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

Abstract 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 blaCTX-M-carrying E. coli and plasmids from food-animal sources in causing human community-acquired urinary tract infections (CA-UTIs). Methods During 2014-2015, 9,090 samples were collected from CA-UTI patients (urines, n=8,564), pigs/chickens from farms and slaughterhouses (faeces, carcasses, n=448), and from the slaughterhouse environment (surface-swabs, water, n=78). E. coli were identified in 2,084 samples. ESBL production was confirmed in 235, and blaCTX-M in 198 strains by PCR that underwent short-read plasmid sequencing. Fourteen strains were long-read sequenced to enable plasmid reconstruction. Results Majority of the ESBL-producing E. coli harboured blaCTX-M (n=198/235, 84%). High clonal diversity (48 STs) and distinct, dominant STs in human (ST1193, n=38/137; ST131, n=30/137) and non-human sources (ST155, n=25/61) indicated lack of clonal transmission between habitats. Eight blaCTX-M variants were identified; 5 were present in at least two sample sources. Human and food-animal strains did not show similar plasmids carrying shared blaCTX-M genes. However, IS6 elements flanking ISEcp1–blaCTX-M–orf477/IS903B structures were common across habitats. Conclusions In this study, animal-associated blaCTX-M-E. coli or blaCTX-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 blaCTX-M variants in different plasmid backbones, however, highlighted the potential of these transposable elements for AMR transmission either within or across habitats.