Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya
BackgroundCholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed Vibrio cholerae genomes from clinical and environmental samples collected during the 2022–2023 outbreak. These strains were compared with historical genomes from Kenya, Uganda, Tanzania, and...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-07-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1603736/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849416075640307712 |
|---|---|
| author | Lydia M. Mageto Lydia M. Mageto Gabriel Oluga Aboge Zelalem H. Mekuria Peter Gathura John Juma Michael Mugo Collins Kipkorir Kebenei Diana Imoli Beatrice Atieno Ongadi Kelvin Kering Cecilia Kathure Mbae Samuel Kariuki |
| author_facet | Lydia M. Mageto Lydia M. Mageto Gabriel Oluga Aboge Zelalem H. Mekuria Peter Gathura John Juma Michael Mugo Collins Kipkorir Kebenei Diana Imoli Beatrice Atieno Ongadi Kelvin Kering Cecilia Kathure Mbae Samuel Kariuki |
| author_sort | Lydia M. Mageto |
| collection | DOAJ |
| description | BackgroundCholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed Vibrio cholerae genomes from clinical and environmental samples collected during the 2022–2023 outbreak. These strains were compared with historical genomes from Kenya, Uganda, Tanzania, and Haiti to inform strategies for cholera prevention, control, and elimination in Kenya.MethodsClinical (stool) and environmental (wastewater, drinking water, and household effluent) samples were collected from Nairobi county. Samples were analyzed for V. cholerae using culture and real time PCR. The environmental (n = 17) and clinical (n = 70) isolates were then subjected to phenotypic antimicrobial susceptibility testing using the Kirby-Bauer disk diffusion method. Whole genome sequencing was employed to characterize the genome, detect antimicrobial resistance genes, virulence factors, and mobile genetic elements. Phylogenetic analysis was performed to assess the genetic relationship and diversity of isolates from 2022 to 2023 outbreak, comparing them with isolates from historical outbreaks.ResultsClinical isolates carried key virulence genes (ctxA, ctxB7, zot, and hlyA) and were 100% resistant to multiple antibiotics, including ampicillin, cefotaxime, ceftriaxone, and cefpodoxime, but remained susceptible to gentamicin and chloramphenicol. In contrast, environmental isolates lacked ctxB gene but harbored toxR, als, and hlyA, showing variable antibiotic resistance (59% to ampicillin, 41% to trimethoprim-sulfamethoxazole, and 47% to nalidixic acid). All clinical isolates from 2022 to 2023 outbreak harbored IncA/C2 plasmids and several antimicrobial resistance genes including blaPER–7. Phylogenetic analysis revealed high genetic diversity in environmental strains, clustering outside the 7th pandemic El Tor lineage, while clinical isolates were highly clonal. Genomes from 2022 to 2023 outbreak were closely related to Kenyan cholera outbreak genomes from 2016 (15 single nucleotide polymorphisms, T13 lineage).ConclusionThe 2022–2023 outbreak likely resulted from re-emergence of previously circulating strains rather than a new introduction. While the role of environmental reservoirs as a source of human infection remains unclear in our study, environmental isolates possess virulent and antimicrobial resistance genes that may spread via horizontal gene transfer. This highlights the need for continuous genomic surveillance to monitor V. cholerae evolution, track transmission patterns, and mitigate the spread of antimicrobial resistance. |
| format | Article |
| id | doaj-art-22c51fec34a84db4ba2df5f1a1b69e3b |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-22c51fec34a84db4ba2df5f1a1b69e3b2025-08-20T03:33:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-07-011610.3389/fmicb.2025.16037361603736Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in KenyaLydia M. Mageto0Lydia M. Mageto1Gabriel Oluga Aboge2Zelalem H. Mekuria3Peter Gathura4John Juma5Michael Mugo6Collins Kipkorir Kebenei7Diana Imoli8Beatrice Atieno Ongadi9Kelvin Kering10Cecilia Kathure Mbae11Samuel Kariuki12Department of Public Health, Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, KenyaWashington State University, Global Health Kenya, Nairobi, KenyaDepartment of Public Health, Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, KenyaDepartment of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, United StatesDepartment of Public Health, Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, KenyaInternational Livestock Research Institute (ILRI), Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaCentre for Microbiology Research, Kenya Medical Research Institute, Nairobi, KenyaBackgroundCholera remains a public health challenge in Kenya. To better understand its dynamics, we analyzed Vibrio cholerae genomes from clinical and environmental samples collected during the 2022–2023 outbreak. These strains were compared with historical genomes from Kenya, Uganda, Tanzania, and Haiti to inform strategies for cholera prevention, control, and elimination in Kenya.MethodsClinical (stool) and environmental (wastewater, drinking water, and household effluent) samples were collected from Nairobi county. Samples were analyzed for V. cholerae using culture and real time PCR. The environmental (n = 17) and clinical (n = 70) isolates were then subjected to phenotypic antimicrobial susceptibility testing using the Kirby-Bauer disk diffusion method. Whole genome sequencing was employed to characterize the genome, detect antimicrobial resistance genes, virulence factors, and mobile genetic elements. Phylogenetic analysis was performed to assess the genetic relationship and diversity of isolates from 2022 to 2023 outbreak, comparing them with isolates from historical outbreaks.ResultsClinical isolates carried key virulence genes (ctxA, ctxB7, zot, and hlyA) and were 100% resistant to multiple antibiotics, including ampicillin, cefotaxime, ceftriaxone, and cefpodoxime, but remained susceptible to gentamicin and chloramphenicol. In contrast, environmental isolates lacked ctxB gene but harbored toxR, als, and hlyA, showing variable antibiotic resistance (59% to ampicillin, 41% to trimethoprim-sulfamethoxazole, and 47% to nalidixic acid). All clinical isolates from 2022 to 2023 outbreak harbored IncA/C2 plasmids and several antimicrobial resistance genes including blaPER–7. Phylogenetic analysis revealed high genetic diversity in environmental strains, clustering outside the 7th pandemic El Tor lineage, while clinical isolates were highly clonal. Genomes from 2022 to 2023 outbreak were closely related to Kenyan cholera outbreak genomes from 2016 (15 single nucleotide polymorphisms, T13 lineage).ConclusionThe 2022–2023 outbreak likely resulted from re-emergence of previously circulating strains rather than a new introduction. While the role of environmental reservoirs as a source of human infection remains unclear in our study, environmental isolates possess virulent and antimicrobial resistance genes that may spread via horizontal gene transfer. This highlights the need for continuous genomic surveillance to monitor V. cholerae evolution, track transmission patterns, and mitigate the spread of antimicrobial resistance.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1603736/fullcholeraantimicrobial resistancewhole genome sequencingphylogenetic analysisvirulence |
| spellingShingle | Lydia M. Mageto Lydia M. Mageto Gabriel Oluga Aboge Zelalem H. Mekuria Peter Gathura John Juma Michael Mugo Collins Kipkorir Kebenei Diana Imoli Beatrice Atieno Ongadi Kelvin Kering Cecilia Kathure Mbae Samuel Kariuki Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya Frontiers in Microbiology cholera antimicrobial resistance whole genome sequencing phylogenetic analysis virulence |
| title | Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya |
| title_full | Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya |
| title_fullStr | Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya |
| title_full_unstemmed | Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya |
| title_short | Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022–2023 cholera outbreak in Kenya |
| title_sort | genomic characterization of vibrio cholerae isolated from clinical and environmental sources during the 2022 2023 cholera outbreak in kenya |
| topic | cholera antimicrobial resistance whole genome sequencing phylogenetic analysis virulence |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1603736/full |
| work_keys_str_mv | AT lydiammageto genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT lydiammageto genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT gabrielolugaaboge genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT zelalemhmekuria genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT petergathura genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT johnjuma genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT michaelmugo genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT collinskipkorirkebenei genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT dianaimoli genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT beatriceatienoongadi genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT kelvinkering genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT ceciliakathurembae genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya AT samuelkariuki genomiccharacterizationofvibriocholeraeisolatedfromclinicalandenvironmentalsourcesduringthe20222023choleraoutbreakinkenya |