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Xiao S, Abade A, Boru W, Kasambara W, Mwaba J, Ongole F, Mmanywa M, Trovão NS, Chilengi R, Kwenda G, Orach CG, Chibwe I, Bwire G, Stine OC, Milstone AM, Lessler J, Azman AS, Luo W, Murt K, Sack DA, Debes AK, Wohl S. New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission. medRxiv 2024:2024.03.28.24302717. [PMID: 38585829 PMCID: PMC10996759 DOI: 10.1101/2024.03.28.24302717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.
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Affiliation(s)
- Shaoming Xiao
- Division of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ahmed Abade
- Ministry of Health, Dar es Salaam, Tanzania
- Field Epidemiology and Laboratory Training Program, Nairobi, Kenya
| | - Waqo Boru
- Field Epidemiology and Laboratory Training Program, Nairobi, Kenya
| | | | - John Mwaba
- Center for Infectious Disease Research, Zambia
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | | | | | | | - Roma Chilengi
- Zambia National Public Health Institute, Lusaka, Zambia
| | | | | | | | | | - O Colin Stine
- University of Maryland School of Medicine, Baltimore, USA
| | - Aaron M Milstone
- Division of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Wensheng Luo
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kelsey Murt
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - David A Sack
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amanda K Debes
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
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Jere KC, Chibwe I, Chaima D, Kasambala W, Mhango C, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Kamng'ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Cunliffe NA, Msefula CL, Chaguza C. Draft genomes of Aeromonas caviae from patients with cholera-like illness during the 2022-2023 cholera outbreak in Malawi. Microbiol Resour Announc 2023; 12:e0058023. [PMID: 37768056 PMCID: PMC10586119 DOI: 10.1128/mra.00580-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Aeromonas caviae is an increasingly recognized etiological agent of acute gastroenteritis. Here, we report five draft genomes of A. caviae isolated from suspected cholera cases during the 2022-2023 cholera outbreak in Malawi.
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Affiliation(s)
- Khuzwayo C. Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Innocent Chibwe
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - David Chaima
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Watipaso Kasambala
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Chimwemwe Mhango
- Malawi-Liverpool-Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Joseph Bitilinyu-Bangoh
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Bernard Mvula
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Wakisa Kipandula
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox W. Kamng'ona
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - A. Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Annie Chauma-Mwale
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Daniel Hungerford
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Matthew Kagoli
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State, South Africa
| | - Queen Dube
- Malawi Ministry of Health, Lilongwe, Malawi
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nigel A. Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Chisomo L. Msefula
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, YaleUniversity, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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Mseka UL, Mandolo J, Nyoni K, Divala O, Kambalame D, Mapemba D, Kamzati M, Chibwe I, Henrion MY, Manda K, Thindwa D, Mvula M, Odala B, Kamng'ona R, Dzinza N, Jere KC, Feasey N, Ho A, Amoah AS, Gordon M, Swarthout TD, Crampin A, Heyderman RS, Kagoli M, Chitsa-Banda E, Mitambo C, Phuka J, Chilima B, Kasambara W, Jambo KC, Chauma-Mwale A. Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi. EClinicalMedicine 2023; 56:101800. [PMID: 36600885 PMCID: PMC9800171 DOI: 10.1016/j.eclinm.2022.101800] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Background The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions. Methods We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalisations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. A multivariable logistic regression model was developed to investigate the factors associated with SARS-CoV-2 seropositivity. Findings Serum samples were analysed from 4619 participants (57% female; 60% aged 18-50 years), of whom 878/3794 (23%) of vaccine eligible adults had received a single dose of any COVID-19 vaccine. The overall assay-adjusted seroprevalence was 83.7% (95% confidence interval (CI), 79.3%-93.4%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18-50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (1 dose, 94% vs. 77%, adjusted odds ratio 4.89 [95% CI, 3.43-7.22]; 2 doses, 97% vs. 77%, aOR 6.62 [95% CI, 4.14-11.3]). Urban residents were more likely to be seropositive than those from rural settings (91% vs. 78%, aOR 2.76 [95% CI, 2.16-3.55]). There was at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalisations, 10.7% (95% CI, 10.2-11.3) vs. 4.86% (95% CI, 4.52-5.23), p < 0.0001; deaths, 3.48% (95% CI, 3.18-3.81) vs. 1.15% (95% CI, 1.00-1.34), p < 0.0001). Interpretation We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence and low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of reported at-risk populations. Funding Supported by the Bill and Melinda Gates Foundation (INV-039481).
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Affiliation(s)
- Upendo L. Mseka
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Public Health Institute of Malawi, Lilongwe, Malawi
| | | | | | - Oscar Divala
- Public Health Institute of Malawi, Lilongwe, Malawi
| | | | | | | | | | - Marc Y.R. Henrion
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Deus Thindwa
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Memory Mvula
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Bright Odala
- Public Health Institute of Malawi, Lilongwe, Malawi
| | | | | | - Khuzwayo C. Jere
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Kamuzu University of Health Sciences (formerly University of Malawi, College of Medicine) Blantyre, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Antonia Ho
- University of Glasgow, Glasgow, United Kingdom
| | - Abena S. Amoah
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Epidemiology and Intervention Unit, Lilongwe, Malawi
| | - Melita Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Todd D. Swarthout
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Amelia Crampin
- University of Glasgow, Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Epidemiology and Intervention Unit, Lilongwe, Malawi
| | - Robert S. Heyderman
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | | | | | | | - John Phuka
- Kamuzu University of Health Sciences (formerly University of Malawi, College of Medicine) Blantyre, Malawi
| | | | | | - Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Kamuzu University of Health Sciences (formerly University of Malawi, College of Medicine) Blantyre, Malawi
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Chibwe I, Kasambara W, Kagoli M, Milala H, Gondwe C, Azman AS. Field Evaluation of Cholkit Rapid Diagnostic Test for Vibrio Cholerae O1 During a Cholera Outbreak in Malawi, 2018. Open Forum Infect Dis 2020; 7:ofaa493. [PMID: 33241067 PMCID: PMC7676503 DOI: 10.1093/ofid/ofaa493] [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] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022] Open
Abstract
Rapid diagnostic tests (RDTs) for cholera are an important emerging tool for surveillance, yet the currently available tests have several limitations. We assess the performance of a new RDT, Cholkit, during a cholera outbreak in Malawi compared with culture and find a sensitivity of 93.0% (95% CI, 83.0%–98.1%) and a specificity of 95.7% (95% CI, 78.1%–100.0%).
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Affiliation(s)
- Innocent Chibwe
- National Microbiology Reference Laboratory/Public Health Institute of Malawi, Malawi Ministry of Health, Lilongwe, Malawi
| | - Watipaso Kasambara
- National Microbiology Reference Laboratory/Public Health Institute of Malawi, Malawi Ministry of Health, Lilongwe, Malawi
| | - Mathews Kagoli
- National Microbiology Reference Laboratory/Public Health Institute of Malawi, Malawi Ministry of Health, Lilongwe, Malawi
| | - Harry Milala
- National Microbiology Reference Laboratory/Public Health Institute of Malawi, Malawi Ministry of Health, Lilongwe, Malawi
| | - Charity Gondwe
- National Microbiology Reference Laboratory/Public Health Institute of Malawi, Malawi Ministry of Health, Lilongwe, Malawi
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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