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Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen.

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Al-Shalali, Salah 
Njamkepo, Elisabeth  ORCID logo
Bashir, Ismail Mahat 


Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.


Acknowledgements: This research was funded in whole, or in part, by the Wellcome Trust (grant nos 206194 and 108413/A/15/D). This work was supported by Institut Pasteur, Santé publique France, and by the French Government’s Investissement d’Avenir programme, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant no. ANR-10-LABX-62-IBEID). F.L., M.J.D., G.A.B., A.T.-B., M.A.B., A.C. and N.R.T. were supported by Wellcome funding to the Sanger Institute (grant nos 206194 and 108413/A/15/D). E.N., J.R., M.-L.Q. and F.-X.W. were supported by French Government funding to Institute Pasteur (grant no. ANR-10-LABX-62-IBEID). We thank J. Woolfolk, S. Clare and C. Tolley for their support in sample management at Wellcome Sanger Institute, as well as the Sanger Pipelines team for support. M.J.D. is an Official Fellow of Churchill College, Cambridge, and was previously supported by a Junior Research Fellowship at the College. For the purpose of Open Access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

Funder: LABoratoire d’EXcellence IBEID (Labex IBEID); ANR-10-LABX-62-IBEID


Humans, Cholera, Vibrio cholerae O1, Yemen, Plasmids, Genomics

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Nat Microbiol

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Springer Science and Business Media LLC
Wellcome Trust (Wellcome) (206194, 108413/A/15/D, 206194, 206194, 108413/A/15/D, 206194, 108413/A/15/D, 206194, 108413/A/15/D, 206194, 108413/A/15/D, 206194)