Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment

Abstract

SummaryBackgroundAntimicrobial resistance is a major public health threat, affecting not only humans but also animals and the environment. Although the “One Health” dimension of resistance is well recognized, data are lacking on the circulation of resistance, particularly in low-income countries. The World Health Organization has proposed a protocol called Tricycle, focusing on extended-spectrum beta-lactamase (ESBL)-Escherichia colisurveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL-E. coliprevalence and describe intra- and inter-sector circulation of ESBL-E. coliand plasmids.Methods289 pregnant women, 246 farm chickens and 28 surface waters were sampled in Antananarivo (the capital city) area and tested for ESBL-E. coli. Isolates were sequenced by short-(Illumina) and long-(Nanopore) read methods.FindingsESBL-E. coliprevalence was 29·8%, 56·9% and 100% in pregnant women, chickens, and the environment, respectively. The wet season was associated with higher rates of carriage in humans (OR=3·1, 95%CI 1·8-5·3) and animals (OR=2·8 95%CI 1·7-4·8). Sequencing of 277 non-duplicated isolates (82, 118 and 77 from each sector, respectively) showed high genetic diversity (90 STs identified) with differences between sectors. Single nucleotide polymorphism (SNP) analysis revealed 169/277 (61%) isolates grouped into 44 clusters (≥2 isolates) of closely related isolates (<40 SNPs), of which 24 contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were allblaCTX-M(77.6%blaCTX-M-15), chromosomally integrated in 57·4% (159/277) of isolates, and plasmidic in 40·8% (113/277). The 114 ESBL-carrying plasmids were mainly IncF (55·2%, n=63) and IncY (36·8%, n=42). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) subtypes, and all IncY plasmids, highly conserved, were observed in isolates of differing genetic backgrounds from all sectors.InterpretationDespite varying strain population structures in the three sectors, both ESBL-E. colistrains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar.FundingFondation Mérieux, INSERM, Université Paris Cité