Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs

Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

Insights into the effects of pulsed antimicrobials on the chicken resistome and microbiota from fecal metagenomes

Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes(ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump(marA, soxS, sdiA, rob, evgS and phoP).These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin,chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.

Identification of blaIMI-mediated carbapenem-resistant Enterobacter from a duck farm in China

Carbapenem-and colistin-resistant Enterobacter has been a clinical and therapy problem in recent years.Here,we report the carbapenem-and colistin-resistant Enterobacter harboring bla_(IMI) isolated from intestinal samples and the environment of a duck farm in China.Four bla_(IMI)-positive Enterobacter isolates were resistant to carbapenem and colistin.Three bla_(IMI) subtypes were detected in different molecular categories of Enterobacter.The detection of the various IMI producers highlights the diversity of carbapenemases in a duck farm.Whole-genome sequencing demonstrated the bla_(IMI) genes were present in chromosomes or plasmids in these strains.The conjugation experiment demonstrated the ability of bla_(IMI)-carrying plasmid to transmit horizontally.The molecular evolution characteristics were examined through comparative genetic analysis.The study demonstrated the presence of chromosomal and plasmid bla_(IMI) and the bla_(IMI)-carrying plasmid exhibits a horizontal transmission between Enterobacter and Escherichia coli C600.The similar genetic content was discovered between two bla_(IMI-16)-positive Enterobacter asburiae.In addition,a bla_(IMI-16)-carrying plasmid is an IncFII(Yp)plasmid,and a substantial amount of mobile genetic elements were identified around bla_(IMI-16).The IS-like elements and IncFII(Yp)plasmid are significant in the propagation of bla_(IMI).Our study provides evidence for the transmission of diverse bla_(IMI) genes in China and supplies additional reference data for bla_(IMI)-positive antimicrobialresistant Enterobacter.Routine surveys of bla_(IMI)-positive Enterobacter from animal-raising environments must be given more focus.