Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
Title of the talk: Whole genome sequencing reveals limited contribution of non-intensive chicken farming to extended-spectrum beta-lactamase producing Escherichia coli colonization in humans in southern Vietnam
Overuse of antimicrobials in agriculture in Asia has been reported, but the risk of acquisition of extended-spectrum beta-lactamase (ESBLs) in humans through non-intensive chicken farming still remains unclear. We collected faecal samples from 204 randomly selected farmers and their chickens, and from 306 community-based individuals who did not raise poultry in Vietnam. Whole genome sequencing was employed to examine genomic relatedness of ESBL-Ec colonizing chickens and humans in Vietnam. The prevalence of ESBL-Ec colonization was 20.0% in chicken farms, 31.1% in chicken farmers, 49.5% in rural individuals and 38.3% in urban individuals. Multivariable analysis showed that colonization with ESBL-Ec in humans was associated with human usage of antimicrobial drugs (OR=2.52, 95%CI=1.08–5.87). Whole-genome sequencing revealed that CTX-M genes were the most predominant ESBL genes, found in 468/486 (96.2%) of ESBL-Ec isolates. However, the distribution of CTX-M genes across chicken and human isolates was different. CTX-M-55 was identified as the most common ESBL-encoding gene in chicken isolates (72.1% versus 12.9% in human isolates, p<0.001), whilst CTX-M-27 was more prevalent in human isolates (44.2% versus 7.0% in chicken isolates; p<0.001). On 16/204 farms (6.9%; 95%CI=3.4–10.3%) ESBL-Ec were detected phenotypically in both the farmers and their chickens. On 3/204 farms (1.5%; 95%CI=0–3.1%), ESBL genes of ESBL-Ec isolated from the farmers and their chickens were identical. However, we detected identical sequence types of ESBL-Ec between chicken and farmer isolates in only one farm. Isolates also revealed 1 pairwise SNP distance based on core gene alignment, indicating potential sharing of ESBL-Ec between the chickens and farmer on that farm. The findings suggest that non-intensive chicken farming is not a major source of ESBL-Ec colonization in humans and human antimicrobial drug usage appears to be an important driver of ESBL-Ec colonization in humans in Vietnam.
Dr. Nguyen Vinh Trung is a researcher at the Oxford University Clinical Research Unit in Ho Chi Minh City, Vietnam. His research interests include epidemiology of zoonotic pathogens and dynamics of antimicrobial resistance in bacterial populations