Changes in drug resistance of poultry and livestock sourced Escherichia coli in Chongqing

【Objective】 To compare the changes in antimicrobial resistance rates and the prevalence of horizontally transferable drug resistance genes in Escherichia coli from livestock and poultry in Chongqing over the past decade，providing scientific basis for controlling E. coli antimicrobial resistance in this region. 【Method】 Fecal samples were collected from livestock and poultry on 13 farms across 12 districts in Chongqing. A total of 157 E. coli strains（76 from 2007-2008 and 81 from 2020）were obtained after bacterial isolation and purification. Antimicrobial susceptibility to 18 antibiotics was evaluated through in vitro bacteriostatic tests. PCR was used to detect 17 horizontally transferable drug resistance genes in 39 multi-drug resistant E. coli strains. Molecular evolution relationships were analyzed using multilocus sequence typing（MLST）and phylogenetic clustering. Nine multidrug resistant E. coli strains were selected for whole-genome sequencing based on their resistance spectrum. 【Result】 The multi-drug resistance rate of livestock and poultry E. coli in Chongqing decreased from 96.05% during 2007-2008 to 75.31% in 2020. Resistance rates to tetracyclines（oxytetracycline，minocycline），amphenicols（florfenicol），fluoroquinolones（enrofloxacin，ciprofloxacin），and aminoglycosides （streptomycin，gentamicin，amikacin）declined from 13.16%-85.53% to 0-45.68%. The resistance spectrum shifted from predominantly five- to six-drug resistance to two- to four-drug resistance. Compared to 2007-2008 isolates，2020 isolates showed decreased detection rates of resistance genes for sulfonamides（sul1），β -lactams（bla_TEM），aminoglycosides ［aadA1 and aph（3'）-Ia and polymyxins（mcr-1），but increased detection rates for genes related to amphenicols（floR） and quinolones（qnrS）. Among the 39 tested strains，29 sequence types（STs）were identified，including 3 novel STs： ST12677，ST12678，and ST12679. Phylogenetic clustering revealed similar distributions，with all isolates grouped into A，B1，and D clusters. Horizontally transferable drug resistance genes were abundant in quantity and types，with isolates from 2007-2008 carrying 10-14 genes（4-7 types）and those from 2020 carrying 9-18 genes（6-10 types）. 【Conclusion】 While resistance of E. coli strains from livestock and poultry to certain antibiotics has greatly declined in Chongqing，and multi-drug resistance has been alleviated to some extents，some strains still carry a substantial number of transferable drug resistance genes. This highlights the importance of further investigation into horizontal transmission mechanisms and control strategies. Developing suitable alternative antimicrobial programs based on resistance trends may help mitigate multidrug resistance and safeguard public health.