Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producing Escherichia coli strains and plasmids among humans, chickens and the environment

Background Antimicrobial 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 coli surveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL- E. coli prevalence and describe intra- and inter-sector circulation of ESBL- E. coli and plasmids. Methods 289 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. Findings ESBL- E. coli prevalence 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 all bla CTX-M (77.6% bla CTX-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. Interpretation Despite varying strain population structures in the three sectors, both ESBL- E. coli strains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar. Funding Fondation Mérieux, INSERM, Université Paris Cité ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Protocols ### Funding Statement This study was funded by Merieux Foundation and INSERM. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Ethics Committee of Ministry of Health, Madagascar gave ethical approval for this work (authorization number 038-MSANP/CERBM). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.