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Hackman J, Sheppard C, Phelan J, Jones-Warner W, Sobkowiak B, Shah S, Litt D, Fry NK, Toizumi M, Yoshida LM, Hibberd M, Miller E, Flasche S, Hué S. Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. Wellcome Open Res 2023; 8:427. [PMID: 38638914 PMCID: PMC11024593 DOI: 10.12688/wellcomeopenres.19219.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 04/20/2024] Open
Abstract
Background: Inference on pneumococcal transmission has mostly relied on longitudinal studies which are costly and resource intensive. Therefore, we conducted a pilot study to test the ability to infer who infected whom from cross-sectional pneumococcal sequences using phylogenetic inference. Methods: Five suspected transmission pairs, for which there was epidemiological evidence of who infected whom, were selected from a household study. For each pair, Streptococcus pneumoniae full genomes were sequenced from nasopharyngeal swabs collected on the same day. The within-host genetic diversity of the pneumococcal population was used to infer the transmission direction and then cross-validated with the direction suggested by the epidemiological records. Results: The pneumococcal genomes clustered into the five households from which the samples were taken. The proportion of concordantly inferred transmission direction generally increased with increasing minimum genome fragment size and single nucleotide polymorphisms. We observed a larger proportion of unique polymorphic sites in the source bacterial population compared to that of the recipient in four of the five pairs, as expected in the case of a transmission bottleneck. The only pair that did not exhibit this effect was also the pair that had consistent discordant transmission direction compared to the epidemiological records suggesting potential misdirection as a result of false-negative sampling. Conclusions: This pilot provided support for further studies to test if the direction of pneumococcal transmission can be reliably inferred from cross-sectional samples if sequenced with sufficient depth and fragment length.
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Affiliation(s)
- Jada Hackman
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Carmen Sheppard
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - William Jones-Warner
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ben Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sonal Shah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - David Litt
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Norman K. Fry
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
- Immunisation & Countermeasures Division, UK Health Security Agency, London, UK
| | - Michiko Toizumi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Lay-Myint Yoshida
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Elizabeth Miller
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stefan Flasche
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stéphane Hué
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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2
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Qu F, Weschler LB, Zhang Y, Spengler JD. Childhood pneumonia in Beijing: Associations and interactions among selected demographic and environmental factors. ENVIRONMENTAL RESEARCH 2023; 231:116211. [PMID: 37257739 DOI: 10.1016/j.envres.2023.116211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 06/02/2023]
Abstract
Among infectious diseases, pneumonia is the greatest cause of mortality in children less than 5 years old. Approximately 27% of Beijing's 3-8 year-old children have had pneumonia at least once. The sole reservoir of pneumonia pathogens is the human nasopharynx. We investigated associations and interactions among two kinds of environmental risk factors: i) airborne pathogens, namely closed bedroom window and shared bedroom and ii) pollutants, namely traffic pollution and environmental tobacco smoke (ETS). We evaluated breastfeeding's (BF) protective value against childhood pneumonia. The database consists of responses to a questionnaire in a cross-sectional study. Crude and adjusted Odds Ratios were assessed independently for each risk factor. Combinations of the studied risk factors were analyzed using multivariate logistic regression. Risk factors were evaluated for interactions on the additive scale using the metrics Relative Excess Risk due to Interaction (RERI), Attributable Proportion (AP) and Synergy Index (S). All independent risk factors were significant for children's pneumonia. We also found evidence of possible synergistic interaction between pairs of risk factors that was stronger when one of the risk factors was a closed bedroom window. Remarkably, window opening was associated with reduced risk of pneumonia for children living near heavy traffic pollution. Longer duration BF was more protective than shorter, and exclusive BF was more protective than partial BF against childhood pneumonia. In conclusion, low ventilation (closed bedroom windows), shared bedroom, ETS, and traffic exposure were associated with increased risk of pneumonia. Exclusive BF for more than six months had the greatest protective value against pneumonia.
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Affiliation(s)
- Fang Qu
- China Meteorological Administration Training Center, China Meteorological Administration, Beijing, 100081, China; Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, United States
| | - Louise B Weschler
- Independent Researcher, 161 Richdale Road, Colts Neck, NJ, 07722, United States.
| | - Yinping Zhang
- Department of Building Science, Tsinghua University, Beijing, 100084, China
| | - John D Spengler
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, United States
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3
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Adamu AL, Ojal J, Abubakar IA, Odeyemi KA, Bello MM, Okoromah CAN, Karia B, Karani A, Akech D, Inem V, Scott JAG, Adetifa IMO. The impact of introduction of the 10-valent pneumococcal conjugate vaccine on pneumococcal carriage in Nigeria. Nat Commun 2023; 14:2666. [PMID: 37160867 PMCID: PMC10169786 DOI: 10.1038/s41467-023-38277-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/24/2023] [Indexed: 05/11/2023] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) protect against invasive pneumococcal disease (IPD) among vaccinees. However, at population level, this protection is driven by indirect effects. PCVs prevent nasopharyngeal acquisition of vaccine-serotype (VT) pneumococci, reducing onward transmission. Each disease episode is preceded by infection from a carrier, so vaccine impacts on carriage provide a minimum estimate of disease reduction in settings lacking expensive IPD surveillance. We documented carriage prevalence and vaccine coverage in two settings in Nigeria annually (2016-2020) following PCV10 introduction in 2016. Among 4,684 rural participants, VT carriage prevalence fell from 21 to 12% as childhood (<5 years) vaccine coverage rose from 7 to 84%. Among 2,135 urban participants, VT carriage prevalence fell from 16 to 9% as uptake rose from 15 to 94%. Within these ranges, carriage prevalence declined with uptake. Increasing PCV10 coverage reduced pneumococcal infection at all ages, implying at least a comparable reduction in IPD.
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Affiliation(s)
- Aishatu L Adamu
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Community Medicine, College of Health Sciences, Bayero University, Kano/Aminu Kano Teaching Hospital, Kano, Nigeria.
| | - J Ojal
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Isa A Abubakar
- Department of Community Medicine, College of Health Sciences, Bayero University, Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Kofo A Odeyemi
- Department of Community Medicine and Primary Care, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Musa M Bello
- Department of Community Medicine, College of Health Sciences, Bayero University, Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Christy A N Okoromah
- Department of Paediatrics and Child Health, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | - Angela Karani
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Donald Akech
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Victor Inem
- Department of Community Medicine and Primary Care, College of Medicine, University of Lagos, Lagos, Nigeria
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Ifedayo M O Adetifa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Department of Paediatrics and Child Health, College of Medicine, University of Lagos, Lagos, Nigeria
- Nigeria Centre for Disease Control, Abuja, Nigeria
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4
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Carrim M, Tempia S, Thindwa D, Martinson NA, Kahn K, Flasche S, Hellferscee O, Treurnicht FK, McMorrow ML, Moyes J, Mkhencele T, Mathunjwa A, Kleynhans J, Lebina L, Mothlaoleng K, Wafawanaka F, Gómez-Olivé FX, Cohen C, von Gottberg A, Wolter N. Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study. Clin Infect Dis 2023; 76:e710-e717. [PMID: 35717655 PMCID: PMC10169447 DOI: 10.1093/cid/ciac499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Longitudinal pneumococcus colonization data in high human immunodeficiency virus (HIV) prevalence settings following pneumococcal conjugate vaccine introduction are limited. METHODS In 327 randomly selected households, 1684 individuals were enrolled and followed-up for 6 to 10 months during 2016 through 2018 from 2 communities. Nasopharyngeal swabs were collected twice weekly and tested for pneumococcus using quantitative lytA real-time polymerase chain reaction. A Markov model was fitted to the data to define the start and end of an episode of colonization. We assessed factors associated with colonization using logistic regression. RESULTS During the study period, 98% (1655/1684) of participants were colonized with pneumococcus at least once. Younger age (<5 years: adjusted odds ratio [aOR], 14.1; 95% confidence [CI], 1.8-111.3, and 5-24 years: aOR, 4.8, 95% CI, 1.9-11.9, compared with 25-44 years) and HIV infection (aOR, 10.1; 95% CI, 1.3-77.1) were associated with increased odds of colonization. Children aged <5 years had fewer colonization episodes (median, 9) than individuals ≥5 years (median, 18; P < .001) but had a longer episode duration (<5 years: 35.5 days; interquartile range, 17-88) vs. ≥5 years: 5.5 days (4-12). High pneumococcal loads were associated with age (<1 year: aOR 25.4; 95% CI, 7.4-87.6; 1-4 years: aOR 13.5, 95% CI 8.3-22.9; 5-14 years: aOR 3.1, 95% CI, 2.1-4.4 vs. 45-65 year old patients) and HIV infection (aOR 1.7; 95% CI 1.2-2.4). CONCLUSIONS We observed high levels of pneumococcus colonization across all age groups. Children and people with HIV were more likely to be colonized and had higher pneumococcal loads. Carriage duration decreased with age highlighting that children remain important in pneumococcal transmission.
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Affiliation(s)
- 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
| | - 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, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- MassGenics, Duluth, Georgia, USA
| | - Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Neil A Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, 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, USA
| | - 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
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Orienka Hellferscee
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, 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
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, 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
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Katlego Mothlaoleng
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, 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
| | - 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
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5
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van Zandvoort K, Bobe MO, Hassan AI, Abdi MI, Ahmed MS, Soleman SM, Warsame MY, Wais MA, Diggle E, McGowan CR, Satzke C, Mulholland K, Egeh MM, Hassan MM, Hergeeye MA, Eggo RM, Checchi F, Flasche S. Social contacts and other risk factors for respiratory infections among internally displaced people in Somaliland. Epidemics 2022; 41:100625. [PMID: 36103782 DOI: 10.1016/j.epidem.2022.100625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/16/2022] [Accepted: 08/25/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Populations affected by humanitarian crises experience high burdens of acute respiratory infections (ARI), potentially driven by risk factors for severe disease such as poor nutrition and underlying conditions, and risk factors that may increase transmission such as overcrowding and the possibility of high social mixing. However, little is known about social mixing patterns in these populations. METHODS We conducted a cross-sectional social contact survey among internally displaced people (IDP) living in Digaale, a permanent IDP camp in Somaliland. We included questions on household demographics, shelter quality, crowding, travel frequency, health status, and recent diagnosis of pneumonia, and assessed anthropometric status in children. We present the prevalence of several risk factors relevant to transmission of respiratory infections, and calculated age-standardised social contact matrices to assess population mixing. RESULTS We found crowded households with high proportions of recent self-reported pneumonia (46% in children). 20% of children younger than five are stunted, and crude death rates are high in all age groups. ARI risk factors were common. Participants reported around 10 direct contacts per day. Social contact patterns are assortative by age, and physical contact rates are very high (78%). CONCLUSIONS ARI risk factors are very common in this population, while the large degree of contacts that involve physical touch could further increase transmission. Such IDP settings potentially present a perfect storm of risk factors for ARIs and their transmission, and innovative approaches to address such risks are urgently needed.
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Affiliation(s)
- Kevin van Zandvoort
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | - Mohamed Omer Bobe
- Save the Children International, Maansoor area, Jig-jiga yar, Hargeisa, Somaliland
| | - Abdirahman Ibrahim Hassan
- Republic of Somaliland Ministry of Health Development, 26 June District, Presidential Road, Hargeisa, Somaliland
| | - Mohamed Ismail Abdi
- Save the Children International, Maansoor area, Jig-jiga yar, Hargeisa, Somaliland
| | - Mohammed Saed Ahmed
- Save the Children International, Maansoor area, Jig-jiga yar, Hargeisa, Somaliland
| | - Saeed Mohamood Soleman
- Republic of Somaliland Ministry of Health Development, 26 June District, Presidential Road, Hargeisa, Somaliland
| | - Mohamed Yusuf Warsame
- Republic of Somaliland Ministry of Health Development, 26 June District, Presidential Road, Hargeisa, Somaliland
| | - Muna Awil Wais
- Save the Children International, Maansoor area, Jig-jiga yar, Hargeisa, Somaliland
| | - Emma Diggle
- Save the Children UK, 1 St John's Lane, London EC1M 4AR, United Kingdom
| | - Catherine R McGowan
- Save the Children UK, 1 St John's Lane, London EC1M 4AR, United Kingdom; Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, The University of Melbourne Department of Paediatrics at the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Kim Mulholland
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Infection and Immunity, Murdoch Children's Research Institute, The University of Melbourne Department of Paediatrics at the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | | | | | - Mohamed Abdi Hergeeye
- Republic of Somaliland Ministry of Health Development, 26 June District, Presidential Road, Hargeisa, Somaliland
| | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Francesco Checchi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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6
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Thindwa D, Mwalukomo TS, Msefula J, Jambo KC, Brown C, Kamng’ona A, Mwansambo C, Ojal J, Flasche S, French N, Heyderman RS, Swarthout TD. Risk factors for pneumococcal carriage in adults living with HIV on antiretroviral therapy in the infant pneumococcal vaccine era in Malawi. AIDS 2022; 36:2045-2055. [PMID: 35983828 PMCID: PMC10503545 DOI: 10.1097/qad.0000000000003365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Adults living with HIV (ALWHIV) on antiretroviral therapy (ART) are at high risk of pneumococcal carriage and disease. To help evaluate carriage risk in African ALWHIV at least 4 years after infant pneumococcal conjugate vaccination introduction in 2011, we assessed association between pneumococcal carriage and potential risk factors. METHODS Nasopharyngeal swabs were collected from adults aged 18-40 years attending an ART clinic during rolling, cross-sectional surveys in Blantyre, Malawi between 2015 and 2019. We fitted generalized additive models to estimate the risk of sex, social economic status (SES), living with a child less than 5 years, and ART duration on carriage. RESULTS Of 2067 adults, median age was 33 years (range 28-37), 1427 (69.0%) were women, 1087 (61.4%) were in low-middle socioeconomic-status (SES), 910 (44.0%) were living with a child less than 5 years, and median ART duration was 3 years (range 0.004-17). We estimated 38.2 and 60.6% reductions in overall and vaccine-serotype carriage prevalence. Overall carriage was associated with low SES, living with a child less than 5 years and shorter duration on ART. By contrast, vaccine-type carriage was associated with living without a child less than 5 years and male sex. CONCLUSION Despite temporal reductions in overall and vaccine-serotype carriage, there is evidence of incomplete vaccine-serotype indirect protection. A targeted-vaccination campaign should be considered for ALWHIV, along with other public health measures to further reduce vaccine-serotype carriage and therefore disease.
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Affiliation(s)
- Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Malawi-Liverpool-Wellcome Programme
| | - Thandie S. Mwalukomo
- School of Life Sciences and Allied Health Professions, Department of Biomedical Sciences, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Programme
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Arox Kamng’ona
- School of Life Sciences and Allied Health Professions, Department of Biomedical Sciences, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - John Ojal
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- KEMRI-Wellcome Research Programme, Geographic Medicine Centre, Kilifi, Kenya
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Neil French
- Institute of Infection, Veterinary and Ecological Science, Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool
| | - Robert S. Heyderman
- Division of Infection and Immunity, Research Department of Infection, NIHR Mucosal Pathogens Research Unit, University College London, London, UK
| | - Todd D. Swarthout
- Malawi-Liverpool-Wellcome Programme
- Division of Infection and Immunity, Research Department of Infection, NIHR Mucosal Pathogens Research Unit, University College London, London, UK
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7
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Qian G, Toizumi M, Clifford S, Le LT, Papastylianou T, Satzke C, Quilty B, Iwasaki C, Kitamura N, Takegata M, Bui MX, Nguyen HAT, Dang DA, van Hoek AJ, Yoshida LM, Flasche S. Association of pneumococcal carriage in infants with the risk of carriage among their contacts in Nha Trang, Vietnam: A nested cross-sectional survey. PLoS Med 2022; 19:e1004016. [PMID: 35639774 PMCID: PMC9197035 DOI: 10.1371/journal.pmed.1004016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 06/14/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Infants are at highest risk of pneumococcal disease. Their added protection through herd effects is a key part in the considerations on optimal pneumococcal vaccination strategies. Yet, little is currently known about the main transmission pathways to this vulnerable age group. Hence, this study investigates pneumococcal transmission routes to infants in the coastal city of Nha Trang, Vietnam. METHODS AND FINDINGS In October 2018, we conducted a nested cross-sectional contact and pneumococcal carriage survey in randomly selected 4- to 11-month-old infants across all 27 communes of Nha Trang. Bayesian logistic regression models were used to estimate age specific carriage prevalence in the population, a proxy for the probability that a contact of a given age could lead to pneumococcal exposure for the infant. We used another Bayesian logistic regression model to estimate the correlation between infant carriage and the probability that at least one of their reported contacts carried pneumococci, controlling for age and locality. In total, 1,583 infants between 4 and 13 months old participated, with 7,428 contacts reported. Few infants (5%, or 86 infants) attended day care, and carriage prevalence was 22% (353 infants). Most infants (61%, or 966 infants) had less than a 25% probability to have had close contact with a pneumococcal carrier on the surveyed day. Pneumococcal infection risk and contact behaviour were highly correlated: If adjusted for age and locality, the odds of an infant's carriage increased by 22% (95% confidence interval (CI): 15 to 29) per 10 percentage points increase in the probability to have had close contact with at least 1 pneumococcal carrier. Moreover, 2- to 6-year-old children contributed 51% (95% CI: 39 to 63) to the total direct pneumococcal exposure risks to infants in this setting. The main limitation of this study is that exposure risk was assessed indirectly by the age-dependent propensity for carriage of a contact and not by assessing carriage of such contacts directly. CONCLUSIONS In this study, we observed that cross-sectional contact and infection studies could help identify pneumococcal transmission routes and that preschool-age children may be the largest reservoir for pneumococcal transmission to infants in Nha Trang, Vietnam.
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Affiliation(s)
- George Qian
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail: (GQ); (SF)
| | - Michiko Toizumi
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Sam Clifford
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Lien Thuy Le
- Department of Bacteriology, the Pasteur Institute in Nha Trang, Nha Trang, Vietnam
| | - Tasos Papastylianou
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, United Kingdom
| | - Catherine Satzke
- Translational Microbiology Group, Murdoch Children’s Research Institute at the Royal Children’s Hospital, University of Melbourne, Parkville, Australia
| | - Billy Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Chihiro Iwasaki
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Noriko Kitamura
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Mizuki Takegata
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | | | | | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Albert Jan van Hoek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lay Myint Yoshida
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Stefan Flasche
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail: (GQ); (SF)
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8
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Neal EFG, Chan J, Nguyen CD, Russell FM. Factors associated with pneumococcal nasopharyngeal carriage: A systematic review. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000327. [PMID: 36962225 PMCID: PMC10021834 DOI: 10.1371/journal.pgph.0000327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022]
Abstract
Pneumococcal disease is a major contributor to global childhood morbidity and mortality and is more common in low- and middle-income countries (LMICs) than in high-income countries. Pneumococcal carriage is a prerequisite for pneumococcal disease. Pneumococcal conjugate vaccine reduces vaccine-type carriage and disease. However, pneumococcal carriage and disease persist, and it is important to identify other potentially modifiable factors associated with pneumococcal carriage and determine if risk factors differ between low, middle, and high-income countries. This information may help inform pneumococcal disease prevention programs. This systematic literature review describes factors associated with pneumococcal carriage stratified by country income status and summarises pneumococcal carriage rates for included studies. We undertook a systematic search of English-language pneumococcal nasopharyngeal carriage studies up to 30th June 2021. Peer-reviewed studies reporting factors associated with overall pneumococcal nasopharyngeal carriage in healthy, community-based study populations were eligible for inclusion. Two researchers independently reviewed studies to determine eligibility. Results are presented as narrative summaries. This review is registered with PROSPERO, CRD42020186914. Eighty-two studies were included, and 46 (56%) were conducted in LMICs. There was heterogeneity in the factors assessed in each study. Factors positively associated with pneumococcal carriage in all income classification were young age, ethnicity, symptoms of respiratory tract infection, childcare attendance, living with young children, poverty, exposure to smoke, season, and co-colonisation with other pathogens. Breastfeeding and antibiotic use were protective against carriage in all income classifications. Median (interquartile range) pneumococcal carriage rates differed by income classification, ranging from 51% (19.3-70.2%), 38.5% (19.3-51.6%), 31.5% (19.0-51.0%), 28.5% (16.8-35.4%), (P = 0.005) in low-, lower-middle, upper-middle, and high-income classifications, respectively. Our findings suggest that where measured, factors associated with pneumococcal nasopharyngeal carriage are similar across income classifications, despite the highest pneumococcal carriage rates being in low-income classifications. Reducing viral transmission through vaccination and public health interventions to address social determinants of health would play an important role.
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Affiliation(s)
- Eleanor Frances Georgina Neal
- Infection & Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Jocelyn Chan
- Infection & Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Cattram Duong Nguyen
- Infection & Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Fiona Mary Russell
- Infection & Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
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9
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Korsten K, Adriaenssens N, Coenen S, Butler CC, Pirçon JY, Verheij TJM, Bont LJ, Wildenbeest JG. Contact With Young Children Increases the Risk of Respiratory Infection in Older Adults in Europe-the RESCEU Study. J Infect Dis 2021; 226:S79-S86. [PMID: 34908153 PMCID: PMC9374513 DOI: 10.1093/infdis/jiab519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Knowledge about how older adults get a respiratory infection is crucial for planning preventive strategies. We aimed to determine how contact with young children living outside of the household affects the risk of acute respiratory tract infections (ARTI) in community-dwelling older adults. Methods This study is part of the European RESCEU older adult study. Weekly surveillance was performed to detect ARTI throughout 2 winter seasons (2017-2018, 2018-2019). Child exposure, defined as having regular contact with children under 5 living outside of the subject’s household, was assessed at baseline. The average attributable fraction was calculated to determine the fraction of ARTI explained by exposure to these children. Results We prospectively established that 597/1006 (59%) participants experienced at least 1 ARTI. Child exposure increased the risk of all-cause ARTI (adjusted odds ratio [aOR], 1.58; 95% confidence interval [CI], 1.21 -2.08; P = .001). This risk was highest in those with the most frequent contact (aOR, 1.80; 95% CI, 1.23-2.63; P = .003). The average attributable fraction of child exposure explaining ARTI was 10% (95% CI, 5%-15%). Conclusions One of 10 ARTI in community-dwelling older adults is attributable to exposure to preschool children living outside of the household. Clinical Trials Registration NCT03621930.
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Affiliation(s)
- Koos Korsten
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Adriaenssens
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Primary and Interdisciplinary Care-Centre for General Practice, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Samuel Coenen
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Primary and Interdisciplinary Care-Centre for General Practice, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Epidemiology and Social Medicine, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Chris C Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Theo J M Verheij
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Louis J Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joanne G Wildenbeest
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
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10
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Mousa A, Winskill P, Watson OJ, Ratmann O, Monod M, Ajelli M, Diallo A, Dodd PJ, Grijalva CG, Kiti MC, Krishnan A, Kumar R, Kumar S, Kwok KO, Lanata CF, le Polain de Waroux O, Leung K, Mahikul W, Melegaro A, Morrow CD, Mossong J, Neal EF, Nokes DJ, Pan-Ngum W, Potter GE, Russell FM, Saha S, Sugimoto JD, Wei WI, Wood RR, Wu J, Zhang J, Walker P, Whittaker C. Social contact patterns and implications for infectious disease transmission: a systematic review and meta-analysis of contact surveys. eLife 2021; 10:70294. [PMID: 34821551 PMCID: PMC8765757 DOI: 10.7554/elife.70294] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focused on high-income settings. Methods: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys, we explored how contact characteristics (number, location, duration, and whether physical) vary across income settings. Results: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, with low-income settings characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income strata on the frequency, duration, and type of contacts individuals made. Conclusions: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens and the effectiveness of different non-pharmaceutical interventions. Funding: This work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1). Infectious diseases, particularly those caused by airborne pathogens like SARS-CoV-2, spread by social contact, and understanding how people mix is critical in controlling outbreaks. To explore these patterns, researchers typically carry out large contact surveys. Participants are asked for personal information (such as gender, age and occupation), as well as details of recent social contacts, usually those that happened in the last 24 hours. This information includes, the age and gender of the contact, where the interaction happened, how long it lasted, and whether it involved physical touch. These kinds of surveys help scientists to predict how infectious diseases might spread. But there is a problem: most of the data come from high-income countries, and there is evidence to suggest that social contact patterns differ between places. Therefore, data from these countries might not be useful for predicting how infections spread in lower-income regions. Here, Mousa et al. have collected and combined data from 27 contact surveys carried out before the COVID-19 pandemic to see how baseline social interactions vary between high- and lower-income settings. The comparison revealed that, in higher-income countries, the number of daily contacts people made decreased with age. But, in lower-income countries, younger and older individuals made similar numbers of contacts and mixed with all age groups. In higher-income countries, more contacts happened at work or school, while in low-income settings, more interactions happened at home and people were also more likely to live in larger, intergenerational households. Mousa et al. also found that gender affected how long contacts lasted and whether they involved physical contact, both of which are key risk factors for transmitting airborne pathogens. These findings can help researchers to predict how infectious diseases might spread in different settings. They can also be used to assess how effective non-medical restrictions, like shielding of the elderly and workplace closures, will be at reducing transmissions in different parts of the world.
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Affiliation(s)
- Andria Mousa
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Oliver John Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, United States
| | - Aldiouma Diallo
- VITROME, Institut de Recherche pour le Developpement, Dakar, Senegal
| | - Peter J Dodd
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Carlos G Grijalva
- Division of Pharmacoepidemiology, Department of Health Policy, Vanderbilt University Medical Center, Nashville, United States
| | | | - Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Supriya Kumar
- Bill and Melinda Gates Foundation, Seattle, WA, United States
| | - Kin O Kwok
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Kathy Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wiriya Mahikul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Alessia Melegaro
- Dondena Centre for Research on Social Dynamics and Public Policy, Department of Social and Political Sciences, Bocconi University, Milano, Italy
| | - Carl D Morrow
- Desmond Tutu HIV Centre, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Eleanor Fg Neal
- Infection and Immunity, Murdoch Children's Research Institute, Victoria, Australia
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Gail E Potter
- National Institute for Allergies and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Fiona M Russell
- Infection and Immunity, Murdoch Children's Research Institute, Victoria, Australia
| | - Siddhartha Saha
- US Centers for Disease Control and Prevention, New Delhi, India
| | - Jonathan D Sugimoto
- Seattle Epidemiologic Research and Information Center, United States Department of Veterans Affairs, Seattle, United States
| | - Wan In Wei
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Robin R Wood
- Desmond Tutu HIV Centre, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Joseph Wu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Shanghai, China
| | - Patrick Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
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11
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Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. Proc Natl Acad Sci U S A 2021; 118:2112605118. [PMID: 34753823 PMCID: PMC8609560 DOI: 10.1073/pnas.2112605118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Schools play a central role in the transmission of many respiratory infections. Heterogeneous social contact patterns associated with the social structures of schools (i.e., classes/grades) are likely to influence the within-school transmission dynamics, but data-driven evidence on fine-scale transmission patterns between students has been limited. Using a mathematical model, we analyzed a large-scale dataset of seasonal influenza outbreaks in Matsumoto city, Japan, to infer social interactions within and between classes/grades from observed transmission patterns. While the relative contribution of within-class and within-grade transmissions to the reproduction number varied with the number of classes per grade, the overall within-school reproduction number, which determines the initial growth of cases and the risk of sustained transmission, was only minimally associated with class sizes and the number of classes per grade. This finding suggests that interventions that change the size and number of classes, e.g., splitting classes and staggered attendance, may have a limited effect on the control of school outbreaks. We also found that vaccination and mask-wearing of students were associated with reduced susceptibility (vaccination and mask-wearing) and infectiousness (mask-wearing), and hand washing was associated with increased susceptibility. Our results show how analysis of fine-grained transmission patterns between students can improve understanding of within-school disease dynamics and provide insights into the relative impact of different approaches to outbreak control.
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12
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Mousa A, Winskill P, Watson OJ, Ratmann O, Monod M, Ajelli M, Diallo A, Dodd PJ, Grijalva CG, Kiti MC, Krishnan A, Kumar R, Kumar S, Kwok KO, Lanata CF, Le Polain de Waroux O, Leung K, Mahikul W, Melegaro A, Morrow CD, Mossong J, Neal EFG, Nokes DJ, Pan-ngum W, Potter GE, Russell FM, Saha S, Sugimoto JD, Wei WI, Wood RR, Wu JT, Zhang J, Walker PGT, Whittaker C. Social Contact Patterns and Implications for Infectious Disease Transmission: A Systematic Review and Meta-Analysis of Contact Surveys. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.10.21258720. [PMID: 34159341 PMCID: PMC8219108 DOI: 10.1101/2021.06.10.21258720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings. METHODS Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings. RESULTS Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, but low-income settings were characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made. CONCLUSIONS These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions. FUNDING This work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1).
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Affiliation(s)
- Andria Mousa
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA
| | - Aldiouma Diallo
- VITROME, Institut de Recherche pour le Developpement, Senegal
| | - Peter J Dodd
- School of Health and Related Research, University of Sheffield, UK
| | - Carlos G Grijalva
- Division of Pharmacoepidemiology, Department of Health Policy. Vanderbilt University Medical Center. Nashville, TN, USA
| | | | - Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | | | - Kin On Kwok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Shenzhen Research Institute of The Chinese University of Hong Kong, Shenzhen, China
| | - Claudio F Lanata
- Instituto de Investigación Nutricional, Lima, Peru
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Wiriya Mahikul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Alessia Melegaro
- Dondena Centre for Research on Social Dynamics and Public Policy, Department of Social and Political Sciences, Bocconi University, Milan, Italy
| | - Carl D Morrow
- Desmond Tutu HIV Centre, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research (CIDER), School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town South Africa
| | | | - Eleanor FG Neal
- Infection & Immunity, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - David J Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences, University of Warwick, Coventry UK
| | - Wirichada Pan-ngum
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Gail E Potter
- National Institute for Allergies and Infectious Diseases, National Institutes of Health, Rockville MD, USA
- The Emmes Company, Rockville MD, USA
| | - Fiona M Russell
- Infection & Immunity, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Siddhartha Saha
- Influenza Programme, US Centers for Disease Control and Prevention, India Office, US Embassy, New Delhi
| | - Jonathan D Sugimoto
- Seattle Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, United States Department of Veterans Affairs, USA
- Department of Epidemiology, University of Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wan In Wei
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Robin R Wood
- Desmond Tutu HIV Centre, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Patrick GT Walker
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
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13
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Kleynhans J, Tempia S, McMorrow ML, von Gottberg A, Martinson NA, Kahn K, Moyes J, Mkhencele T, Lebina L, Gómez-Olivé FX, Wafawanaka F, Mathunjwa A, Cohen C. A cross-sectional study measuring contact patterns using diaries in an urban and a rural community in South Africa, 2018. BMC Public Health 2021; 21:1055. [PMID: 34078327 PMCID: PMC8172361 DOI: 10.1186/s12889-021-11136-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Describing contact patterns is crucial to understanding infectious disease transmission dynamics and guiding targeted transmission mitigation interventions. Data on contact patterns in Africa, especially South Africa, are limited. We measured and compared contact patterns in a rural and urban community, South Africa. We assessed participant and contact characteristics associated with differences in contact rates. METHODS We conducted a cross-sectional study nested in a prospective household cohort study. We interviewed participants to collect information on persons in contact with for one day. We described self-reported contact rates as median number people contacted per day, assessed differences in contact rates based on participant characteristics using quantile regression, and used a Poisson model to assess differences in contact rates based on contact characteristics within age groups. We also calculated cumulative person hours in contact within age groups at different locations. RESULTS We conducted 535 interviews (269 rural, 266 urban), with 17,252 contacts reported. The overall contact rate was 14 (interquartile range (IQR) 9-33) contacts per day. Those ≤18 years had higher contact rates at the rural site (coefficient 17, 95% confidence interval (95%CI) 10-23) compared to the urban site, for those aged 14-18 years (13, 95%CI 3-23) compared to < 7 years. No differences were observed for adults. There was a strong age-based mixing, with age groups interacting more with similar age groups, but also interaction of participants of all ages with adults. Children aged 14-18 years had the highest cumulative person hours in contact (116.3 rural and 76.4 urban). CONCLUSIONS Age played an important role in the number and duration of contact events, with children at the rural site having almost double the contact rate compared to the urban site. These contact rates can be utilized in mathematical models to assess transmission dynamics of infectious diseases in similar communities.
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Affiliation(s)
- 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.
| | - Stefano Tempia
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- MassGenics, Duluth, Georgia, USA
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- United States Public Health Service, Rockville, MD, USA
| | - 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
| | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for Tuberculosis Research, Baltimore, MD, USA
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - 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, 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
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - F 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, 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, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, 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
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14
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Thindwa D, Pinsent A, Ojal J, Gallagher KE, French N, Flasche S. Vaccine strategies to reduce the burden of pneumococcal disease in HIV-infected adults in Africa. Expert Rev Vaccines 2020; 19:1085-1092. [PMID: 33269987 PMCID: PMC8315211 DOI: 10.1080/14760584.2020.1843435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Streptococcus pneumoniae is the leading cause of invasive bacterial disease, globally. Despite antiretroviral therapy, adults infected with human immunodeficiency virus (HIV) are also at high risk of pneumococcal carriage and disease. Pneumococcal conjugate vaccines (PCVs) provide effective protection against vaccine serotype (VT) carriage and disease in children, and have been introduced worldwide, including most HIV-affected low- and middle-income countries. Unlike high-income countries, the circulation of VT persists in the PCV era in some low-income countries and results in a continued high burden of pneumococcal disease in HIV-infected adults. Moreover, no routine vaccination that directly protects HIV-infected adults in such settings has been implemented. AREAS COVERED Nonsystematic review on the pneumococcal burden in HIV-infected adults and vaccine strategies to reduce this burden. EXPERT OPINION We propose and discuss the relative merit of changing the infant PCV program to use (1a) a two prime plus booster dose schedule, (1b) a two prime plus booster dose schedule with an additional booster dose at school entry, to directly vaccinate (2a) HIV-infected adults or vaccinating (2b) HIV-infected pregnant women for direct protection, with added indirect protection to the high-risk neonates. We identify key knowledge gaps for such an evaluation and propose strategies to overcome them.
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Affiliation(s)
- Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK,Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi,CONTACT Deus Thindwa Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, United Kingdom
| | - Amy Pinsent
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK,Aquarius Population Health, London, UK
| | - John Ojal
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine, Coast, Kilifi, Kenya
| | - Katherine E Gallagher
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Neil French
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi,Institute of Infection and Global Health, Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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Flasche S, Lipsitch M, Ojal J, Pinsent A. Estimating the contribution of different age strata to vaccine serotype pneumococcal transmission in the pre vaccine era: a modelling study. BMC Med 2020; 18:129. [PMID: 32517683 PMCID: PMC7285529 DOI: 10.1186/s12916-020-01601-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Herd protection through interruption of transmission has contributed greatly to the impact of pneumococcal conjugate vaccines (PCVs) and may enable the use of cost-saving reduced dose schedules. To aid PCV age targeting to achieve herd protection, we estimated which population age groups contribute most to vaccine serotype (VT) pneumococcal transmission. METHODS We used transmission dynamic models to mirror pre-PCV epidemiology in England and Wales, Finland, Kilifi in Kenya and Nha Trang in Vietnam where data on carriage prevalence in infants, pre-school and school-aged children and adults as well as social contact patterns was available. We used Markov Chain Monte Carlo methods to fit the models and then extracted the per capita and population-based contribution of different age groups to VT transmission. RESULTS We estimated that in all settings, < 1-year-old infants cause very frequent secondary vaccine type pneumococcal infections per capita. However, 1-5-year-old children have the much higher contribution to the force of infection at 51% (28, 73), 40% (27, 59), 37% (28, 48) and 67% (41, 86) of the total infection pressure in E&W, Finland, Kilifi and Nha Trang, respectively. Unlike the other settings, school-aged children in Kilifi were the dominant source for VT infections with 42% (29, 54) of all infections caused. Similarly, we estimated that the main source of VT infections in infants are pre-school children and that in Kilifi 39% (28, 51) of VT infant infections stem from school-aged children whereas this was below 15% in the other settings. CONCLUSION Vaccine protection of pre-school children is key for PCV herd immunity. However, in high transmission settings, school-aged children may substantially contribute to transmission and likely have waned much of their PCV protection under currently recommended schedules.
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Affiliation(s)
- Stefan Flasche
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK.
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - John Ojal
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Amy Pinsent
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
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Isolation and Identification of Streptococcus pneumonia Causing Respiratory and Thoracic Diseases in Najaf Province. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15. PLoS Comput Biol 2019; 15:e1007589. [PMID: 31877122 PMCID: PMC6959609 DOI: 10.1371/journal.pcbi.1007589] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/14/2020] [Accepted: 12/08/2019] [Indexed: 12/19/2022] Open
Abstract
Households are important settings for the transmission of seasonal influenza. Previous studies found that the per-person risk of within-household transmission decreases with household size. However, more detailed heterogeneities driven by household composition and contact patterns have not been studied. We employed a mathematical model that accounts for infections both from outside and within the household. The model was applied to citywide primary school seasonal influenza surveillance and household surveys from 10,486 students during the 2014/15 season in Matsumoto city, Japan. We compared a range of models to estimate the structure of household transmission and found that familial relationship and household composition strongly influenced the transmission patterns of seasonal influenza in households. Children had a substantially high risk of infection from outside the household (up to 20%) compared with adults (1–3%). Intense transmission was observed within-generation (between children/parents/grandparents) and also between mother and child, with transmission risks typically ranging from 5–20% depending on the transmission route and household composition. Children were identified as the largest source of secondary transmission, with family structure influencing infection risk. We characterised detailed heterogeneity in household transmission patterns of influenza by applying a mathematical model to citywide primary school influenza survey data from 10,486 students in Matsumoto city, Japan, one of the largest-scale household surveys on seasonal influenza. Children were identified as the largest source of secondary transmission, with family structure influencing infection risk. This suggests that vaccinating children would have stronger secondary effects on transmission than would be assumed without taking into account transmission patterns within the household.
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Neal EFG, Flasche S, Nguyen CD, Ratu FT, Dunne EM, Koyamaibole L, Reyburn R, Rafai E, Kama M, Ortika BD, Boelsen LK, Kado J, Tikoduadua L, Devi R, Tuivaga E, Satzke C, Mulholland EK, Edmunds WJ, Russell FM. Associations between ethnicity, social contact, and pneumococcal carriage three years post-PCV10 in Fiji. Vaccine 2019; 38:202-211. [PMID: 31668367 PMCID: PMC6964150 DOI: 10.1016/j.vaccine.2019.10.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/10/2019] [Accepted: 10/10/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pneumococcal carriage is a prerequisite for pneumococcal disease. Little is known about whether social contact frequency and intensity are associated with pneumococcal carriage. In Fiji, indigenous iTaukei have higher prevalence of pneumococcal carriage compared with Fijians of Indian Descent (FID). We hypothesised that contact differences may contribute to ethnic differences in pneumococcal carriage prevalence and density. METHODS In 2015, young infants (5-8 weeks), toddlers (12-23 months), children (2-6 years), and caregivers from Suva and surrounding areas, participated in a cross-sectional survey (n = 2014), three years post pneumococcal conjugate vaccine introduction. Demographic and contact data, and nasopharyngeal swabs were collected. Pneumococci were detected, and quantified using quantitative real-time PCR, with molecular serotyping by microarray. Associations between ethnicity, contact, and pneumococcal carriage and density were estimated using multivariable generalised estimating equation regression models. RESULTS iTaukei participants had larger household sizes, higher pneumococcal carriage rates, more contacts, and more frequent contacts of longer duration, compared with FID. The odds of vaccine-type carriage increased by 28% (95% CI 8-53%) P < 0.01 in association with physical contact with 7-14 year old children. iTaukei ethnicity was associated with vaccine-type carriage (aOR) 1.73; 95% CI 1.06-2.82, P = 0.03) and non-vaccine type carriage (aOR 5.98; 95% CI 4.47-8.00, P < 0.01). Ethnicity and contact were not associated with pneumococcal density. CONCLUSIONS iTaukei had greater frequency and intensity of contact compared with FID. Physical contact was associated with pneumococcal carriage. Observed differences in pneumococcal nasopharyngeal carriage prevalence between iTaukei and FID were not explained by differences in social contact patterns by ethnicity.
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Affiliation(s)
- Eleanor F G Neal
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Cattram D Nguyen
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - F Tupou Ratu
- Ministry of Health and Medical Services, Suva, Fiji
| | - Eileen M Dunne
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Rita Reyburn
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Eric Rafai
- Ministry of Health and Medical Services, Suva, Fiji
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Belinda D Ortika
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Laura K Boelsen
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Joseph Kado
- College of Medicine Nursing and Health Sciences, Fiji National University, Suva, Fiji; Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, Australia
| | | | - Rachel Devi
- Ministry of Health and Medical Services, Suva, Fiji
| | | | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - E Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fiona M Russell
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
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Heinsbroek E, Tafatatha T, Phiri A, Swarthout TD, Alaerts M, Crampin AC, Chisambo C, Mwiba O, Read JM, French N. Pneumococcal carriage in households in Karonga District, Malawi, before and after introduction of 13-valent pneumococcal conjugate vaccination. Vaccine 2018; 36:7369-7376. [PMID: 30352744 PMCID: PMC6238076 DOI: 10.1016/j.vaccine.2018.10.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 08/24/2018] [Accepted: 10/05/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Thirteen-valent pneumococcal conjugate vaccine (PCV13) was introduced in Malawi in November 2011 and is offered to infants at 6, 10 and 14 weeks of age as part of routine immunisation. PCV13 is expected to reduce vaccine type (VT) nasopharyngeal carriage, leading to reduced transmission and herd protection. METHODS We compared pneumococcal carriage in rural Karonga District, Malawi, pre-vaccine in 2009-2011 and post-vaccine in 2014 using a combination of cross-sectional and longitudinal analyses. Nasopharyngeal swabs were collected from a cohort of mother-infant pairs and household members <16 years. Pneumococci from 2009 to 2011 were serogrouped using latex agglutination and serotyped by Quellung reaction. In 2014, latex agglutination was used for both steps. Carriage prevalence ratios using prevalence data from before and after vaccine introduction were calculated by log-binomial regression, adjusted for age, seasonality and household composition. Participating infants in 2014 received PCV13 as part of routine immunisation. RESULTS VT carriage prior to PCV-13 introduction was 11.4%, 45.1%, 28.2%, 21.2% and 6.6% for 6-week old infants, 18-week old infants, children 1-4 years, children 5-15 years and mothers, respectively. After vaccine introduction, VT carriage decreased among vaccinated 18-week old infants (adjusted prevalence ratio 0.24 (95%CI 0.08-0.75)), vaccinated children 1-4 years (0.54 (0.33-0.88)), unvaccinated children 5-15 years (0.37 (0.17-0.78)) and mothers (0.34 (0.15-0.79)). No decrease in VT carriage was observed for 6-week old infants too young to be vaccinated (1.07 (0.38-3.02)) and PCV-13 ineligible children 1-4 years (0.84 (0.53-1.33)). Non-VT carriage increased only among vaccinated children 1-4 years (1.58 (1.21-2.06)). CONCLUSIONS There is evidence of reduced VT pneumococcal carriage three years after vaccine introduction in this rural Malawian population with good vaccine coverage using a 3 + 0 schedule. However carriage was sustained among 6-week-old infants and PCV13 ineligible 1-4 year olds, and there was some indication of serotype replacement in vaccinated 1-4 year olds.
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Affiliation(s)
- Ellen Heinsbroek
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Amos Phiri
- Karonga Prevention Study, Chilumba, Malawi
| | - Todd D Swarthout
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi; Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Maaike Alaerts
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Amelia C Crampin
- Karonga Prevention Study, Chilumba, Malawi; London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Jonathan M Read
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Centre for Health Informatics Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Neil French
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi.
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Brooks LRK, Mias GI. Streptococcus pneumoniae's Virulence and Host Immunity: Aging, Diagnostics, and Prevention. Front Immunol 2018; 9:1366. [PMID: 29988379 PMCID: PMC6023974 DOI: 10.3389/fimmu.2018.01366] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pneumoniae is an infectious pathogen responsible for millions of deaths worldwide. Diseases caused by this bacterium are classified as pneumococcal diseases. This pathogen colonizes the nasopharynx of its host asymptomatically, but overtime can migrate to sterile tissues and organs and cause infections. Pneumonia is currently the most common pneumococcal disease. Pneumococcal pneumonia is a global health concern and vastly affects children under the age of five as well as the elderly and individuals with pre-existing health conditions. S. pneumoniae has a large selection of virulence factors that promote adherence, invasion of host tissues, and allows it to escape host immune defenses. A clear understanding of S. pneumoniae's virulence factors, host immune responses, and examining the current techniques available for diagnosis, treatment, and disease prevention will allow for better regulation of the pathogen and its diseases. In terms of disease prevention, other considerations must include the effects of age on responses to vaccines and vaccine efficacy. Ongoing work aims to improve on current vaccination paradigms by including the use of serotype-independent vaccines, such as protein and whole cell vaccines. Extending our knowledge of the biology of, and associated host immune response to S. pneumoniae is paramount for our improvement of pneumococcal disease diagnosis, treatment, and improvement of patient outlook.
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Affiliation(s)
- Lavida R. K. Brooks
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI, United States
| | - George I. Mias
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI, United States
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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Flasche S, Ojal J, Le Polain de Waroux O, Otiende M, O'Brien KL, Kiti M, Nokes DJ, Edmunds WJ, Scott JAG. Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: a modelling study based on data from PCV10 introduction in Kilifi, Kenya. BMC Med 2017; 15:113. [PMID: 28592303 PMCID: PMC5463405 DOI: 10.1186/s12916-017-0882-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The World Health Organisation recommends the use of catch-up campaigns as part of the introduction of pneumococcal conjugate vaccines (PCVs) to accelerate herd protection and hence PCV impact. The value of a catch-up campaign is a trade-off between the costs of vaccinating additional age groups and the benefit of additional direct and indirect protection. There is a paucity of observational data, particularly from low- and middle-income countries, to quantify the optimal breadth of such catch-up campaigns. METHODS In Kilifi, Kenya, PCV10 was introduced in 2011 using the three-dose Expanded Programme on Immunisation infant schedule and a catch-up campaign in children <5 years old. We fitted a transmission dynamic model to detailed local data, including nasopharyngeal carriage and invasive pneumococcal disease (IPD), to infer the marginal impact of the PCV catch-up campaign over hypothetical routine cohort vaccination in that setting and to estimate the likely impact of alternative campaigns and their dose efficiency. RESULTS We estimated that, within 10 years of introduction, the catch-up campaign among children <5 years old prevents an additional 65 (48-84) IPD cases across age groups, compared to PCV cohort introduction alone. Vaccination without any catch-up campaign prevented 155 (121-193) IPD cases and used 1321 (1058-1698) PCV doses per IPD case prevented. In the years after implementation, the PCV programme gradually accrues herd protection, and hence its dose efficiency increases: 10 years after the start of cohort vaccination alone the programme used 910 (732-1184) doses per IPD case averted. We estimated that a two-dose catch-up among children <1 year old uses an additional 910 (732-1184) doses per additional IPD case averted. Furthermore, by extending a single-dose catch-up campaign to children aged 1 to <2 years and subsequently to those aged 2 to <5 years, the campaign uses an additional 412 (296-606) and 543 (403-763) doses per additional IPD case averted. These results were not sensitive to vaccine coverage, serotype competition, the duration of vaccine protection or the relative protection of infants. CONCLUSIONS We find that catch-up campaigns are a highly dose-efficient way to accelerate population protection against pneumococcal disease.
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Affiliation(s)
- Stefan Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.
| | - John Ojal
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Olivier Le Polain de Waroux
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - Mark Otiende
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katherine L O'Brien
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Moses Kiti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- University of Warwick and WIDER, Coventry, UK
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - J Anthony G Scott
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
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