| Antibiotic resistance(AR)is recognized as one of the most serious global threats to public health and food safety.Antibiotic resistance genes(ARGs)are important factors causing AR,which have attracted international public health concerns.These concerns are exemplified by the rapid increase in carbapenem-resistant Enterobacteriaceae expressing enzymes(for example,blaKPC-1 and blaNDM-1)and the plasmid-mediated colistin resistance genes,such as mcr-1.Gut microbiota of chicken,pig,and human is a huge reservoir of antibiotic-resistant bacteria and resistance genes.We previously characterized poultry gut antibiotic resistome profile(in live poultry markets,LPMs),but we did not compare the LPMs with farm samples.More importantly,we found no reports addressing the difference of antibiotic resistome between the LPM workers and those who have no contact with the LPMs.Moreover,limited information is available regarding the presence(metagenomic DNA level)and expression profiles(metatranscriptomic RNA level)of ARGs in the gut microbiota of chicken,pig,and human.Notably,Salmonella enterica(S.enterica)is a major pathogen of humans and animals,and also an important source and reservoir of genes that encode AR.Although systematic studies on the trends and geographical distribution of AR-Salmonella enterica and dominant serovars have been well studied in America,Canada,Australia,Europe,and other countries or regions,while limited data is available in China.Therefore,we carried out this research to shed light on these fundamental issues mentioned above,the main content is as follows:First,we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance,diversity,and expression of ARGs in human,chicken,and pig gut microbiomes in China.Based on deep sequencing data and ARG databases,a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human,chicken,and pig fecal samples.Metatranscriptomic analysis revealed that 49.4,66.5,and 56.6%of ARGs identified in human,chicken,and pig gut microbiota,respectively,were expressed,indicating that a large proportion of ARGs was not transcriptionally active.Further analysis demonstrated that transcript abundance of tetracycline,aminoglycoside,and beta-lactam resistance genes was mainly contributed by acquired ARGs.We also found that various biocide,chemical,and metal resistance genes were actively transcribed in human and animal guts.The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts,providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota.Taken together,these data deepen our understanding of the distribution,evolution,and dissemination of ARGs and metal resistance genes in human,chicken,and pig gut microbiota.Second,we characterized the resistome and bacterial microbiome of farm chickens and LPMs,and LPM workers and control subjects using whole-metagenomic sequencing.The mobile ARGs identified in chickens and the distribution of the MCR-family genes in publicly bacterial genomes and chicken gut metagenomes was analyzed,respectively.In addition,the prevalence of mcr-1 in LPMs following the ban on colistin-positive additives in China was explored.By profiling the microbiomes and resistomes in chicken farms,LPMs,LPM workers,and LPM environments,we found that the bacterial community composition and resistomes were significantly different between the farms and the LPMs,and the LPM samples possessed more diversified ARGs(59 types)than the farms.Some mobile ARGs,such as mcr-1 and tet(X3),identified in chicken farms,LPMs,LPM workers,and LPM environments were also harbored by human clinical pathogens.Moreover,we found that the resistomes were significantly different between the LPM workers and those who have no contact with the LPMs,and more diversified ARGs(1 88 types)were observed in the LPM workers.It is also worth noting that mcr-10 was identified in both human(5.2%.96/1,859)and chicken(1.5%,14/910)gut microbiomes.Although mcr-1 prevalence decreased significantly in the LPMs across the seven provinces in China,from 190/333(57.1%)samples in September 2016-March 2017 to 208/544(38.2%)samples in August 2018-May 2019,it is widespread and continuous in the LPMs.Live poultry trade has a significant effect on the diversity of ARGs in LPM workers,chickens,and environments in China,driven by human selection with the live poultry trade.Our findings highlight the live poultry trade as ARG disseminators into LPMs,which serve as an interface of LPM environments even LPM workers,and that could urge Government to have better control of LPMs in China.Further studies on the factors that promote antibiotic resistance exchange between LPM environments,human commensals,and pathogens,are warranted.Third,taking the One-Health strategy,we used 35,382 S.enterica isolates collected from 1982 to 2019,covering a large set of multiple sources including healthy person,inpatients,wet markets,farm animals,and wild animals to explore the temporal and spatial dynamics of dominant serovars of Salmonella in China.Moreover,we selected 1,572 isolates for comparative genomics and antibiotic resistance studies.Our data confirmed S.Typhimurium was the dominant serovar of Salmonella in China,which was consistent with Belgium and Australia,and inconsistent with the United States,Canada,and Europe.The proportion of Salmonella serovars Typhimurium,I 1,4,[5],12:i:-,London,Rissen,Corvallis,Meleagridis,Kentucky,and Goldcoast showing an increasing trend during 2006-2019.Based on 1572 WGS data,we used SeqSero2 and SISTR to determine the Salmonella serovars that fully match laboratory test results.The proportion of AR isolates(genotype)have an increasing trend over time,especially multidrug-resistant(MDR)isolates with 20.93%in 2006.increasing to 51.75%in 2017.Moreover,isolates from non-human origin possessed more antibiotic resistance determinants,virulence factors,and mobile genetic elements.Our results fill in the data gap on the trends of AR-Salmonella enterica and dominant serovars in China.These data provide useful information for inform clinical and public health decision-makers in prioritizing interventions for foodborne diseases and food safety.Finally,through comparative genomic analysis of both human and animal gut microbiomes and bacterial genomes generated by both our laboratory and public data available,we have substantially expanded our insights into the diversity and distribution of mcr and tet(X)-like genes.Notably,MCR-family genes were extensively distributed in human microbiomes and clinical pathogens,for example,Klebsiella pneumoniae and S.enterica,Moreover,we reported the identification of the plasmid-mediated tigecycline resistance gene tet(X4)in a conjugative plasmid of the S.enterica serovar Llandoff strain SH16G3606 isolated from a man in China in 2016,the first reported serovar Llandoff in China as a novel sequence type ST8300.The tet(X4)-mediated resistance phenotype could be successfully transferred from the S.Llandoff strain into E.coli J53.resulting in a 32-fold increase in the minimal inhibitory concentration(MIC)of tigecycline.The tet(X4)gene was located between two copies of ISCR2 in the plasmid pSal21GXH-tetX4.To our knowledge,this is the first report of the plasmid-mediated tigecycline resistance gene tet(X4)in a S.Llandoff strain isolated from a human stool sample in China.In addition,our findings demonstrated that a total of 171 isolates carrying tet(X)-like genes distributed in 21 countries or areas across 6 continents,posing a potential threat to public health and food safety.Overall,we assembled the largest dataset to date of sequenced bacterial genomes containing novel tet(X)-like genes through our sequencing efforts and an extensive search of the publicly available sequence datasets and found that the widespread of tet(X)-like genes in different bacterial species,including clinical pathogens. |
