Characterization Of Antibiotic Resistance Genes In Farm Staff,Animal Gut And Environment

The discovery and usage of antibiotics not only promoted the health of people but also contributed to the rapid development of livestock and poultry industry.However,the emergence of antibiotic resistant genes(ARGs)and antibiotic resistance bacteria(ARB)due to the intensive use of antibiotics is a difficult problem to be solved.The intensity of anthropogenic activities promoted the accumulation of ARGs among different environments,which has brought a new challenge to public health security.High abundance of ARGs had been found in sewage,sludge,poultry manure,human feces and intestines.The resistance genes in these specific environments can reflect the determinants of resistance gene selection,the extension of ARB contamination and the potential risk of transmission.Bacteria that were originally sensitive to antibiotics can capture ARGs in the natural environment and integrate them into their own genomes to develop resistance to antibiotics through vertical gene transfer(VGT)or horizontal gene transfer(HGT).Researchers confirmed that the superbug carrying ARGs(such as mcr-1)in the environments had been widely spread by HGT.In order to assess the risk of contamination and spread of ARGs in different environments,we uses metagenomics methods combined with bioinformatics analysis to explore the distribution of ARGs and their hosts in staff,pond water and soil from livestock farm in Guangdong province.Besides,the ARGs in human intestinal and environmental samples from the short reads archive(SRA)of National Center for Biotechnology Information(NCBI)were compared comprehensively and systematically.The metagenomic samples from the livestock farming were collected,including 11 human gut samples,15 pond water samples and 13 soil samples.In addition,the metagenomic samples were randomly downloaded from the database,including 36 chicken fecal samples,29 human gut samples,26 pig gut samples,29 seawater samples and 17 soil samples.The total number of samples was 176 in number.The clean data was obtained after the quality control of the sequencing raw data.The annotations of clean data were obtained by de novo assembly,predicting the open reading frames(ORFs)and searching against the database.The Alpha diversity was estimated by calculating the number of unique ARG subtypes and the Shannon index of each sample and the Beta diversity was performed by Principal Component Analysis(PCA).The co-occurrence relationship between the antibiotic resistance genes and their hosts were visualized by a network analysis.We used metagenomics analysis to systemically and comprehensively identify the similarities and differences of ARGs and their hosts in the environments.The results showed that there was significant imparity in the ARGs among different sample types.The abundance of ARGs in the gut-associated environments was significantly higher than that in other environments(P < 0.05).The ARGs coverage in chicken feces was more abundant than the pig gut and human gut.The most abundant ARG type in chicken was multidrug(40.7%),followed by aminoglycoside(9.8%).For pig,the top 2 ARG types were tetracycline(48.8%)and macrolide-lincosamide-streptomycins(16.7%).We found a different ARGs composition in human gut between the samples collected from NCBI and Guangdong province.Tetracycline(41.0%)was the most abundant ARG type found in human gut samples from SRA,while the gene encoding multidrug(29.1%)was the most abundant in human gut samples from Guangdong.Various distributions of ARGs in human gut from different countries might be due to the conception of rational use of antibiotics and the government’s supervision of antibiotics.The ARG types of multidrug,sulfonamide and bacitracin were dominant in natural environments.Metagenomic host-tracking analysis identified Escherichia,Bacteroides,and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments,while Alteromonas,Mycobacteriuma and Polynucleobacter and Proteobacteria as the predominant bacterial hosts of ARGs in natural environments.This thesis described the broad diversity and distribution of ARGs and their hosts in gut-associated environments and natural environments collected from Guangdong province and NCBI.The high abundance of ARGs in gut-associated environments,especially in livestock and poultry,indicated that more attention should be paid to the global surveillance and rational use of antibiotics.The results could help us evaluate the ARGs that may pose risks to environmental pollution and public health.