One Health compartment analysis of ESBL-producing Escherichia coli reveals multiple transmission events in a rural area of Madagascar

Gay Noellie, Rabenandrasana Mamitina Alain Noah, Panandiniaina Harielle Prisca, Rakotoninidrina Marie Florence, Ramahatafandry Ilo Tsimok'Haja, Enouf Vincent, Roger François, Collard Jean-Marc, Cardinale Eric, Rieux Adrien, Loire Etienne. 2023. One Health compartment analysis of ESBL-producing Escherichia coli reveals multiple transmission events in a rural area of Madagascar. Journal of Antimicrobial Chemotherapy, 78 (8) : 1848-1858.

https://doi.org/10.1093/jac/dkad125

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Url - autres données associées : https://github.com/loire/AMR_mada2020

Résumé : Background: ESBL-producing Escherichia coli (ESBL-Ec) is considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human and environment compartments. There is likelihood of ESBL-Ec animal–human transmission but proof of cross-compartment transmission is still unclear. Objectives: To characterize ESBL-Ec genetic similarity in various compartments (humans, animals and environment) from a rural area of Madagascar. Methods: We collected ESBL-Ec isolates prospectively from humans, animals and the environment (water) between April and October 2018. These isolates were subject to WGS and analysed with cutting-edge phylogenomic methods to characterize population genetic structure and infer putative transmission events among compartments. Results: Of the 1454 samples collected, 512 tested positive for ESBL-Ec. We successfully sequenced 510 samples, and a phylogenomic tree based on 179 365 SNPs was produced. Phylogenetic distances between and amongst compartments were indistinguishable, and 104 clusters of recent transmission events between compartments were highlighted. Amongst a large diversity of ESBL-Ec genotypes, no lineage host specificity was observed, indicating the regular occurrence of ESBL-Ec transfer among compartments in rural Madagascar. Conclusions: Our findings stress the importance of using a phylogenomic approach on ESBL-Ec samples in various putative compartments to obtain a clear baseline of AMR transmissions in rural settings, where one wants to identify risk factors associated with transmission or to measure the effect of 'One Health' interventions in low- and middle-income countries.

Mots-clés Agrovoc : épidémiologie, phylogénie, surveillance épidémiologique, genre humain, santé animale, résistance aux antimicrobiens, transmission des maladies, génétique des populations, Escherichia coli, zone rurale, antimicrobien, élevage, facteur de risque