Macrogenomics-based analysis of microbial resistance of microbes in pig and chicken faeces in Anhui region
Objective In order to gain insight into the phenomenon that the misuse of antibiotics in the production of food animals has forced intestinal commensal bacteria to become one of the important hosts of antimicrobial resistance(AMR).Therefore,the present study was conducted to analyze the intestinal bacterial AMR in food animals using macro-genomics.Methods AMR and mobile genetic elements in pig and chicken faeces from Anhui region were quantified and characterised using macrogenomics techniques,and the resistance profiles of the commensal bacterial communities in pigs and chickens were observed at the level of the core resistance gene subtype.Results In terms of the abundance and di-versity of antimicrobial resistance gene(ARG),the diversity and detection rate of ARG were higher in chicken intestinal commensal bacteria than in pigs,whereas the total abundance of ARG was higher in porcine intestinal commensal bacteria than in chickens.Macrolide-Lincosamide-Streptozotocin-like resistance genes and Tetracycline resistance genes were the two most abundant ARG in all the samples.The study also detected ARG prevalent worldwide,including optrA,qnrS,lsaE,and tem,etc..At the same time,a number of removable genetic elements including phage,plasmid and insertion se-quences were also shown to have some correlation with ARG,which revealed the horizontal transfer potential of ARG.In addition,a statistically positive correlation was demonstrated between resistance groups and microbiomes of food chain an-imals.Host traceability analyses showed that Bacteroides and Escherichia coli were detected to contain high levels of ARG in chicken samples,whereas rich ARG were detected in Ruminococcus and Roseburia in pig samples.Conclusion Intest-inal microbiota is one of the important hosts and transmission routes of ARG.The study provides a scientific basis for eval-uating the safety of food animals and the subsequent construction of a database of pan-resistant genes,which is of great sig-nificance for public health.
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