1
|
Rautman LH, Maiga-Ascofaré O, Eibach D, Hogan B, Dekker D, Jaeger A, Akenten CW, Owusu-Dabo E, Boateng FO, Hanson H, Boahen KG, Sarpong N, Adu-Sarkodie Y, Kreuels B, May J, Krumkamp R. Fever in focus: Symptoms, diagnoses and treatment of febrile children in Ghana-A longitudinal hospital study. Trop Med Int Health 2024; 29:206-213. [PMID: 38093593 DOI: 10.1111/tmi.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
BACKGROUND Healthcare resources are often limited in areas of sub-Saharan Africa. This makes accurate and timely diagnoses challenging and delays treatment of childhood febrile illness. We explored longitudinal characteristics related to symptoms, diagnosis and treatment of hospitalised febrile children in a rural area of Ghana highly endemic for malaria. METHODS Febrile children under 15 years, admitted to the study hospital paediatric ward, were recruited to the study and clinical data were collected throughout hospitalisation. Descriptive statistics were reported for all cases; for longitudinal analyses, a subset of visits with limited missing data was used. RESULTS There were 801 hospitalised children included in longitudinal analyses. Malaria (n = 581, 73%) and sepsis (n = 373, 47%) were the most prevalent suspected diagnoses on admission. One-third of malaria suspected diagnoses (n = 192, 33%) were changed on the discharge diagnosis, compared to 84% (n = 315) of sepsis suspected diagnoses. Among malaria-only discharge diagnoses, 98% (n/N = 202/207) received an antimalarial and 33% (n/N = 69/207) an antibiotic; among discharge diagnoses without malaria, 28% (n/N = 108/389) received an antimalarial and 83% (n/N = 324/389) an antibiotic. CONCLUSIONS Suspected diagnoses were largely based on clinical presentation and were frequently changed; changed diagnoses were associated with lingering symptoms, underscoring the need for faster and more accurate diagnostics. Medications were over-prescribed regardless of diagnosis stability, possibly because of a lack of confidence in suspected diagnoses. Thus, better diagnostic tools are needed for childhood febrile illnesses to enhance the accuracy of and confidence in diagnoses, and to cut down unjustified medication use, reducing the risk of antimicrobial and malaria resistance.
Collapse
Affiliation(s)
- Lydia Helen Rautman
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Oumou Maiga-Ascofaré
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | | | - Ellis Owusu-Dabo
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Felix Osei Boateng
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Henry Hanson
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Benno Kreuels
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| |
Collapse
|
2
|
Badr HS, Colston JM, Nguyen NLH, Chen YT, Burnett E, Ali SA, Rayamajhi A, Satter SM, Van Trang N, Eibach D, Krumkamp R, May J, Adegnika AA, Manouana GP, Kremsner PG, Chilengi R, Hatyoka L, Debes AK, Ateudjieu J, Faruque ASG, Hossain MJ, Kanungo S, Kotloff KL, Mandomando I, Nisar MI, Omore R, Sow SO, Zaidi AKM, Lambrecht N, Adu B, Page N, Platts-Mills JA, Mavacala Freitas C, Pelkonen T, Ashorn P, Maleta K, Ahmed T, Bessong P, Bhutta ZA, Mason C, Mduma E, Olortegui MP, Peñataro Yori P, Lima AAM, Kang G, Humphrey J, Ntozini R, Prendergast AJ, Okada K, Wongboot W, Langeland N, Moyo SJ, Gaensbauer J, Melgar M, Freeman M, Chard AN, Thongpaseuth V, Houpt E, Zaitchik BF, Kosek MN. Spatiotemporal variation in risk of Shigella infection in childhood: a global risk mapping and prediction model using individual participant data. Lancet Glob Health 2023; 11:e373-e384. [PMID: 36796984 PMCID: PMC10020138 DOI: 10.1016/s2214-109x(22)00549-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/18/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
BACKGROUND Diarrhoeal disease is a leading cause of childhood illness and death globally, and Shigella is a major aetiological contributor for which a vaccine might soon be available. The primary objective of this study was to model the spatiotemporal variation in paediatric Shigella infection and map its predicted prevalence across low-income and middle-income countries (LMICs). METHODS Individual participant data for Shigella positivity in stool samples were sourced from multiple LMIC-based studies of children aged 59 months or younger. Covariates included household-level and participant-level factors ascertained by study investigators and environmental and hydrometeorological variables extracted from various data products at georeferenced child locations. Multivariate models were fitted and prevalence predictions obtained by syndrome and age stratum. FINDINGS 20 studies from 23 countries (including locations in Central America and South America, sub-Saharan Africa, and south and southeast Asia) contributed 66 563 sample results. Age, symptom status, and study design contributed most to model performance followed by temperature, wind speed, relative humidity, and soil moisture. Probability of Shigella infection exceeded 20% when both precipitation and soil moisture were above average and had a 43% peak in uncomplicated diarrhoea cases at 33°C temperatures, above which it decreased. Compared with unimproved sanitation, improved sanitation decreased the odds of Shigella infection by 19% (odds ratio [OR]=0·81 [95% CI 0·76-0·86]) and open defecation decreased them by 18% (OR=0·82 [0·76-0·88]). INTERPRETATION The distribution of Shigella is more sensitive to climatological factors, such as temperature, than previously recognised. Conditions in much of sub-Saharan Africa are particularly propitious for Shigella transmission, although hotspots also occur in South America and Central America, the Ganges-Brahmaputra Delta, and the island of New Guinea. These findings can inform prioritisation of populations for future vaccine trials and campaigns. FUNDING NASA, National Institutes of Health-The National Institute of Allergy and Infectious Diseases, and Bill & Melinda Gates Foundation.
Collapse
Affiliation(s)
- Hamada S Badr
- Department of Earth and Planetary Sciences, Johns Hopkins Krieger School of Arts and Sciences, Baltimore, MA, USA
| | - Josh M Colston
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Yen Ting Chen
- Department of Emergency Medicine, Chi-Mei Medical Center, Tainan, Taiwan
| | - Eleanor Burnett
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Ajit Rayamajhi
- Department of Pediatrics, National Academy of Medical Sciences, Kanti Children's Hospital, Kathmandu, Nepal
| | - Syed M Satter
- Programme for Emerging Infections, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ayola Akim Adegnika
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | | | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Luiza Hatyoka
- Enteric diseases and Vaccines Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Amanda K Debes
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jerome Ateudjieu
- Faculty of Medicine and Pharmaceutical Sciences, University of Dschang, Dschang, Cameroon; Department of Health Research, M A SANTE (Meileur Acces aux Soins en Santé), Yaoundé, Cameroon; Division of Health Operations Research, Cameroon Ministry of Public Health, Yaoundé, Cameroon
| | - Abu S G Faruque
- Centre for Nutrition & Food Security, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - M Jahangir Hossain
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Suman Kanungo
- National Institute of Cholera and Enteric Diseases, Kolkota, India
| | - Karen L Kotloff
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - M Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Richard Omore
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Nyanza, Kenya
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Mali, Bamako, Mali
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Nathalie Lambrecht
- Institute of Public Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Research Department 2, Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Nicola Page
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Pretoria, South Africa
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Tuula Pelkonen
- New Children's Hospital, Pediatric Research Center and Helsinki University Hospital, Helsinki, Finland
| | - Per Ashorn
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Kenneth Maleta
- College of Medicine, University of Malawi, Blantyre, Malawi
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Pascal Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, Limpopo, South Africa
| | - Zulfiqar A Bhutta
- Center of Excellence in Women and Child Health, Aga Khan University, Karachi, Pakistan
| | - Carl Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | | | | | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Aldo A M Lima
- Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Gagandeep Kang
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jean Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Kazuhisa Okada
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Warawan Wongboot
- Department of Medical Sciences, National Institute of Health, Nonthaburi, Thailand
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Sabrina J Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - James Gaensbauer
- Center for Global Health, Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Mario Melgar
- Pediatric Infectious Diseases, Hospital Roosevelt, Guatemala City, Guatemala
| | - Matthew Freeman
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, 30322, GA, USA
| | - Anna N Chard
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, 30322, GA, USA
| | - Vonethalom Thongpaseuth
- Laboratory and Treatment Unit, Center for Malariology, Parasitology, and Entomology, Ministry of Health, Vientiane, Lao PDR
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Benjamin F Zaitchik
- Department of Earth and Planetary Sciences, Johns Hopkins Krieger School of Arts and Sciences, Baltimore, MA, USA.
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA
| |
Collapse
|
3
|
Heinemann M, Kleinjohann L, Rolling T, Winter D, Hackbarth N, Ramharter M, Addo M, Eibach D, Phillips RO, Owusu-Ofori A, Vinnemeier CD. Impact of antibiotic intake on the incidence of extended-spectrum β-lactamase-producing Enterobacterales in sub-Saharan Africa: results from a community-based longitudinal study. Clin Microbiol Infect 2023; 29:340-345. [PMID: 36150674 DOI: 10.1016/j.cmi.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES The global prevalence of intestinal extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) is approximately 17% in communities, with significant variations among regions. This longitudinal study aimed to assess the impact of antibiotic intake on the incidence of intestinal ESBL-PE in Ghanaian pharmacy customers outside of hospitals. METHODS Screening for ESBL-PE was performed in four independent pharmacies in Kumasi, Ghana, using rectal swabs and an ESBL-PE-selective medium. Pharmacy customers purchasing antibiotics were recruited, and those buying non-antibiotic drugs served as controls. Participants who were negative for ESBL-PE provided follow-up swabs for up to 28 days. RESULTS At baseline, 302 (75%) of 404 participants were colonized with ESBL-PE. Sixty-three participants who were negative for ESBL-PE at baseline received per-protocol follow-up, including 28 individuals who took antibiotics and 35 controls. The cumulative proportions of ESBL-PE in the antibiotics and control groups were 71% (20/28) and 54% (19/35) at the first follow-up (p 0.258), 86% (24/28) and 80% (28/35) at the second follow-up (p 0.741) and 86% (24/28) and 94% (33/35) at the third follow-up (p 0.393), respectively. DISCUSSION The rate of intestinal ESBL-PE carriage among pharmacy customers outside of hospitals was higher than expected at baseline and further increased during the 28 days of follow-up, irrespective of antibiotic intake. This alarming finding needs to be considered in the antibiotic treatment of outpatients and emphasizes the urgent need for improved prevention strategies, development of new antibiotic drugs and potential future elimination strategies. Further longitudinal studies on ESBL-PE in African communities, also outside of pharmacy settings, are required.
Collapse
Affiliation(s)
- Melina Heinemann
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Lukas Kleinjohann
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thierry Rolling
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Doris Winter
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany; Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Nina Hackbarth
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Michael Ramharter
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marylyn Addo
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Richard O Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Alex Owusu-Ofori
- Department of Clinical Microbiology, School of Medical Science, College of Health Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christof D Vinnemeier
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| |
Collapse
|
4
|
Krumkamp R, Kohsar M, Nolte K, Hogan B, Eibach D, Jaeger A, Akenten CW, Drosten C, Boahen KG, Sarpong N, Eckerle I, Binger T, Owusu-Dabo E, May J, Kreuels B. Pathogens associated with hospitalization due to acute lower respiratory tract infections in children in rural Ghana: a case-control study. Sci Rep 2023; 13:2443. [PMID: 36765075 PMCID: PMC9916495 DOI: 10.1038/s41598-023-29410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Respiratory infections are one of the most common causes of death among children under the age of five years. Data on prevalence and relevance of specific organisms in African children are still lacking. This case-control-study investigated prevalence and relevance of specific organisms in Ghanaian children admitted to hospital with symptoms of lower respiratory tract infection (LRTI). Pharyngeal swabs were taken and tested by PCR for 19 respiratory isolates. Adjusted odds ratios (aORs) were calculated to estimate associations between isolates and admission with LRTI. Population attributable fractions (PAFs) were calculated to assess the proportion of LRTI cases due to a particular pathogen. The study included 327 cases and 562 controls. We found associations between detection and admission for LRTI for influenza (aOR 98.6; 95% confidence interval (CI) 20.0-1789.6), respiratory syncytial virus (aOR 40.2; 95% CI 7.2-758.6), H. influenzae (aOR 4.1; 95% CI 2.2-7.9) and S. pneumoniae (aOR 2.4; 95% CI 1.7-3.4). PAFs ≥ 10% were observed for S. pneumoniae (30%; 95% CI 26-42), H. influenzae (10%; 95% CI 2-19) and influenza (10%; 95% CI 2-18). This study highlights the need for heightened surveillance and development of effective vaccines for respiratory pathogens other than SARS-CoV-2 in the future.
Collapse
Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | - Matin Kohsar
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Kolja Nolte
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Deutsche Gesellschaft Für Internationale Zusammenarbeit (GIZ GmbH), Berlin, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Isabella Eckerle
- Department of Medicine, University of Geneva, Geneva, Switzerland
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Benno Kreuels
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany.
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Research Group Snakebite Envenoming, Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| |
Collapse
|
5
|
Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Punčochář M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614:125-135. [PMID: 36653448 PMCID: PMC9892008 DOI: 10.1038/s41586-022-05620-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/02/2022] [Indexed: 01/19/2023]
Abstract
The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.
Collapse
Affiliation(s)
| | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Elisa Piperni
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | | | - Liviana Ricci
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Olivia Farrant
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Goncalves
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Marta Selma-Royo
- Department CIBIO, University of Trento, Trento, Italy
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Ana G Binetti
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jimmy E Becerra
- Grupo de Investigación Alimentación y Comportamiento Humano, Universidad Metropolitana, Barranquilla, Colombia
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - John Lusingu
- National Institute for Medical Research, Tanga Medical Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire M Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Qian Xu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Nan Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Huanlong Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples 'Federico II', Portici, Italy
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Enrico Domenici
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Computational and Systems Biology (COSBI), Microsoft Research Foundation, Rovereto, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
| |
Collapse
|
6
|
Akenten CW, Ofori LA, Khan NA, Mbwana J, Sarpong N, May J, Thye T, Obiri-Danso K, Paintsil EK, Fosu D, Philipps RO, Eibach D, Krumkamp R, Dekker D. Prevalence, Characterization, and Antimicrobial Resistance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Domestic Free-Range Poultry in Agogo, Ghana. Foodborne Pathog Dis 2023; 20:59-66. [PMID: 36779941 DOI: 10.1089/fpd.2022.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Poultry has been suggested as an important source for extended-spectrum beta-lactamase (ESBL)-producing bacteria that can lead to difficult-to treat infections in humans. Therefore, this study aims to determine the frequency, the genetics, and antimicrobial resistance profiles of ESBL-producing Escherichia coli in domestic free-range poultry in Agogo, Ghana. The study was set up and piloted from January 2019 until June 2019. Between June and December 2019, fecal samples (N = 144) were collected from free-roaming chickens from domestic farms in the regions of Sukuumu, Bontodiase, and Freetown and cultured on ESBL screening agar. Strain identification and antibiotic susceptibility were performed using the VITEK 2 compact system. ESBL-producing E. coli were confirmed using the double disk synergy test. Molecular characterization of ESBL-associated genes (blaTEM, blaSHV, and blaCTX-M) were performed using conventional polymerase chain reaction (PCR) and further sequencing of obtained PCR amplicons. The result showed that 56.2% (n/N = 81/144) of collected fecal samples were positive for ESBL-producing E. coli. Majority of the isolates showed resistance to tetracycline (93.8%, n/N = 76/81) and trimethoprim-sulfamethoxazole (66.7, n/N = 54/81), whereas resistance to carbapenems was not found. The majority of ESBL-producing E. coli carried the blaCTX-M genes, with blaCTX-M-15 being the dominant (95.1%, n/N = 77/81) genotype. In this study, we report high frequencies of ESBL-producing E. coli in smallholder free-range poultry representing a potential source of infection, highlighting the need for control of antibiotic use and animal hygiene/sanitation measures, both important from a One Health perspective.
Collapse
Affiliation(s)
| | - Linda Aurelia Ofori
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Neyaz Ahmed Khan
- Research Group One Health Bacteriology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Joyce Mbwana
- National Institute for Medical Research (NIMR), Tanga, Tanzania
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Jürgen May
- Department Infectious Disease epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.,German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Tropical Medicine II, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Thorsten Thye
- Department Infectious Disease epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | | | - Dennis Fosu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | | | - Daniel Eibach
- Department Infectious Disease epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ralf Krumkamp
- Department Infectious Disease epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.,German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Denise Dekker
- Research Group One Health Bacteriology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| |
Collapse
|
7
|
Moirongo RM, Aglanu LM, Lamshöft M, Adero BO, Yator S, Anyona S, May J, Lorenz E, Eibach D. Laboratory-based surveillance of antimicrobial resistance in regions of Kenya: An assessment of capacities, practices, and barriers by means of multi-facility survey. Front Public Health 2022; 10:1003178. [PMID: 36518572 PMCID: PMC9742437 DOI: 10.3389/fpubh.2022.1003178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
Background Adequate laboratory capacity is critical in the implementation of coherent surveillance for antimicrobial resistance (AMR). We describe capacities and deficiencies in laboratory infrastructure and AMR surveillance practices among health facilities in Kenya to support progress toward broader sustainable laboratory-based AMR surveillance. Methods A convenience sample of health facilities from both public and private sectors across the country were selected. Information was obtained cross-sectionally between 5th October and 8th December 2020 through online surveys of laboratory managers. The assessment covered quality assurance, management and dissemination of AMR data, material and equipment, staffing, microbiology competency, biosafety and certification. A scoring scheme was developed for the evaluation and interpreted as (80% and above) facility is adequate (60-79%) requires some strengthening and (<60%) needing significant strengthening. Average scores were compared across facilities in public and private sectors, rural and urban settings, as well as national, county, and community levels. Results Among the participating facilities (n = 219), the majority (n = 135, 61.6%) did not offer bacterial culture testing, 47 (21.5%) offered culture services only and 37 (16.9%) performed antimicrobial susceptibility testing (AST). The major gaps identified among AST facilities were poor access to laboratory information management technology (LIMT) (score: 45.9%) and low uptake of external quality assessment (EQA) programs for cultures (score 67.7%). Access to laboratory technology was more than two-fold higher in facilities in urban (58.6%) relative to rural (25.0%) areas. Whilst laboratories that lacked culture services were found to have significant infrastructural gaps (average score 59.4%), facilities that performed cultures only (average score: 83.6%) and AST (average score: 82.9%) recorded significantly high scores that were very similar across areas assessed. Lack of equipment was identified as the leading challenge to the implementation of susceptibility testing among 46.8% of laboratories. Conclusions We identified key gaps in laboratory information management technology, external quality assurance and material and equipment among the surveyed health facilities in Kenya. Our findings suggest that by investing in equipment, facilities performing cultures can be successfully upgraded to provide additional antimicrobial susceptibility testing, presenting a chance for a major leap toward improved AMR diagnostics and surveillance in the country.
Collapse
Affiliation(s)
- Rehema Moraa Moirongo
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany,*Correspondence: Rehema Moraa Moirongo
| | - Leslie Mawuli Aglanu
- Global Health and Infectious Diseases Research Group, Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana,Department of Internal Medicine/Infectious Diseases, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Maike Lamshöft
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany,German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | - Solomon Yator
- Department of Biochemistry and Molecular Biology, University of Bremen, Bremen, Germany
| | - Stephen Anyona
- Centre for Microbiology Research (KEMRI-CMR), Kenya Medical Research Institute, Nairobi, Kenya
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany,German Center for Infection Research (DZIF), Braunschweig, Germany,Department of Tropical Medicine I, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Eva Lorenz
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany,German Center for Infection Research (DZIF), Braunschweig, Germany,Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| |
Collapse
|
8
|
Struck NS, Lorenz E, Deschermeier C, Eibach D, Kettenbeil J, Loag W, Brieger SA, Ginsbach AM, Obirikorang C, Maiga-Ascofare O, Sarkodie YA, Boham EEA, Adu EA, Asare G, Amoako-Adusei A, Yawson A, Boakye AO, Deke J, Almoustapha NS, Adu-Amoah L, Duah IK, Ouedraogo TA, Boudo V, Rushton B, Ehmen C, Fusco D, Gunga L, Benke D, Höppner Y, Rasolojaona ZT, Rasamoelina T, Rakotoarivelo RA, Rakotozandrindrainy R, Coulibaly B, Sié A, Awuah AAA, Amuasi JH, Souares A, May J. High seroprevalence of SARS-CoV-2 in Burkina-Faso, Ghana and Madagascar in 2021: a population-based study. BMC Public Health 2022; 22:1676. [PMID: 36064368 PMCID: PMC9441841 DOI: 10.1186/s12889-022-13918-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/07/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The current COVID-19 pandemic affects the entire world population and has serious health, economic and social consequences. Assessing the prevalence of COVID-19 through population-based serological surveys is essential to monitor the progression of the epidemic, especially in African countries where the extent of SARS-CoV-2 spread remains unclear. METHODS A two-stage cluster population-based SARS-CoV-2 seroprevalence survey was conducted in Bobo-Dioulasso and in Ouagadougou, Burkina Faso, Fianarantsoa, Madagascar and Kumasi, Ghana between February and June 2021. IgG seropositivity was determined in 2,163 households with a specificity improved SARS-CoV-2 Enzyme-linked Immunosorbent Assay. Population seroprevalence was evaluated using a Bayesian logistic regression model that accounted for test performance and age, sex and neighbourhood of the participants. RESULTS Seroprevalence adjusted for test performance and population characteristics were 55.7% [95% Credible Interval (CrI) 49·0; 62·8] in Bobo-Dioulasso, 37·4% [95% CrI 31·3; 43·5] in Ouagadougou, 41·5% [95% CrI 36·5; 47·2] in Fianarantsoa, and 41·2% [95% CrI 34·5; 49·0] in Kumasi. Within the study population, less than 6% of participants performed a test for acute SARS-CoV-2 infection since the onset of the pandemic. CONCLUSIONS High exposure to SARS-CoV-2 was found in the surveyed regions albeit below the herd immunity threshold and with a low rate of previous testing for acute infections. Despite the high seroprevalence in our study population, the duration of protection from naturally acquired immunity remains unclear and new virus variants continue to emerge. This highlights the importance of vaccine deployment and continued preventive measures to protect the population at risk.
Collapse
Affiliation(s)
- Nicole S Struck
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.
| | - Eva Lorenz
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg, University Mainz, Mainz, Germany
| | - Christina Deschermeier
- Diagnostics Development Laboratory, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany
| | - Jenny Kettenbeil
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Wibke Loag
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Steven A Brieger
- University of Sussex Business School, University of Sussex, Falmer, UK
| | - Anna M Ginsbach
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Christian Obirikorang
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oumou Maiga-Ascofare
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Eric Ebenezer Amprofi Boham
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Evans Asamoah Adu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gracelyn Asare
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Amos Amoako-Adusei
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alfred Yawson
- Department of Community Health, University of Ghana, Accra, Ghana
| | - Alexander Owusu Boakye
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - James Deke
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Nana Safi Almoustapha
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Louis Adu-Amoah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ibrahim Kwaku Duah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Valentin Boudo
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Ben Rushton
- Diagnostics Development Laboratory, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christa Ehmen
- Diagnostics Development Laboratory, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniela Fusco
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany
| | - Leonard Gunga
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Dominik Benke
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Yannick Höppner
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | | | | | | | | | - Boubacar Coulibaly
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.,Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Ali Sié
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.,Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso.,Heidelberg Institute of Global Health (HIGH), Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Anthony Afum-Adjei Awuah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John H Amuasi
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Aurélia Souares
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.,Heidelberg Institute of Global Health (HIGH), Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Heidelberg, Germany.,Department of Tropical Medicine I, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| |
Collapse
|
9
|
Krumkamp R, Conraths FJ, Caccio S, Schares G, Hogan B, Winter D, Jaeger A, Melhem S, Rakotozandrindrainy N, May J, Rakotozandrindrainy R, Eibach D. Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar. Parasit Vectors 2022; 15:304. [PMID: 36031635 PMCID: PMC9422120 DOI: 10.1186/s13071-022-05434-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/12/2022] [Indexed: 12/02/2022] Open
Abstract
Background The aim of this study was to identify local transmission patterns of Cryptosporidium spp. infections among livestock and humans in four extremely rural and remote highland communities in Madagascar. Methods In this cross-sectional study, households were randomly sampled throughout a 1-year study period, with one feces sample collected from each child (≤ 5 years old), sheep and cattle. Cryptosporidium spp. were identified using a nested PCR assay targeting the 18S ribosomal RNA gene. All samples positive for Cryptosporidium hominis were further subtyped by sequencing the 60-kDa glycoprotein gene (gp60). Spatial clustering methods were applied to analyze potential transmission patterns. Results In total, 252 households participated in the study, and samples from 197 children, 862 cattle and 334 sheep were collected and included in the study. Of the samples collected, 11 (5.6%) from children, 30 (3.5%) from cattle and 42 (12.6%) from sheep tested positive for Cryptosporidium spp. Very little overlap in the species distribution between human and animal infections was found. Global (overall) and local (spatially defined) clustering was observed for Cryptosporidium spp. infections in sheep and for Cryptosporidium xiaoi/bovis infections among sheep and cattle. Discussion The results of this analysis do not support the occurrence of defined disease outbreaks, rather they point to a continuous series of transmission events that are spatially aggregated. Despite the close coexistence between humans, sheep and cattle in the study area, mutual transmission was not observed. Hence, the study underlines the importance of sustained sanitation and hygiene measures to prevent cryptosporidiosis transmission among infants, since asymptomatic children serve as an infection reservoir. Similarly, the study highlights the importance of improving hygiene to reduce the transmission of Cryptosporidium spp. in livestock, an infection with serious consequences, especially in newborn calves. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05434-0.
Collapse
|
10
|
Fuesslin V, Krautwurst S, Srivastava A, Winter D, Liedigk B, Thye T, Herrera-León S, Wohl S, May J, Fobil JN, Eibach D, Marz M, Schuldt K. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. Front Microbiol 2022; 13:909692. [PMID: 35814690 PMCID: PMC9257098 DOI: 10.3389/fmicb.2022.909692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
Collapse
Affiliation(s)
- Valeria Fuesslin
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Doris Winter
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Britta Liedigk
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thorsten Thye
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Silvia Herrera-León
- National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jürgen May
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Julius N. Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Daniel Eibach
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Kathrin Schuldt
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
11
|
Hein W, Aglanu LM, Mensah-Sekyere M, Harant A, Brinkel J, Lamshöft M, Lorenz E, Eibach D, Amuasi J. Fighting Antimicrobial Resistance: Development and Implementation of the Ghanaian National Action Plan (2017–2021). Antibiotics (Basel) 2022; 11:antibiotics11050613. [PMID: 35625257 PMCID: PMC9137880 DOI: 10.3390/antibiotics11050613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
In recent years, Ghana has been recognised as a leading player in addressing antimicrobial resistance (AMR) in Africa. However, based on our literature review, we could not ascertain whether the core elements of the national action plan (NAP) were implemented in practice. In this paper, we present a qualitative analysis of the development of AMR-related policies in Ghana, including the NAP. We conducted 13 semi-structured expert interviews to obtain at a more thorough understanding of the implementation process for the AMR NAP and to highlight its accomplishments and shortcomings. The results show that AMR policies, as embodied in the NAP, have led to an extended network of cooperation between stakeholders in many political fields. Broadly, limited allocation of financial resources from the government and from international cooperation have been deplored. Furthermore, the opportunity for using the NAP in mainstreaming the response to the threat of AMR has not been seized. To the general public, this remained hidden behind a number of other relevant health topics such as infection prevention, veterinary services and pharmaceutical regulation. As a One Health (OH) challenge, developing countries could integrate AMR NAPs into other health and environmental programmes to improve its implementation in practice.
Collapse
Affiliation(s)
- Wolfgang Hein
- German Institute of Global and Area Studies (GIGA), 20354 Hamburg, Germany
- Faculty of Business, Economics and Social Sciences, University of Hamburg, 20146 Hamburg, Germany;
- Correspondence:
| | - Leslie Mawuli Aglanu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), PMB UPO, Kumasi, Ghana; (L.M.A.); (J.A.)
- University Medical Centre Groningen (UMCG), University of Groningen, 9713 GZ Groningen, The Netherlands
| | | | - Anne Harant
- Faculty of Business, Economics and Social Sciences, University of Hamburg, 20146 Hamburg, Germany;
| | - Johanna Brinkel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany; (J.B.); (M.L.); (E.L.)
- German Centre for Infection Research (DZIF), 20354 Hamburg, Germany
| | - Maike Lamshöft
- Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany; (J.B.); (M.L.); (E.L.)
- German Centre for Infection Research (DZIF), 20354 Hamburg, Germany
| | - Eva Lorenz
- Bernhard Nocht Institute for Tropical Medicine (BNITM), 20359 Hamburg, Germany; (J.B.); (M.L.); (E.L.)
- German Centre for Infection Research (DZIF), 20354 Hamburg, Germany
| | - Daniel Eibach
- Federal Ministry for Economic Cooperation and Development (Germany), 53113 Bonn, Germany;
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), PMB UPO, Kumasi, Ghana; (L.M.A.); (J.A.)
- Kwame Nkrumah University of Science and Technology (KNUST), PMB UPO, Kumasi, Ghana;
| |
Collapse
|
12
|
Tichkule S, Cacciò SM, Robinson G, Chalmers RM, Mueller I, Emery-Corbin SJ, Eibach D, Tyler KM, van Oosterhout C, Jex AR. Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution. Mol Biol Evol 2022; 39:6550530. [PMID: 35302613 PMCID: PMC9004413 DOI: 10.1093/molbev/msac056] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidiosis is a major global health problem and a primary cause of diarrhea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America, and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes, including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a co-evolutionary arms race with the host. Finally, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, maybe driving the evolution of more virulent C. hominis variants.
Collapse
Affiliation(s)
- Swapnil Tichkule
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Simone M Cacciò
- Department of Infectious Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, UK.,Swansea University Medical School, Swansea, UK
| | - Rachel M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, UK.,Swansea University Medical School, Swansea, UK
| | - Ivo Mueller
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Samantha J Emery-Corbin
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Kevin M Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.,Center of Excellence for Bionanoscience Research, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Aaron R Jex
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
13
|
Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, Han C, Bisignano C, Rao P, Wool E, Johnson SC, Browne AJ, Chipeta MG, Fell F, Hackett S, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, McManigal B, Achalapong S, Agarwal R, Akech S, Albertson S, Amuasi J, Andrews J, Aravkin A, Ashley E, Babin FX, Bailey F, Baker S, Basnyat B, Bekker A, Bender R, Berkley JA, Bethou A, Bielicki J, Boonkasidecha S, Bukosia J, Carvalheiro C, Castañeda-Orjuela C, Chansamouth V, Chaurasia S, Chiurchiù S, Chowdhury F, Clotaire Donatien R, Cook AJ, Cooper B, Cressey TR, Criollo-Mora E, Cunningham M, Darboe S, Day NPJ, De Luca M, Dokova K, Dramowski A, Dunachie SJ, Duong Bich T, Eckmanns T, Eibach D, Emami A, Feasey N, Fisher-Pearson N, Forrest K, Garcia C, Garrett D, Gastmeier P, Giref AZ, Greer RC, Gupta V, Haller S, Haselbeck A, Hay SI, Holm M, Hopkins S, Hsia Y, Iregbu KC, Jacobs J, Jarovsky D, Javanmardi F, Jenney AWJ, Khorana M, Khusuwan S, Kissoon N, Kobeissi E, Kostyanev T, Krapp F, Krumkamp R, Kumar A, Kyu HH, Lim C, Lim K, Limmathurotsakul D, Loftus MJ, Lunn M, Ma J, Manoharan A, Marks F, May J, Mayxay M, Mturi N, Munera-Huertas T, Musicha P, Musila LA, Mussi-Pinhata MM, Naidu RN, Nakamura T, Nanavati R, Nangia S, Newton P, Ngoun C, Novotney A, Nwakanma D, Obiero CW, Ochoa TJ, Olivas-Martinez A, Olliaro P, Ooko E, Ortiz-Brizuela E, Ounchanum P, Pak GD, Paredes JL, Peleg AY, Perrone C, Phe T, Phommasone K, Plakkal N, Ponce-de-Leon A, Raad M, Ramdin T, Rattanavong S, Riddell A, Roberts T, Robotham JV, Roca A, Rosenthal VD, Rudd KE, Russell N, Sader HS, Saengchan W, Schnall J, Scott JAG, Seekaew S, Sharland M, Shivamallappa M, Sifuentes-Osornio J, Simpson AJ, Steenkeste N, Stewardson AJ, Stoeva T, Tasak N, Thaiprakong A, Thwaites G, Tigoi C, Turner C, Turner P, van Doorn HR, Velaphi S, Vongpradith A, Vongsouvath M, Vu H, Walsh T, Walson JL, Waner S, Wangrangsimakul T, Wannapinij P, Wozniak T, Young Sharma TEMW, Yu KC, Zheng P, Sartorius B, Lopez AD, Stergachis A, Moore C, Dolecek C, Naghavi M. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399:629-655. [PMID: 35065702 PMCID: PMC8841637 DOI: 10.1016/s0140-6736(21)02724-0] [Citation(s) in RCA: 3952] [Impact Index Per Article: 1976.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. FINDINGS On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911-1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in Australasia, at 6·5 deaths (4·3-9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to AMR and 3·57 million (2·62-4·78) deaths associated with AMR in 2019. One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. INTERPRETATION To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
Collapse
|
14
|
Colston JM, Zaitchik BF, Badr HS, Burnett E, Ali SA, Rayamajhi A, Satter SM, Eibach D, Krumkamp R, May J, Chilengi R, Howard LM, Sow SO, Jahangir Hossain M, Saha D, Imran Nisar M, Zaidi AKM, Kanungo S, Mandomando I, Faruque ASG, Kotloff KL, Levine MM, Breiman RF, Omore R, Page N, Platts‐Mills JA, Ashorn U, Fan Y, Shrestha PS, Ahmed T, Mduma E, Yori PP, Bhutta Z, Bessong P, Olortegui MP, Lima AAM, Kang G, Humphrey J, Prendergast AJ, Ntozini R, Okada K, Wongboot W, Gaensbauer J, Melgar MT, Pelkonen T, Freitas CM, Kosek MN. Associations Between Eight Earth Observation-Derived Climate Variables and Enteropathogen Infection: An Independent Participant Data Meta-Analysis of Surveillance Studies With Broad Spectrum Nucleic Acid Diagnostics. Geohealth 2022; 6:e2021GH000452. [PMID: 35024531 PMCID: PMC8729196 DOI: 10.1029/2021gh000452] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/12/2021] [Accepted: 11/18/2021] [Indexed: 05/10/2023]
Abstract
Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined. Infection status for 10 common enteropathogens-adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Campylobacter, ETEC, Shigella, Cryptosporidium and Giardia-was matched by date with hydrometeorological variables from a global Earth observation dataset-precipitation and runoff volume, humidity, soil moisture, solar radiation, air pressure, temperature, and wind speed. Models were fitted for each pathogen, accounting for lags, nonlinearity, confounders, and threshold effects. Different variables showed complex, non-linear associations with infection risk varying in magnitude and direction depending on pathogen species. Rotavirus infection decreased markedly following increasing 7-day average temperatures-a relative risk of 0.76 (95% confidence interval: 0.69-0.85) above 28°C-while ETEC risk increased by almost half, 1.43 (1.36-1.50), in the 20-35°C range. Risk for all pathogens was highest following soil moistures in the upper range. Humidity was associated with increases in bacterial infections and decreases in most viral infections. Several virus species' risk increased following lower-than-average rainfall, while rotavirus and ETEC increased with heavier runoff. Temperature, soil moisture, and humidity are particularly influential parameters across all enteropathogens, likely impacting pathogen survival outside the host. Precipitation and runoff have divergent associations with different enteric viruses. These effects may engender shifts in the relative burden of diarrhea-causing agents as the global climate changes.
Collapse
|
15
|
Lorenz E, Souares A, Amuasi J, Loag W, Deschermeier C, Fusco D, Benke D, A Rakotoarivelo R, Rasamoelina MT, Rakotozandrindrainy R, Sie A, Afum-Adjei Awuah A, May J, Eibach D, Struck N. Seroprevalence of SARS-CoV-2 in urban settings in three sub-Saharan African countries (SeroCoV): a study protocol for a household-based cross-sectional prevalence study using two-stage cluster sampling. BMJ Open 2021; 11:e056853. [PMID: 34921091 PMCID: PMC8685532 DOI: 10.1136/bmjopen-2021-056853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/23/2021] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION The current COVID-19 pandemic has impacted the entire world with increasing morbidity and mortality and has resulted in serious economic and social consequences. Assessing the burden of COVID-19 is essential for developing efficient pandemic preparedness and response strategies and for determining the impact of implemented control measures. Population-based seroprevalence surveys are critical to estimate infection rates, monitor the progression of the epidemic and to allow for the identification of persons exposed to the infection who may either have been asymptomatic or were never tested. This is especially important for countries where effective testing and tracking systems could not be established and where non-severe cases or under-reported deaths might have blurred the true burden of COVID-19. Most seroprevalence surveys performed in sub-Saharan Africa have targeted specific high risk or more easily accessible populations such as healthcare workers or blood donors, and household-based estimates are rarely available. Here, we present the study protocol for a SARS-CoV-2 seroprevalence estimation in the general population of Burkina Faso, Ghana and Madagascar in 2021. METHODS AND ANALYSIS The SeroCoV study is a household-based cross-sectional prevalence investigation in persons aged 10 years and older living in urban areas in six cities using a two-stage geographical cluster sampling method stratified by age and sex. The presence of anti-SARS-CoV-2 IgG antibodies will be determined using a sensitive and specific SARS-CoV-2 IgG ELISA. In addition, questionnaires will cover sociodemographic information, episodes of diseases and history of testing and treatment for COVID-like symptoms, travel history and safety measures. We will estimate the seroprevalence of SARS-CoV-2, taking into account test performance and adjusting for the age and sex of the respective populations. ETHICS AND DISSEMINATION Ethical approval was received for all participating countries. Results will be disseminated through reports and presentations at the country level as well as peer-reviewed publications and international scientific conferences presentations.
Collapse
Affiliation(s)
- Eva Lorenz
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
- German Center for Infection Research Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Aurélia Souares
- Universitatsklinikum Heidelberg Institut fur Global Health, Heidelberg, Germany
- German Center for Infection Research Heidelberg Site, Heidelberg, Baden-Württemberg, Germany
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Wibke Loag
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
| | - Christina Deschermeier
- Infectious Disease Diagnostics, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
| | - Daniela Fusco
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
- German Center for Infection Research Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
| | - Dominik Benke
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
| | | | | | | | - Ali Sie
- German Center for Infection Research Heidelberg Site, Heidelberg, Baden-Württemberg, Germany
- Centre de Recherche en Sante de Nouna, Nouna, Boucle du Mouhoun, Burkina Faso
| | - Anthony Afum-Adjei Awuah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
- German Center for Infection Research Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
- German Center for Infection Research Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
| | - Nicole Struck
- Infectious Disease Epidemiology, Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany
- German Center for Infection Research Hamburg-Lübeck-Borstel-Riems Site, Hamburg, Germany
| |
Collapse
|
16
|
Manouana GP, Niendorf S, Tomazatos A, Mbong Ngwese M, Nzamba Maloum M, Nguema Moure PA, Bingoulou Matsougou G, Ategbo S, Rossatanga EG, Bock CT, Borrmann S, Mordmüller B, Eibach D, Kremsner PG, Velavan TP, Adegnika AA. Molecular surveillance and genetic divergence of rotavirus A antigenic epitopes in Gabonese children with acute gastroenteritis. EBioMedicine 2021; 73:103648. [PMID: 34706308 PMCID: PMC8551588 DOI: 10.1016/j.ebiom.2021.103648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023] Open
Abstract
Background Rotavirus A (RVA) causes acute gastroenteritis in children <5 years of age in sub-Saharan Africa. In this study, we described the epidemiology and genetic diversity of RVA infecting Gabonese children and examined the antigenic variability of circulating strains in relation to available vaccine strains to maximize the public health benefits of introducing rotavirus vaccine through the Expanded Programme on Immunization (EPI) in Gabon. Methods Stool samples were collected consecutively between April 2018 and November 2019 from all hospitalized children <5 years with gastroenteritis and community controls without gastroenteritis. Children were tested for rotavirus A by quantitative RT-PCR and subsequently sequenced to identify circulating rotavirus A genotypes in the most vulnerable population. The VP7 and VP4 (VP8*) antigenic epitopes were mapped to homologs of vaccine strains to assess structural variability and potential impact on antigenicity. Findings Infections were mostly acquired during the dry season. Rotavirus A was detected in 98/177 (55%) hospitalized children with gastroenteritis and 14/67 (21%) of the control children. The most common RVA genotypes were G1 (18%), G3 (12%), G8 (18%), G9 (2%), G12 (25%), with G8 and G9 reported for the first time in Gabon. All were associated either with P[6] (31%) or P[8] (38%) genotypes. Several non-synonymous substitutions were observed in the antigenic epitopes of VP7 (positions 94 and 147) and VP8* (positions 89, 116, 146 and 150), which may modulate the elicited immune responses. Interpretation This study contributes to the epidemiological surveillance of rotavirus A required before the introduction of rotavirus vaccination in the EPI for Gabonese children.
Collapse
Affiliation(s)
- Gédéon Prince Manouana
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Sandra Niendorf
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Alexandru Tomazatos
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | - Gedeon Bingoulou Matsougou
- Département de Pédiatrie, Faculté de Médecine, Université des Sciences de la Santé (USS), BP 4009, Libreville, Gabon
| | - Simon Ategbo
- Département de Pédiatrie, Faculté de Médecine, Université des Sciences de la Santé (USS), BP 4009, Libreville, Gabon
| | | | - C Thomas Bock
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Steffen Borrmann
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon; Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherland
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Viet Nam.
| | - Ayola Akim Adegnika
- Institute of Tropical Medicine, University of Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon; Centre Hospitalier Régional Georges Rawiri de Lambaréné, Lambaréné, Gabon; Fondation pour la Recherche Scientifique, Cotonou, Bénin.
| |
Collapse
|
17
|
Manouana GP, Byrne N, Mbong Ngwese M, Nguema Moure A, Hofmann P, Bingoulou Matsougou G, Lotola Mougeni F, Nnoh Dansou E, Agbanrin MD, Mapikou Gouleu CS, Ategbo S, Zinsou JF, Adegbite BR, Edoa JR, Kremsner PG, Mordmüller B, Eibach D, McCall M, Abraham A, Borrmann S, Adegnika AA. Prevalence of Pathogens in Young Children Presenting to Hospital with Diarrhea from Lambaréné, Gabon. Am J Trop Med Hyg 2021; 105:254-260. [PMID: 34232911 DOI: 10.4269/ajtmh.20-1290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/08/2021] [Indexed: 11/07/2022] Open
Abstract
Diarrheal disease is the second most frequent cause of mortality in children younger than 5 years worldwide, causing more than half a million deaths each year. Our knowledge of the epidemiology of potentially pathogenic agents found in children suffering from diarrhea in sub-Saharan African countries is still patchy, and thereby hinders implementation of effective preventative interventions. The lack of cheap, easy-to-use diagnostic tools leads to mostly symptomatic and empirical case management. An observational study with a total of 241 participants was conducted from February 2017 to August 2018 among children younger than 5 years with diarrhea in Lambaréné, Gabon. Clinical and demographic data were recorded, and a stool sample was collected. The samples were examined using a commercial rapid immunoassay to detect Rotavirus/adenovirus, conventional bacterial culture for Salmonella spp., and multiplex real-time PCR for Cryptosporidium spp., Giardia lamblia, Cyclospora cayetanensis, enterotoxigenic Escherichia coli (ETEC), and enteroinvasive Escherichia coli (EIEC)/Shigella. At least one infectious agent was present in 121 of 241 (50%) samples. The most frequently isolated pathogens were EIEC/Shigella and ETEC (54/179; 30.2% and 44/179; 24.6%, respectively), followed by G. lamblia (33/241; 13.7%), Cryptosporidium spp. (31/241; 12.9%), and Rotavirus (23/241; 9.5%). Coinfection with multiple pathogens was observed in 33% (40/121) of the positive cases with EIEC/Shigella, ETEC, and Cryptosporidium spp. most frequently identified. Our results provide new insight into the possible causes of diarrheal disease in the Moyen-Ogooué region of Gabon and motivate further research on possible modes of infection and targeted preventive measures.
Collapse
Affiliation(s)
- Gédéon Prince Manouana
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany
| | - Natalie Byrne
- 2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany
| | | | | | - Philipp Hofmann
- 3German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Greifswald - Insel Riems, Germany
| | - Gedeon Bingoulou Matsougou
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,4Département de Pédiatrie, Faculté de Médecine, Université des Sciences de la Santé (USS), Libreville, Gabon
| | | | | | | | | | - Simon Ategbo
- 4Département de Pédiatrie, Faculté de Médecine, Université des Sciences de la Santé (USS), Libreville, Gabon
| | | | - Bayode Romeo Adegbite
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,5Department of Infectious Diseases, Center of Tropical Medicine and Travel Medicine, Amsterdam University Medical Centers, Location Amsterdam, Amsterdam, The Netherlands.,6Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Peter Gottfried Kremsner
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany.,7German Center for Infection Research (DZIF), Tübingen, Germany
| | - Benjamin Mordmüller
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany.,7German Center for Infection Research (DZIF), Tübingen, Germany
| | - Daniel Eibach
- 3German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Greifswald - Insel Riems, Germany.,8Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Matthew McCall
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany.,9Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
| | - Alabi Abraham
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon
| | - Steffen Borrmann
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany.,7German Center for Infection Research (DZIF), Tübingen, Germany
| | - Ayola Akim Adegnika
- 1Centre de Recherche Médicales de Lambaréné, Lambaréné, Gabon.,2Institut für Tropenmedizin, Eberhad Karls Universität Tübingen, Tübingen, Germany.,7German Center for Infection Research (DZIF), Tübingen, Germany
| |
Collapse
|
18
|
Riba A, Hassani K, Walker A, van Best N, von Zezschwitz D, Anslinger T, Sillner N, Rosenhain S, Eibach D, Maiga-Ascofaré O, Rolle-Kampczyk U, Basic M, Binz A, Mocek S, Sodeik B, Bauerfeind R, Mohs A, Trautwein C, Kiessling F, May J, Klingenspor M, Gremse F, Schmitt-Kopplin P, Bleich A, Torow N, von Bergen M, Hornef MW. Disturbed gut microbiota and bile homeostasis in Giardia-infected mice contributes to metabolic dysregulation and growth impairment. Sci Transl Med 2021; 12:12/565/eaay7019. [PMID: 33055245 DOI: 10.1126/scitranslmed.aay7019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Although infection with the human enteropathogen Giardia lamblia causes self-limited diarrhea in adults, infant populations in endemic areas experience persistent pathogen carriage in the absence of diarrhea. The persistence of this protozoan parasite in infants has been associated with reduced weight gain and linear growth (height-for-age). The mechanisms that support persistent infection and determine the different disease outcomes in the infant host are incompletely understood. Using a neonatal mouse model of persistent G. lamblia infection, we demonstrate that G. lamblia induced bile secretion and used the bile constituent phosphatidylcholine as a substrate for parasite growth. In addition, we show that G. lamblia infection altered the enteric microbiota composition, leading to enhanced bile acid deconjugation and increased expression of fibroblast growth factor 15. This resulted in elevated energy expenditure and dysregulated lipid metabolism with reduced adipose tissue, body weight gain, and growth in the infected mice. Our results indicate that this enteropathogen's modulation of bile acid metabolism and lipid metabolism in the neonatal mouse host led to an altered body composition, suggesting how G. lamblia infection could contribute to growth restriction in infants in endemic areas.
Collapse
Affiliation(s)
- Ambre Riba
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany
| | - Kasra Hassani
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625 Hannover, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Niels van Best
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany.,Department of Medical Microbiology and NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Dunja von Zezschwitz
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany
| | - Teresa Anslinger
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany
| | - Nina Sillner
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Rosenhain
- Institute for Experimental Molecular Imaging, University Hospital Aachen, 52074 Aachen, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | | | - Ulrike Rolle-Kampczyk
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, 04318 Leipzig, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Anne Binz
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Sabine Mocek
- Chair for Molecular Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Rudolf Bauerfeind
- Research Core Unit for Laser Microscopy, Hannover Medical School, 30625 Hannover, Germany
| | - Antje Mohs
- Medizinische Klinik III, RWTH University Hospital, Aachen, 52074 Aachen, Germany
| | - Christian Trautwein
- Medizinische Klinik III, RWTH University Hospital, Aachen, 52074 Aachen, Germany
| | - Fabian Kiessling
- Institute for Experimental Molecular Imaging, University Hospital Aachen, 52074 Aachen, Germany.,Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.,Fraunhofer Institute for Digital Medicine MEVIS, Bremen, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Felix Gremse
- Institute for Experimental Molecular Imaging, University Hospital Aachen, 52074 Aachen, Germany.,Software Tools for Computational Engineering, RWTH Aachen University, 52072 Aachen, Germany.,Gremse-IT GmbH, 52068 Aachen, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany.,Analytical Food Chemistry, Technical University of Munich, 85354 Freising, Germany
| | - André Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia Torow
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Bruderstrase 34, D-04103 Leipzig, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany.
| |
Collapse
|
19
|
Krumkamp R, Aldrich C, Maiga-Ascofare O, Mbwana J, Rakotozandrindrainy N, Borrmann S, Caccio SM, Rakotozandrindrainy R, Adegnika AA, Lusingu JPA, Amuasi J, May J, Eibach D. Transmission of Cryptosporidium Species Among Human and Animal Local Contact Networks in Sub-Saharan Africa: A Multicountry Study. Clin Infect Dis 2021; 72:1358-1366. [PMID: 32150243 PMCID: PMC8075035 DOI: 10.1093/cid/ciaa223] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/03/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Cryptosporidiosis has been identified as one of the major causes of diarrhea and diarrhea-associated deaths in young children in sub-Saharan Africa. This study traces back Cryptosporidium-positive children to their human and animal contacts to identify transmission networks. METHODS Stool samples were collected from children < 5 years of age with diarrhea in Gabon, Ghana, Madagascar, and Tanzania. Cryptosporidium-positive and -negative initial cases (ICs) were followed to the community, where stool samples from households, neighbors, and animal contacts were obtained. Samples were screened for Cryptosporidium species by immunochromatographic tests and by sequencing the 18S ribosomal RNA gene and further subtyped at the 60 kDa glycoprotein gene (gp60). Transmission clusters were identified and risk ratios (RRs) calculated. RESULTS Among 1363 pediatric ICs, 184 (13%) were diagnosed with Cryptosporidium species. One hundred eight contact networks were sampled from Cryptosporidium-positive and 68 from negative ICs. Identical gp60 subtypes were detected among 2 or more contacts in 39 (36%) of the networks from positive ICs and in 1 contact (1%) from negative ICs. In comparison to Cryptosporidium-negative ICs, positive ICs had an increased risk of having Cryptosporidium-positive household members (RR, 3.6 [95% confidence interval {CI}, 1.7-7.5]) or positive neighboring children (RR, 2.9 [95% CI, 1.6-5.1]), but no increased risk of having positive animals (RR, 1.2 [95% CI, .8-1.9]) in their contact network. CONCLUSIONS Cryptosporidiosis in rural sub-Saharan Africa is characterized by infection clusters among human contacts, to which zoonotic transmission appears to contribute only marginally.
Collapse
Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Cassandra Aldrich
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany.,Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Oumou Maiga-Ascofare
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Joyce Mbwana
- National Institute for Medical Research, Tanga Research Centre, Tanga, United Republic of Tanzania
| | | | - Steffen Borrmann
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Tübingen, Germany
| | - Simone M Caccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Tübingen, Germany
| | - John P A Lusingu
- National Institute for Medical Research, Tanga Research Centre, Tanga, United Republic of Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | | |
Collapse
|
20
|
Emmerich P, Murawski C, Ehmen C, von Possel R, Pekarek N, Oestereich L, Duraffour S, Pahlmann M, Struck N, Eibach D, Krumkamp R, Amuasi J, Maiga-Ascofaré O, Rakotozandrindrainy R, Asogun D, Ighodalo Y, Kann S, May J, Tannich E, Deschermeier C. Limited specificity of commercially available SARS-CoV-2 IgG ELISAs in serum samples of African origin. Trop Med Int Health 2021; 26:621-631. [PMID: 33666297 PMCID: PMC8014856 DOI: 10.1111/tmi.13569] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Specific serological tests are mandatory for reliable SARS-CoV-2 diagnostics and seroprevalence studies. Here, we assess the specificities of four commercially available SARS-CoV-2 IgG ELISAs in serum/plasma panels originating from Africa, South America, and Europe. METHODS 882 serum/plasma samples collected from symptom-free donors before the COVID-19 pandemic in three African countries (Ghana, Madagascar, Nigeria), Colombia, and Germany were analysed with three nucleocapsid-based ELISAs (Euroimmun Anti-SARS-CoV-2-NCP IgG, EDI™ Novel Coronavirus COVID-19 IgG, Mikrogen recomWell SARS-CoV-2 IgG), one spike/S1-based ELISA (Euroimmun Anti-SARS-CoV-2 IgG), and in-house common cold CoV ELISAs. RESULTS High specificity was confirmed for all SARS-CoV-2 IgG ELISAs for Madagascan (93.4-99.4%), Colombian (97.8-100.0%), and German (95.9-100.0%) samples. In contrast, specificity was much lower for the Ghanaian and Nigerian serum panels (Ghana: NCP-based assays 77.7-89.7%, spike/S1-based assay 94.3%; Nigeria: NCP-based assays 39.3-82.7%, spike/S1-based assay 90.7%). 15 of 600 African sera were concordantly classified as positive in both the NCP-based and the spike/S1-based Euroimmun ELISA, but did not inhibit spike/ACE2 binding in a surrogate virus neutralisation test. IgG antibodies elicited by previous infections with common cold CoVs were found in all sample panels, including those from Madagascar, Colombia, and Germany and thus do not inevitably hamper assay specificity. Nevertheless, high levels of IgG antibodies interacting with OC43 NCP were found in all 15 SARS-CoV-2 NCP/spike/S1 ELISA positive sera. CONCLUSIONS Depending on the chosen antigen and assay protocol, SARS-CoV-2 IgG ELISA specificity may be significantly reduced in certain populations probably due to interference of immune responses to endemic pathogens like other viruses or parasites.
Collapse
Affiliation(s)
- Petra Emmerich
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, Rostock, Germany
| | - Carolin Murawski
- Department for Infectious Disease Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christa Ehmen
- Department for Infectious Disease Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ronald von Possel
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Neele Pekarek
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Lisa Oestereich
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany
| | - Sophie Duraffour
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany
| | - Meike Pahlmann
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany
| | - Nicole Struck
- German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany.,Department for Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany.,Department for Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ralf Krumkamp
- German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany.,Department for Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Amuasi
- Global Health and Infectious Disease Research Group, Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Oumou Maiga-Ascofaré
- German Center for Infection Research, Hamburg - Lübeck - Borstel - Riems, Germany.,Infectious Disease Epidemiology Research Group, Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Danny Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Yemisi Ighodalo
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Simone Kann
- Medical Mission Institute, Würzburg, Germany
| | - Jürgen May
- Department for Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Egbert Tannich
- Department for Infectious Disease Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,National Reference Centre for Tropical Pathogens, Hamburg, Germany
| | - Christina Deschermeier
- Department for Infectious Disease Diagnostics, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
21
|
Marlene Ihling C, Schnitzler P, Heinrich N, Mangu C, Sudi L, Souares A, Gies S, Sié A, Coulibaly B, Thierry Ouédraogo A, Mordmüller B, Held J, Akim Adegnika A, Fernandes JF, Eckerle I, May J, Hogan B, Eibach D, Tabatabai J. Molecular epidemiology of Respiratory Syncytial Virus in children in sub‐Saharan Africa. Trop Med Int Health 2021. [DOI: 10.1111/tmi.13582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clara Marlene Ihling
- Center of Infectious Diseases Virology, Heidelberg University Hospital Heidelberg Germany
- German Center for Infection Research (DZIF), City?, Germany
- Dr. von Haunersches Kinderspital University Hospital of the LMU Munich Munich Germany
| | - Paul Schnitzler
- Center of Infectious Diseases Virology, Heidelberg University Hospital Heidelberg Germany
| | - Norbert Heinrich
- German Center for Infection Research (DZIF), City?, Germany
- Division for Infectious Diseases University Hospital of the LMU Munich Munich Germany
| | - Chacha Mangu
- NIMR‐Mbeya Medical Research Center Mbeya Tanzania
| | - Lwitiho Sudi
- NIMR‐Mbeya Medical Research Center Mbeya Tanzania
| | - Aurélia Souares
- German Center for Infection Research (DZIF), City?, Germany
- Heidelberg Institute of Global Health Heidelberg University Hospital Heidelberg Germany
| | - Sabine Gies
- German Center for Infection Research (DZIF), City?, Germany
- Heidelberg Institute of Global Health Heidelberg University Hospital Heidelberg Germany
| | - Ali Sié
- Centre de Recherche en Santé de Nouna Nouna Burkina Faso
| | | | | | - Benjamin Mordmüller
- German Center for Infection Research (DZIF), City?, Germany
- Eberhard Karls University Tuebingen Tübingen Germany
| | - Jana Held
- German Center for Infection Research (DZIF), City?, Germany
- Eberhard Karls University Tuebingen Tübingen Germany
| | - Ayola Akim Adegnika
- German Center for Infection Research (DZIF), City?, Germany
- Eberhard Karls University Tuebingen Tübingen Germany
- Centre de Recherches Médicales de Lambaréné Lambaréné Gabon
| | - José F. Fernandes
- Eberhard Karls University Tuebingen Tübingen Germany
- Centre de Recherches Médicales de Lambaréné Lambaréné Gabon
| | - Isabella Eckerle
- Institute of Virology University of Bonn Medical Center Bonn Germany
- Geneva Center for Emerging Viral Diseases University Hospitals of Geneva Faculty of Medicine University of Geneva Geneva Switzerland
| | - Juergen May
- German Center for Infection Research (DZIF), City?, Germany
- Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Benedikt Hogan
- German Center for Infection Research (DZIF), City?, Germany
- Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Daniel Eibach
- German Center for Infection Research (DZIF), City?, Germany
- Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Julia Tabatabai
- Center of Infectious Diseases Virology, Heidelberg University Hospital Heidelberg Germany
- German Center for Infection Research (DZIF), City?, Germany
- Center for Pediatric and Adolescent Medicine University Hospital Heidelberg Heidelberg Germany
| |
Collapse
|
22
|
Ihling CM, Schnitzler P, Heinrich N, Mangu C, Sudi L, Souares A, Gies S, Sié A, Coulibaly B, Ouédraogo AT, Mordmüller B, Held J, Adegnika AA, Fernandes JF, Eckerle I, May J, Hogan B, Eibach D, Tabatabai J. Molecular epidemiology of respiratory syncytial virus in children in sub-Saharan Africa. Trop Med Int Health 2021; 26:810-822. [PMID: 33683751 DOI: 10.1111/tmi.13573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study investigated the molecular epidemiology of respiratory syncytial virus (RSV) among febrile children with acute respiratory tract infection in Ghana, Gabon, Tanzania and Burkina Faso between 2014 and 2017 as well as the evolution and diversification of RSV strains from other sub-Saharan countries. METHODS Pharyngeal swabs were collected at four study sites (Agogo, Ghana: n = 490; Lambaréné, Gabon: n = 182; Mbeya, Tanzania: n = 293; Nouna, Burkina Faso: n = 115) and analysed for RSV and other respiratory viruses using rtPCR. For RSV-positive samples, sequence analysis of the second hypervariable region of the G gene was performed. A dataset of RSV strains from sub-Saharan Africa (2011-2017) currently available in GenBank was compiled. Phylogenetic analysis was conducted to identify the diversity of circulating RSV genotypes. RESULTS In total, 46 samples were tested RSV positive (Ghana n = 31 (6.3%), Gabon n = 4 (2.2%), Tanzania n = 9 (3.1%) and Burkina Faso n = 2 (1.7%)). The most common RSV co-infection was with rhinovirus. All RSV A strains clustered with genotype ON1 strains with a 72-nucleotide duplication and all RSV B strains belonged to genotype BAIX. Phylogenetic analysis of amino acid sequences from sub-Saharan Africa revealed the diversification into 11 different ON1 and 22 different BAIX lineages and differentiation of ON1 and BAIX strains into potential new sub-genotypes, provisionally named ON1-NGR, BAIX-KEN1, BAIX-KEN2 and BAIX-KEN3. CONCLUSION The study contributes to an improved understanding of the molecular epidemiology of RSV infection in sub-Saharan Africa. It provides the first phylogenetic data for RSV from Tanzania, Gabon and Burkina Faso and combines it with RSV strains from all other sub-Saharan countries currently available in GenBank.
Collapse
Affiliation(s)
- Clara Marlene Ihling
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany.,Dr. von Haunersches Kinderspital, University Hospital of the LMU Munich, Munich, Germany
| | - Paul Schnitzler
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Norbert Heinrich
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Division for Infectious Diseases, University Hospital of the LMU Munich, Munich, Germany
| | - Chacha Mangu
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Lwitiho Sudi
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Aurélia Souares
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Heidelberg Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Sabine Gies
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Heidelberg Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Ali Sié
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | | | - Benjamin Mordmüller
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Jana Held
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Ayola Akim Adegnika
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - José F Fernandes
- Eberhard Karls University Tuebingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Isabella Eckerle
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany.,Faculty of Medicine, Geneva Center for Emerging Viral Diseases, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland
| | - Juergen May
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia Tabatabai
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany.,Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| |
Collapse
|
23
|
Strauss RA, Herrera-Leon L, Guillén AC, Castro JS, Lorenz E, Carvajal A, Hernandez E, Navas T, Vielma S, Lopez N, Lopez MG, Aurenty L, Navas V, Rosas MA, Drummond T, Martínez JG, Hernández E, Bertuglia F, Andrade O, Torres J, May J, Herrera-Leon S, Eibach D. Molecular and epidemiologic characterization of the diphtheria outbreak in Venezuela. Sci Rep 2021; 11:6378. [PMID: 33737710 PMCID: PMC7973433 DOI: 10.1038/s41598-021-85957-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/09/2021] [Indexed: 11/09/2022] Open
Abstract
In 2016, Venezuela faced a large diphtheria outbreak that extended until 2019. Nasopharyngeal or oropharyngeal samples were prospectively collected from 51 suspected cases and retrospective data from 348 clinical records was retrieved from 14 hospitals between November 2017 and November 2018. Confirmed pathogenic Corynebactrium isolates were biotyped. Multilocus Sequence Typing (MLST) was performed followed by next-generation-based core genome-MLST and minimum spanning trees were generated. Subjects between 10 and 19 years of age were mostly affected (n = 95; 27.3%). Case fatality rates (CFR) were higher in males (19.4%), as compared to females (15.8%). The highest CFR (31.1%) was observed among those under 5, followed by the 40 to 49 age-group (25.0%). Nine samples corresponded to C. diphtheriae and 1 to C. ulcerans. Two Sequencing Types (ST), ST174 and ST697 (the latter not previously described) were identified among the eight C. diphtheriae isolates from Carabobo state. Cg-MLST revealed only one cluster also from Carabobo. The Whole Genome Sequencing analysis revealed that the outbreak seemed to be caused by different strains with C. diphtheriae and C. ulcerans coexisting. The reemergence and length of this outbreak suggest vaccination coverage problems and an inadequate control strategy.
Collapse
Affiliation(s)
| | | | | | - Julio S Castro
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Eva Lorenz
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ana Carvajal
- Hospital Universitario de Caracas, Caracas, Venezuela
| | | | - Trina Navas
- Hospital General Los Magallanes de Catia, Caracas, Venezuela
| | | | | | - Maria G Lopez
- Hospital de Niños José Manuel de Los Ríos, Caracas, Venezuela
| | - Lisbeth Aurenty
- Hospital de Niños José Manuel de Los Ríos, Caracas, Venezuela
| | - Valeria Navas
- Hospital Universitario de Maracaibo, Maracaibo, Venezuela
| | - Maria A Rosas
- Ciudad Hospitalaria Dr Henrique Tejera, Carabobo, Venezuela
| | | | | | | | | | - Omaira Andrade
- Centro Clinico-Materno Leopoldo Aguerrevere, Caracas, Venezuela
| | - Jaime Torres
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
24
|
Akenten CW, Boahen KG, Marfo KS, Sarpong N, Dekker D, Struck NS, Osei-Tutu L, May J, Amuasi JH, Eibach D. Bloodstream infection with Acinetobacter baumanii in a Plasmodium falciparum positive infant: a case report. J Med Case Rep 2021; 15:46. [PMID: 33541431 PMCID: PMC7863459 DOI: 10.1186/s13256-020-02648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/21/2020] [Indexed: 12/03/2022] Open
Abstract
Background The increasing incidence of multi-antibiotic-resistant bacterial infections, coupled with the risk of co-infections in malaria-endemic regions, complicates accurate diagnosis and prolongs hospitalization, thereby increasing the total cost of illness. Further, there are challenges in making the correct choice of antibiotic treatment and duration, precipitated by a lack of access to microbial culture facilities in many hospitals in Ghana. The aim of this case report is to highlight the need for blood cultures or alternative rapid tests to be performed routinely in malaria patients, to diagnose co-infections with bacteria, especially when symptoms persist after antimalarial treatment. Case presentation A 6-month old black female child presented to the Agogo Presbyterian Hospital with fever, diarrhea, and a 3-day history of cough. A rapid diagnostic test for malaria and Malaria microscopy was positive for P. falciparum with a parasitemia of 224 parasites/μl. The patient was treated with Intravenous Artesunate, parental antibiotics (cefuroxime and gentamicin) and oral dispersible zinc tablets in addition to intravenous fluids. Blood culture yielded Acinetobacter baumanii, which was resistant to all of the third-generation antibiotics included in the susceptibility test conducted, but sensitive to ciprofloxacin and gentamicin. After augmenting treatment with intravenous ciprofloxacin, all symptoms resolved. Conclusion Even though this study cannot confirm whether the bacterial infection was nosocomial or otherwise, the case highlights the necessity to test malaria patients for possible co-infections, especially when fever persists after parasites have been cleared from the bloodstream. Bacterial blood cultures and antimicrobial susceptibility testing should be routinely performed to guide treatment options for febril illnesses in Ghana in order to reduce inappropriate use of broad-spectrum antibiotics and limit the development of antimicrobial resistance.
Collapse
Affiliation(s)
- Charity Wiafe Akenten
- Kumasi Centre for Collaborative Research in Tropical Medicine, P.O Box PMB KNUST, Kumasi, Ghana.
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, P.O Box PMB KNUST, Kumasi, Ghana
| | - Kwadwo Sarfo Marfo
- Kumasi Centre for Collaborative Research in Tropical Medicine, P.O Box PMB KNUST, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, P.O Box PMB KNUST, Kumasi, Ghana
| | - Denise Dekker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Juergen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Humphrey Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, P.O Box PMB KNUST, Kumasi, Ghana.,School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
25
|
Struck NS, Zimmermann M, Krumkamp R, Lorenz E, Jacobs T, Rieger T, Wurr S, Günther S, Gyau Boahen K, Marks F, Sarpong N, Owusu-Dabo E, May J, Eibach D. Cytokine Profile Distinguishes Children With Plasmodium falciparum Malaria From Those With Bacterial Blood Stream Infections. J Infect Dis 2021; 221:1098-1106. [PMID: 31701142 PMCID: PMC7075412 DOI: 10.1093/infdis/jiz587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/05/2019] [Indexed: 12/29/2022] Open
Abstract
Background Malaria presents with unspecific clinical symptoms that frequently overlap with other infectious diseases and is also a risk factor for coinfections, such as non-Typhi Salmonella. Malaria rapid diagnostic tests are sensitive but unable to distinguish between an acute infection requiring treatment and asymptomatic malaria with a concomitant infection. We set out to test whether cytokine profiles could predict disease status and allow the differentiation between malaria and a bacterial bloodstream infection. Methods We created a classification model based on cytokine concentration levels of pediatric inpatients with either Plasmodium falciparum malaria or a bacterial bloodstream infection using the Luminex platform. Candidate markers were preselected using classification and regression trees, and the predictive strength was calculated through random forest modeling. Results Analyses revealed that a combination of 7–15 cytokines exhibited a median disease prediction accuracy of 88% (95th percentile interval, 73%–100%). Haptoglobin, soluble Fas-Ligand, and complement component C2 were the strongest single markers with median prediction accuracies of 82% (with 95th percentile intervals of 71%–94%, 62%–94%, and 62%–94%, respectively). Conclusions Cytokine profiles possess good median disease prediction accuracy and offer new possibilities for the development of innovative point-of-care tests to guide treatment decisions in malaria-endemic regions.
Collapse
Affiliation(s)
- Nicole S Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Correspondence: Nicole S. Struck, PhD, Bernhard Nocht Institute for Tropical Medicine, Department of Infectious Disease Epidemiology, Bernhard Nocht Strasse 74, 20359 Hamburg, Germany ()
| | - Marlow Zimmermann
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Eva Lorenz
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Thomas Jacobs
- Department of Immunology, Bernhard-Nocht-Institute of Tropical Medicine, Hamburg, Germany
| | - Toni Rieger
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Virology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephanie Wurr
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Virology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Virology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nimako Sarpong
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
26
|
Tichkule S, Jex AR, van Oosterhout C, Sannella AR, Krumkamp R, Aldrich C, Maiga-Ascofare O, Dekker D, Lamshöft M, Mbwana J, Rakotozandrindrainy N, Borrmann S, Thye T, Schuldt K, Winter D, Kremsner PG, Oppong K, Manouana P, Mbong M, Gesase S, Minja DTR, Mueller I, Bahlo M, Nader J, May J, Rakotozandrindrain R, Adegnika AA, Lusingu JPA, Amuasi J, Eibach D, Caccio SM. Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa. Microb Genom 2021; 7:mgen000493. [PMID: 33355530 PMCID: PMC8115899 DOI: 10.1099/mgen.0.000493] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/26/2020] [Indexed: 12/02/2022] Open
Abstract
Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C. hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide diversity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses; (2) local anthroponotic transmission underpins the spread of this pathogen in Africa; (3) hybridization occurs between distinct geographical lineages; and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host-parasite coevolution.
Collapse
Affiliation(s)
- Swapnil Tichkule
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Aaron R. Jex
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Anna Rosa Sannella
- Department of Infectious Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Cassandra Aldrich
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich 80802, Germany
| | - Oumou Maiga-Ascofare
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Maike Lamshöft
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Joyce Mbwana
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | | | - Steffen Borrmann
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - Thorsten Thye
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Kathrin Schuldt
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Peter G. Kremsner
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - Kwabena Oppong
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Prince Manouana
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
| | - Mirabeau Mbong
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
| | - Samwel Gesase
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Daniel T. R. Minja
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Ivo Mueller
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Melanie Bahlo
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Johanna Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - John P. A. Lusingu
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Simone Mario Caccio
- Department of Infectious Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| |
Collapse
|
27
|
Krumkamp R, Struck NS, Lorenz E, Zimmermann M, Boahen KG, Sarpong N, Owusu-Dabo E, Pak GD, Jeon HJ, Marks F, Jacobs T, May J, Eibach D. Classification of invasive bloodstream infections and Plasmodium falciparum malaria using autoantibodies as biomarkers. Sci Rep 2020; 10:21168. [PMID: 33273605 PMCID: PMC7712777 DOI: 10.1038/s41598-020-78155-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/20/2020] [Indexed: 01/25/2023] Open
Abstract
A better understanding of disease-specific biomarker profiles during acute infections could guide the development of innovative diagnostic methods to differentiate between malaria and alternative causes of fever. We investigated autoantibody (AAb) profiles in febrile children (≤ 5 years) admitted to a hospital in rural Ghana. Serum samples from 30 children with a bacterial bloodstream infection and 35 children with Plasmodium falciparum malaria were analyzed using protein microarrays (Protoplex Immune Response Assay, ThermoFisher). A variable selection algorithm was applied to identify the smallest set of AAbs showing the best performance to classify malaria and bacteremia patients. The selection procedure identified 8 AAbs of which IFNGR2 and FBXW5 were selected in repeated model run. The classification error was 22%, which was mainly due to non-Typhi Salmonella (NTS) diagnoses being misclassified as malaria. Likewise, a cluster analysis grouped patients with NTS and malaria together, but separated malaria from non-NTS infections. Both current and recent malaria are a risk factor for NTS, therefore, a better understanding about the function of AAb in disease-specific immune responses is required in order to support their application for diagnostic purposes.
Collapse
Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nicole Sunaina Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany. .,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Eva Lorenz
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marlow Zimmermann
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Kennedy Gyau Boahen
- Department of Infectious Disease Epidemiology, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Nimako Sarpong
- Department of Infectious Disease Epidemiology, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Gi Deok Pak
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea
| | - Hyon Jin Jeon
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea
| | - Florian Marks
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea.,The Department of Medicine, the University of Cambridge, Cambridge, UK
| | - Thomas Jacobs
- Research Group Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,First Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| |
Collapse
|
28
|
Kiemde D, Ribeiro I, Sanou S, Coulibaly B, Sie A, Ouedraogo AS, Souares A, Eibach D. Molecular characterization of beta-lactamase genes produced by community-acquired uropathogenic Escherichia coli in Nouna. J Infect Dev Ctries 2020; 14:1274-1280. [PMID: 33296340 DOI: 10.3855/jidc.11737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/31/2019] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Extended-Spectrum Beta-Lactamases (ESBL) are a common mechanism of bacterial resistance in Enterobacteriaceae. The purpose of this study is to characterize the ESBL genes produced by community-acquired uropathogenic Escherichia coli strains in the Nouna District, in the West-African country, Burkina Faso. METHODOLOGY Samples were collected from non-hospitalized patients who came for consultation at the CMA (Centre Médical avec Antenne chirurgicale) in Nouna and were sent to the laboratory for a urine culture test. The detection of ESBL production by the bacteria was carried out with the double-disc synergy test and the extraction of the ESBL genes with the heat shock method. Molecular characterization of ESBL genes was performed with three sequential multiplex polymerase chain reaction (PCR) assays. RESULTS One hundred and eighty-two (182) bacteriological cultures were analyzed and 29 E. coli isolated, between 01/07/2017 and 01/07/2018. The ESBL phenotype was found in 13/29 (44.8%). Multiplex PCR yielded many beta-lactamase genes, predominantly blaCTX-M-1,3,15 (12/13; 92.3%) followed by beta-lactamase genes blaOXA-1,4,30 (8/13; 61.5%) and beta-lactamase genes blaTEM-1,2 (7/13; 53.8%). CONCLUSION This study showed that the blaCTX-M-1,3,15 genes produced by uropathogenic E. coli were predominant. Sequencing of these genes would be needed to better characterize the different types of ESBL circulating in Nouna.
Collapse
Affiliation(s)
- Dramane Kiemde
- Nouna Health Research Center/CMA (Centre Médical avec Antenne Chirurgicale) Biological Analysis Laboratory, Burkina Faso.
| | - Inês Ribeiro
- Heidelberg Institute of Global Health (HIGH), Heidelberg University Hospital, Germany.
| | - Soufiane Sanou
- Department of Medical Bacteriology and Virology, National Reference Laboratory for Antimicrobial Resistance, University Hospital Centre Sanou Sourou, Bobo Dioulasso, Burkina Faso.
| | - Boubacar Coulibaly
- Nouna Health Research Center/CMA (Centre Médical avec Antenne Chirurgicale) Biological Analysis Laboratory, Burkina Faso.
| | - Ali Sie
- Nouna Health Research Center/CMA (Centre Médical avec Antenne Chirurgicale) Biological Analysis Laboratory, Burkina Faso.
| | - Abdoul-Salam Ouedraogo
- Department of Medical Bacteriology and Virology, National Reference Laboratory for Antimicrobial Resistance, University Hospital Centre Sanou Sourou, Bobo Dioulasso, Burkina Faso.
| | - Aurélia Souares
- German Center for Infection Research (DZIF), Heidelberg, Hamburg-Lübeck-Borstel-Riems, Heidelberg, Germany.
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.
| |
Collapse
|
29
|
Toy T, Pak GD, Duc TP, Campbell JI, El Tayeb MA, Von Kalckreuth V, Im J, Panzner U, Cruz Espinoza LM, Eibach D, Dekker DM, Park SE, Jeon HJ, Konings F, Mogeni OD, Cosmas L, Bjerregaard-Andersen M, Gasmelseed N, Hertz JT, Jaeger A, Krumkamp R, Ley B, Thriemer K, Kabore LP, Niang A, Raminosoa TM, Sampo E, Sarpong N, Soura A, Owusu-Dabo E, Teferi M, Yeshitela B, Poppert S, May J, Kim JH, Chon Y, Park JK, Aseffa A, Breiman RF, Schütt-Gerowitt H, Aaby P, Adu-Sarkodie Y, Crump JA, Rakotozandrindrainy R, Meyer CG, Sow AG, Clemens JD, Wierzba TF, Baker S, Marks F. Multicountry Distribution and Characterization of Extended-spectrum β-Lactamase-associated Gram-negative Bacteria From Bloodstream Infections in Sub-Saharan Africa. Clin Infect Dis 2020; 69:S449-S458. [PMID: 31665776 PMCID: PMC6821266 DOI: 10.1093/cid/ciz450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is a major global health concern, yet, there are noticeable gaps in AMR surveillance data in regions such as sub-Saharan Africa. We aimed to measure the prevalence of extended-spectrum β-lactamase (ESBL) producing Gram-negative bacteria in bloodstream infections from 12 sentinel sites in sub-Saharan Africa. Methods Data were generated during the Typhoid Fever Surveillance in Africa Program (TSAP), in which standardized blood cultures were performed on febrile patients attending 12 health facilities in 9 sub-Saharan African countries between 2010 and 2014. Pathogenic bloodstream isolates were identified at the sites and then subsequently confirmed at a central reference laboratory. Antimicrobial susceptibility testing, detection of ESBL production, and conventional multiplex polymerase chain reaction (PCR) testing for genes encoding for β-lactamase were performed on all pathogens. Results Five hundred and five pathogenic Gram-negative bloodstream isolates were isolated during the study period and available for further characterization. This included 423 Enterobacteriaceae. Phenotypically, 61 (12.1%) isolates exhibited ESBL activity, and genotypically, 47 (9.3%) yielded a PCR amplicon for at least one of the screened ESBL genes. Among specific Gram-negative isolates, 40 (45.5%) of 88 Klebsiella spp., 7 (5.7%) of 122 Escherichia coli, 6 (16.2%) of 37 Acinetobacter spp., and 2 (1.3%) of 159 of nontyphoidal Salmonella (NTS) showed phenotypic ESBL activity. Conclusions Our findings confirm the presence of ESBL production among pathogens causing bloodstream infections in sub-Saharan Africa. With few alternatives for managing ESBL-producing pathogens in the African setting, measures to control the development and proliferation of AMR organisms are urgently needed.
Collapse
Affiliation(s)
- Trevor Toy
- International Vaccine Institute, Seoul, South Korea
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, South Korea
| | - Trung Pham Duc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Justin Im
- International Vaccine Institute, Seoul, South Korea
| | | | | | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Denise Myriam Dekker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | - Se Eun Park
- International Vaccine Institute, Seoul, South Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, South Korea.,Department of Medicine, Cambridge University, United Kingdom
| | | | - Ondari D Mogeni
- International Vaccine Institute, Seoul, South Korea.,Kenya Medical Research Institute-Centre for Global Health Research (KEMRI-CGHR), Nairobi
| | - Leonard Cosmas
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
| | - Morten Bjerregaard-Andersen
- Bandim Health Project, Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines, Copenhagen, Denmark
| | - Nagla Gasmelseed
- Faculty of Medicine, University of Gezira, Wad Medani, Sudan.,Faculty of Science, University of Hafr Al Batin, Saudi Arabia
| | - Julian T Hertz
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina
| | - Anna Jaeger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Ley
- International Vaccine Institute, Seoul, South Korea.,Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia
| | - Kamala Thriemer
- International Vaccine Institute, Seoul, South Korea.,Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Australia
| | | | | | | | - Emmanuel Sampo
- Institut Supérieur des Sciences de la Population, University of Ouagadougou, Burkina Faso
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Ghana
| | - Abdramane Soura
- Institut Supérieur des Sciences de la Population, University of Ouagadougou, Burkina Faso
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Ghana.,Department of Global and International Health, School of Public Health, KNUST, Kumasi, Ghana
| | | | | | - Sven Poppert
- Infectious Diseases Department, University Hospital Eppendorf, Hamburg, Germany
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | - Jerome H Kim
- International Vaccine Institute, Seoul, South Korea
| | - Yun Chon
- International Vaccine Institute, Seoul, South Korea
| | | | | | - Robert F Breiman
- Kenya Medical Research Institute-Centre for Global Health Research (KEMRI-CGHR), Nairobi.,Global Health Institute, Emory University, Atlanta, Georgia
| | - Heidi Schütt-Gerowitt
- International Vaccine Institute, Seoul, South Korea.,Institute of Medical Microbiology, University of Cologne, Germany
| | - Peter Aaby
- Bandim Health Project, Bissau, Guinea-Bissau.,Research Center for Vitamins and Vaccines, Copenhagen, Denmark
| | - Yaw Adu-Sarkodie
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology (KNUST), Ghana.,Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John A Crump
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Christian G Meyer
- Institute of Tropical Medicine, Eberhard-Karls University Tübingen, Germany.,Duy Tan University, Da Nang, Vietnam
| | - Amy Gassama Sow
- Institute Pasteur de Dakar, Senegal.,Université Cheikh Anta Diop de Dakar, Senegal
| | - John D Clemens
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh.,University of California, Fielding School of Public Health, Los Angeles.,School of Medicine, Korea University, Seoul, South Korea
| | | | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Department of Medicine, Cambridge University, United Kingdom
| | - Florian Marks
- International Vaccine Institute, Seoul, South Korea.,Department of Medicine, Cambridge University, United Kingdom
| |
Collapse
|
30
|
Moirongo RM, Lorenz E, Ntinginya NE, Dekker D, Fernandes J, Held J, Lamshöft M, Schaumburg F, Mangu C, Sudi L, Sie A, Souares A, Heinrich N, Wieser A, Mordmüller B, Owusu-Dabo E, Adegnika AA, Coulibaly B, May J, Eibach D. Regional Variation of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacterales, Fluoroquinolone-Resistant Salmonella enterica and Methicillin-Resistant Staphylococcus aureus Among Febrile Patients in Sub-Saharan Africa. Front Microbiol 2020; 11:567235. [PMID: 33101240 PMCID: PMC7546812 DOI: 10.3389/fmicb.2020.567235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Background Antimicrobial resistance (AMR) thwarts the curative power of drugs and is a present-time global problem. We present data on antimicrobial susceptibility and resistance determinants of bacteria the WHO has highlighted as being key antimicrobial resistance concerns in Africa, to strengthen knowledge of AMR patterns in the region. Methods Blood, stool, and urine specimens of febrile patients, aged between ≥ 30 days and ≤ 15 years and hospitalized in Burkina Faso, Gabon, Ghana, and Tanzania were cultured from November 2013 to March 2017 (Patients > 15 years were included in Tanzania). Antimicrobial susceptibility testing was performed for all Enterobacterales and Staphylococcus aureus isolates using disk diffusion method. Extended-spectrum beta-lactamase (ESBL) production was confirmed by double-disk diffusion test and the detection of blaCTX–M, blaTEM and blaSHV. Multilocus sequence typing was conducted for ESBL-producing Escherichia coli and Klebsiella pneumoniae, ciprofloxacin-resistant Salmonella enterica and S. aureus. Ciprofloxacin-resistant Salmonella enterica were screened for plasmid-mediated resistance genes and mutations in gyrA, gyrB, parC, and parE. S. aureus isolates were tested for the presence of mecA and Panton-Valentine Leukocidin (PVL) and further genotyped by spa typing. Results Among 4,052 specimens from 3,012 patients, 219 cultures were positive of which 88.1% (n = 193) were Enterobacterales and 7.3% (n = 16) S. aureus. The prevalence of ESBL-producing Enterobacterales (all CTX-M15 genotype) was 45.2% (14/31; 95% CI: 27.3, 64.0) in Burkina Faso, 25.8% (8/31; 95% CI: 11.9, 44.6) in Gabon, 15.1% (18/119; 95% CI: 9.2, 22.8) in Ghana and 0.0% (0/12; 95% CI: 0.0, 26.5) in Tanzania. ESBL positive non-typhoid Salmonella (n = 3) were detected in Burkina Faso only and methicillin-resistant S. aureus (n = 2) were detected in Ghana only. While sequence type (ST)131 predominated among ESBL E. coli (39.1%;9/23), STs among ESBL K. pneumoniae were highly heterogenous. Ciprofloxacin resistant nt Salmonella were commonest in Burkina Faso (50.0%; 6/12) and all harbored qnrB genes. PVL were found in 81.3% S. aureus. Conclusion Our findings reveal a distinct susceptibility pattern across the various study regions in Africa, with notably high rates of ESBL-producing Enterobacterales and ciprofloxacin-resistant nt Salmonella in Burkina Faso. This highlights the need for local AMR surveillance and reporting of resistances to support appropriate action.
Collapse
Affiliation(s)
- Rehema Moraa Moirongo
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Eva Lorenz
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nyanda E Ntinginya
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Denise Dekker
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - José Fernandes
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Jana Held
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Maike Lamshöft
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - Frieder Schaumburg
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Chacha Mangu
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Lwitiho Sudi
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Ali Sie
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Aurelia Souares
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Heidelberg Institute of Global Health (HIGH), Heidelberg University Hospital, Heidelberg, Germany
| | - Norbert Heinrich
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Department of Infectious Diseases & Tropical Medicine, Ludwig Maximilians University of Munich, Munich, Germany
| | - Andreas Wieser
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Department of Infectious Diseases & Tropical Medicine, Ludwig Maximilians University of Munich, Munich, Germany.,Faculty of Medicine, Max Von Pettenkofer Institute, Ludwig Maximilians University of Munich, Munich, Germany
| | - Benjamin Mordmüller
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), African Partner Institution, Lambaréné, Gabon
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Akim Ayola Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), African Partner Institution, Lambaréné, Gabon
| | | | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| |
Collapse
|
31
|
Herr W, Krumkamp R, Hogan B, Dekker D, Gyau K, Owusu-Dabo E, Sarpong N, Jaeger A, Loag W, Winter D, Akenten CW, Eibach D, Fickenscher H, Eis-Hübinger A, May J, Kreuels B. A cross-sectional study on risk factors for infection with Parvovirus B19 and the association with anaemia in a febrile paediatric population in Ghana. Sci Rep 2020; 10:15695. [PMID: 32973247 PMCID: PMC7515863 DOI: 10.1038/s41598-020-72657-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
Parvovirus B19 (B19V) occurs globally and can cause severe anaemia. The role of co-infections with Plasmodium falciparum (P. falciparum) has been controversially discussed. The study aimed to determine prevalence and severity of B19V infection, and the effect of co-infections on the risk for anaemia. Between November 2013 and April 2015 a total of 1186 hospital visits of children with fever admitted to a hospital in Ghana were recorded. Malaria, B19V and additional diagnostics for fever causes were performed. Recent B19V infection was defined as PCR and/or IgM positivity. Risk factors for a B19V infection and for anaemia were analysed. The prevalence of anaemia was compared between children with/without B19V infection, stratified for the presence of malaria. B19V IgM/PCR was positive in 6.4% (n = 76; 40 IgM + , 30 PCR + , 6 IgM + and PCR +). Among the B19V cases 60.5% had a simultaneous P. falciparum infection. B19V IgM positivity but not PCR positivity was associated with moderate-severe anaemia (OR = 2.6; 95%-CI: 1.3-5.3; P < 0.01 vs. OR = 0.9; 95%-CI: 0.4-1.8; P = 0.70). P. falciparum and IgM positive B19V infection were independent risk factors for anaemia with no evidence of effect modification. Our data show a significant association between B19V infection, defined as IgM but not PCR positivity, and moderate-severe anaemia. A multiplicative effect of B19V and P. falciparum infection was not found.
Collapse
Affiliation(s)
- Wiebke Herr
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany.,Institute for Infection Medicine, Christian-Albrecht University of Kiel, University Medical Center Schleswig-Holstein, 24105, Kiel, Germany.,DZIF-German Center for Infection Research, Partnersite Hamburg-Lübeck-Borstel, 38124, Braunschweig, Germany
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany.,DZIF-German Center for Infection Research, Partnersite Hamburg-Lübeck-Borstel, 38124, Braunschweig, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Kennedy Gyau
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Wibke Loag
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Charity Wiafe Akenten
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, Christian-Albrecht University of Kiel, University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Anna Eis-Hübinger
- University of Bonn Medical Center, Institute of Virology, 53127, Bonn, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany.,DZIF-German Center for Infection Research, Partnersite Hamburg-Lübeck-Borstel, 38124, Braunschweig, Germany
| | - Benno Kreuels
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany. .,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany. .,DZIF-German Center for Infection Research, Partnersite Hamburg-Lübeck-Borstel, 38124, Braunschweig, Germany.
| |
Collapse
|
32
|
Manouana GP, Lorenz E, Mbong Ngwese M, Nguema Moure PA, Maiga Ascofaré O, Akenten CW, Amuasi J, Rakotozandrindrainy N, Rakotozandrindrainy R, Mbwana J, Lusingu J, Byrne N, Melhem S, Zinsou JF, Adegbite RB, Hogan B, Winter D, May J, Kremsner PG, Borrmann S, Eibach D, Adegnika AA. Performance of a rapid diagnostic test for the detection of Cryptosporidium spp. in African children admitted to hospital with diarrhea. PLoS Negl Trop Dis 2020; 14:e0008448. [PMID: 32658930 PMCID: PMC7377516 DOI: 10.1371/journal.pntd.0008448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 07/23/2020] [Accepted: 06/02/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cryptosporidium is a protozoan parasite that causes mild to severe diarrhoeal disease in humans. To date, several commercial companies have developed rapid immunoassays for the detection of Cryptosporidium infection. However, the challenge is to identify an accurate, simple and rapid diagnostic tool for the estimation of cryptosporidiosis burden. This study aims at evaluating the accuracy of CerTest Crypto, a commercialized rapid diagnostic test (RDT) for the detection of Cryptosporidium antigens in the stool of children presenting with diarrhoea. METHODS A cross-sectional study was conducted in four study sites in Sub-Saharan Africa (Gabon, Ghana, Madagascar, and Tanzania), from May 2017 to April 2018. Stool samples were collected from children under 5 years with diarrhoea or a history of diarrhoea within the last 24 hours. All specimens were processed and analyzed using CerTest Crypto RDT against a composite diagnostic panel involving two polymerase chain reaction (PCR) tests (qPCR and RFLP-PCR,) as the gold standard. RESULTS A total of 596 stool samples were collected. Evaluation of the RDT yielded a very low overall sensitivity of 49.6% (confidence interval (CI) 40.1-59.0), a specificity of 92.5% (CI 89.8-94.7), positive predictive value of 61.3% (CI 50.6-71.2), and negative predictive value of 88.5% (85.3-91.1) when compared to the composite reference standard of qPCR and RFLP-PCR for the detection of Cryptosporidium species. Moreover, the performance of this test varied across different sites. CONCLUSION The weak performance of the studied RDT suggests the need to carefully evaluate available commercial RDTs before their use as standard tools in clinical trials and community survey of Cryptosporidium infections in pediatric cohorts.
Collapse
Affiliation(s)
- Gédéon Prince Manouana
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
- Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Eva Lorenz
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Germany
| | - Mirabeau Mbong Ngwese
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | | | - Oumou Maiga Ascofaré
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | | | - Joyce Mbwana
- National Institute for Medical Research (NIMR) & University of Copenhagen, Denmark
| | - John Lusingu
- National Institute for Medical Research (NIMR) & University of Copenhagen, Denmark
| | - Natalie Byrne
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Sophia Melhem
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Jeannot Frejus Zinsou
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Roméo Bayodé Adegbite
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Benedikt Hogan
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Doris Winter
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Jurgen May
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
| | - Peter Gottfried Kremsner
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
- Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Steffen Borrmann
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Insitute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné
- German Center for Infection Research (DZIF), African partner institution, CERMEL, Gabon
- Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- * E-mail:
| |
Collapse
|
33
|
Strauss R, Lorenz E, Kristensen K, Eibach D, Torres J, May J, Castro J. Investigating the utility of Google trends for Zika and Chikungunya surveillance in Venezuela. BMC Public Health 2020; 20:947. [PMID: 32546159 PMCID: PMC7298838 DOI: 10.1186/s12889-020-09059-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/04/2020] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Chikungunya and Zika Virus are vector-borne diseases responsible for a substantial disease burden in the Americas. Between 2013 and 2016, no cases of Chikungunya or Zika Virus were reported by the Venezuelan Ministry of Health. However, peaks of undiagnosed fever cases have been observed during the same period. In the context of scarce data, alternative surveillance methods are needed. Assuming that unusual peaks of acute fever cases correspond to the incidences of both diseases, this study aims to evaluate the use of Google Trends as an indicator of the epidemic behavior of Chikungunya and Zika. METHODS Time-series cross-correlations of acute fever cases reported by the Venezuelan Ministry of Health and data on Google search queries related to Chikungunya and Zika were calculated. RESULTS A temporal distinction has been made so that acute febrile cases occurring between 25th of June 2014 and 23rd of April 2015 were attributed to the Chikungunya virus, while cases occurring between 30th of April 2015 and 29th of April 2016 were ascribed to the Zika virus. The highest cross-correlations for each disease were shown at a lag of 0 (r = 0.784) for Chikungunya and at + 1 (r = 0.754) for Zika. CONCLUSION The strong positive correlation between Google search queries and official data on acute febrile cases suggests that this resource can be used as an indicator of endemic urban arboviruses activity. In the Venezuelan context, Internet search queries might help to overcome some of the gaps that exist in the national surveillance system.
Collapse
Affiliation(s)
- Ricardo Strauss
- Bernhard Nocht Institute for Tropical Medicine, Research Group Infectious Disease Epidemiology, Hamburg, Germany.
| | - Eva Lorenz
- Bernhard Nocht Institute for Tropical Medicine, Research Group Infectious Disease Epidemiology, Hamburg, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center, Mainz, Germany
| | - Kaja Kristensen
- Bernhard Nocht Institute for Tropical Medicine, Research Group Infectious Disease Epidemiology, Hamburg, Germany.,Faculty of Life Sciences, Hamburg University of Applied Sciences, Ulmenliet 20, 21033, Hamburg, Germany
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Research Group Infectious Disease Epidemiology, Hamburg, Germany
| | - Jaime Torres
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Research Group Infectious Disease Epidemiology, Hamburg, Germany
| | - Julio Castro
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| |
Collapse
|
34
|
Fernandes JF, Held J, Dorn M, Lalremruata A, Schaumburg F, Alabi A, Agbanrin MD, Kokou C, Ben Adande A, Esen M, Eibach D, Adegnika AA, Agnandji ST, Lell B, Eckerle I, Henrichfreise B, Hogan B, May J, Kremsner PG, Grobusch MP, Mordmüller B. Causes of fever in Gabonese children: a cross-sectional hospital-based study. Sci Rep 2020; 10:2080. [PMID: 32034188 PMCID: PMC7005879 DOI: 10.1038/s41598-020-58204-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/13/2020] [Indexed: 11/28/2022] Open
Abstract
The causes of infections in pediatric populations differ between age groups and settings, particularly in the tropics. Such differences in epidemiology may lead to misdiagnosis and ineffective empirical treatment. Here, we investigated the current spectrum of pathogens causing febrile diseases leading to pediatric hospitalization in Lambaréné, Gabon. From August 2015 to March 2016, we conducted a prospective, cross-sectional, hospital-based study in a provincial hospital. Patients were children ≤ 15 years with fever ≥ 38 °C and required hospitalization. A total of 600 febrile patients were enrolled. Malaria was the main diagnosis found in 52% (311/600) patients. Blood cultures revealed septicemia in 3% (17/593), among them four cases of typhoid fever. The other causes of fever were heterogeneously distributed between both bacteria and viruses. Severe infections identified by Lambaréné Organ Dysfunction Score (LODS) were also most often caused by malaria, but children with danger signs did not have more coinfections than others. In 6% (35/600) of patients, no pathogen was isolated. In Gabon, malaria is still the major cause of fever in children, followed by a bacterial and viral disease. Guidelines for both diagnosis and management should be tailored to the spectrum of pathogens and resources available locally.
Collapse
Affiliation(s)
- José Francisco Fernandes
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.,Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Jana Held
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon. .,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany. .,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Magdalena Dorn
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon
| | - Albert Lalremruata
- Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, 48149, Münster, Germany
| | - Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon
| | - Maradona Daouda Agbanrin
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon
| | - Cosme Kokou
- Albert Schweitzer Hospital, Lambaréné, BP: 118, Lambaréné, Gabon
| | - Abel Ben Adande
- Albert Schweitzer Hospital, Lambaréné, BP: 118, Lambaréné, Gabon
| | - Meral Esen
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74 D-, 20359, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sélidji Todagbé Agnandji
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Isabella Eckerle
- Institute of Virology, University of Bonn Medical Centre, 53127, Bonn, Germany
| | - Beate Henrichfreise
- Pharmaceutical Microbiology, University Hospital Bonn, University Bonn, 53115, Bonn, Germany
| | - Benedikt Hogan
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74 D-, 20359, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74 D-, 20359, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Peter Gottfried Kremsner
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Martin Peter Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon. .,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany. .,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany. .,Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam University Medical Centers, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Benjamin Mordmüller
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, B.P: 242, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| |
Collapse
|
35
|
Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe 2019; 26:666-679.e7. [PMID: 31607556 PMCID: PMC6854460 DOI: 10.1016/j.chom.2019.08.018] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/05/2019] [Accepted: 08/28/2019] [Indexed: 12/29/2022]
Abstract
Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.
Collapse
Affiliation(s)
- Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy.
| | - Kun D Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy
| | | | - Hannah Fehlner-Peach
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Kevin Bonham
- The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Moreno Zolfo
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Cara Magnabosco
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA; Departments of Biology and Computer Science, New York University, New York, NY 10003, USA
| | - John Lusingu
- National Institute for Medical Research, Tanga Centre, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Ghana
| | - Karl Reinhard
- Hardin Hall, School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0987, USA
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Fredrik Boulund
- Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Lars Engstrand
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain
| | - Dan R Littman
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, 20359 Hamburg, Germany
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 1 38010 S, San Michele all'Adige, Italy
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Biostatistics Department, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy.
| |
Collapse
|
36
|
Hogan B, Eibach D, Krumkamp R, Sarpong N, Dekker D, Kreuels B, Maiga-Ascofaré O, Gyau Boahen K, Wiafe Akenten C, Adu-Sarkodie Y, Owusu-Dabo E, May J. Malaria Coinfections in Febrile Pediatric Inpatients: A Hospital-Based Study From Ghana. Clin Infect Dis 2019; 66:1838-1845. [PMID: 29408951 PMCID: PMC5982794 DOI: 10.1093/cid/cix1120] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/06/2018] [Indexed: 11/12/2022] Open
Abstract
Background The epidemiology of pediatric febrile illness is shifting in sub-Saharan Africa, but malaria remains a major cause of childhood morbidity and mortality. The present study describes causes of febrile illness in hospitalized children in Ghana and aims to determine the burden of malaria coinfections and their association with parasite densities. Methods In a prospective study, children (aged ≥30 days and ≤15 years) with fever ≥38.0°C were recruited after admission to the pediatric ward of a primary hospital in Ghana. Malaria parasitemia was determined and blood, stool, urine, respiratory, and cerebrospinal fluid specimens were screened for parasitic, bacterial, and viral pathogens. Associations of Plasmodium densities with other pathogens were calculated. Results From November 2013 to April 2015, 1238 children were enrolled from 4169 admissions. A clinical/microbiological diagnosis could be made in 1109/1238 (90%) patients, with Plasmodium parasitemia (n = 728/1238 [59%]) being predominant. This was followed by lower respiratory tract infections/pneumonia (n = 411/1238 [34%]; among detected pathogens most frequently Streptococcus pneumoniae, n = 192/299 [64%]), urinary tract infections (n = 218/1238 [18%]; Escherichia coli, n = 21/32 [66%]), gastrointestinal infections (n = 210 [17%]; rotavirus, n = 32/97 [33%]), and invasive bloodstream infections (n = 62 [5%]; Salmonella species, n = 47 [76%]). In Plasmodium-infected children the frequency of lower respiratory tract, gastrointestinal, and bloodstream infections increased with decreasing parasite densities. Conclusions In a hospital setting, the likelihood of comorbidity with a nonmalarial disease is inversely correlated with increasing blood levels of malaria parasites. Hence, parasite densities provide important information as an indicator for the probability of coinfection, in particular to guide antimicrobial medication.
Collapse
Affiliation(s)
- Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | - Nimako Sarpong
- German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | - Benno Kreuels
- German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany.,Division of Tropical Medicine, I. Department of Internal Medicine, University Medical Centre Hamburg Eppendorf, Germany
| | - Oumou Maiga-Ascofaré
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kennedy Gyau Boahen
- German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Charity Wiafe Akenten
- German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany.,Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, School of Public Health, College of Health Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Global Health, School of Public Health, College of Health Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck, Germany
| | | |
Collapse
|
37
|
Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L. Detection of dicistroviruses RNA in blood of febrile Tanzanian children. Emerg Microbes Infect 2019; 8:613-623. [PMID: 30999808 PMCID: PMC6493270 DOI: 10.1080/22221751.2019.1603791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.
Collapse
Affiliation(s)
- Samuel Cordey
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Florian Laubscher
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Mary-Anne Hartley
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland
| | - Thomas Junier
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,e Global Health Institute, School of Life Sciences , École Polytechnique Fédérale de Lausanne Lausanne , Switzerland
| | | | - Kristina Keitel
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Gael Vieille
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Josephine Samaka
- g Ifakara Health Institute , Dar es Salaam , Tanzania.,h Amana Hospital , Dar es Salaam , Tanzania
| | | | - Frank Kagoro
- g Ifakara Health Institute , Dar es Salaam , Tanzania
| | - Noémie Boillat-Blanco
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland.,i Infectious Diseases Service , Lausanne University Hospital Lausanne , Switzerland
| | | | - Mylène Docquier
- k iGE3 Genomics Platform , University of Geneva Geneva , Switzerland
| | - Francisco Brito
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,l Department of Genetic Medicine and Development , Faculty of Medicine of Geneva Geneva , Switzerland
| | - Daniel Eibach
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Jürgen May
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Peter Sothmann
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany.,o Division of Tropical Medicine, 1st Department of Medicine , University Medical Center Hamburg-Eppendorf Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - Cassandra Aldrich
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - John Lusingu
- q National Institute for Medical Research , Tanga Research Centre , Tanga , Tanzania
| | | | - Valérie D'Acremont
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland.,f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Laurent Kaiser
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland.,r Geneva Centre for Emerging Viral Diseases Geneva , Switzerland
| |
Collapse
|
38
|
Aldrich C, Hartman H, Feasey N, Chattaway MA, Dekker D, Al-Emran HM, Larkin L, McCormick J, Sarpong N, Le Hello S, Adu-Sarkodie Y, Panzner U, Park SE, Im J, Marks F, May J, Dallman TJ, Eibach D. Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana. PLoS Negl Trop Dis 2019; 13:e0007485. [PMID: 31220112 PMCID: PMC6605661 DOI: 10.1371/journal.pntd.0007485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 07/02/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Salmonella enterica serovar Enteritidis is a cause of both poultry- and egg-associated enterocolitis globally and bloodstream-invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa (sSA). Distinct, multi-drug resistant genotypes associated with iNTS disease in sSA have recently been described, often requiring treatment with fluoroquinolone antibiotics. In industrialised countries, antimicrobial use in poultry production has led to frequent fluoroquinolone resistance amongst globally prevalent enterocolitis-associated lineages. METHODOLOGY/PRINCIPAL FINDINGS Twenty seven S. Enteritidis isolates from patients with iNTS disease and two poultry isolates, collected between 2007 and 2015 in the Ashanti region of Ghana, were whole-genome sequenced. These isolates, notable for a high rate of diminished ciprofloxacin susceptibility (DCS), were placed in the phyletic context of 1,067 sequences from the Public Health England (PHE) S. Enteritidis genome database to understand whether DCS was associated with African or globally-circulating clades of S. Enteritidis. Analysis showed four of the major S. Enteritidis clades were represented, two global and two African. All thirteen DCS isolates, containing a single gyrA mutation at codon 87, belonged to a global PT4-like clade responsible for epidemics of poultry-associated enterocolitis. Apart from two DCS isolates, which clustered with PHE isolates associated with travel to Spain and Brazil, the remaining DCS isolates, including one poultry isolate, belonged to two monophyletic clusters in which gyrA 87 mutations appear to have developed within the region. CONCLUSIONS/SIGNIFICANCE Extensive phylogenetic diversity is evident amongst iNTS disease-associated S. Enteritidis in Ghana. Antimicrobial resistance profiles differed by clade, highlighting the challenges of devising empirical sepsis guidelines. The detection of fluoroquinolone resistance in phyletically-related poultry and human isolates is of major concern and surveillance and control measures within the region's burgeoning poultry industry are required to protect a human population at high risk of iNTS disease.
Collapse
Affiliation(s)
- Cassandra Aldrich
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Hassan Hartman
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Nicholas Feasey
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Hassan M. Al-Emran
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Jessore University of Science and Technology, Jessore, Bangladesh
| | - Lesley Larkin
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Jacquelyn McCormick
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Simon Le Hello
- Institut Pasteur, French National Reference Center for Escherichia coli, Shigella and Salmonella, Paris, France
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea
| | - Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Timothy J. Dallman
- National Infections Service, Public Health England, Colindale, United Kingdom
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
39
|
Manouana GP, Matsougou GB, Byrne N, Hofmann P, Ngwese MM, A Nguema Moure P, Zinsou JF, Dejon Agobe JC, R Adegbite B, R Edoa J, J Honkpehedji Y, Mccall MB, S Alabi A, Eibach D, G Kremsner P, Borrmann S, A Adegnika A. PO 8444 CHARACTERISATION OF PATHOGENS CAUSING DIARRHOEA IN CHILDREN UNDER FIVE IN LAMBARÉNÉ, GABON. BMJ Glob Health 2019. [DOI: 10.1136/bmjgh-2019-edc.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundDiarrhoeal disease remains the second leading cause of death in children under five years, being associated with about 525,000 deaths every year. The most common pathogens worldwide are Shigella spp/EIEC, rotavirus, adenovirus 40/41, ST-ETEC and Cryptosporidium spp. Public health interventions rely on estimates of pathogen-specific burden for prioritisation. Sadly, comprehensive data on the aetiology of diarrhoea in children is lacking for Gabon. This study aimed to identify the spectrum of pathogens found in Lambaréné, Gabon and provide baseline data on their prevalence, needed for implementation of effective control measures.MethodsA cross-sectional study was conducted at Albert Schweitzer and Georges Rawiri Regional hospitals in Lambaréné from February 2017 to February 2018. A consecutive sample of children under 5 year old with diarrhoea or a history of diarrhoea within the previous three days were prospectively studied. A single stool sample was collected from each study participant and processed using commercial rapid immunoassays to detect antigens of rotavirus, adenovirus, and Cryptosporidium spp. Multiplex PCR was used for Cryptosporidium spp., Giardia lamblia and Cyclospora cayetanensis detection, and characterisation of E. coli strains.ResultsOut of 188 participants who provided stool samples, one or more pathogens could be detected in 34.6% of the cases. The most prevalent parasites were Giardia lamblia (14.9%), Cryptosporidium spp. (11.7%), and Cyclospora cayetanensis (2.7%). Enteric viruses also were identified in these children: 10.6% and 1.6% of rotavirus and adenovirus, respectively. Multiple pathogens were detected in 5.3% of samples.ConclusionThis analysis of the causes of diarrhoea in children under 5 years of age in our setting showed three main pathogens: Giardia lamblia, Cryptosporidium spp. and rotavirus. Our study confirms major agents of acute diarrhoeal diseases in children, highlights research needs (Cryptosporidium) and supports the introduction of new tools such as the implementation of the rotavirus vaccine in the national immunisation programme.
Collapse
|
40
|
Dekker D, Eibach D, Boahen KG, Akenten CW, Pfeifer Y, Zautner AE, Mertens E, Krumkamp R, Jaeger A, Flieger A, Owusu-Dabo E, May J. Fluoroquinolone-Resistant Salmonella enterica, Campylobacter spp., and Arcobacter butzleri from Local and Imported Poultry Meat in Kumasi, Ghana. Foodborne Pathog Dis 2019; 16:352-358. [PMID: 30907631 PMCID: PMC6529854 DOI: 10.1089/fpd.2018.2562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Salmonella and Campylobacter are important gastroenteric pathogens. Arcobacter butzleri is an emerging enteric pathogen. Data on the frequencies of these poultry-associated pathogens on meat products sold in sub-Saharan Africa are scarce. This study aimed to analyze the frequency of Salmonella, Campylobacter, and Arcobacter antibiotic resistance and underlying mechanisms of resistance to fluoroquinolones in locally produced and imported poultry sold in urban Ghana. Chicken meat was collected and cultured on standard media. Bacterial strains were identified by biochemical methods and by mass spectrometry. Antibiotic susceptibility was tested by disk diffusion. Ciprofloxacin-resistant strains were assessed for molecular mechanisms of resistance. Among 200 samples, comprising 34% (n = 68) from the Ghanaian poultry industry and 66% (n = 132) from imports, 9% (n = 17) contained Salmonella, 11% (n = 22) Campylobacter, and 26.5% (n = 53) A. butzleri. Higher overall contamination frequencies were found in local meat. Most common Salmonella serovars identified were Kentucky (n/N = 5/16; 31%) and Poona (n/N = 4/16; 25%). Campylobacter were C. coli (n/N = 10/19; 53%) and C. jejuni (n/N = 9/19; 47%). Resistance to fluoroquinolones was high with 63% (n = 10), 75% (n = 15), and 52% (n = 25) in Salmonella, Campylobacter, and Arcobacter, respectively. A link between Salmonella Kentucky [sequence type (ST) 198] and a ciprofloxacin minimum inhibitory concentration of 16 μg/mL was found. Salmonella Poona-ST308 revealed transferable qnrB2 fluoroquinolone resistance genes. Markedly high frequencies of resistant Salmonella, Campylobacter, and Arcobacter predominant in locally produced meat represent a probable transmission reservoir for human infections. These findings highlight the need for implementation of surveillance systems that focus on food hygiene, use of antibiotics in animal husbandry, and continuous monitoring of the quality of meat products from imports.
Collapse
Affiliation(s)
- Denise Dekker
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.,2 German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Daniel Eibach
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Kennedy G Boahen
- 3 Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Charity Wiafe Akenten
- 3 Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Yvonne Pfeifer
- 4 Robert Koch Institute (RKI), FG13 Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | - Andreas E Zautner
- 5 Institute for Medical Microbiology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Eva Mertens
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Ralf Krumkamp
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.,2 German Centre for Infection Research (DZIF), Hamburg-Borstel-Luebeck, Germany
| | - Anna Jaeger
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Antje Flieger
- 6 Robert Koch Institute (RKI), Division of Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Ellis Owusu-Dabo
- 3 Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Jürgen May
- 1 Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| |
Collapse
|
41
|
Eibach D, Hogan B, Sarpong N, Winter D, Struck NS, Adu-Sarkodie Y, Owusu-Dabo E, Schmidt-Chanasit J, May J, Cadar D. Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana. Sci Rep 2019; 9:2360. [PMID: 30787417 PMCID: PMC6382885 DOI: 10.1038/s41598-019-38975-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
The cause of acute encephalitis/meningoencephalitis in pediatric patients remains often unexplained despite extensive investigations for large panel of pathogens. To explore a possible viral implication, we investigated the virome of cerebrospinal fluid specimens of 70 febrile pediatric inpatients with clinical compatible encephalitis/meningoencephalitis. Using viral metagenomics, we detected and genetically characterized three novel human Torque teno mini virus (TTMV) species (TTMV-G1-3). Phylogenetically, TTMV-G1-3 clustered in three novel monophyletic lineages within genus Betatorquevirus of the Anelloviridae family. TTMV-G1-3 were highly prevalent in diseased children, but absent in the healthy cohort which may indicate an association of TTMV species with febrile illness. With 2/3 detected malaria co-infection, it remains unclear if these novel anellovirus species are causative agents or increase disease severity by interaction with malaria parasites. The presence of the viruses 28 days after initiating antimalarial and/or antibiotic treatment suggests a still active viral infection likely as effect of parasitic and/or bacterial co-infection that may have initiated a modulated immune system environment for viral replication or a defective virus clearance. This study increases the current knowledge on the genetic diversity of TTMV and strengthens that human anelloviruses can be considered as biomarkers for strong perturbations of the immune system in certain pathological conditions.
Collapse
Affiliation(s)
- Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Nicole S Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, 40080, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, 40080, Ghana
| | - Jonas Schmidt-Chanasit
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany.,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.,German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany
| | - Daniel Cadar
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Borstel, 20359, Germany. .,Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, 20359, Germany.
| |
Collapse
|
42
|
Strauss R, Guillen A, Torres J, Castro J, Eibach D, Leon LH, Leon SH, Navas T, Carvajal A, Drummond T, Hernandez E, Aurenty L, Lopez M, Vielma S, Hernández E, Lopez N, Navas V, Lopez S, Rosas M. Clinical and molecular epidemiology of the current Venezuelan diphtheria epidemic. A hospital-based experience. Int J Infect Dis 2019. [DOI: 10.1016/j.ijid.2018.11.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
43
|
Frickmann H, Wiemer DF, Wassill L, Hinz R, Rojak S, Wille A, Loderstädt U, Schwarz NG, von Kalckreuth V, Im J, Jin Jeon H, Marks F, Owusu-Dabo E, Sarpong N, May J, Eibach D, Dekker D. Loop-mediated isothermal amplification-based detection of typhoid fever on an automated Genie II Mk2 system - A case-control-based approach. Acta Trop 2019; 190:293-295. [PMID: 30528158 DOI: 10.1016/j.actatropica.2018.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022]
Abstract
Typhoid fever, caused by the bacterium Salmonella enterica subsp. enterica serovar Typhi, is an important cause of blood stream infections in the tropics, for which easy-to-apply molecular diagnostic approaches are desirable. The diagnostic performance of a newly introduced and a previously described loop-mediated isothermal amplification (LAMP) approach using different primer sets on a Genie II Mk2 device for the identification of Salmonella enterica ssp. enterica ser. Typhi was evaluated with well-characterized residual materials from the tropics in a case control-based approach. After in-vitro confirmation of binding characteristics of both LAMP primer sets with culture isolates (n = 112), sensitivity and specificity were 100% for the newly designed new LAMP primer set 1 with incubated blood culture materials, while specificity was reduced to 97.1% for primer set 2. For 170 EDTA blood samples, sensitivity and specificity were 10% and 98.3% for primer set 1 as well as 38.0% and 83.3% for primer set 2, respectively; qPCR from EDTA blood did not score much better with 10% sensitivity and 100% specificity. LAMP using a Genie II Mk2 device is suitable for the identification of Salmonella enterica spp. enterica ser. Typhi from incubated blood culture materials. Sensitivity and specificity were insufficient for diagnosis directly from EDTA blood samples but LAMP showed similar sensitivity as qPCR.
Collapse
|
44
|
Falgenhauer L, Imirzalioglu C, Oppong K, Akenten CW, Hogan B, Krumkamp R, Poppert S, Levermann V, Schwengers O, Sarpong N, Owusu-Dabo E, May J, Eibach D. Detection and Characterization of ESBL-Producing Escherichia coli From Humans and Poultry in Ghana. Front Microbiol 2019; 9:3358. [PMID: 30697208 PMCID: PMC6340976 DOI: 10.3389/fmicb.2018.03358] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/31/2018] [Indexed: 11/13/2022] Open
Abstract
Introduction: The increasing incidence of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in sub-Saharan Africa is of serious concern. Studies from countries with a highly industrialized poultry industry suggest the poultry production-food-consumer chain as a potential transmission route. In Africa, integrated studies at this human-animal interface are still missing. Aim: To determine the molecular epidemiology of ESBL-producing E. coli from the intestinal tract of humans and poultry in rural Ghana. Methods: During a 6-month period, fecal samples from all children admitted to the Agogo Hospital (Ghana) and broilers at eight poultry farms located within the hospital catchment area were collected. After screening on selective ESBL agar, whole genome sequencing (WGS) was performed on all ESBL isolates. The genomes were analyzed using multilocus sequence typing (MLST), ESBL genotyping and genome-based phylogenetic analyses. Results: Of 140 broilers and 54 children, 41 (29%) and 33 (61%) harbored ESBL E. coli, respectively, with prevalences on farms ranging between 0 and 85%. No predominant sequence type (ST) was detected among humans. ST10 was most prevalent among broilers (n = 31, 69%). The ESBL gene bla CTX-M-15 was predominant among broilers (n = 43, 96%) and humans (n = 32, 97%). Whole-genome-based phylogenetic analysis revealed three very closely related broiler/human isolate clusters (10% of ESBL isolates) with chromosomal and plasmid-mediated ESBL genes. Conclusion: The findings demonstrate a high frequency of intestinal ESBL-producing E. coli in rural Ghana. Considering that animal and human samples are independent specimens from the same geographic location, the number of closely related ESBL isolates circulating across these two reservoirs is substantial. Hence, poultry farms or meat products might be an important source for ESBL-producing bacteria in rural Ghana leading to difficult-to-treat infections in humans.
Collapse
Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Kwabena Oppong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Benedikt Hogan
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Ralf Krumkamp
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Vinzent Levermann
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
45
|
Dekker D, Krumkamp R, Eibach D, Sarpong N, Boahen KG, Frimpong M, Fechtner E, Poppert S, Hagen RM, Schwarz NG, Adu-Sarkodie Y, Owusu-Dabo E, Im J, Marks F, Frickmann H, May J. Characterization of Salmonella enterica from invasive bloodstream infections and water sources in rural Ghana. BMC Infect Dis 2018; 18:47. [PMID: 29351771 PMCID: PMC5775569 DOI: 10.1186/s12879-018-2957-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Background Non-typhoidal Salmonella (NTS) cause the majority of bloodstream infections in Ghana, however the mode of transmission and source of invasive NTS in Africa are poorly understood. This study compares NTS from water sources and invasive bloodstream infections in rural Ghana. Methods Blood from hospitalised, febrile children and samples from drinking water sources were analysed for Salmonella spp. Strains were serotyped to trace possible epidemiological links between human and water-derived isolates.. Antibiotic susceptibility testing was performed, Results In 2720 blood culture samples, 165 (6%) NTS were isolated. S. Typhimurium (70%) was the most common serovar followed by S. Enteritidis (8%) and S. Dublin (8%). Multidrug resistance (MDR) was found in 95 (58%) NTS isolates, including five S. Enteritidis. One S. Typhimurium showed reduced fluroquinolone susceptibility. In 511 water samples, 19 (4%) tested positive for S. enterica with two isolates being resistant to ampicillin and one isolate being resistant to cotrimoxazole. Serovars from water samples were not encountered in any of the clinical specimens. Conclusion Water analyses demonstrated that common drinking water sources were contaminated with S. enterica posing a potential risk for transmission. However, a link between S. enterica from water sources and patients could not be established, questioning the ability of water-derived serovars to cause invasive bloodstream infections.
Collapse
Affiliation(s)
- Denise Dekker
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany. .,German Center for Infection Research (DZIF), Hamburg-Borstel, Lübeck, Germany.
| | - Ralf Krumkamp
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel, Lübeck, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel, Lübeck, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Elina Fechtner
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany
| | - Sven Poppert
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany
| | - Ralf Matthias Hagen
- Bundeswehr Hospital of Hamburg, Germany, Department of Tropical Medicine at the Bernhard Nocht Institute, Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany
| | - Norbert Georg Schwarz
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Justin Im
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea
| | - Florian Marks
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea.,The Department of Medicine, The University of Cambridge, Cambridge, UK
| | - Hagen Frickmann
- Bundeswehr Hospital of Hamburg, Germany, Department of Tropical Medicine at the Bernhard Nocht Institute, Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18055, Rostock, Germany
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel, Lübeck, Germany
| |
Collapse
|
46
|
Bühl H, Eibach D, Nagel M, Greub G, Borel N, Sarpong N, Rettig T, Pesch T, Aeby S, Klöckner A, Brunke M, Krannich S, Kreuels B, Owusu-Dabo E, Hogan B, May J, Henrichfreise B. Chlamydiae in febrile children with respiratory tract symptoms and age-matched controls, Ghana. New Microbes New Infect 2018; 22:44-48. [PMID: 29511568 PMCID: PMC5832669 DOI: 10.1016/j.nmni.2017.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/30/2017] [Accepted: 12/21/2017] [Indexed: 11/29/2022] Open
Abstract
Members of the Chlamydiales order are obligate intracellular pathogens causing acute and chronic infectious diseases. Chlamydiaceae are established agents of community- and zoonotically acquired respiratory tract infections, and emerging pathogens among the Chlamydia-related bacteria have been implicated in airway infections. The role of both in airway infections in Africa is underexplored. We performed a case -control study on the prevalence of Chlamydiaceae and Chlamydia-related emerging pathogens in children with febrile respiratory tract infections in West Africa, Ghana. Using a pan-Chlamydiales broad-range real-time PCR, we detected chlamydial DNA in 11 (1.9%) of 572 hospitalized febrile children with respiratory tract symptoms and in 24 (4.3%) of 560 asymptomatic age-matched controls (p 0.03). Chlamydiaceae were found to be common among both symptomatic and healthy Ghanaian children, with Chlamydia pneumoniae being the most prevalent species. Parachlamydiaceae were detected in two children without symptoms but not in the symptomatic group. We identified neither Chlamydia psittaci nor Simkania negevensis but a member of a new chlamydial family that shared 90.2% sequence identity with the 16S rRNA gene of the zoonotic pathogen Chlamydia pecorum. In addition, we found a new Chlamydia-related species that belonged to a novel family sharing 91.3% 16S rRNA sequence identity with Candidatus Syngnamydia venezia. The prevalence and spectrum of chlamydial species differed from previous results obtained from children of other geographic regions and our study indicates that both, Chlamydiaceae and Chlamydia-related bacteria, are not clearly linked to clinical symptoms in Ghanaian children.
Collapse
Affiliation(s)
- H Bühl
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - D Eibach
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - M Nagel
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - G Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - N Borel
- Institute of Veterinary Pathology, University of Zurich, Vetsuisse Faculty, Zurich, Switzerland
| | - N Sarpong
- German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany.,Agogo Presbyterian Hospital, Department of Child Health, Agogo, Ghana
| | - T Rettig
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - T Pesch
- Institute of Veterinary Pathology, University of Zurich, Vetsuisse Faculty, Zurich, Switzerland
| | - S Aeby
- Institute of Microbiology, University Hospital Center and University of Lausanne, Switzerland
| | - A Klöckner
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany.,German Center for Infection Research (DZIF), Bonn, Germany
| | - M Brunke
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - S Krannich
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| | - B Kreuels
- Division of Tropical Medicine, I. Department of Internal Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - E Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.,Department of Global Health, School of Public Health, College of Health Sciences, KNUST, Kumasi, Ghana
| | - B Hogan
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - J May
- Bernhard Nocht Institute for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck, Germany
| | - B Henrichfreise
- Institute for Pharmaceutical Microbiology, University Clinic, University of Bonn, Germany
| |
Collapse
|
47
|
Hogan B, Ammer L, Zimmermann M, Binger T, Krumkamp R, Sarpong N, Rettig T, Dekker D, Kreuels B, Reigl L, Boahen KG, Wiafe C, Adu‐Sarkodie Y, Owusu‐Dabo E, May J, Eibach D. Burden of influenza among hospitalized febrile children in Ghana. Influenza Other Respir Viruses 2017; 11:497-501. [PMID: 28991406 PMCID: PMC5705687 DOI: 10.1111/irv.12507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2017] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Influenza surveillance data from Africa indicate a substantial disease burden with high mortality. However, local influenza data from district hospitals with limited laboratory facilities are still scarce. OBJECTIVES To identify the frequency and seasonal distribution of influenza among hospitalized febrile children in a rural hospital in Ghana and to describe differential diagnoses to other severe febrile infections. METHODS Between January 2014 and April 2015, all children with a temperature of ≥38°C admitted to a district hospital in Ghana were screened for influenza A and B by RT-PCR and differentiated to subtypes A(H1N1)pdm09 and A(H3N2). Malaria microscopy and blood cultures were performed for each patient. RESULTS A total of 1063 children with a median age of 2 years (IQR: 1-4 years) were recruited. Of those, 271 (21%) were classified as severe acute respiratory infection (SARI) and 47 (4%) were positive for influenza, namely 26 (55%) influenza B, 15 (32%) A(H1N1)pdm09, and 6 (13%) A(H3N2) cases. Influenza predominantly occurred in children aged 3-5 years and was more frequently detected in the major rainy season (OR = 2.9; 95% CI: 1.47-6.19) during the first half of the year. Two (4%) and seven (15%) influenza-positive children were co-diagnosed with an invasive bloodstream infection or malaria, respectively. CONCLUSION Influenza contributes substantially to the burden of hospitalized febrile children in Ghana being strongly dependent on age and corresponds with the major rainy season during the first half-year.
Collapse
MESH Headings
- Bacteremia/diagnosis
- Bacteremia/epidemiology
- Child, Hospitalized/statistics & numerical data
- Child, Preschool
- Coinfection/diagnosis
- Coinfection/epidemiology
- Coinfection/microbiology
- Coinfection/parasitology
- Cost of Illness
- Female
- Fever/epidemiology
- Fever/virology
- Ghana/epidemiology
- Humans
- Infant
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza, Human/complications
- Influenza, Human/diagnosis
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Betainfluenzavirus/genetics
- Betainfluenzavirus/isolation & purification
- Malaria/diagnosis
- Malaria/epidemiology
- Male
- Polymerase Chain Reaction
- Respiratory Tract Infections/epidemiology
- Respiratory Tract Infections/virology
- Seasons
Collapse
Affiliation(s)
- Benedikt Hogan
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Luise Ammer
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Marlow Zimmermann
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
| | - Tabea Binger
- College of Health SciencesKumasi Centre for Collaborative Research in Tropical Medicine (KCCR)KNUSTKumasiGhana
| | - Ralf Krumkamp
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Nimako Sarpong
- College of Health SciencesKumasi Centre for Collaborative Research in Tropical Medicine (KCCR)KNUSTKumasiGhana
| | - Theresa Rettig
- Department of Child HealthAgogo Presbyterian HospitalAgogoGhana
| | - Denise Dekker
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Benno Kreuels
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
- Division of Tropical MedicineI. Department of Internal MedicineUniversity Medical Centre Hamburg‐Eppendorf (UKE)HamburgGermany
| | - Lisa Reigl
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Kennedy G. Boahen
- College of Health SciencesKumasi Centre for Collaborative Research in Tropical Medicine (KCCR)KNUSTKumasiGhana
| | - Charity Wiafe
- College of Health SciencesKumasi Centre for Collaborative Research in Tropical Medicine (KCCR)KNUSTKumasiGhana
| | - Yaw Adu‐Sarkodie
- Department of Clinical MicrobiologyKwame Nkrumah University of Science and Technology (KNUST)KumasiGhana
| | - Ellis Owusu‐Dabo
- College of Health SciencesKumasi Centre for Collaborative Research in Tropical Medicine (KCCR)KNUSTKumasiGhana
- Department of Global HealthSchool of Public HealthCollege of Health SciencesKNUSTKumasiGhana
| | - Jürgen May
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
- German Center for Infection Research (DZIF)Hamburg‐Borstel‐LübeckGermany
| | - Daniel Eibach
- Infectious Disease EpidemiologyBernhard Nocht Institute for Tropical Medicine HamburgHamburgGermany
| |
Collapse
|
48
|
Casalegno JS, Eibach D, Valette M, Enouf V, Daviaud I, Behillil S, Vabret A, Soulary JC, Benchaib M, Cohen JM, van der Werf S, Mosnier A, Lina B. Performance of influenza case definitions for influenza community surveillance: based on the French influenza surveillance network GROG, 2009-2014. ACTA ACUST UNITED AC 2017; 22:30504. [PMID: 28422004 PMCID: PMC5388124 DOI: 10.2807/1560-7917.es.2017.22.14.30504] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/14/2016] [Indexed: 11/20/2022]
Abstract
International case definitions recommended by the Centers for Disease Control and Prevention (CDC), the European Centre for Disease Prevention and Control (ECDC), and the World Health Organization (WHO) are commonly used for influenza surveillance. We evaluated clinical factors associated with the laboratory-confirmed diagnosis of influenza and the performance of these influenza case definitions by using a complete dataset of 14,994 patients with acute respiratory infection (ARI) from whom a specimen was collected between August 2009 and April 2014 by the Groupes Régionaux d'Observation de la Grippe (GROG), a French national influenza surveillance network. Cough and fever ≥ 39 °C most accurately predicted an influenza infection in all age groups. Several other symptoms were associated with an increased risk of influenza (headache, weakness, myalgia, coryza) or decreased risk (adenopathy, pharyngitis, shortness of breath, otitis/otalgia, bronchitis/ bronchiolitis), but not throughout all age groups. The WHO case definition for influenza-like illness (ILI) had the highest specificity with 21.4%, while the ECDC ILI case definition had the highest sensitivity with 96.1%. The diagnosis among children younger than 5 years remains challenging. The study compared the performance of clinical influenza definitions based on outpatient surveillance and will contribute to improving the comparability of data shared at international level.
Collapse
Affiliation(s)
- Jean-Sebastien Casalegno
- Univ Lyon, Virpath, CIRI, INSERM U1111, CNRS, ENS, Université Claude Bernard Lyon 1, Lyon, France.,These authors contributed equally.,National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
| | - Daniel Eibach
- These authors contributed equally.,Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Martine Valette
- National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
| | - Vincent Enouf
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Isabelle Daviaud
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Sylvie Behillil
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Astrid Vabret
- UNICAEN, EA4655 - U2RM, Normandie University, Caen, France.,Department of Virology, University Hospital, Caen, France
| | | | - Mehdi Benchaib
- Service de Médecine de la Reproduction, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
| | - Jean Marie Cohen
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Sylvie van der Werf
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Anne Mosnier
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Bruno Lina
- Univ Lyon, Virpath, CIRI, INSERM U1111, CNRS, ENS, Université Claude Bernard Lyon 1, Lyon, France.,National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
| |
Collapse
|
49
|
Krumkamp R, Hogan B, Eibach D, Sarpong N, Kreuels B, Maiga-Ascofaré O, Adu-Sarkodie Y, Owusu-Dabo E, May J. Co-diagnoses in hospitalised children – revealing the cause of admission in a malaria endemic area. Das Gesundheitswesen 2017. [DOI: 10.1055/s-0037-1605873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R Krumkamp
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
- Deutsches Zentrum für Infektionsforschung, Hamburg
| | - B Hogan
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
| | - D Eibach
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
| | - N Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi
| | - B Kreuels
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
- Deutsches Zentrum für Infektionsforschung, Hamburg
- Universitätsklinikum Hamburg-Eppendorf, Hamburg
| | - O Maiga-Ascofaré
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi
| | - Y Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi
| | - E Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi
| | - J May
- Bernhard-Nocht-Institut für Tropenmedizin, Hamburg
- Deutsches Zentrum für Infektionsforschung, Hamburg
| |
Collapse
|
50
|
Sothmann P, Keller C, Krumkamp R, Kreuels B, Aldrich C, Sarpong N, Steierberg S, Winter D, Boahen KG, Owusu-Dabo E, May J, Eibach D. Rickettsia felis Infection in Febrile Children, Ghana. Am J Trop Med Hyg 2017; 96:783-785. [PMID: 28115672 DOI: 10.4269/ajtmh.16-0754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractRickettsial infections are an underrecognized cause of febrile illness in sub-Saharan Africa. To evaluate the epidemiology and clinical features of rickettsial disease in pediatric patients in Ghana, we screened blood samples from febrile children aged less than 15 years presenting to an outpatient department in Ghana's Ashanti Region for the presence of rickettsial DNA. We detected Rickettsia felis in 7/470 (1.5%) blood samples, using two independent real-time polymerase chain reactions. No other Rickettsia species were found. R. felis was detected repeatedly in one patient, and coinfection with Plasmodium falciparum was found in 3/7 samples. Symptoms apart from fever included cough (6/7) and vomiting (4/7). None of the R. felis-positive patients reported a rash. This study is the first report on R. felis in Ghana and adds to the growing evidence for its widespread occurrence with and without malaria coinfection in sub-Saharan Africa.
Collapse
Affiliation(s)
- Peter Sothmann
- Division of Tropical Medicine, 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christian Keller
- Institute of Virology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Ralf Krumkamp
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck, Hamburg, Germany
| | - Benno Kreuels
- Division of Tropical Medicine, 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck, Hamburg, Germany
| | - Cassandra Aldrich
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Stefanie Steierberg
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Doris Winter
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|