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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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Dharanendra S, Gillet AS, Geer B, Hall MAK, Hwang PR. Watery Diarrhea Is Not Always Clostridioides difficile: A Case Report of Aeromonas hydrophila Gastroenteritis. Cureus 2024; 16:e51940. [PMID: 38333475 PMCID: PMC10851916 DOI: 10.7759/cureus.51940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Aeromonas species can cause acute gastroenteritis but are much less commonly observed in the hospital setting than other bacteria. Most cases of Aeromonas hydrophila gastroenteritis reported in the literature have occurred in pediatric, elderly, and/or immunocompromised patients. We present a case of subacute watery diarrhea due to A. hydrophila infection in an otherwise healthy 48-year-old female patient with prior abdominal surgeries and recent hospitalization for a catheter-associated urinary tract infection (CAUTI) for which she received antibiotics. The patient presented with 10 days of increasingly frequent non-bloody, watery, foul-smelling diarrhea as well as decreased oral intake, cramping bilateral upper abdominal pain, chills, and malaise. Initial diagnoses considered included Clostridioides difficile in the setting of CAUTI and antibiotic use, small intestinal bacterial overgrowth, dumping syndrome related to bariatric surgery, and malabsorption. A computed tomography scan of her abdomen/pelvis, admission labs, and flexible sigmoidoscopy showed no relevant findings. Stool cultures eventually returned positive for A. hydrophila. The case is an uncommon presentation of Aeromonas infection that could be easily missed while other diagnoses are pursued. Early treatment of Aeromonas infection can be crucial in preventing advanced forms of disease such as septicemia and necrotizing fasciitis.
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Affiliation(s)
| | - Aaron S Gillet
- Department of Medicine, Division of Hospital Medicine, Emory University School of Medicine, Atlanta, USA
| | - Bashir Geer
- Department of Medicine, Division of Hospital Medicine, Emory University School of Medicine, Atlanta, USA
| | - Mary Ann Kirkconnell Hall
- Department of Medicine, Division of Hospital Medicine, Emory University School of Medicine, Atlanta, USA
| | - Patricia R Hwang
- Department of Medicine, Division of Hospital Medicine, Emory University School of Medicine, Atlanta, USA
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3
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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] [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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da Silva S, Guedes FADF, Amaral JRV, Ribeiro JRDA, de Souza YPA, de Freitas-Almeida ÂC, Thompson FL, Ramos RTJ, Whiteley AS, Macrae A, de Oliveira SS. Aeromonas allosaccharophila Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us? Life (Basel) 2022; 12:1492. [PMID: 36294926 PMCID: PMC9605075 DOI: 10.3390/life12101492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila.
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Affiliation(s)
- Sheila da Silva
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - Fernanda Alves de Freitas Guedes
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - João Ricardo Vidal Amaral
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - José Roberto de Assis Ribeiro
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | | | - Ângela Correa de Freitas-Almeida
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro Biomédico, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Av. 28 de Setembro, 87, 3° Andar, Fundos, Vila Isabel, Rio de Janeiro 20550-170, Brazil
| | - Fabiano Lopes Thompson
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Instituto de Biologia, 2° Andar-Sala 93, Rio de Janeiro 219410-970, Brazil
| | - Rommel Thiago Jucá Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas da Universidade Federal do Pará (UFPA), Rua Augusto Corrêa, 01 Guamá, Belém 66075-970, Brazil
| | - Andrew Steven Whiteley
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Canberra, ACT 2601, Australia
| | - Andrew Macrae
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
| | - Selma Soares de Oliveira
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
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