Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China

Abstract

Escherichia coli is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 E. coli strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the E. coli isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes blaNDM-5 (1.10%, 2/181), mcr-1 (1.10%, 2/181), tet(X4) (1.10%, 2/181), and cfr (6.08%, 2/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified astA (37.02%, 67/181), hlyA (1.66%, 3/181), hlyB (1.66%, 3/181) and hlyD (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China

“…Some of these antibiotics had no previously known association with these ARGs. In particular, 14 ARGs (aadA16, aph(3′)-Ia, aph(3′)-VIa, bla CARB-16 , catQ, dfrA15, dfrA16, dfrA27, bla OXA-58 , bla PER-1 , qnrD1, tet(Z), tet (39) and bla SHV-110 ) found to be associated with resistance to the highest number of antibiotics had previously been found in earlier studies on poultry in China [40][41][42] , confirming our method. However, we found a cluster of gut bacteria that correlated well with E. coli resistance to five different antibiotics.…”

Machine learning and metagenomics enhance surveillance of antimicrobial resistance in chicken production in China

“…In our study 68 clinically relevant ARGs correlated with resistance to multiple antibiotics, and some of these antibiotics had no previously known association with these ARGs. In particular, the six ARGs (aadA16, aadA22, PER-1, AAC(6')-Ia, tet (39) and SHV-110) that we found associated to resistance to the highest number of antibiotics, had been previously found in earlier studies on poultry in China [34][35][36] , con rming our method. However, we found a cluster of further gut bacteria that correlated well with E. coli resistance to ve different antibiotics.…”

Transmission of linezolid-resistant Enterococcus isolates carrying optrA and poxtA genes in slaughterhouses

“…The complete genome sequence can effectively analyze the genome characteristics, ARGs, plasmids, and other elements (Wang et al, 2013;Zhu et al, 2015;Peng et al, 2017), and has been an essential means of antimicrobial resistance research in recent years (Tang et al, 2022a,b). The ARGs predicted by the genome have a corresponding good relationship with the AMR phenotype (Zheng et al, 2022;Zhou et al, 2022;Li et al, 2022b;Tang et al, 2022b).…”