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Background <p>Cholera remains a significant public health issue in Kenya, primarily driven by recurrent outbreaks associated with <i>Vibrio cholerae</i> O1 sequence type 69 (ST 69). Recently, non-O1/non-O139 strains have emerged and are associated with sporadic cases; however limited genomic data hinder our understanding of strain diversity, virulence, and antimicrobial resistance (AMR). This study characterized the genetic diversity, virulence, and AMR profiles of <i>V. cholerae</i> isolated in Western Kenya between 2015 and 2023 through an enteric pathogen surveillance study.</p> Methods <p>Twenty-four <i>V. cholerae</i> isolates from diarrheal patients aged 2 to 77 years were analyzed. Antimicrobial susceptibility testing was performed using E-test strips for azithromycin, tetracycline, ciprofloxacin, chloramphenicol, and trimethoprim–sulfamethoxazole, interpreted according to CLSI M45 guidelines. Hybrid whole genome sequencing (Illumina and Oxford Nanopore) was used to characterize sequence types, virulence determinants, AMR genes, mobile genetic elements, and phylogenetic relationships. The Kenyan isolates were contextualized within a global phylogeny of publicly available genomes.</p> Results <p>Two sequence types (STs) were identified: pandemic O1/ST69 (15/24, 62.5%) and non-O1/non-O139 ST8 (9/24, 37.5%). All ST69 isolates were susceptible to ciprofloxacin, tetracycline, and chloramphenicol. However, 10/15; 66.7% were resistant to azithromycin and trimethoprim–sulfamethoxazole. All azithromycin-resistant isolates were isolated in 2023. In contrast, all ST8 were 100% susceptible to all antibiotics tested. ST69 isolates carried classical virulence determinants, including <i>ctxAB</i>, seventh pandemic-associated pathogenicity islands, and consistently harbored fluoroquinolone resistance mutations (<i>gyrA</i> S83I and <i>parC</i> S85L). Notably, all ST69 isolates from 2023 possessed a conserved IncC plasmid encoding multiple AMR genes, including <i>bla</i><sub>PER−7</sub>, <i>sul1</i>,<i> aadA2</i>, and macrolide resistance determinants, explaining the observed multidrug resistance. Conversely, ST8 isolates lacked cholera toxin genes, carried fewer virulence and resistance determinants, and were detected only in 2019 at a single site. Phylogenomic analysis placed ST69 isolates within the seventh pandemic wave 3, contained in the 13-transmision event (AFR13), were closely related to African and Asian strains. In contrast, ST8 isolates were contained in the third transmission event and clustered with older European and South American lineages.</p> Conclusion <p>Our findings suggest persistent endemic circulation of pandemic ST69 in western Kenya alongside sporadic non-pandemic ST8 lineages. The recent detection of plasmid-mediated multidrug resistance among ST69 highlights ongoing pathogen evolution and underscores the need for sustained genomic surveillance to guide cholera control and antimicrobial stewardship.</p>

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Genomic analysis of Vibrio cholerae in Western Kenya (2015–2023) reveals persistence of pandemic ST69 and presence of the European-associated ST8 lineage

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月29日

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  • Erick C Kipkirui,
  • Vanessa Natasha,
  • Collins Kigen,
  • James W Muturi,
  • Ronald K Kirera,
  • Margaret C Koech,
  • Mary C Kirui,
  • Nancy C Kipkemoi,
  • Janet N Ndonye,
  • Sheilla Jerotich,
  • Luis Pow Sang,
  • Lillian Musila,
  • Elizabeth A Odundo

摘要

Background

Cholera remains a significant public health issue in Kenya, primarily driven by recurrent outbreaks associated with Vibrio cholerae O1 sequence type 69 (ST 69). Recently, non-O1/non-O139 strains have emerged and are associated with sporadic cases; however limited genomic data hinder our understanding of strain diversity, virulence, and antimicrobial resistance (AMR). This study characterized the genetic diversity, virulence, and AMR profiles of V. cholerae isolated in Western Kenya between 2015 and 2023 through an enteric pathogen surveillance study.

Methods

Twenty-four V. cholerae isolates from diarrheal patients aged 2 to 77 years were analyzed. Antimicrobial susceptibility testing was performed using E-test strips for azithromycin, tetracycline, ciprofloxacin, chloramphenicol, and trimethoprim–sulfamethoxazole, interpreted according to CLSI M45 guidelines. Hybrid whole genome sequencing (Illumina and Oxford Nanopore) was used to characterize sequence types, virulence determinants, AMR genes, mobile genetic elements, and phylogenetic relationships. The Kenyan isolates were contextualized within a global phylogeny of publicly available genomes.

Results

Two sequence types (STs) were identified: pandemic O1/ST69 (15/24, 62.5%) and non-O1/non-O139 ST8 (9/24, 37.5%). All ST69 isolates were susceptible to ciprofloxacin, tetracycline, and chloramphenicol. However, 10/15; 66.7% were resistant to azithromycin and trimethoprim–sulfamethoxazole. All azithromycin-resistant isolates were isolated in 2023. In contrast, all ST8 were 100% susceptible to all antibiotics tested. ST69 isolates carried classical virulence determinants, including ctxAB, seventh pandemic-associated pathogenicity islands, and consistently harbored fluoroquinolone resistance mutations (gyrA S83I and parC S85L). Notably, all ST69 isolates from 2023 possessed a conserved IncC plasmid encoding multiple AMR genes, including blaPER−7, sul1, aadA2, and macrolide resistance determinants, explaining the observed multidrug resistance. Conversely, ST8 isolates lacked cholera toxin genes, carried fewer virulence and resistance determinants, and were detected only in 2019 at a single site. Phylogenomic analysis placed ST69 isolates within the seventh pandemic wave 3, contained in the 13-transmision event (AFR13), were closely related to African and Asian strains. In contrast, ST8 isolates were contained in the third transmission event and clustered with older European and South American lineages.

Conclusion

Our findings suggest persistent endemic circulation of pandemic ST69 in western Kenya alongside sporadic non-pandemic ST8 lineages. The recent detection of plasmid-mediated multidrug resistance among ST69 highlights ongoing pathogen evolution and underscores the need for sustained genomic surveillance to guide cholera control and antimicrobial stewardship.