1
|
Cohen C, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit J, Gómez-Olivé FX, Dawood FS, Mkhencele T, Tempia S. Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST-C community cohort study, South Africa, 2020-2021. BMC Infect Dis 2024; 24:336. [PMID: 38515050 PMCID: PMC10956206 DOI: 10.1186/s12879-024-09209-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. METHODS We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. RESULTS We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value <30 (vs >35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged <5 (aOR 6.7, 95%CI1.4-31.2) and 5-12 years (aOR 6.6 95%CI2.6-16.7)(vs 19-39) and Ct value <30 (aOR 4.5, 95%CI 1.3-15.5) and 30-35 (aOR 6.0, 95%CI 2.3-15.7)(vs >35). CONCLUSIONS Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness.
Collapse
Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Africa Health Research Institute, Mtubatuba, KwaZulu-Natal, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacques du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatimah S Dawood
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centers for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America
| |
Collapse
|
2
|
Lovelock T, du Plessis M, van der Westhuizen C, Janson JT, Lawrence C, Parker A, Pecoraro A, Prozesky H, von Gottberg A, Taljaard J. Non-toxigenic Corynebacterium diphtheriae endocarditis: A cluster of five cases. S Afr J Infect Dis 2024; 39:539. [PMID: 38444885 PMCID: PMC10913159 DOI: 10.4102/sajid.v39i1.539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/08/2023] [Indexed: 03/07/2024] Open
Abstract
Background Classical toxin-mediated respiratory diphtheria has become less common because of widespread effective vaccination globally but invasive disease as a result of non-toxigenic strains of Corynebacterium diphtheriae is not prevented by vaccination and may result in severe disease, including infective endocarditis (IE). Objectives To describe the outbreak and subsequent investigation of a cluster of five cases of non-toxigenic C. diphtheriae endocarditis. Method A retrospective observational case series of five cases of non-toxigenic C. diphtheriae endocarditis identified in the rural West Coast district of the Western Cape province of South Africa between May 2021 and June 2021. Results Non-toxigenic C. diphtheriae IE had an aggressive clinical course with high mortality in this cohort. Only one of five patients survived to hospital discharge. The surviving patient received a prompt diagnosis with early surgical intervention but still had a complicated clinical course. Notably, only one case had a pre-existing risk factor for IE, namely a prosthetic valve. Whole genome sequencing of clinical isolates confirmed that all isolates were of the same novel sequence type of non-toxigenic C. diphtheriae but despite a thorough investigation no epidemiological link was ever found between the cases. Conclusion Non-toxigenic strains of C. diphtheriae are less well known but may be highly virulent and cause severe invasive disease. Contribution This is the largest cluster of non-toxigenic C. diphtheriae IE ever described in South Africa and expands the body of literature on this unusual but possibly emerging infection.
Collapse
Affiliation(s)
- Tamsin Lovelock
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clinton van der Westhuizen
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Microbiology and Immunology, Department of Pathology, Tygerberg Hospital/Stellenbosch University, Cape Town, South Africa
| | - Jacques T Janson
- Division of Cardiothoracic Surgery, Department of Surgery, Tygerberg Hospital/Stellenbosch University, Cape Town, South Africa
| | - Charlene Lawrence
- Western Cape Government, Department of Health and Wellness, Emergency and Clinical Services Support, Service Priorities Coordination, Communicable Disease Control and Outbreak Response, Cape Town, South Africa
| | - Arifa Parker
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Alfonso Pecoraro
- Division of Cardiology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Hans Prozesky
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jantjie Taljaard
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| |
Collapse
|
3
|
Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom 2023; 9:001162. [PMID: 38117675 PMCID: PMC10763497 DOI: 10.1099/mgen.0.001162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.
Collapse
Affiliation(s)
- Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dineo Mogale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J. Zar
- Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
4
|
Shaw D, Abad R, Amin-Chowdhury Z, Bautista A, Bennett D, Broughton K, Cao B, Casanova C, Choi EH, Chu YW, Claus H, Coelho J, Corcoran M, Cottrell S, Cunney R, Cuypers L, Dalby T, Davies H, de Gouveia L, Deghmane AE, Demczuk W, Desmet S, Domenech M, Drew R, du Plessis M, Duarte C, Erlendsdóttir H, Fry NK, Fuursted K, Hale T, Henares D, Henriques-Normark B, Hilty M, Hoffmann S, Humphreys H, Ip M, Jacobsson S, Johnson C, Johnston J, Jolley KA, Kawabata A, Kozakova J, Kristinsson KG, Krizova P, Kuch A, Ladhani S, Lâm TT, León ME, Lindholm L, Litt D, Maiden MCJ, Martin I, Martiny D, Mattheus W, McCarthy ND, Meehan M, Meiring S, Mölling P, Morfeldt E, Morgan J, Mulhall R, Muñoz-Almagro C, Murdoch D, Murphy J, Musilek M, Mzabi A, Novakova L, Oftadeh S, Perez-Argüello A, Pérez-Vázquez M, Perrin M, Perry M, Prevost B, Roberts M, Rokney A, Ron M, Sanabria OM, Scott KJ, Sheppard C, Siira L, Sintchenko V, Skoczyńska A, Sloan M, Slotved HC, Smith AJ, Steens A, Taha MK, Toropainen M, Tzanakaki G, Vainio A, van der Linden MPG, van Sorge NM, Varon E, Vohrnova S, von Gottberg A, Yuste J, Zanella R, Zhou F, Brueggemann AB. Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium. Lancet Digit Health 2023; 5:e582-e593. [PMID: 37516557 PMCID: PMC10914672 DOI: 10.1016/s2589-7500(23)00108-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/22/2023] [Accepted: 05/25/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.
Collapse
Affiliation(s)
- David Shaw
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Raquel Abad
- National Reference Laboratory for Meningococci, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Zahin Amin-Chowdhury
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | | | - Desiree Bennett
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Karen Broughton
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Carlo Casanova
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Yiu-Wai Chu
- Department of Health, Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Hong Kong Special Administrative Region, China
| | - Heike Claus
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | - Juliana Coelho
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Mary Corcoran
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lize Cuypers
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Tine Dalby
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Copenhagen, Denmark
| | - Heather Davies
- Meningococcal Reference Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ala-Eddine Deghmane
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stefanie Desmet
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Mirian Domenech
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Richard Drew
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Clinical Innovation Unit, Rotunda, Dublin, Ireland
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Helga Erlendsdóttir
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Norman K Fry
- Immunisation and Vaccine Preventable Diseases Division and Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Kurt Fuursted
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Thomas Hale
- Blavatnik School of Government, University of Oxford, Oxford, UK
| | - Desiree Henares
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Birgitta Henriques-Normark
- Karolinska Institutet, Karolinska University Hospital, Public Health Agency of Sweden, Stockholm, Sweden
| | - Markus Hilty
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Steen Hoffmann
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Hilary Humphreys
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susanne Jacobsson
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | | | | | - Jana Kozakova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Pavla Krizova
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alicja Kuch
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Shamez Ladhani
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | - Thiên-Trí Lâm
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | | | - Laura Lindholm
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | | | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Delphine Martiny
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium; Faculty of Medicine and Pharmacy, University of Mons, Mons, Belgium
| | | | - Noel D McCarthy
- Population Health Medicine, Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Paula Mölling
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Julie Morgan
- Streptococcal Reference Laboratory, Institute of Environmental Science and Research Limited, Porirua, New Zealand
| | - Robert Mulhall
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Carmen Muñoz-Almagro
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain; Medicine Department, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | | | - Martin Musilek
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alexandre Mzabi
- Ministère de la Santé - Direction de la santé, Luxembourg, Luxembourg
| | - Ludmila Novakova
- National Reference Laboratory for Haemophilus Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Shahin Oftadeh
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia
| | - Amaresh Perez-Argüello
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Maria Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Benoit Prevost
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium
| | | | - Assaf Rokney
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Merav Ron
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Kevin J Scott
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Lotta Siira
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Vitali Sintchenko
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia; Sydney Institute for Infectious Diseases, University of Sydney, NSW, Australia
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | | | | | - Andrew J Smith
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK; College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Anneke Steens
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Muhamed-Kheir Taha
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | | | - Georgina Tzanakaki
- National Meningitis Reference Laboratory, Department of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Anni Vainio
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mark P G van der Linden
- Department of Medical Microbiology, German National Reference Centre for Streptococci, University Hospital RWTH Aachen, Aachen, Germany
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, and Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Emmanuelle Varon
- Laboratory of Medical Biology and National Reference Centre for Pneumococci, Intercommunal Hospital of Créteil, Créteil, France
| | - Sandra Vohrnova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jose Yuste
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosemeire Zanella
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz, São Paulo, Brazil
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK.
| |
Collapse
|
5
|
Naidoo K, Msimang M, du Plessis M, Naidoo DP. Diphtheritic myocarditis: a case report, with toxinmediated complications and multi-organ involvement. Cardiovasc J Afr 2023; 34:117-120. [PMID: 36063382 PMCID: PMC10512040 DOI: 10.5830/cvja-2022-032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023] Open
Abstract
The re-emergence of diphtheria in South Africa in recent years warns of incomplete vaccination coverage. Recent outbreaks have been associated with a high mortality rate, due to late presentation, limited access to antitoxin and the occurrence of serious systemic complications. Death due to diphtheria is most commonly associated with diphtheritic myocarditis, which presents with heart failure, cardiogenic shock and conduction abnormalities. This case highlights the key clinical features and systemic complications, and examines the reasons for the return of diphtheria in our community.
Collapse
Affiliation(s)
- Kumari Naidoo
- Department of Internal Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Mpumelelo Msimang
- Department of Histopathology, University of KwaZulu-Natal, Durban; National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Datshana Prakesh Naidoo
- Department of Cardiology, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| |
Collapse
|
6
|
Hawkins PA, Chochua S, Lo SW, Belman S, Antonio M, Kwambana-Adams B, von Gottberg A, du Plessis M, Cornick J, Beall B, Breiman RF, Bentley SD, McGee L. A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction. Microb Genom 2023; 9. [PMID: 37083600 DOI: 10.1099/mgen.0.000998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against Streptococcus pneumoniae has led to serotype replacement by non-vaccine serotypes, including serotype 15A. Clonal complex 63 (CC63) is associated with many serotypes and has been reported in association with 15A after introduction of PCVs. A total of 865 CC63 isolates were included in this study, from the USA (n=391) and a global collection (n=474) from 1998-2019 and 1995-2018, respectively. We analysed the genomic sequences to identify serotypes and penicillin-binding protein (PBP) genes 1A, 2B and 2X, and other resistance determinants, to predict minimum inhibitory concentrations (MICs) against penicillin, erythromycin, clindamycin, co-trimoxazole and tetracycline. We conducted phylogenetic and spatiotemporal analyses to understand the evolutionary history of the 15A-CC63 sub-lineage. Overall, most (89.5 %, n=247) pre-PCV isolates in the CC63 cluster belonged to serotype 14, with 15A representing 6.5 % of isolates. Conversely, serotype 14 isolates represented 28.2 % of post-PCV CC63 isolates (n=618), whilst serotype 15A isolates represented 65.4 %. Dating of the CC63 lineage determined the most recent common ancestor emerged in the 1980s, suggesting the 15A-CC63 sub-lineage emerged from its closest serotype 14 ancestor prior to the development of pneumococcal vaccines. This sub-lineage was predominant in the USA, Israel and China. Multidrug resistance (to three or more drug classes) was widespread among isolates in this sub-lineage. We show that the CC63 lineage is globally distributed and most of the isolates are penicillin non-susceptible, and thus should be monitored.
Collapse
Affiliation(s)
- Paulina A Hawkins
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Martin Antonio
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Anne von Gottberg
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jen Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
7
|
Moosa F, Tempia S, Kleynhans J, McMorrow M, Moyes J, du Plessis M, Carrim M, Treurnicht FK, Helferscee O, Mkhencele T, Mathunjwa A, Martinson NA, Kahn K, Lebina L, Wafawanaka F, Cohen C, von Gottberg A, Wolter N. Incidence and Transmission Dynamics of Bordetella pertussis Infection in Rural and Urban Communities, South Africa, 2016‒2018. Emerg Infect Dis 2023; 29:294-303. [PMID: 36692337 PMCID: PMC9881781 DOI: 10.3201/eid2902.221125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We conducted 3 prospective cohort studies (2016-2018), enrolling persons from 2 communities in South Africa. Nasopharyngeal swab specimens were collected twice a week from participants. Factors associated with Bordetella pertussis incidence, episode duration, and household transmission were determined by using Poisson regression, Weibull accelerated time-failure, and logistic regression hierarchical models, respectively. Among 1,684 participants, 118 episodes of infection were detected in 107 participants (incidence 0.21, 95% CI 0.17-0.25 infections/100 person-weeks). Children <5 years of age who had incomplete vaccination were more likely to have pertussis infection. Episode duration was longer for participants who had higher bacterial loads. Transmission was more likely to occur from male index case-patients and persons who had >7 days infection duration. In both communities, there was high incidence of B. pertussis infection and most cases were colonized.
Collapse
|
8
|
Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo S, McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae. bioRxiv 2023:2023.01.18.524577. [PMID: 36711799 PMCID: PMC9882368 DOI: 10.1101/2023.01.18.524577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location. The extent and mechanisms of spread, and vaccine-driven changes in fitness and antimicrobial resistance (AMR), remain largely unquantified. Using geolocated genome sequences from South Africa (N=6910, 2000-2014) we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately we estimated the population level changes in fitness of strains that are (vaccine type, VT) and are not (non-vaccine type, NVT) included in the vaccine, first implemented in 2009, as well as differences in strain fitness between those that are and are not resistant to penicillin. We estimated that pneumococci only become homogenously mixed across South Africa after about 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Further, in the years following vaccine implementation the relative fitness of NVT compared to VT strains increased (RR: 1.29 [95% CI 1.20-1.37]) - with an increasing proportion of these NVT strains becoming penicillin resistant. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in AMR may be transient.
Collapse
Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute; Hinxton, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Susan Nzenze
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | - Sarah Downs
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute; Hinxton, UK
| | | | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service; Johannesburg, South Africa
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge; Cambridge, UK
| |
Collapse
|
9
|
Müller A, Lekhuleni C, Hupp S, du Plessis M, Holivololona L, Babiychuk E, Leib SL, Grandgirard D, Iliev AI, von Gottberg A, Hathaway LJ. Meningitis-associated pneumococcal serotype 8, ST 53, strain is hypervirulent in a rat model and has non-haemolytic pneumolysin which can be attenuated by liposomes. Front Cell Infect Microbiol 2023; 12:1106063. [PMID: 36683678 PMCID: PMC9852819 DOI: 10.3389/fcimb.2022.1106063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Streptococcus pneumoniae bacteria cause life-threatening invasive pneumococcal disease (IPD), including meningitis. Pneumococci are classified into serotypes, determined by differences in capsular polysaccharide and both serotype and pneumolysin toxin are associated with disease severity. Strains of serotype 8, ST 53, are increasing in prevalence in IPD in several countries. Methods Here we tested the virulence of such an isolate in a rat model of meningitis in comparison with a serotype 15B and a serotype 14 isolate. All three were isolated from meningitis patients in South Africa in 2019, where serotype 8 is currently the most common serotype in IPD. Results and Discussion Only the serotype 8 isolate was hypervirulent causing brain injury and a high mortality rate. It induced a greater inflammatory cytokine response than either the serotype 15B or 14 strain in the rat model and from primary mixed-glia cells isolated from mouse brains. It had the thickest capsule of the three strains and produced non-haemolytic pneumolysin. Pneumolysin-sequestering liposomes reduced the neuroinflammatory cytokine response in vitro indicating that liposomes have the potential to be an effective adjuvant therapy even for hypervirulent pneumococcal strains with non-haemolytic pneumolysin.
Collapse
Affiliation(s)
- Annelies Müller
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Cebile Lekhuleni
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sabrina Hupp
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lalaina Holivololona
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | | | - Stephen L Leib
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Denis Grandgirard
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | | | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| |
Collapse
|
10
|
Walaza S, Tempia S, von Gottberg A, Wolter N, Bhiman JN, Buys A, Amoako D, Moosa F, du Plessis M, Moyes J, McMorrow ML, Dawood H, Variava E, Reubenson G, Nel J, Zar HJ, Makhasi M, Meiring S, Quan V, Cohen C. Risk Factors for Severe Coronavirus Disease 2019 Among Human Immunodeficiency Virus-Infected and -Uninfected Individuals in South Africa, April 2020-March 2022: Data From Sentinel Surveillance. Open Forum Infect Dis 2022; 9:ofac578. [PMID: 36570970 PMCID: PMC9772867 DOI: 10.1093/ofid/ofac578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/22/2022] [Indexed: 12/24/2022] Open
Abstract
Background Data on risk factors for coronavirus disease 2019 (COVID-19)-associated hospitalization and mortality in high human immunodeficiency virus (HIV) prevalence settings are limited. Methods Using existing syndromic surveillance programs for influenza-like-illness and severe respiratory illness at sentinel sites in South Africa, we identified factors associated with COVID-19 hospitalization and mortality. Results From April 2020 through March 2022, severe acute respiratory syndrome coronavirus 2 was detected in 24.0% (660 of 2746) of outpatient and 32.5% (2282 of 7025) of inpatient cases. Factors associated with COVID-19-associated hospitalization included the following: older age (25-44 [adjusted odds ratio {aOR}= 1.8, 95% confidence interval (CI) = 1.1-2.9], 45-64 [aOR = 6.8, 95% CI = 4.2-11.0] and ≥65 years [aOR = 26.6, 95% CI = 14.4-49.1] vs 15-24 years); black race (aOR, 3.3; 95% CI, 2.2-5.0); obesity (aOR, 2.3; 95% CI, 1.4-3.9); asthma (aOR, 3.5; 95% CI, 1.4-8.9); diabetes mellitus (aOR, 5.3; 95% CI, 3.1-9.3); HIV with CD4 ≥200/mm3 (aOR, 1.5; 95% CI, 1.1-2.2) and CD4 <200/mm3 (aOR, 10.5; 95% CI, 5.1-21.6) or tuberculosis (aOR, 12.8; 95% CI, 2.8-58.5). Infection with Beta (aOR, 0.5; 95% CI, .3-.7) vs Delta variant and being fully vaccinated (aOR, 0.1; 95% CI, .1-.3) were less associated with COVID-19 hospitalization. In-hospital mortality was increased in older age (45-64 years [aOR, 2.2; 95% CI, 1.6-3.2] and ≥65 years [aOR, 4.0; 95% CI, 2.8-5.8] vs 25-44 years) and male sex (aOR, 1.3; 95% CI, 1.0-1.6) and was lower in Omicron-infected (aOR, 0.3; 95% CI, .2-.6) vs Delta-infected individuals. Conclusions Active syndromic surveillance encompassing clinical, laboratory, and genomic data identified setting-specific risk factors associated with COVID-19 severity that will inform prioritization of COVID-19 vaccine distribution. Elderly people with tuberculosis or people with HIV, especially severely immunosuppressed, should be prioritized for vaccination.
Collapse
Affiliation(s)
- Sibongile Walaza
- Correspondence: Sibongile Walaza, MBBCh, PhD, Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131, Gauteng, South Africa ()
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,MassGenics, Atlanta, Georgia, USA,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Daniel Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Program, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Halima Dawood
- Department of Medicine, Greys Hospital, Pietermaritzburg, South Africa,Caprisa, University of KwaZulu - Natal, Pietermaritzburg, South Africa
| | - Ebrahim Variava
- Department of Medicine, Klerksdorp-Tshepong Hospital Complex, Klerksdorp, South Africa,Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gary Reubenson
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Rahima Moosa Mother and Child Hospital, Johannesburg, South Africa
| | - Jeremy Nel
- Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J Zar
- Department of Paediatrics, Red Cross War Memorial Hospital, andSouth African-Medical Research Council on Child and Adolescent Health, University of Cape Town, South Africa
| | - Mvuyo Makhasi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Susan Meiring
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Divison of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Vanessa Quan
- Divison of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | |
Collapse
|
11
|
Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B, Ravikumar KL, Kandasamy R, Pollard SAJ, Saha SK, Bigogo G, Antonio M, Kwambana-Adams B, Mirza S, Shakoor S, Nisar I, Cornick JE, Lehmann D, Ford RL, Sigauque B, Turner P, Moïsi J, Obaro SK, Dagan R, Diawara I, Skoczyńska A, Wang H, Carter PE, Klugman KP, Rodgers G, Breiman RF, McGee L, Bentley SD, Almagro CM, Varon E, Corso A, Davydov A, Maguire A, Kiran A, Moiane B, Beall B, Zhao C, Aanensen D, Everett D, Faccone D, Foster-Nyarko E, Bojang E, Egorova E, Voropaeva E, Sampane-Donkor E, Sadowy E, Nagaraj G, Mucavele H, Belabbès H, Elmdaghri N, Verani J, Keenan J, Lees J, N Nair Thulasee Bhai J, Ndlangisa K, Zerouali K, Bentley L, Titov L, De Gouveia L, Alaerts M, Ip M, de Cunto Brandileone MC, Hasanuzzaman M, Paragi M, Nurse-Lucas M, du Plessis M, Ali M, Croucher N, Wolter N, Givon-Lavi N, Porat N, Köseoglu Eser Ö, Ho PL, Eberechi Akpaka P, Gagetti P, Tientcheu PE, Law P, Benisty R, Mostowy R, Malaker R, Grassi Almeida SC, Doiphode S, Madhi S, Devi Sekaran S, Clarke S, Srifuengfung S, Nzenze S, Kastrin T, Ochoa T, Hryniewicz W, Urban Y. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study. Lancet Microbe 2022; 3:e735-e743. [PMID: 35985351 PMCID: PMC9519462 DOI: 10.1016/s2666-5247(22)00158-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context. METHODS Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster (GPSC) and a clonal complex (CC) were assigned to each genome. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted using the same 24F collection and supplemented with a global collection of genomes belonging to the lineage of interest from the GPS project database (n=25 590). FINDINGS Serotype 24F was identified in numerous countries mainly due to the clonal spread of three lineages: GPSC10 (CC230), GPSC16 (CC156), and GPSC206 (CC7701). GPSC10 was the only multidrug-resistant lineage. GPSC10 drove the increase in 24F in France and had high invasive disease potential. The international dataset of GPSC10 (n=888) revealed that this lineage expressed 16 other serotypes, with only six included in 13-valent PCV (PCV13). All serotype 24F isolates were clustered in a single clade within the GPSC10 phylogeny and long-range transmissions were detected from Europe to other continents. Spatiotemporal analysis showed GPSC10-24F took 3-5 years to spread across France and a rapid change of serotype composition from PCV13 serotype 19A to 24F during the introduction of PCV13 was observed in neighbouring country Spain. INTERPRETATION Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.
Collapse
Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK,Correspondence to: Dr Stephanie W Lo, Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kate Mellor
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Robert Cohen
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France,GPIP, Groupe de Pathologie Infectieuse Pédiatrique, Paris, France,AFPA, Association Française de Pédiatrie Ambulatoire, Saint-Germain-en-Laye, France,Université Paris Est, IMRB-GRC GEMINI, Créteil, France,Clinical Research Center, Centre Hospitalier Intercommunal de Créteil, Créteil, France,Unité Court Séjour, Petits nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Alba Redin Alonso
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Sophie Belman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rebecca A Gladstone
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK,School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia,Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sir Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Brenda Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Shaper Mirza
- Microbiology and Immunology Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA,International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Ron Dagan
- Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idrissa Diawara
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco,National Reference Laboratory, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Hui Wang
- Peking University People ‘s Hospital, Beijing, China
| | - Philip E Carter
- Institute of Environmental Science and Research Limited, Kenepuru Science Centre, Porirua, New Zealand
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Gail Rodgers
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Carmen Muñoz Almagro
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Emmanuelle Varon
- National Reference Center for Pneumococci, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Meiring S, Tempia S, Bhiman JN, Buys A, Kleynhans J, Makhasi M, McMorrow M, Moyes J, Quan V, Walaza S, du Plessis M, Wolter N, von Gottberg A, Cohen C. Prolonged Shedding of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at High Viral Loads Among Hospitalized Immunocompromised Persons Living With Human Immunodeficiency Virus (HIV), South Africa. Clin Infect Dis 2022; 75:e144-e156. [PMID: 35134129 PMCID: PMC8903337 DOI: 10.1093/cid/ciac077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding duration and magnitude among persons living with human immunodeficiency virus (HIV, PLHIV). METHODS From May through December 2020, we conducted a prospective cohort study at 20 hospitals in South Africa. Adults hospitalized with symptomatic coronavirus disease 2019 (COVID-19) were enrolled and followed every 2 days with nasopharyngeal/oropharyngeal (NP/OP) swabs until documentation of cessation of SARS-CoV-2 shedding (2 consecutive negative NP/OP swabs). Real-time reverse transcription-polymerase chain reaction testing for SARS-CoV-2 was performed, and cycle-threshold (Ct) values < 30 were considered a proxy for high SARS-CoV-2 viral load. Factors associated with prolonged shedding were assessed using accelerated time-failure Weibull regression models. RESULTS Of 2175 COVID-19 patients screened, 300 were enrolled, and 257 individuals (155 HIV-uninfected and 102 PLHIV) had > 1 swabbing visit (median 5 visits [range 2-21]). Median time to cessation of shedding was 13 days (interquartile range [IQR] 6-25) and did not differ significantly by HIV infection. Among a subset of 94 patients (41 PLHIV and 53 HIV-uninfected) with initial respiratory sample Ct-value < 30, median time of shedding at high SARS-CoV-2 viral load was 8 days (IQR 4-17). This was significantly longer in PLHIV with CD4 count < 200 cells/µL, compared to HIV-uninfected persons (median 27 days [IQR 8-43] vs 7 days [IQR 4-13]; adjusted hazard ratio [aHR] 0.14, 95% confidence interval [CI] .07-.28, P < .001), as well as in unsuppressed-HIV versus HIV-uninfected persons. CONCLUSIONS Although SARS-CoV-2 shedding duration did not differ significantly by HIV infection, among a subset with high initial SARS-CoV-2 viral loads, immunocompromised PLHIV shed SARS-CoV-2 at high viral loads for longer than HIV-uninfected persons. Better HIV control may potentially decrease transmission time of SARS-CoV-2.
Collapse
Affiliation(s)
- Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mvuyo Makhasi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Meredith McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
13
|
Sun K, Tempia S, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit JD, Gómez-Olivé FX, Mkhencele T, Viboud C, Cohen C. SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron's impact in South African population cohorts. Sci Transl Med 2022; 14:eabo7081. [PMID: 35638937 PMCID: PMC9161370 DOI: 10.1126/scitranslmed.abo7081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022]
Abstract
Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa's high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.
Collapse
Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jinal N. Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, 21287, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Jacques D. du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| |
Collapse
|
14
|
Moleleki M, du Plessis M, Ndlangisa K, Reddy C, Hellferscee O, Mekgoe O, McMorrow M, Walaza S, Cohen C, Tempia S, von Gottberg A, Wolter N. Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017. Int J Infect Dis 2022; 122:389-397. [PMID: 35700877 DOI: 10.1016/j.ijid.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/30/2022] [Accepted: 06/08/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES We describe the use of a multi-pathogen platform, TaqMan array card (TAC) real-time PCR, for the detection of pathogens in patients hospitalized with severe respiratory illness (SRI). METHODS Prospective hospital-based syndromic surveillance for acute and chronic SRI was carried out at two sentinel sites in South Africa between January and December 2017. We tested respiratory specimens for 21 respiratory pathogens and blood samples for nine bacteria using TAC. Pathogen detection was compared by age group and HIV status using the chi-squared test. RESULTS During 2017, 956 patients of all ages were enrolled in the SRI surveillance, and of these, 637 (67%) patients were included in this study (637 blood, 487 naso- and oro-pharyngeal swabs and 411 sputum specimens tested). At least one pathogen was detected in 83% (527/637) of patients. Common pathogens detected included H. influenzae (225/637; 35%), S. pneumoniae (224/637; 35%), rhinovirus (144/637; 23%), S. aureus (129/637; 20%), K. pneumoniae (85/637; 13%), M. tuberculosis (75/637; 12%), and respiratory syncytial virus (57/637; 9%). Multiple pathogens (≥2) were co-detected in 57% (364/637) of patients. CONCLUSION While use of a multi-pathogen platform improved pathogen yield, pathogen co-detections were common and would need clinical assessment for usefulness in individual-level treatment and management decisions.
Collapse
Affiliation(s)
- Malefu Moleleki
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kedibone Ndlangisa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cayla Reddy
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Medical Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Omphe Mekgoe
- Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; MassGenics, Duluth, Georgia, United States of America
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
15
|
Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett DB, Dagan R, Hawkins PA, Beall B, Corso A, Grassi Almeida SC, Ochoa TJ, Obaro S, Shakoor S, Donkor ES, Gladstone RA, Ho PL, Paragi M, Doiphode S, Srifuengfung S, Ford R, Moïsi J, Saha SK, Bigogo G, Sigauque B, Eser ÖK, Elmdaghri N, Titov L, Turner P, Kumar KLR, Kandasamy R, Egorova E, Ip M, Breiman RF, Klugman KP, McGee L, Bentley SD, von Gottberg A, The Global Pneumococcal Sequencing Consortium. A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. Microb Genom 2022; 8. [PMID: 35384831 PMCID: PMC9453074 DOI: 10.1099/mgen.0.000746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005–2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005–2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.
Collapse
Affiliation(s)
- Kedibone M Ndlangisa
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Linda de Gouveia
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.,West Africa Partnerships and Strategies, Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | | | - Dean B Everett
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi.,Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Paulina A Hawkins
- Rollins School Public Health, Emory University, Atlanta, USA.,Centers for Disease Control and Prevention, Atlanta, USA
| | - Bernard Beall
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Alejandra Corso
- Administración Nacional de Laboratorios e Institutos de Salud, Buenos Aires, Argentina
| | | | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Eric S Donkor
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | | | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | - Metka Paragi
- National Laboratory of Health, Environment and Food, Ljubljana, Slovenia
| | | | | | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Moçambique
| | - Özgen Köseoglu Eser
- Hacettepe University Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey
| | - Naima Elmdaghri
- Faculty of Medicine and Pharmacy & Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Leonid Titov
- The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K L Ravi Kumar
- Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India
| | - Rama Kandasamy
- University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Ekaterina Egorova
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - Margaret Ip
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, PR China
| | | | - Keith P Klugman
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | |
Collapse
|
16
|
Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, Everatt J, Bhiman JN, Scheepers C, Tebeila N, Chiwandire N, du Plessis M, Govender N, Ismail A, Glass A, Mlisana K, Stevens W, Treurnicht FK, Makatini Z, Hsiao NY, Parboosing R, Wadula J, Hussey H, Davies MA, Boulle A, von Gottberg A, Cohen C. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet 2022; 399:437-446. [PMID: 35065011 PMCID: PMC8769664 DOI: 10.1016/s0140-6736(22)00017-4] [Citation(s) in RCA: 613] [Impact Index Per Article: 306.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. METHODS We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. FINDINGS From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity. INTERPRETATION Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. FUNDING The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.
Collapse
Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Welch
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle Groome
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Naume Tebeila
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicola Chiwandire
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nevashan Govender
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy Stevens
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Zinhle Makatini
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Nei-Yuan Hsiao
- National Health Laboratory Service, Johannesburg, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Raveen Parboosing
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Virology, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Jeannette Wadula
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, CH Baragwanath Academic Hospital, Johannesburg, South Africa
| | - Hannah Hussey
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Boulle
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
17
|
Noble L, Scott L, Munir R, Steegen K, du Plessis M, Hans L, Stevens W. Guidance for SARS-CoV-2 RNA-Based Molecular Assay Analytical Performance Evaluations. Methods Mol Biol 2022; 2511:99-115. [PMID: 35838955 DOI: 10.1007/978-1-0716-2395-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is frequently diagnosed through detection of viral RNA using nucleic acid amplification testing (NAAT) assays that are usually used in centralized settings. Following the publication of the SARS-CoV-2 genetic sequence, multiple diagnostic assays were launched in 2020. These assays require evaluation beyond manufacturer self-reported performance to determine whether they are suitable for use, meet country acceptance criteria, and are compatible with existing in-country platforms. In order to meet the demand for testing services, rapid yet robust assay performance evaluations are required. In our setting, these evaluation protocols required the use of residual patient specimens and reference materials, as typical clinical trials are time-consuming and limited by cost and the cyclical nature of SARS-CoV-2 infection. This protocol is designed to assist in the rapid and robust evaluation of nucleic acid-based assays for the detection of SARS-CoV-2 using limited specimens, reference materials, and test kits. While it is specific for RNA-based assays, it can be adapted for fully automated analyses. The preparation and processing of evaluation panels is described, followed by methods for analytical precision analysis and data visualization. Assay robustness and scalability are briefly discussed as these can be critical for implementation. This protocol is designed to be flexible and alternative options are provided throughout the text where possible.
Collapse
Affiliation(s)
- Lara Noble
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Riffat Munir
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kim Steegen
- National Priority Programme, National Health Laboratory Service, Johannesburg, Gauteng, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, Gauteng, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lucia Hans
- National Priority Programme, National Health Laboratory Service, Johannesburg, Gauteng, South Africa
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Programme, National Health Laboratory Service, Johannesburg, Gauteng, South Africa
| |
Collapse
|
18
|
Cohen C, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit J, Xavier Gómez-Olivé F, Dawood FS, Mkhencele T, Sun K, Viboud C, Tempia S. SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021. medRxiv 2021:2021.07.20.21260855. [PMID: 34909794 PMCID: PMC8669861 DOI: 10.1101/2021.07.20.21260855] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND By August 2021, South Africa experienced three SARS-CoV-2 waves; the second and third associated with emergence of Beta and Delta variants respectively. METHODS We conducted a prospective cohort study during July 2020-August 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Serum was collected every two months and tested for anti-SARS-CoV-2 antibodies. RESULTS Among 115,759 nasal specimens from 1,200 members (follow-up rate 93%), 1976 (2%) were SARS-CoV-2-positive. By rRT-PCR and serology combined, 62% (749/1200) of individuals experienced ≥1 SARS-CoV-2 infection episode, and 12% (87/749) experienced reinfection. Of 662 PCR-confirmed episodes with available data, 15% (n=97) were associated with ≥1 symptom. Among 222 households, 200 (90%) had ≥1 SARS-CoV-2-positive individual. Household cumulative infection risk (HCIR) was 25% (213/856). On multivariable analysis, accounting for age and sex, index case lower cycle threshold value (OR 3.9, 95%CI 1.7-8.8), urban community (OR 2.0,95%CI 1.1-3.9), Beta (OR 4.2, 95%CI 1.7-10.1) and Delta (OR 14.6, 95%CI 5.7-37.5) variant infection were associated with increased HCIR. HCIR was similar for symptomatic (21/110, 19%) and asymptomatic (195/775, 25%) index cases (p=0.165). Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection. People living with HIV who were not virally supressed were more likely to develop symptomatic illness, and shed SARS-CoV-2 for longer compared to HIV-uninfected individuals. CONCLUSIONS In this study, 85% of SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of Beta and Delta variants, likely contributed to successive waves, with >60% of individuals infected by the end of follow-up. RESEARCH IN CONTEXT Evidence before this study: Previous studies have generated wide-ranging estimates of the proportion of SARS-CoV-2 infections which are asymptomatic. A recent systematic review found that 20% (95% CI 3%-67%) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections remained asymptomatic throughout infection and that transmission from asymptomatic individuals was reduced. A systematic review and meta-analysis of 87 household transmission studies of SARS-CoV-2 found an estimated secondary attack rate of 19% (95% CI 16-22). The review also found that household secondary attack rates were increased from symptomatic index cases and that adults were more likely to acquire infection. As of December 2021, South Africa experienced three waves of SARS-CoV-2 infections; the second and third waves were associated with circulation of Beta and Delta variants respectively. SARS-CoV-2 vaccines became available in February 2021, but uptake was low in study sites reaching 5% fully vaccinated at the end of follow up. Studies to quantify the burden of asymptomatic infections, symptomatic fraction, reinfection frequency, duration of shedding and household transmission of SARS-CoV-2 from asymptomatically infected individuals have mostly been conducted as part of outbreak investigations or in specific settings. Comprehensive systematic community studies of SARS-CoV-2 burden and transmission including for the Beta and Delta variants are lacking, especially in low vaccination settings.Added value of this study: We conducted a unique detailed COVID-19 household cohort study over a 13 month period in South Africa, with real time reverse transcriptase polymerase chain reaction (rRT-PCR) testing twice a week irrespective of symptoms and bimonthly serology. By the end of the study in August 2021, 749 (62%) of 1200 individuals from 222 randomly sampled households in a rural and an urban community in South Africa had at least one confirmed SARS-CoV-2 infection, detected on rRT-PCR and/or serology, and 12% (87/749) experienced reinfection. Symptom data were analysed for 662 rRT-PCR-confirmed infection episodes that occurred >14 days after the start of follow-up (of a total of 718 rRT-PCR-confirmed episodes), of these, 15% (n=97) were associated with one or more symptoms. Among symptomatic indvidiausl, 9% (n=9) were hospitalised and 2% (n=2) died. Ninety percent (200/222) of included households, had one or more individual infected with SARS-CoV-2 on rRT-PCR and/or serology within the household. SARS-CoV-2 infected index cases transmitted the infection to 25% (213/856) of susceptible household contacts. Index case ribonucleic acid (RNA) viral load proxied by rRT-PCR cycle threshold value was strongly predictive of household transmission. Presence of symptoms in the index case was not associated with household transmission. Household transmission was four times greater from index cases infected with Beta variant and fifteen times greater from index cases infected with Delta variant compared to wild-type infection. Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection within households. People living with HIV (PLHIV) who were not virally supressed were more likely to develop symptomatic illness when infected with SARS-CoV-2, and shed SARS-CoV-2 for longer when compared to HIV-uninfected individuals.Implications of all the available evidence: We found a high rate of SARS-CoV-2 infection in households in a rural community and an urban community in South Africa, with the majority of infections being asymptomatic in individuals of all ages. Asymptomatic individuals transmitted SARS-CoV-2 at similar levels to symptomatic individuals suggesting that interventions targeting symptomatic individuals such as symptom-based testing and contact tracing of individuals tested because they report symptoms may have a limited impact as control measures. Increased household transmission of Beta and Delta variants, likely contributed to recurrent waves of COVID-19, with >60% of individuals infected by the end of follow-up. Higher attack rates, reinfection and acquisition in adolescents and prolonged SARS-CoV-2 shedding in PLHIV who were not virally suppressed suggests that prioritised vaccination of individuals in these groups could impact community transmission.
Collapse
Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N. Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, South Africa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacques du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatimah S. Dawood
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Kaiyun Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| |
Collapse
|
19
|
du Plessis M, de Gouveia L, Freitas C, Abera NA, Lula BS, Raboba JL, Nhantumbo AA, Jantjies E, Uwimana J, Phungwayo N, Maphalala G, Masona G, Muyombe J, Mugisha D, Nalumansi E, Odongkara M, Lukwesa-Musyani C, Nakazwe R, Dondo V, Macharaga J, Weldegebriel GG, Mwenda JM, Serhan F, Cohen AL, Lessa FC, von Gottberg A. The Role of Molecular Testing in Pediatric Meningitis Surveillance in Southern and East African Countries, 2008-2017. J Infect Dis 2021; 224:S194-S203. [PMID: 34469556 PMCID: PMC8409535 DOI: 10.1093/infdis/jiab092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background As part of the global Invasive Bacterial Vaccine-Preventable Diseases Surveillance Network, 12 African countries referred cerebrospinal fluid (CSF) samples to South Africa’s regional reference laboratory. We evaluated the utility of real-time polymerase chain reaction (PCR) in detecting and serotyping/grouping Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae (HNS). Methods From 2008 to 2017, CSF samples collected from children <5 years old with suspected meningitis underwent routine microbiology testing in-country, and 11 680 samples were submitted for HNS PCR at the regional reference laboratory. Unconditional logistic regression, with adjustment for geographic location, was performed to identify factors associated with PCR positivity. Results The overall HNS PCR positivity rate for all countries was 10% (1195 of 11 626 samples). In samples with both PCR and culture results, HNS PCR positivity was 11% (744 of 6747 samples), and HNS culture positivity was 3% (207 of 6747). Molecular serotype/serogroup was assigned in 75% of PCR-positive specimens (762 of 1016). Compared with PCR-negative CSF samples, PCR-positive samples were more often turbid (adjusted odds ratio, 6.80; 95% confidence interval, 5.67–8.17) and xanthochromic (1.72; 1.29–2.28), had elevated white blood cell counts (6.13; 4.71–7.99) and high protein concentrations (5.80; 4.34–7.75), and were more often HNS culture positive (32.70; 23.18–46.12). Conclusion PCR increased detection of vaccine-preventable bacterial meningitis in countries where confirmation of suspected meningitis cases is impeded by limited culture capacity.
Collapse
Affiliation(s)
- Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Cesar Freitas
- Hospital Pediatrico David Bernardino, Luanda, Angola
| | - Negga Asamene Abera
- Bacteriology National Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Budiaki Sylvie Lula
- Department of Microbiology National Reference Laboratory, Ministry of Health, Maseru, Lesotho
| | - Julia Liliane Raboba
- Department of Child Health, Teaching Hospital, Centre Hospitalier Universitaire Mère Enfant Tsaralàlana, Antananarivo, Madagascar
| | | | - Elana Jantjies
- Namibia Institute of Pathology, Microbiology, and Windhoek Central Reference Laboratory, Windhoek, Namibia
| | | | - Nomcebo Phungwayo
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - Gugu Maphalala
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - Gilbert Masona
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - John Muyombe
- Bacteriology Laboratory, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - David Mugisha
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Esther Nalumansi
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Moses Odongkara
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Chileshe Lukwesa-Musyani
- Ministry of Health, University Teaching Hospital, Pathology and Microbiology Department, Lusaka, Zambia
| | - Ruth Nakazwe
- Ministry of Health, University Teaching Hospital, Pathology and Microbiology Department, Lusaka, Zambia
| | | | | | - Goitom G Weldegebriel
- World Health Organization Regional Office for Africa, Inter-Country Support Team, Harare, Zimbabwe
| | - Jason M Mwenda
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | | | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
20
|
Wolter N, Cohen C, Tempia S, Walaza S, Moosa F, du Plessis M, McMorrow ML, Treurnicht FK, Hellferscee O, Dawood H, Variava E, von Gottberg A. Epidemiology of Pertussis in Individuals of All Ages Hospitalized With Respiratory Illness in South Africa, January 2013-December 2018. Clin Infect Dis 2021; 73:e745-e753. [PMID: 33530100 DOI: 10.1093/cid/ciab089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Policy recommendations on pertussis vaccination need to be guided by data, which are limited from low- and middle-income countries. We aimed to describe the epidemiology of pertussis in South Africa, a country with high human immunodeficiency virus (HIV) prevalence and routine pertussis vaccination for 6 decades including the acellular vaccine since 2009. METHODS Hospitalized patients of all ages were enrolled at 5 sentinel sites as part of a pneumonia surveillance program from January 2013 through December 2018. Nasopharyngeal specimens and induced sputum were tested by polymerase chain reaction (PCR) for Bordetella pertussis. In addition, demographic and clinical information were collected. Incidence rates were calculated for 2013-2016, and multivariable logistic regression performed to identify factors associated with pertussis. RESULTS Over the 6-year period 19 429 individuals were enrolled, of which 239 (1.2%) tested positive for B. pertussis. Detection rate was highest in infants aged <6 months (2.8%, 155/5524). Mean annual incidence was 17 cases per 100 000 population, with the highest incidence in children <1 year of age (228 per 100 000). Age-adjusted incidence was 65.9 per 100 000 in HIV-infected individuals compared to 8.5 per 100 000 in HIV-uninfected individuals (risk ratio 30.4, 95% confidence interval: 23.0-40.2). Ten individuals (4.2%) with pertussis died; of which 7 were infants aged <6 months and 3 were immunocompromised adults. CONCLUSIONS Pertussis continues to be a significant cause of illness and hospitalization in South Africa, despite routine vaccination. The highest burden of disease and death occurred in infants; however, HIV-infected adults were also identified as an important group at risk of B. pertussis infection.
Collapse
Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,MassGenics, Duluth, Georgia, USA.,Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Halima Dawood
- Greys Hospital and Caprisa, University of KwaZulu Natal, KwaZulu Natal, South Africa
| | - Ebrahim Variava
- Department of Medicine, Klerksdorp Tshepong Hospital Complex, Klerksdorp, South Africa.,School of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
21
|
Meiring S, Cohen C, de Gouveia L, du Plessis M, Ganesh K, Kleynhans J, Quan V, Tempia S, von Gottberg A. Human Immunodeficiency Virus Infection Is Associated With Increased Meningococcal Carriage Acquisition Among First-year Students in 2 South African Universities. Clin Infect Dis 2021; 73:e28-e38. [PMID: 32369560 PMCID: PMC8246797 DOI: 10.1093/cid/ciaa521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/30/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Invasive meningococcal disease clusters occur among university students and may reflect higher carriage prevalence among this population. We aimed to measure meningococcal carriage prevalence, acquisition, and risk factors among first-year university students in South Africa. METHODS In summer-autumn 2017, after consenting to participate, we collected oropharyngeal swabs and questionnaires on carriage risk factors and tested students for HIV at 2 universities, during registration week (survey 1) and 6-8 weeks later (survey 2). Meningococci were detected by culture and polymerase chain reaction. RESULTS We enrolled 2120 students at registration. Mean age was 18.5 years, 59% (1252/2120) were female and 0.8% (16/1984) had HIV. Seventy-eight percent of students returned for survey 2 (1655/2120). Among the cohort, carriage prevalence was 4.7% (77/1655) at registration, increasing to 7.9% (130/1655) at survey 2: 5.0% (83) acquired new carriage, 2.8% (47) had persistent carriage, 1.8% (30) cleared the initial carriage, and 90.3% (1495) remained carriage free. At both surveys, nongenogroupable meningococci predominated, followed by genogroups Y, B, W, and C. On multinomial analysis, risk factors for carriage acquisition included attending nightclubs (adjusted relative risk ratio [aRRR], 2.1; 95% CI, 1.1-4.0), having intimate kissing partners (aRRR, 1.8; 95% CI, 1.1-2.9) and HIV (aRRR, 5.0; 95% CI, 1.1-24.4). CONCLUSIONS Meningococcal carriage among first-year university students increased after 2 months. Sociobehavioral risk factors were associated with increased carriage for all analyses. HIV was associated with carriage acquisition. Until vaccination programs become mandatory in South African universities, data suggest that students with HIV could benefit most from meningococcal vaccination.
Collapse
Affiliation(s)
- Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Karistha Ganesh
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
22
|
Diallo K, Feteh VF, Ibe L, Antonio M, Caugant DA, du Plessis M, Deghmane AE, Feavers IM, Fernandez K, Fox LM, Rodrigues CMC, Ronveaux O, Taha MK, Wang X, Brueggemann AB, Maiden MCJ, Harrison OB. Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review. EBioMedicine 2021; 65:103274. [PMID: 33721818 PMCID: PMC7957090 DOI: 10.1016/j.ebiom.2021.103274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.
Collapse
Affiliation(s)
- Kanny Diallo
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Cote d'Ivoire
| | - Vitalis F Feteh
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Lilian Ibe
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dominique A Caugant
- WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo N-0213, Norway
| | - Mignon du Plessis
- A division of the National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | | | - Ian M Feavers
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | | | - LeAnne M Fox
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Department of Paediatric Infectious Diseases, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | | | | | - Xin Wang
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | - Odile B Harrison
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom.
| |
Collapse
|
23
|
Chaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C, Senghore M, Obaro SK, Ousmane S, Pluschke G, Collard JM, Sigaùque B, French N, Klugman KP, Heyderman RS, McGee L, Antonio M, Breiman RF, von Gottberg A, Everett DB, Kadioglu A, Bentley SD. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Commun Biol 2020; 3:559. [PMID: 33033372 PMCID: PMC7545184 DOI: 10.1038/s42003-020-01290-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10-08) and helicase proteins (P = 1.32 × 10-06) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.
Collapse
Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA
- International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire, Niamey, Niger
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Betuel Sigaùque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
24
|
Mwenda JM, Soda E, Weldegebriel G, Katsande R, Biey JNM, Traore T, de Gouveia L, du Plessis M, von Gottberg A, Antonio M, Kwambana-Adams B, Worwui A, Gierke R, Schwartz S, van Beneden C, Cohen A, Serhan F, Lessa FC. Pediatric Bacterial Meningitis Surveillance in the World Health Organization African Region Using the Invasive Bacterial Vaccine-Preventable Disease Surveillance Network, 2011-2016. Clin Infect Dis 2020; 69:S49-S57. [PMID: 31505629 PMCID: PMC6736400 DOI: 10.1093/cid/ciz472] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Bacterial meningitis is a major cause of morbidity and mortality in sub-Saharan Africa. We analyzed data from the World Health Organization's (WHO) Invasive Bacterial Vaccine-preventable Diseases Surveillance Network (2011-2016) to describe the epidemiology of laboratory-confirmed Streptococcus pneumoniae (Spn), Neisseria meningitidis, and Haemophilus influenzae meningitis within the WHO African Region. We also evaluated declines in vaccine-type pneumococcal meningitis following pneumococcal conjugate vaccine (PCV) introduction. METHODS Reports of meningitis in children <5 years old from sentinel surveillance hospitals in 26 countries were classified as suspected, probable, or confirmed. Confirmed meningitis cases were analyzed by age group and subregion (South-East and West-Central). We described case fatality ratios (CFRs), pathogen distribution, and annual changes in serotype and serogroup, including changes in vaccine-type Spn meningitis following PCV introduction. RESULTS Among 49 844 reported meningitis cases, 1670 (3.3%) were laboratory-confirmed. Spn (1007/1670 [60.3%]) was the most commonly detected pathogen; vaccine-type Spn meningitis cases declined over time. CFR was the highest for Spn meningitis: 12.9% (46/357) in the South-East subregion and 30.9% (89/288) in the West-Central subregion. Meningitis caused by N. meningitidis was more common in West-Central than South-East Africa (321/954 [33.6%] vs 110/716 [15.4%]; P < .0001). Haemophilus influenzae (232/1670 [13.9%]) was the least prevalent organism. CONCLUSIONS Spn was the most common cause of pediatric bacterial meningitis in the African region even after reported cases declined following PCV introduction. Sustaining robust surveillance is essential to monitor changes in pathogen distribution and to inform and guide vaccination policies.
Collapse
Affiliation(s)
- Jason M Mwenda
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Elizabeth Soda
- Epidemic Intelligence Service, and, Atlanta, Georgia.,Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Goitom Weldegebriel
- World Health Organization (WHO) Regional Office for Africa, Intercountry Support Team, Harare, Zimbabwe
| | - Regis Katsande
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | - Tieble Traore
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Linda de Gouveia
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Banjul
| | - Brenda Kwambana-Adams
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Banjul
| | - Archibald Worwui
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, Banjul
| | - Ryan Gierke
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stephanie Schwartz
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Chris van Beneden
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| |
Collapse
|
25
|
Meiring S, Cohen C, de Gouveia L, du Plessis M, Kularatne R, Hoosen A, Lekalakala R, Lengana S, Seetharam S, Naicker P, Quan V, Reubenson G, Tempia S, von Mollendorf C, von Gottberg A. Declining Incidence of Invasive Meningococcal Disease in South Africa: 2003-2016. Clin Infect Dis 2020; 69:495-504. [PMID: 30351372 DOI: 10.1093/cid/ciy914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Invasive meningococcal disease (IMD) is endemic to South Africa, where vaccine use is negligible. We describe the epidemiology of IMD in South Africa. METHODS IMD cases were identified through a national, laboratory-based surveillance program, GERMS-SA, from 2003-2016. Clinical data on outcomes and human immunodeficiency virus (HIV) statuses were available from 26 sentinel hospital sites. We conducted space-time analyses to detect clusters of serogroup-specific IMD cases. RESULTS Over 14 years, 5249 IMD cases were identified. The incidence was 0.97 cases per 100 000 persons in 2003, peaked at 1.4 cases per 100 000 persons in 2006, and declined to 0.23 cases per 100 000 persons in 2016. Serogroups were confirmed in 3917 (75%) cases: serogroup A was present in 4.7% of cases, B in 23.3%, C in 9.4%; W in 49.5%; Y in 12.3%, X in 0.3%; Z in 0.1% and 0.4% of cases were non-groupable. We identified 8 serogroup-specific, geo-temporal clusters of disease. Isolate susceptibility was 100% to ceftriaxone, 95% to penicillin, and 99.9% to ciprofloxacin. The in-hospital case-fatality rate was 17% (247/1479). Of those tested, 36% (337/947) of IMD cases were HIV-coinfected. The IMD incidence in HIV-infected persons was higher for all age categories, with an age-adjusted relative risk ratio (aRRR) of 2.5 (95% confidence interval [CI] 2.2-2.8; P < .001) from 2012-2016. No patients reported previous meningococcal vaccine exposure. Patients with serogroup W were 3 times more likely to present with severe disease than those with serogroup B (aRRR 2.7, 95% CI 1.1-6.3); HIV coinfection was twice as common with W and Y diseases (aRRR W = 1.8, 95% CI 1.1-2.9; aRRR Y = 1.9, 95% CI 1.0-3.4). CONCLUSIONS In the absence of significant vaccine use, IMD in South Africa decreased by 76% from 2003-2016. HIV was associated with an increased risk of IMD, especially for serogroup W and Y diseases.
Collapse
Affiliation(s)
- Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg.,School of Public Health, University of the Witwatersrand, Johannesburg
| | - Cheryl Cohen
- School of Public Health, University of the Witwatersrand, Johannesburg.,Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | | | | | - Ruth Lekalakala
- Department of Medical Microbiology, NHLS and University of Limpopo, Polokwane
| | - Sarona Lengana
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | | | - Preneshni Naicker
- Lancet Laboratories, Cape Town.,Division of Medical Microbiology, University of Cape Town
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service (NHLS), Johannesburg
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Empilweni Service & Research Unit, Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Stefano Tempia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centres for Disease Control and Prevention, Pretoria
| | - Claire von Mollendorf
- School of Public Health, University of the Witwatersrand, Johannesburg.,Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, NICD, a Division of the NHLS, Johannesburg.,School of Pathology, University of the Witwatersrand, Johannesburg
| | | |
Collapse
|
26
|
Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ, Quah FX, Blaschke AJ, Pershing NL, Byington CL, Balaji V, Hryniewicz W, Sigauque B, Ravikumar K, Almeida SCG, Ochoa TJ, Ho PL, du Plessis M, Ndlangisa KM, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Pollard AJ, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, Metcalf BJ, Li Y, Beall BW, McGee L, Breiman RF, Aanensen DM, Bentley SD. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microb Genom 2020; 6:e000357. [PMID: 32375991 PMCID: PMC7371119 DOI: 10.1099/mgen.0.000357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.
Collapse
Affiliation(s)
| | - Stephanie W. Lo
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John A. Lees
- Faculty of Medicine, School of Public Health, Imperial College London, UK
| | | | - Andries J. van Tonder
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Leon J. Bentley
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Fu Xiang Quah
- Parasites and microbes, Wellcome Sanger InstituteHinxton, UK
| | - Anne J. Blaschke
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Nicole L. Pershing
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | | | - Waleria Hryniewicz
- National Medicines Institute, Division of Clinical Microbiology and Infection Prevention, Warsaw, Poland
| | - Betuel Sigauque
- Fundação Manhiça / Centro de Investigação em Saúde da Manhiça (CISM), Maputo Mozambique, Instituto Nacional de Saúde, inistério de Saúde, Maputo, Mozambique
| | - K.L. Ravikumar
- Central Research Laboratory, Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India
| | | | - Theresa J. Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Kedibone M. Ndlangisa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | - Susan A. Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel
| | | | - Anne von Gottberg
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | | | - Yuan Li
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F. Breiman
- Rollins School Public Health, Emory University, GA, USA
- Emory Global Health Institute, Atlanta, GA, USA
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | |
Collapse
|
27
|
Mohale T, Wolter N, Allam M, Nzenze SA, Madhi SA, du Plessis M, von Gottberg A. Genomic differences among carriage and invasive nontypeable pneumococci circulating in South Africa. Microb Genom 2019; 5. [PMID: 31617841 PMCID: PMC6861859 DOI: 10.1099/mgen.0.000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Most pneumococci express a polysaccharide capsule, a key virulence factor and target for pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression [nontypeable pneumococci (NTPn)] are more frequently isolated from carriage studies than in invasive disease. Limited data exist about the population structure of carriage NTPn from the African continent. We aimed to characterize carriage NTPn and compare them to previously described invasive NTPn. Carriage and invasive NTPn isolates were obtained from South African cross-sectional studies (2009 and 2012) and laboratory-based surveillance for invasive pneumococcal disease (2003–2013), respectively. Isolates were characterized by capsular locus sequence analysis, multilocus sequence typing, antimicrobial non-susceptibility patterns and phylogenetic analysis. NTPn represented 3.7 % (137/3721) of carriage isolates compared to 0.1 % (39/32 824) of invasive isolates (P<0.001), and 24 % (33/137) of individuals were co-colonized with encapsulated pneumococci. Non-susceptibility to cotrimoxazole [84 % (112/133) vs 44 % (17/39)], penicillin [77 % (102/133) vs 36 % (14/39)], erythromycin [53 % (70/133) vs 31 % (12/39)] and clindamycin [36 % (48/133) vs 18 % (7/39)] was higher (P=0.03) among carriage than invasive NTPn. Ninety-one per cent (124/137) of carriage NTPn had complete deletion of the capsular locus and 9 % (13/137) had capsule genes, compared to 44 % (17/39) and 56 % (22/39) of invasive NTPn, respectively. Carriage NTPn were slightly less diverse [Simpson’s diversity index (D)=0.92] compared to invasive NTPn [D=0.97]. Sixty-seven per cent (92/137) of carriage NTPn belonged to a lineage exclusive to NTPn strains compared to 23 % (9/39) of invasive NTPn. We identified 293 and 275 genes that were significantly associated with carriage and invasive NTPn, respectively. NTPn isolates detected in carriage differed from those causing invasive disease, which may explain their success in colonisation or in causing invasive disease.
Collapse
Affiliation(s)
- Thabo Mohale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Susan A Nzenze
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Research Chair, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|
28
|
Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick JE, Kwambana-Adams B, Law PY, Ho PL, Antonio M, Everett DB, Dagan R, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect Dis 2019; 19:759-769. [PMID: 31196809 PMCID: PMC7641901 DOI: 10.1016/s1473-3099(19)30297-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Invasive pneumococcal disease remains an important health priority owing to increasing disease incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) by analysing 20 027 pneumococcal isolates collected worldwide and from previously published genomic data. In this study, we aimed to investigate the pneumococcal lineages behind the predominant serotypes, the mechanism of serotype replacement in disease, as well as the major pneumococcal lineages contributing to invasive pneumococcal disease in the post-vaccine era and their antibiotic resistant traits. METHODS We whole-genome sequenced 3233 invasive pneumococcal disease isolates from laboratory-based surveillance programmes in Hong Kong (n=78), Israel (n=701), Malawi (n=226), South Africa (n=1351), The Gambia (n=203), and the USA (n=674). The genomes represented pneumococci from before and after pneumococcal conjugate vaccine (PCV) introductions and were from children younger than 3 years. We identified predominant serotypes by prevalence and their major contributing lineages in each country, and assessed any serotype replacement by comparing the incidence rate between the pre-PCV and PCV periods for Israel, South Africa, and the USA. We defined the status of a lineage as vaccine-type GPSC (≥50% 13-valent PCV [PCV13] serotypes) or non-vaccine-type GPSC (>50% non-PCV13 serotypes) on the basis of its initial serotype composition detected in the earliest vaccine period to measure their individual contribution toward serotype replacement in each country. Major pneumococcal lineages in the PCV period were identified by pooled incidence rate using a random effects model. FINDINGS The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. These serotypes were associated with more than one lineage, except for serotype 5 (GPSC8). Serotype replacement was mainly mediated by expansion of non-vaccine serotypes within vaccine-type GPSCs and, to a lesser extent, by increases in non-vaccine-type GPSCs. A globally spreading lineage, GPSC3, expressing invasive serotypes 8 in South Africa and 33F in the USA and Israel, was the most common lineage causing non-vaccine serotype invasive pneumococcal disease in the PCV13 period. We observed that same prevalent non-vaccine serotypes could be associated with distinctive lineages in different countries, which exhibited dissimilar antibiotic resistance profiles. In non-vaccine serotype isolates, we detected significant increases in the prevalence of resistance to penicillin (52 [21%] of 249 vs 169 [29%] of 575, p=0·0016) and erythromycin (three [1%] of 249 vs 65 [11%] of 575, p=0·0031) in the PCV13 period compared with the pre-PCV period. INTERPRETATION Globally spreading lineages expressing invasive serotypes have an important role in serotype replacement, and emerging non-vaccine serotypes associated with different pneumococcal lineages in different countries might be explained by local antibiotic-selective pressures. Continued genomic surveillance of the dynamics of the pneumococcal population with increased geographical representation in the post-vaccine period will generate further knowledge for optimising future vaccine design. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control.
Collapse
Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noga Givon-Lavi
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Pierra Y Law
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Dean B Everett
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA; Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | | |
Collapse
|
29
|
van Tonder AJ, Gladstone RA, Lo SW, Nahm MH, du Plessis M, Cornick J, Kwambana-Adams B, Madhi SA, Hawkins PA, Benisty R, Dagan R, Everett D, Antonio M, Klugman KP, von Gottberg A, Breiman RF, McGee L, Bentley SD. Putative novel cps loci in a large global collection of pneumococci. Microb Genom 2019; 5. [PMID: 31184299 PMCID: PMC6700660 DOI: 10.1099/mgen.0.000274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18 000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6 % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis.
Collapse
Affiliation(s)
- Andries J van Tonder
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rebecca A Gladstone
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Moon H Nahm
- Division of Pulmonary Medicine, Departments of Medicine and Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rachel Benisty
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheeba, Beer-Sheva, Israel
| | - Ron Dagan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheeba, Beer-Sheva, Israel
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Martin Antonio
- Vaccines and Immunity Theme, MRC Unit, Banjul, The Gambia
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Queens Research Institute, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | -
- https://www.pneumogen.net/gps/
| |
Collapse
|
30
|
Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019; 10:2176. [PMID: 31092817 PMCID: PMC6520353 DOI: 10.1038/s41467-019-09976-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.
Collapse
Affiliation(s)
- John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Bart Ferwerda
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Philip H C Kremer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicole E Wheeler
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- The Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Mercedes Valls Serón
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | | | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Alienke J Wijmega-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Anne L Wyllie
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Aeilko H Zwinderman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Zitta B Harboe
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, DK-2300, Denmark
| | - Lene F Lundbo
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Lisette C P G M de Groot
- Department of Human Nutrition, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Natasja M van Schoor
- Amsterdam UMC, VU University, Department of Epidemiology and Biostatistics, Amsterdam Public Health, Van der Boechorststraat 7, Amsterdam, 1007 MB, The Netherlands
| | - Nathalie van der Velde
- Amsterdam UMC, University of Amsterdam, Department of Internal Medicine, Geriatrics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Centre Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Lars H Ängquist
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, DK-2000, Denmark
| | - Thorkild I A Sørensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Copenhagen, DK-2200, Denmark
- The Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-1014, Denmark
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mignon du Plessis
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Susan Nzenze
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Julian Parkhill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Shabir Madhi
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Anne von Gottberg
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Arie van der Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC/RIVM, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Matthijs C Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Jeffrey C Barrett
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Genomics Plc, East Road, Cambridge, CB1 1BH, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
| |
Collapse
|
31
|
Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019; 43:338-346. [PMID: 31003929 PMCID: PMC6557916 DOI: 10.1016/j.ebiom.2019.04.021] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. METHODS Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. FINDINGS The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. INTERPRETATION We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness.
Collapse
Affiliation(s)
| | - Stephanie W Lo
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - John A Lees
- New York University School of Medicine, New York, NY, USA
| | | | | | - Jukka Corander
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK; Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
| | - Andrew J Page
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Pekka Marttinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Espoo, Finland
| | - Leon J Bentley
- Parasites and microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pak Leung Ho
- Department of Microbiology, Carol Yu Centre for Infection, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, Blantyre, Malawi
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia
| | - Rachel Benisty
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, South Africa; Department of Science and Technology, National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, South Africa
| | | | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273 Banjul, the Gambia; Division of Microbiology & Immunity, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, USA; Emory Global Health Institute, Atlanta, USA
| | | |
Collapse
|
32
|
Moosa F, du Plessis M, Wolter N, Carrim M, Cohen C, von Mollendorf C, Walaza S, Tempia S, Dawood H, Variava E, von Gottberg A. Challenges and clinical relevance of molecular detection of Bordetella pertussis in South Africa. BMC Infect Dis 2019; 19:276. [PMID: 30898099 PMCID: PMC6429695 DOI: 10.1186/s12879-019-3869-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/04/2019] [Indexed: 11/30/2022] Open
Abstract
Background We assessed the utility of a multi-target, real-time PCR assay for Bordetella pertussis detection and diagnosis in patients with severe respiratory illness (SRI), influenza-like illness (ILI), and asymptomatic controls. Methods Real-time PCR detection of IS481, pIS1001, hIS1001 and ptxS1 was performed on nasopharyngeal specimens (SRI, ILI and controls) and induced sputum (SRI) collected from June 2012 to May 2016 through respiratory illness surveillance. Using PCR cycle threshold (Ct) value cut-offs, IS481 positive cases were classified as confirmed (Ct < 35) or possible (Ct 35–39) pertussis disease. Results Among 12,922 samples, 146 (1.1%) were IS481 positive of which 62% (90/146) were classified as confirmed. The attributable fraction (AF) was 92.2% (95% CI, 65.6 to 98.2%) and 90.5% (95% CI, 57.5 to 97.9%) amongst SRI and ILI PCR-confirmed pertussis cases, respectively. Amongst possible pertussis cases, AF was 36.9% (95% CI, − 142.3 to 83.6%) and 67.5% (95% CI, − 30.6 to 91.9%) in the SRI and ILI groups, respectively. Conclusion All IS481 positive specimens could be considered as B. pertussis infection, and potentially pertussis disease with supportive clinical information. Electronic supplementary material The online version of this article (10.1186/s12879-019-3869-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| | - Claire von Mollendorf
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Halima Dawood
- Pietermaritzburg Metropolitan Hospitals, KwaZulu-Natal, and Caprisa, University of KwaZulu-Natal, Durban, South Africa
| | - Ebrahim Variava
- University of the Witwatersrand, Johannesburg, South Africa.,Klerksdorp-Tshepong Hospital, North West Province, Klerksdorp, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.,University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
33
|
Carrim M, Wolter N, Benitez AJ, Tempia S, du Plessis M, Walaza S, Moosa F, Diaz MH, Wolff BJ, Treurnicht FK, Hellferscee O, Dawood H, Variava E, Cohen C, Winchell JM, von Gottberg A. Epidemiology and Molecular Identification and Characterization of Mycoplasma pneumoniae, South Africa, 2012-2015. Emerg Infect Dis 2019; 24:506-513. [PMID: 29460736 PMCID: PMC5823326 DOI: 10.3201/eid2403.162052] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2012-2015, we tested respiratory specimens from patients with severe respiratory illness (SRI), patients with influenza-like illness (ILI), and controls in South Africa by real-time PCR for Mycoplasma pneumoniae, followed by culture and molecular characterization of positive samples. M. pneumoniae prevalence was 1.6% among SRI patients, 0.7% among ILI patients, and 0.2% among controls (p<0.001). Age <5 years (adjusted odd ratio 7.1; 95% CI 1.7-28.7) and HIV infection (adjusted odds ratio 23.8; 95% CI 4.1-138.2) among M. pneumonia-positive persons were associated with severe disease. The detection rate attributable to illness was 93.9% (95% CI 74.4%-98.5%) in SRI patients and 80.7% (95% CI 16.7%-95.6%) in ILI patients. The hospitalization rate was 28 cases/100,000 population. We observed the macrolide-susceptible M. pneumoniae genotype in all cases and found P1 types 1, 2, and a type 2 variant with multilocus variable number tandem repeat types 3/6/6/2, 3/5/6/2, and 4/5/7/2.
Collapse
|
34
|
Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA, Clarke SC, Everett D, Cornick J, Sadowy E, Hryniewicz W, Skoczynska A, Moïsi JC, McGee L, Beall B, Metcalf BJ, Breiman RF, Ho PL, Reid R, O’Brien KL, Gladstone RA, Bentley SD, Hanage WP. Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS Pathog 2018; 14:e1007438. [PMID: 30475919 PMCID: PMC6283594 DOI: 10.1371/journal.ppat.1007438] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/06/2018] [Accepted: 10/25/2018] [Indexed: 12/23/2022] Open
Abstract
Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the USA, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3-31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identified a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939-1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last of which resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease, as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development.
Collapse
Affiliation(s)
- Taj Azarian
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Patrick K. Mitchell
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Claudette M. Thompson
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Amel Ghouila
- Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford; NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine (CCVTM), Churchill Hospital, Oxford, United Kingdom
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Martin Antonio
- Medical Research Council Unit The Gambia, Fajara, The Gambia
| | | | - Stuart C. Clarke
- Faculty of Medicine and Institute for Life Sciences and Global Health Research Institute, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, United Kingdom
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer Cornick
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Ewa Sadowy
- National Medicines Institute, Warsaw, Poland
| | | | | | - Jennifer C. Moïsi
- Pfizer Vaccines, Medical Development, Scientific and Clinical Affairs, Paris, France
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Benjamin J. Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Robert F. Breiman
- Global Health Institute, Emory University, Atlanta, Georgia, United States of America
| | - PL Ho
- Department of Microbiology, Queen Mary Hospital University of Hong Kong, Hong Kong, People’s Republic of China
| | - Raymond Reid
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine L. O’Brien
- Center for American Indian Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Rebecca A. Gladstone
- Wellcome Trust, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- Wellcome Trust, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| |
Collapse
|
35
|
du Plessis M, Wolter N, Allam M, de Gouveia L, Moosa F, Ntshoe G, Blumberg L, Cohen C, Smith M, Mutevedzi P, Thomas J, Horne V, Moodley P, Archary M, Mahabeer Y, Mahomed S, Kuhn W, Mlisana K, McCarthy K, von Gottberg A. Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015. Emerg Infect Dis 2018; 23:1308-1315. [PMID: 28726616 PMCID: PMC5547784 DOI: 10.3201/eid2308.162039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of C. diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17) and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate were ST-395, suggesting ongoing circulation of this lineage for >30 years. The absence of preexisting molecular sequence data limits drawing conclusions pertaining to the origin of these strains; however, these findings provide baseline genotypic data for future cases and outbreaks. Neither ST has been reported in any other country; this ST appears to be endemic only in South Africa.
Collapse
|
36
|
Hellferscee O, Tempia S, Walaza S, Variava E, Dawood H, Wolter N, Madhi SA, du Plessis M, Cohen C, Treurnicht FK. Enterovirus genotypes among patients with severe acute respiratory illness, influenza-like illness, and asymptomatic individuals in South Africa, 2012-2014. J Med Virol 2017; 89:1759-1767. [PMID: 28574589 PMCID: PMC5714810 DOI: 10.1002/jmv.24869] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/14/2017] [Indexed: 01/26/2023]
Abstract
Enteroviruses can cause outbreaks of severe acute respiratory illness (SARI) and EV-A, -B, -C, and -D species have different pathogenic profiles and circulation patterns. We aimed to characterize and determine the prevalence of enterovirus genotypes among South African patients with respiratory illness and controls during June 2012 to July 2014. Syndromic SARI and influenza-like illness (ILI) surveillance was performed at two sentinel sites. At each site nasopharyngeal/oropharyngeal specimens were collected from SARI and ILI patients as well as controls. Specimens were tested for enterovirus by real-time PCR. Positive specimens were further genotyped by sequencing a region of the VP1 gene. The prevalence of enterovirus was 5.8% (87/1494), 3.4% (103/3079), and 3.4% (46/1367) among SARI, ILI, and controls, respectively (SARI/controls, P = 0.002 and ILI/control, P = 0.973). Among the 101/236 (42.8%) enterovirus-positive specimens that could be genotyped, we observed a high diversity of circulating enterovirus genotypes (a total of 33 genotypes) from all four human enterovirus species with high prevalence of Enterovirus-B (60.4%; 61/101) and Enterovirus-A (21.8%; 22/101) compared to Enterovirus-C (10.9%; 11/101) and Enterovirus-D (6.9%; 7/101) (P = 0.477). Of the enterovirus genotypes identified, Echovirus 30 (9.9%, 10/101), Coxsackie virus B5 (7.9%, 8/101) and Enterovirus-D68 (6.9%, 7/101) were most prevalent. There was no difference in disease severity (SARI or ILI compared to controls) between the different enterovirus species (P = 0.167). We observed a high number of enterovirus genotypes in patients with respiratory illness and in controls from South Africa with no disease association of EV species with disease severity.
Collapse
Affiliation(s)
- Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- Centres for Disease Control and PreventionAtlantaGeorgia
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Ebrahim Variava
- University of the WitwatersrandJohannesburgSouth Africa
- Department of MedicineKlerksdorp‐Tshepong Hospital ComplexKlerksdorpSouth Africa
| | - Halima Dawood
- Pietermaritzburg Metropolitan HospitalPietermaritzburgSouth Africa
- CaprisaUniversity of KwaZulu‐NatalSouth Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Shabir A. Madhi
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Florette K. Treurnicht
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| |
Collapse
|
37
|
Ganesh K, Allam M, Wolter N, Bratcher HB, Harrison OB, Lucidarme J, Borrow R, de Gouveia L, Meiring S, Birkhead M, Maiden MCJ, von Gottberg A, du Plessis M. Molecular characterization of invasive capsule null Neisseria meningitidis in South Africa. BMC Microbiol 2017; 17:40. [PMID: 28222677 PMCID: PMC5320719 DOI: 10.1186/s12866-017-0942-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/31/2017] [Indexed: 12/15/2022] Open
Abstract
Background The meningococcal capsule is an important virulence determinant. Unencapsulated meningococci lacking capsule biosynthesis genes and containing the capsule null locus (cnl) are predominantly non-pathogenic. Rare cases of invasive meningococcal disease caused by cnl isolates belonging to sequence types (ST) and clonal complexes (cc) ST-845 (cc845), ST-198 (cc198), ST-192 (cc192) and ST-53 (cc53) have been documented. The clinical significance of these isolates however remains unclear. We identified four invasive cnl meningococci through laboratory-based surveillance in South Africa from 2003 through 2013, which we aimed to characterize using whole genome data. Results One isolate [NG: P1.7-2,30: F1-2: ST-53 (cc53)] contained cnl allele 12, and caused empyema in an adult male with bronchiectasis from tuberculosis, diabetes mellitus and a smoking history. Three isolates were NG: P1.18-11,42-2: FΔ: ST-192 (cc192) and contained cnl allele 2. One patient was an adolescent male with meningitis. The remaining two isolates were from recurrent disease episodes (8 months apart) in a male child with deficiency of the sixth complement component, and with the exception of two single nucleotide polymorphisms, contained identical core genomes. The ST-53 (cc53) isolate possessed alleles for NHBA peptide 191 and fHbp variant 2; whilst the ST-192 (cc192) isolates contained NHBA peptide 704 and fHbp variant 3. All four isolates lacked nadA. Comparison of the South African genomes to 61 additional cnl genomes on the PubMLST Neisseria database (http://pubmlst.org/neisseria/), determined that most putative virulence genes could be found in both invasive and carriage phenotypes. Conclusions Although rare, invasive disease by cnl meningococci may be associated with host immunodeficiency and such patients may benefit from protein-based meningococcal vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0942-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Karistha Ganesh
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa. .,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Mushal Allam
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Manchester, UK
| | - Linda de Gouveia
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monica Birkhead
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases (NICD), A division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
38
|
Cornick JE, Tastan Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, Govindpershad S, Ousmane S, Senghore M, du Plessis M, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Bentley SD, Kadioglu A, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Alderson M, Everett DB. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1. Vaccine 2017; 35:972-980. [PMID: 28081968 PMCID: PMC5287219 DOI: 10.1016/j.vaccine.2016.12.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/29/2016] [Accepted: 12/15/2016] [Indexed: 11/28/2022]
Abstract
Serotype 1 is one of the most common causes of pneumococcal disease worldwide. Pneumococcal protein vaccines are currently being developed as an alternate intervention strategy to pneumococcal conjugate vaccines. Pre-requisites for an efficacious pneumococcal protein vaccine are universal presence and minimal variation of the target antigen in the pneumococcal population, and the capability to induce a robust human immune response. We used in silico analysis to assess the prevalence of seven protein vaccine candidates (CbpA, PcpA, PhtD, PspA, SP0148, SP1912, SP2108) among 445 serotype 1 pneumococci from 26 different countries, across four continents. CbpA (76%), PspA (68%), PhtD (28%), PcpA (11%) were not universally encoded in the study population, and would not provide full coverage against serotype 1. PcpA was widely present in the European (82%), but not in the African (2%) population. A multi-valent vaccine incorporating CbpA, PcpA, PhtD and PspA was predicted to provide coverage against 86% of the global population. SP0148, SP1912 and SP2108 were universally encoded and we further assessed their predicted amino acid, antigenic and structural variation. Multiple allelic variants of these proteins were identified, different allelic variants dominated in different continents; the observed variation was predicted to impact the antigenicity and structure of two SP0148 variants, one SP1912 variant and four SP2108 variants, however these variants were each only present in a small fraction of the global population (<2%). The vast majority of the observed variation was predicted to have no impact on the efficaciousness of a protein vaccine incorporating a single variant of SP0148, SP1912 and/or SP2108 from S. pneumoniae TIGR4. Our findings emphasise the importance of taking geographic differences into account when designing global vaccine interventions and support the continued development of SP0148, SP1912 and SP2108 as protein vaccine candidates against this important pneumococcal serotype.
Collapse
Affiliation(s)
- Jennifer E Cornick
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK.
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Feyruz Yalcin
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anmol M Kiran
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Benjamin Kumwenda
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Chrispin Chaguza
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Shanil Govindpershad
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire, Niamey, Niger
| | - Madikay Senghore
- Medical Research Council, Banjul, Gambia; Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, UK
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Beutel Sigaùque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | | | - Stephen D Bentley
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Aras Kadioglu
- Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Martin Antonio
- Medical Research Council, Banjul, Gambia; Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, USA
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | | | - Dean B Everett
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi; Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| |
Collapse
|
39
|
Ndlangisa KM, du Plessis M, Allam M, Wolter N, Mohale T, de Gouveia L, Birkhead M, Klugman KP, von Gottberg A. Two cases of serotypeable and non-serotypeable variants of Streptococcus pneumoniae detected simultaneously during invasive disease. BMC Microbiol 2016; 16:126. [PMID: 27342074 PMCID: PMC4921036 DOI: 10.1186/s12866-016-0745-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 06/15/2016] [Indexed: 01/13/2023] Open
Abstract
Background More than 94 serotypes of Streptococcus pneumoniae have been described to date, however the majority of disease is caused by approximately 20 serotypes. Some pneumococci do not react with commercially available antisera used for serotyping and are thus regarded as non-serotypeable (NT). These pneumococci are commonly isolated during carriage studies and very rarely cause invasive disease. Colonization may occur with more than one serotype however disease with more than one serotype is rarely detected. Thus there are limited data describing cases of pneumococcal disease caused by more than one isolate. Results In two cases of invasive pneumococcal disease in South Africa, a non-serotypeable and a serotypeable isolate were co-detected during routine serotyping. A serotype 1 and 18C isolate were each co-detected with a non-serotypeable isolate in 2009 (case A) and 2010 (case B), from cerebrospinal fluid and blood, respectively. Both patients were 10–14 years old. For case A, the serotypeable isolate could not be obtained due to low representation in the mixed culture. Using electron microscopy we confirmed lack of capsule for the non-serotypeable isolates. Comparison of the case A non-serotypeable isolate with a serotype 1 genome revealed only the presence of the rhamnose biosynthesis genes (rmlA, B, C and D) in the capsular locus, all other capsular genes were absent. Nonetheless it had a multilocus sequence type (ST) associated with serotype 1 (ST217 and ribosomal ST3462) and its core genome clustered with other ST217 isolates. The case B non-serotypeable isolate had all serotype 18C capsular genes except for variation in the wchA and wze genes, compared to the 18C isolate. Both case B isolates were ST9817 and their core genomes were identical. Conclusions The ability of pneumococci to alter capsule production is a potential vaccine escape mechanism and therefore non-serotypeable pneumococci should be monitored as such organisms may increase under vaccine pressure. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0745-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kedibone M Ndlangisa
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa. .,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mushal Allam
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thabo Mohale
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Monica Birkhead
- Centre for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
40
|
Lucidarme J, Hill DMC, Bratcher HB, Gray SJ, du Plessis M, Tsang RSW, Vazquez JA, Taha MK, Ceyhan M, Efron AM, Gorla MC, Findlow J, Jolley KA, Maiden MCJ, Borrow R. Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. J Infect 2015; 71:544-52. [PMID: 26226598 PMCID: PMC4635312 DOI: 10.1016/j.jinf.2015.07.007] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/16/2015] [Accepted: 07/17/2015] [Indexed: 10/31/2022]
Abstract
OBJECTIVES Neisseria meningitidis is a leading cause of meningitis and septicaemia. The hyperinvasive ST-11 clonal complex (cc11) caused serogroup C (MenC) outbreaks in the US military in the 1960s and UK universities in the 1990s, a global Hajj-associated serogroup W (MenW) outbreak in 2000-2001, and subsequent MenW epidemics in sub-Saharan Africa. More recently, endemic MenW disease has expanded in South Africa, South America and the UK, and MenC cases have been reported among European and North American men who have sex with men (MSM). Routine typing schemes poorly resolve cc11 so we established the population structure at genomic resolution. METHODS Representatives of these episodes and other geo-temporally diverse cc11 meningococci (n = 750) were compared across 1546 core genes and visualised on phylogenetic networks. RESULTS MenW isolates were confined to a distal portion of one of two main lineages with MenB and MenC isolates interspersed elsewhere. An expanding South American/UK MenW strain was distinct from the 'Hajj outbreak' strain and a closely related endemic South African strain. Recent MenC isolates from MSM in France and the UK were closely related but distinct. CONCLUSIONS High resolution 'genomic' multilocus sequence typing is necessary to resolve and monitor the spread of diverse cc11 lineages globally.
Collapse
Affiliation(s)
- Jay Lucidarme
- Vaccine Evaluation Unit, Public Health England, Manchester Medical Microbiology Partnership, Second Floor, Clinical Sciences Building II, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WZ, UK.
| | | | | | - Steve J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Second Floor, Clinical Sciences Building II, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WZ, UK.
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.
| | - Raymond S W Tsang
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada.
| | - Julio A Vazquez
- Reference Laboratory for Meningococci, Institute of Health Carlos III, Majadahonda, Spain.
| | - Muhamed-Kheir Taha
- Institut Pasteur, Unité des Infections Bactériennes invasives, Département Infection et Epidémiologie, Paris, France.
| | - Mehmet Ceyhan
- Faculty of Medicine, Hacettepe University, Ankara, Turkey.
| | - Adriana M Efron
- Servicio Bacteriología Clínica, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina.
| | - Maria C Gorla
- Division of Medical Biology, Bacteriology Department, Adolfo Lutz Institute, São Paulo 01246-902, Brazil.
| | - Jamie Findlow
- Vaccine Evaluation Unit, Public Health England, Manchester Medical Microbiology Partnership, Second Floor, Clinical Sciences Building II, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WZ, UK.
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, UK.
| | | | - Ray Borrow
- Vaccine Evaluation Unit, Public Health England, Manchester Medical Microbiology Partnership, Second Floor, Clinical Sciences Building II, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WZ, UK; Meningococcal Reference Unit, Public Health England, Manchester Medical Microbiology Partnership, Second Floor, Clinical Sciences Building II, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WZ, UK.
| |
Collapse
|
41
|
Ndlangisa KM, du Plessis M, Wolter N, de Gouveia L, Klugman KP, von Gottberg A, GERMS-SA F. Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines. PLoS One 2014; 9:e107666. [PMID: 25233455 PMCID: PMC4169438 DOI: 10.1371/journal.pone.0107666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/12/2014] [Indexed: 11/23/2022] Open
Abstract
We determined the sequence types of isolates that caused invasive pneumococcal disease (IPD) prior to routine use of pneumococcal conjugate vaccines (PCV) in South Africa. PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, laboratory-based surveillance for IPD, were selected for genetic characterization. In addition, all 134 non-PCV isolates from children <2 years were selected for characterization. Sequence type diversity by serotype and age category (children <5 years vs. individuals ≥5 years) was assessed for PCV serotypes using Simpson’s index of diversity. Similar genotypes circulated among isolates from children and adults and the majority of serotypes were heterogeneous. While globally disseminated clones were common among some serotypes (e.g., serotype 1 [clonal complex (CC) 217, 98% of all serotype 1] and 14 [CC230, 43%)]), some were represented mainly by clonal complexes rarely reported elsewhere (e.g., serotype 3 [CC458, 60%] and 19A [CC2062, 83%]). In children <2 years, serotype 15B and 8 were the most common serotypes among non-PCV isolates (16% [22/134] and 15% [20/134] isolates, respectively). Sequence type 7052 and 53 were most common among serotypes 15B and 8 isolates and accounted for 58% (7/12) and 64% (9/14) of the isolates, respectively. Serotype 19F, 14, 19A and 15B had the highest proportions of penicillin non-susceptible isolates. Genotypes rarely reported in other parts of the world but common among some of our serotypes highlight the importance of our data as these genotypes may emerge post PCV introduction.
Collapse
Affiliation(s)
- Kedibone M. Ndlangisa
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council, Johannesburg, South Africa
- * E-mail:
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Medical Research Council, Johannesburg, South Africa
| | - Keith P. Klugman
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
- Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Medical Research Council, Johannesburg, South Africa
| | | |
Collapse
|
42
|
Wolter N, Tempia S, Cohen C, Madhi SA, Venter M, Moyes J, Walaza S, Malope-Kgokong B, Groome M, du Plessis M, Magomani V, Pretorius M, Hellferscee O, Dawood H, Kahn K, Variava E, Klugman KP, von Gottberg A. High nasopharyngeal pneumococcal density, increased by viral coinfection, is associated with invasive pneumococcal pneumonia. J Infect Dis 2014; 210:1649-57. [PMID: 24907383 DOI: 10.1093/infdis/jiu326] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND We identified factors associated with pneumococcal colonization, high colonization density, and invasive pneumococcal pneumonia among patients hospitalized with acute lower respiratory tract infections (ALRTIs). METHODS In 2010, 4025 cases were enrolled in surveillance in South Africa. A total of 969 of 4025 systematically selected nasopharyngeal-oropharyngeal specimens (24%) were tested for respiratory viruses and Streptococcus pneumoniae by real-time polymerase chain reaction. Of these, 749 (77%) had blood tested for S. pneumoniae. RESULTS Pneumococcal colonization was detected in 55% of cases (534 of 969). On multivariable analysis that controlled for age and tuberculosis treatment, infection with influenza virus (adjusted odds ratio [OR], 2.2; 95% confidence interval [CI], 1.1-4.5), adenovirus (adjusted OR, 1.7; 95% CI, 1.1-2.7), rhinovirus (adjusted OR, 1.6; 95% CI, 1.1-2.3), and human immunodeficiency virus (HIV; adjusted OR, 1.6; 95% CI, 1.1-2.4) were associated with pneumococcal colonization. High colonization density was associated with respiratory virus coinfection (adjusted OR, 1.7; 95% CI, 1.1-2.6) and invasive pneumococcal pneumonia (adjusted OR, 2.3; 95% CI, 1.3-4.0), after adjustment for age and sex. Seven percent (52 of 749) had pneumococci detected in blood. On multivariable analysis among colonized cases, invasive pneumococcal pneumonia was associated with HIV (adjusted OR, 3.2; 95% CI, 1.4-7.5), influenza virus (adjusted OR, 8.2; 95% CI, 2.7-25.0), high colonization density (adjusted OR, 18.7; 95% CI, 2.3-155.1), and ≥5 days of hospitalization (adjusted OR, 3.7; 95% CI, 1.7-8.2). CONCLUSIONS Respiratory virus infection was associated with elevated colonization density and, in turn, invasive pneumococcal pneumonia.
Collapse
Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Influenza Division, Centers for Disease Control and Prevention
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences
| | - Shabir A Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Medical Research Council: Respiratory and Meningeal Pathogens Research Unit Department of Science and Technology/National Research Foundation: Vaccine-Preventable Diseases
| | - Marietjie Venter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Zoonoses Research Unit, Department of Medical Virology, University of Pretoria
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Babatyi Malope-Kgokong
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Michelle Groome
- Department of Science and Technology/National Research Foundation: Vaccine-Preventable Diseases
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Victoria Magomani
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Marthi Pretorius
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | - Halima Dawood
- Pietermaritzburg Metropolitan Hospitals University of KwaZulu Natal
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transition Research Unit Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg Centre for Global Health Research, Umeå University, Sweden INDEPTH Network, Accra, Ghana
| | | | - Keith P Klugman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Hubert Department of Global Health, Rollins School of Public Health Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service Faculty of Health Sciences Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| |
Collapse
|
43
|
du Plessis M, Wolter N, Crowther-Gibson P, Hamstra HJ, Schipper K, Moodley C, Cohen C, van de Beek D, van der Ley P, von Gottberg A, van der Ende A. Meningococcal serogroup Y lpxL1 variants from South Africa are associated with clonal complex 23 among young adults. J Infect 2014; 68:455-61. [DOI: 10.1016/j.jinf.2013.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/21/2013] [Accepted: 12/29/2013] [Indexed: 11/25/2022]
|
44
|
Wolter N, Cohen C, Tempia S, Madhi SA, Venter M, Moyes J, Walaza S, Malope Kgokong B, Groome M, du Plessis M, Pretorius M, Dawood H, Kahn K, Variava E, Klugman KP, von Gottberg A. HIV and influenza virus infections are associated with increased blood pneumococcal load: a prospective, hospital-based observational study in South Africa, 2009-2011. J Infect Dis 2013; 209:56-65. [PMID: 23922370 DOI: 10.1093/infdis/jit427] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Increased pneumococcal loads are associated with severe outcomes. We determined the prevalence of pneumococcal DNA in blood specimens from patients hospitalized with acute lower respiratory tract infection and identified factors associated with invasive pneumococcal pneumonia, bacterial loads, and death. METHODS A total of 8523 patients were enrolled as part of prospective hospital-based surveillance. Blood was collected for quantitative pneumococcal (lytA) detection, and nasopharyngeal specimens were collected for detection of influenza virus and other respiratory viruses by real-time polymerase chain reaction. RESULTS Of 6396 cases (75%) with lytA results, 422 (7%) were positive for pneumococcal DNA. The prevalences of human immunodeficiency virus (HIV) and influenza virus were 51% (2965/5855) and 8% (485/6358), respectively. On multivariable analysis, HIV infection (adjusted odds ratio [aOR], 2.4; 95% confidence interval [CI], 1.6-3.6), influenza virus coinfection (aOR, 1.4; 95% CI, 1.2-2.1), oxygen therapy during admission (aOR, 1.6; 95% CI, 1.1-2.3) and in-hospital death (aOR, 2.1; 95% CI, 1.1-4.0) were significantly associated with increased pneumococcal load. Among lytA-positive patients, after adjustment for length of hospitalization, duration of symptoms, and oxygen therapy during admission, pneumococcal loads ≥10,000 DNA copies/mL (aOR, 3.6; 95% CI, 1.8-7.2) were associated with increased risk of death. CONCLUSIONS HIV and influenza virus infections were associated with elevated pneumococcal loads, which, in turn, were associated with increased risk of death.
Collapse
Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mothibeli KM, du Plessis M, von Gottberg A, Murphy E, Hoiseth SK, Zlotnick G, Klugman KP. Distribution of factor H binding protein beyond serogroup B: Variation among five serogroups of invasive Neisseria meningitidis in South Africa. Vaccine 2011; 29:2187-92. [PMID: 21144918 DOI: 10.1016/j.vaccine.2010.11.072] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 11/11/2010] [Accepted: 11/20/2010] [Indexed: 10/18/2022]
|
46
|
Fali A, du Plessis M, Wolter N, Klugman KP, von Gottberg A. Single report of β-lactam resistance in an invasive Haemophilus influenzae isolate from South Africa mediated by mutations in penicillin-binding protein 3, 2003-2008. Int J Antimicrob Agents 2010; 36:480-2. [PMID: 20846827 DOI: 10.1016/j.ijantimicag.2010.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 07/26/2010] [Indexed: 10/19/2022]
|
47
|
du Plessis M, de Gouveia L, Skosana H, Thomas J, Blumberg L, Klugman KP, von Gottberg A. Invasive Neisseria meningitidis with decreased susceptibility to fluoroquinolones in South Africa, 2009. J Antimicrob Chemother 2010; 65:2258-60. [PMID: 20688769 DOI: 10.1093/jac/dkq291] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
48
|
Murphy E, Andrew L, Lee KL, Dilts DA, Nunez L, Fink PS, Ambrose K, Borrow R, Findlow J, Taha MK, Deghmane AE, Kriz P, Musilek M, Kalmusova J, Caugant DA, Alvestad T, Mayer LW, Sacchi CT, Wang X, Martin D, von Gottberg A, du Plessis M, Klugman KP, Anderson AS, Jansen KU, Zlotnick GW, Hoiseth SK. Sequence diversity of the factor H binding protein vaccine candidate in epidemiologically relevant strains of serogroup B Neisseria meningitidis. J Infect Dis 2009; 200:379-89. [PMID: 19534597 DOI: 10.1086/600141] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Recombinant forms of Neisseria meningitidis human factor H binding protein (fHBP) are undergoing clinical trials in candidate vaccines against invasive meningococcal serogroup B disease. We report an extensive survey and phylogenetic analysis of the diversity of fhbp genes and predicted protein sequences in invasive clinical isolates obtained in the period 2000-2006. METHODS Nucleotide sequences of fhbp genes were obtained from 1837 invasive N. meningitidis serogroup B (MnB) strains from the United States, Europe, New Zealand, and South Africa. Multilocus sequence typing (MLST) analysis was performed on a subset of the strains. RESULTS Every strain contained the fhbp gene. All sequences fell into 1 of 2 subfamilies (A or B), with 60%-75% amino acid identity between subfamilies and at least 83% identity within each subfamily. One fHBP sequence may have arisen via inter-subfamily recombination. Subfamily B sequences were found in 70% of the isolates, and subfamily A sequences were found in 30%. Multiple fHBP variants were detected in each of the common MLST clonal complexes. All major MLST complexes include strains in both subfamily A and subfamily B. CONCLUSIONS The diversity of strains observed underscores the importance of studying the distribution of the vaccine antigen itself rather than relying on common epidemiological surrogates such as MLST.
Collapse
Affiliation(s)
- Ellen Murphy
- Wyeth Vaccines Research, Pearl River, New York 10965, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
McGee L, Biek D, Ge Y, Klugman M, du Plessis M, Smith AM, Beall B, Whitney CG, Klugman KP. In vitro evaluation of the antimicrobial activity of ceftaroline against cephalosporin-resistant isolates of Streptococcus pneumoniae. Antimicrob Agents Chemother 2009; 53:552-6. [PMID: 19015339 PMCID: PMC2630653 DOI: 10.1128/aac.01324-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 10/31/2008] [Accepted: 11/09/2008] [Indexed: 11/20/2022] Open
Abstract
Increasing pneumococcal resistance to extended-spectrum cephalosporins warrants the search for novel agents with activity against such resistant strains. Ceftaroline, a parenteral cephalosporin currently in phase 3 clinical development, has demonstrated potent in vitro activity against resistant gram-positive organisms, including penicillin-resistant Streptococcus pneumoniae. In this study, the activity of ceftaroline was evaluated against highly cefotaxime-resistant isolates of pneumococci from the Active Bacterial Core surveillance program of the Centers for Disease Control and Prevention and against laboratory-derived cephalosporin-resistant mutants of S. pneumoniae. The MICs of ceftaroline and comparators were determined by broth microdilution. In total, 120 U.S. isolates of cefotaxime-resistant (MIC > or = 4 microg/ml) S. pneumoniae were tested along with 18 laboratory-derived R6 strains with known penicillin-binding protein (PBP) mutations. Clinical isolates were characterized by multilocus sequence typing, and the DNAs of selected isolates were sequenced to identify mutations affecting pbp genes. Ceftaroline (MIC(90) = 0.5 microg/ml) had greater in vitro activity than penicillin, cefotaxime, or ceftriaxone (MIC(90) = 8 microg/ml for all comparators) against the set of highly cephalosporin-resistant clinical isolates of S. pneumoniae. Ceftaroline was also more active against the defined R6 PBP mutant strains, which suggests that ceftaroline can overcome common mechanisms of PBP-mediated cephalosporin resistance. These data indicate that ceftaroline has significant potency against S. pneumoniae strains resistant to existing parenteral cephalosporins and support its continued development for the treatment of infections caused by resistant S. pneumoniae strains.
Collapse
|
50
|
von Gottberg A, Klugman KP, Cohen C, Wolter N, de Gouveia L, du Plessis M, Mpembe R, Quan V, Whitelaw A, Hoffmann R, Govender N, Meiring S, Smith AM, Schrag S. Emergence of levofloxacin-non-susceptible Streptococcus pneumoniae and treatment for multidrug-resistant tuberculosis in children in South Africa: a cohort observational surveillance study. Lancet 2008; 371:1108-13. [PMID: 18359074 DOI: 10.1016/s0140-6736(08)60350-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Use of fluoroquinolones to treat paediatric cases of multidrug-resistant tuberculosis could affect the emergence of resistance to this class of drugs. Our aim was to estimate the incidence of, and risk factors for, invasive pneumococcal disease caused by fluoroquinolone-resistant Streptococcus pneumoniae in children in South Africa. METHODS 21,521 cases of invasive pneumococcal disease were identified by active national surveillance between 2000 and 2006, with enhanced surveillance at 15 sentinel hospitals in seven provinces introduced in 2003. We screened 19,404 isolates (90% of cases) for ofloxacin resistance and measured levofloxacin minimum inhibitory concentrations (MICs) for all isolates that were ofloxacin resistant. Non-susceptibility to levofloxacin was defined as an MIC of 4 mg/L or more. Nasopharyngeal pneumococcal carriage was assessed in 65 children in two tuberculosis hospitals where invasive pneumococcal disease caused by levofloxacin-non-susceptible S pneumoniae had been detected. FINDINGS 12 cases of invasive pneumococcal disease were identified as being non-susceptible to levofloxacin, all in children aged under 15 years. All isolates were rifampicin resistant. Outcome was known for 11 of these patients; five (45%) died. Invasive disease caused by levofloxacin-non-susceptible S pneumoniae was associated with a history of tuberculosis treatment (eight [89%] of nine children with non-susceptible isolates had a history of treatment vs 396 [18%] of 2202 children with susceptible isolates; relative risk [RR] 35.78, 95% CI 4.49-285.30) and nosocomial invasive pneumococcal disease (eight [80%] of ten children with non-susceptible isolates had acquired infection nosocomially vs 109 [4%] of 2709 with susceptible isolates; RR 88.96, 19.10-414.29). 31 (89%) of 35 pneumococcal carriers had bacteria that were non-susceptible to levofloxacin. INTERPRETATION Our data suggest that the use of fluoroquinolones to treat multidrug-resistant tuberculosis in children has led to the emergence of invasive pneumococcal disease caused by levofloxacin-non-susceptible S pneumoniae and its nosocomial spread.
Collapse
Affiliation(s)
- Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|