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Volume 11, Issue 12

Genomic analysis and antimicrobial resistance of isolated during Zambia’s 2023 cholera epidemic Open Access

Abstract

Cholera, caused by , remains a priority public health concern, particularly in developing countries. The first cholera outbreak in Zambia was documented in the 1970s, with recurring epidemics reported since then. In 2023, a cholera outbreak affected Zambia, particularly in districts bordering Malawi, Mozambique and the Democratic Republic of Congo, with significant cases reported in these neighbouring countries. This study aims to analyse cholera cases and isolates obtained during the 2023 epidemic, focusing on geographical distribution, genetic relatedness of isolates and their antibiotic resistance profiles.

Stool samples were collected from patients presenting with cholera-like symptoms across three provinces of Zambia. A total of 98 samples were cultured on thiosulphate citrate bile salts sucrose agar, resulting in 32 sequenced isolates. Whole-genome sequencing was performed using Oxford Nanopore Technology, and phylogenetic inference was also achieved by the analysis of SNPs. Phenotypic antimicrobial resistance testing was conducted following Clinical and Laboratory Standards Institute guidelines. The genomic data were analysed for virulence factors and antimicrobial resistance profiles.

Of the 98 stool samples tested, 38 confirmed cholera cases were identified. A subset of 32 confirmed isolates, predominantly from the Eastern Province of Zambia (=21), was selected for whole-genome sequencing. Genomic analysis revealed that all isolates belonged to the seventh pandemic El Tor lineage and the O1 serogroup, with two distinct clades identified corresponding to the 10th (T10) and 15th (T15) transmission events. Geographical analysis indicated a predominance of Ogawa serotypes in Eastern Province and Inaba in Northern Province. The virulence gene analysis confirmed the presence of key cholera toxin genes ( and ) and intestinal colonization factors. All isolates carried genes or mutations predicted to confer resistance to multiple antibiotics, including decreased susceptibility to ciprofloxacin, recommended for the treatment of cholera by the World Health Organization.

The findings highlight the critical need for enhanced surveillance and targeted interventions to mitigate cholera outbreaks in Zambia. The emergence of resistant strains necessitates innovative strategies, including improved water sanitation, vaccination efforts and novel therapeutic approaches to combat this enduring public health threat.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , epidemic , Oxford Nanopore Technologies , Vibrio cholerae and Zambia
Funding
This study was supported by the:
  • Wellcome Trust (Award DEL-22-012)
    • Principal Award Recipient: SamuelBosomprah
  • Wellcome Trust (Award 206194)
    • Principal Award Recipient: NicholasR. Thomson
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-12-16

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Genomic analysis and antimicrobial resistance of Vibrio cholerae isolated during Zambia’s 2023 cholera epidemic
M Gen 11, 001566 (2025); https://doi.org/10.1099/mgen.0.001566
/content/journal/mgen/10.1099/mgen.0.001566
/content/journal/mgen/10.1099/mgen.0.001566
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