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Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka UL, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Bonongwe P, Munthali RJ, Ngwira S, Mwendera CA, Kalizang'oma A, Jambo KC, Kambalame D, Kamng'ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Msefula CL, Cunliffe NA, Jere KC. Genomic insights into the 2022-2023Vibrio cholerae outbreak in Malawi. Nat Commun 2024; 15:6291. [PMID: 39060226 PMCID: PMC11282309 DOI: 10.1038/s41467-024-50484-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Malawi experienced its deadliest Vibrio cholerae (Vc) outbreak following devastating cyclones, with >58,000 cases and >1700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022-2023 Vc outbreak isolates. Our results demonstrate the predominance of ST69 clone, also known as the seventh cholera pandemic El Tor (7PET) lineage, expressing O1 Ogawa (~ 80%) serotype followed by Inaba (~ 16%) and sporadic non-O1/non-7PET serogroups (~ 4%). Phylogenetic reconstruction revealed that the Malawi outbreak strains correspond to a recent importation from Asia into Africa (sublineage AFR15). These isolates harboured known antimicrobial resistance and virulence elements, notably the ICEGEN/ICEVchHai1/ICEVchind5 SXT/R391-like integrative conjugative elements and a CTXφ prophage with the ctxB7 genotype compared to historical Malawian Vc isolates. These data suggest that the devastating cyclones coupled with the recent importation of 7PET serogroup O1 strains, may explain the magnitude of the 2022-2023 cholera outbreak in Malawi.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK.
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Innocent Chibwe
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - David Chaima
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Patrick Musicha
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Latif Ndeketa
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | | | | | - Upendo L Mseka
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | | | - Bernard Mvula
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Wakisa Kipandula
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Patrick Bonongwe
- Ministry of Health, Balaka District Hospital, Balaka, Machinga, Malawi
| | - Richard J Munthali
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Selemani Ngwira
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Chikondi A Mwendera
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - 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, 0204, Pretoria, South Africa
| | | | - Daniel Hungerford
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Matthew Kagoli
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, 9300, 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, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Chisomo L Msefula
- 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, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Khuzwayo C Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi.
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi.
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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Okeke IN, Aboderin AO, Egwuenu A, Underwood A, Afolayan AO, Kekre M, Oaikhena AO, Odih EE, Omotayo HT, Dada-Adegbola H, Ogunleye VO, Ikhimiukor OO, Aanensen DM, Ihekweazu C. Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35980376 DOI: 10.1099/mic.0.001208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.
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Affiliation(s)
- Iruka N Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | | | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
| | - Ayorinde O Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Anderson O Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Hamzat T Omotayo
- World Health Organization, Nigeria Country Office, Abuja, Nigeria
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Veronica O Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Odion O Ikhimiukor
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK.,Wellcome Genome Campus, Hinxton, UK
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