Prospective One Health genetic surveillance in Vietnam identifies distinct blaCTX-M-harbouring Escherichia coli in food-chain and human-derived samples

Objectives: We performed a One Health surveillance in Hanoi-a region with a high-density human population and livestock production, and a recognized hotspot of animal-associated antimicrobial resistance (AMR)-to study the contribution of bla(CTX-M)-carrying Escherichia coli and plasmids from food animal sources in causing human community-acquired urinary tract infections (CA-UTIs). Methods: During 2014-2015, 9090 samples were collected from CA-UTI patients (urine, n = 8564), pigs/chickens from farms and slaughterhouses (faeces, carcasses, n = 448), and from the slaughterhouse environment (surface swabs, water, n = 78). E. coli was identified in 2084 samples. Extended-spectrum b-lactamase (ESBL) production was confirmed in 235 and bla(CTX-M) in 198 strains by PCR with short-read plasmid sequencing. Fourteen strains were long-read sequenced to enable plasmid reconstruction. Results: The majority of the ESBL-producing E. coli strains harboured bla(CTX-M) (n = 198/235, 84%). High clonal diversity (48 sequence types, STs) and distinct, dominant STs in human sources (ST1193, n = 38/137; ST131, n = 30/137) and non-human sources (ST155, n = 25/61) indicated lack of clonal transmission between habitats. Eight bla(CTX-M) variants were identified; five were present in at least two sample sources. Human and food-animal strains did not show similar plasmids carrying shared bla(CTX-M) genes. However, IS6 elements flanking ISEcp1-blaCTX-M-orf477/IS903B structures were common across habitats. Conclusions: In this study, animal-associated bla(CTX-M) E. coli strains or bla(CTX-M) plasmids were not direct sources of CA-UTIs or ESBL resistance in humans, respectively, suggesting evolutionary bottlenecks to their adaptation to a new host species. Presence of common IS6 elements flanking bla(CTX-M) variants in different plasmid backbones, however, highlighted the potential of these transposable elements for AMR transmission either within or across habitats. (C) 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Automated summary

A One Health surveillance was conducted in Hanoi to study the contribution of bla(CTX-M)-carrying Escherichia coli from food animal sources in causing human community-acquired urinary tract infections. The study found that animal-associated bla(CTX-M) E. coli strains were not direct sources of CA-UTIs in humans, suggesting evolutionary bottlenecks to their adaptation to a new host species. Additionally, common IS6 elements flanking bla(CTX-M) variants in different plasmid backbones highlighted the potential of these transposable elements for AMR transmission within or across habitats.