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

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.

Bibliographic Details

Main Authors:	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
Format:	article biblioteca
Language:	eng
Subjects:	S50 - Santé humaine, L73 - Maladies des animaux, E51 - Population rurale, 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, http://aims.fao.org/aos/agrovoc/c_2615, http://aims.fao.org/aos/agrovoc/c_13325, http://aims.fao.org/aos/agrovoc/c_16411, http://aims.fao.org/aos/agrovoc/c_4586, http://aims.fao.org/aos/agrovoc/c_431, http://aims.fao.org/aos/agrovoc/c_662faf6f, http://aims.fao.org/aos/agrovoc/c_2329, http://aims.fao.org/aos/agrovoc/c_34326, http://aims.fao.org/aos/agrovoc/c_33700, http://aims.fao.org/aos/agrovoc/c_6699, http://aims.fao.org/aos/agrovoc/c_509, http://aims.fao.org/aos/agrovoc/c_8532, http://aims.fao.org/aos/agrovoc/c_32668, http://aims.fao.org/aos/agrovoc/c_4510,
Online Access:	http://agritrop.cirad.fr/608002/ http://agritrop.cirad.fr/608002/1/dkad125.pdf
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