| The discovery and application of antibiotics have an indelible contribution to the development of human civilization,but with the abuse of antibiotics,antibiotic residues and the spread of resistance genes have been a serious threat on the ecological environment and human health.Presently,antibiotic-resistant pathogens have become an important factor in endangering public health and food safety.Understanding drug resistance is the prerequisite to defeat it.Recently,scientists have realized the importance of the epidemiological of antibiotic resistance and the horizontal transfer of resistance genes,and explored the transmission mechanism of bacterial resistance.This paper explored antibiotic resistance in two main lines: first,analyzed the difference of antibiotic resistance genes(ARGs)in gut microbiota of bovines from different breeding environments;second,from the perspective of pathogenic bacteria,analyzed the epidemiology of Shigella from calves,and the epidemiological characteristics of antibiotics resistance profiles,ARGs,and virulence genes of Shigella from calves.1.From a macro perspective,we conducted a comprehensive investigation of the gut microbiota structure and reservoir of ARGs in yaks,beef and dairy cattle from different regions and breeding environments of Gansu province by the metagenomic approach.The diversity and abundance of ARGs in the gut microbiota of yaks were significantly lower than those in dairy and beef cattle.2.By SS and MacConkey(MAC)selective media,16 S rDNA,API20 E biochemical assay kit,Serum agglutination test and multiplex PCR,we isolated 136 Shigella strains.Among them,54 strains were Shigella flexneri(S.flexneri),44 strains were Shigella sonneri(S.sonneri),and 38 strains were Shigella dysenteriae(S.dysenteriae).The data filled the gaps in the study of Shigella spp.from bovines in the northwest region and also laid a foundation for the subsequent study of Shigella in animials.3.The pulsed fcield gel electrophoresis(PFGE),multilocus sequence typing(MLST),and multiple-locus variable number tandem repeat analysis(MLVA)were established for studying the molecular genotyping characterization of S.flexneri,S.sonneri and S.dysenteriae.These three methods revealed the genetic relationship,epidemic background,and the intrinsic relationship between the classification characteristics and different phenotypic resistance stains in each aspect.4.7 virulence genes including ipaH,ial,sen,set1 A,set1B,stx and ipaBCD were detected in this study.Among them,ipaH(100%)and ipaBCD(94.85%)were the most prevalent virulence gene,followed by ial(75%)and sen(66.91%).Meanwhile,set1 A and set1 B genes were only found in S.flexneri,while stx gene was only found in S.dysenteriae.5.For the 51 third-cephalosporin resistant isolates,only three ?-lactamase gene types TEM(100%)?OXA(81.48%)?CTX-M(90.2%)were observed.Among them,TEM and OXA have only one subtype,namely TEM-1 and OXA-1,While CTX-M has three subtypes: CTX-M-14,CTX-M-3,CTX-M-79 and CTX-M-14(40/51,78.43%)was the major subtype.6.For the 55 fluoroquinolone-resistant isolates,three mutations in gyrA gene and two mutations in parC gene were detected.GyrA mutations were Ser83Leu(100%),Asp87Asn/Tyr(63.46%)and His211Tyr(50.91%),and parC mutations were Ser80Ile(50.91%)and Ser83Leu(56.36%).Besides,the detection rates of three PMQR genes were 100%,25.45% and 3.64% for aac(6?)-Ib-cr,qnr and qepA,respectively.7.S.dysenteriae Sd170912 has been assembled with one chromosome and three plasmid sequences by SMRT sequencing platform.The lengths of three plasmid sequences were 4,601,880 bp,104,574 bp,149,516 bp,and 34,156 bp,respectively.The Sd170912 genome contained a total of 4796 genes,of which 467 genes were virulence related genes and 96 genes were ARGs.Genomic composition analysis showed there were twenty-three genomics islands(GIs)and eight prophages sequences in Sd170912.Among them,six GIs and three prophages carried ARGs,and thirteen GIs and seven prophages carried virulence genes. |
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