Diverse And Ecological Distribution Of Antibiotic Resistance Genes In Chinese Live Poultry Markets

Antibiotic-resistance poses a serious risk in public health and food safety worldwide in recent years.Antibiotic resistance genes(ARGs)can spread to or circulate among the "one-health"setting,i.e.,human,environments and animals via vertical transfer and horizontal tansfer.Live poultry market(LPM)as a trading place where a large number of animals were frequent transport,contribute to spread not only virus but also the resistant-bacteria and antibiotic resistance genes.However,the ecological distribution of ARGs in Chinese live poultry markets are unknown,so we focused on revealing the diversity and abundance of the ARGs in the gut microbiomes of live poultry in Chinese live poultry markets.We carried out this research on this problem,selected Chinese live poultry markets as the research object,by collecting samples on a large scale,through metagenomics sequencing study the pollution characteristic of ARGs in LPMs and diversity of poultry intestinal microorganism,and compared with pig,human and mouse gut reference set,the main content are as follows:Firstly,we collected a variety of live poultry fresh feces from 26 LPMs in 18 provinces and municipalities in China where were sampling for influenza virus detection for a long-term,directly extract the total DNA,then sequencing through lllumina platform.A comprehensive bioinformatics analysis carried out to analyze the intestinal microorganism and functional diversity of 102 chickens.The results showed that more than 90.71%of the intestinal microorganism in chickens were the bacteria,divided into 16 phylum,30 order,48 class,110 families,213 genus,433 species at each level of classification.The poultry gut metagenome catalogue compared to the pig,human and mouse gut metagenome catalogues.The gut microbial had a big difference,the pairwise overlap at the gene level was also modest,a remarkably low percentage of the genes identified in the poultry,pig,human and mouse catalogues shared by all four groups.The chicken metagenome exhibited a higher alpha diversity than both the human and mouse microbiomes and lower diversity than the pig microbiomes at the gene level,and lower alpha diversity than both the pig and human microbiomes at the KO level.By contrast,the intestinal microorganism of chicken,pig,human and mouse showed higher similarity,and a larger proportion of KO functions were shared(4,316 KO identifiers,50.1%of the total number)at the functional level.Secondly,the comprehensive antibiotic resistance database was used to annotation the antibiotic resistance genes.The results showed that ARGs were widely distribution in each LPM with a total of 235 ARG genotypes,and the number of ARGs in the southern markets in China was significantly higher than that in the northern markets.Among 130 samples,mcr-1 gene was found present in 71 samples,we also surveyed the distribution of the colistin resistance gene mcr-1 in 753 samples from 18 provinces and municipalities in China using PCR amplification,and 59.63%(449/753)live poultry market samples carried mcr-1 gene.Moreover,the results of metagenomics sequencing show that there were many other ARGs in the LPMs.What's more,high-risk genes such as mcr-3,mcr-4,mcr-5 and NDM-1 were also found in our samples.Finally,through comparative analysis of the reference gene set of live poultry,pig,human and mouse,the results showed that four groups shared many kind of ARGs(43 types).In general,there was difference among the distribution of ARGs in four groups.The number of ARGs and abundance in live poultry were significantly higher than that in pig,mouse and human.It was worth noting that tetracycline resistance genes were the most abundant in all the four groups.In conclusion,live poultry with various ARGs transported to LPMs for frequent trade,mcr-1 gene showed a very high positive rate in samples collected from LPMs.ARGs in different animals showed high sharing rate,suggested that it may be caused by cross transmission in LPMs,and multiple ARGs also shared among the gut microbes of human,pig,mouse and poultry,but lower identical genes at the gene level,and higher at the functional level.In this paper,we illustrated the ecological distribution of ARGs in Chinese LPMs,and revealed that the difference between ARGs and gut microbiomes in different species and area through deep sequencing of metagenomics method,which is of great significance for the prevention and control of public health and assessment of food safety.