| Campylobacter is an important food-borne zoonotic pathogen,which genome sequence is characterized by high variation.Mobile genetic elements(MGEs)can be obtained through frameshift mutation or horizontal gene transfer(HGT)to quickly adapt to the environment,so that it can survive in a complex environment with different ecology.There are few reports on the high variation of Campylobacter genome.Chicken is the natural host of Campylobacter,and the prevalence rate at the rearing stage is high(60%-100%).Campylobacter is easy to colonize during the rearing process of chicken,and the chicken has become the main place for the change of Campylobacter.The prevalence and the antibiotic resistance of Campylobacter in poultry have been extensively studied,but the analysis of the genetic characteristics and genetic changes of the Campylobacter genome during the rearing stage has not been reported.In this study,Campylobacter isolated during the rearing process of large-scale chicken farms were used as templates.Based on whole-genome sequencing(WGS),the genetic characteristics and mobile genetic elements of the Campylobacter genome during chicken rearing stage were analyzed from different chicken farms,different rearing stages,and different sources,to analyze the genetic characteristics of the genome in a relatively closed microenvironment and explore the horizontal gene transfer between Campylobacter and the host or environment.1.Analysis of the genomic epidemiological and genetic characteristics of Campylobacter genome at different rearing stagesIn this study,Campylobacter jejuni(C.jejuni)and Campylobacter coli(C.coli)isolated from 6 chickens at different rearing stages and the environment in two chicken farms were selected for whole-genome sequencing.Quality control was performed on raw data and contigs were assembled.Annotation,phylogenetic analysis,MLST typing and CRISPR analysis were performed on the sequenced Campylobacter genome.CRISPR analysis showed that 81.82%of C.jejuni isolates and 62.96%of C.coli isolates contained CRISPR.The number of CRISPR contained in the two chicken farms was different.With the increase of time,the CRISPR rate of chicken farm A increased,but chicken farm B did not change.Analysis of antibiotic resistance genes(ARGs)revealed that Campylobacter contained ARGs,and C.jejuni(8)had fewer ARGs than C.coli(6).Isolates with the same sequence type(ST)basically had the same drug resistance,indicating a certain correspondence between ST and the antibiotic resistance pattern.The type and number of ARGs contained in chicken farm A(5 types,11 ARGs)were higher than those in chicken farm B(4 types,7 t ARGs).At different rearing process,the types of ARGs contained in C.jejuni in chicken farm A showed a decreasing trend,while C.coli showed a trend of increasing.The environmental isolates of chicken farm A contained a relatively large number of ARGs,while those of chicken farm B had less number of ARGs.Meanwhile,it was found that ARGs could spread from the environment to the chicken.The virulence genes analysis showed that 87 virulence genes including adhesion,colonization and immune evasion,glycosylation,motility,secretion system,toxins and other related genes were detected in Campylobacter.C.jejuni contained 85 virulence genes,which was more than C.coli(83).The virulence genes of Campylobacter isolates from different chicken farms were different.In addition to flaB and virB genes,other virulence factors in the two chicken farms were similar.The genes are similar.In different rearing stages,C.jejuni in chicken farm A showed an increasing trend,while C.coli revealed a stable trend.2.Analysis of mobile genetic elements of Campylobacter isolates in rearing stagesCampylobacter uses mobile genetic elements as carriers to exchange for exogenous genes.The Campylobacter genome in this study contained abundant mobile genetic elements,but plasmids and integrons were not detected.There were a total of 2790 insertion sequences(IS),distributed in 30 IS families,of which there were 609 unique sequences of C.jejuni,574 unique sequences of C.coli,and 1607 common sequences of Campylobacter.Campylobacter has many sources of IS.The unique sequences of C.jejuni had the most fragments from and the unique sequences of C.coli had the most fragments from Pseudomonas,and the consensus sequences had the most fragments from Mycoplasma,which indicated that Campylobacter had frequent sequence exchanges with the microorganisms in the chicken or the environment.The IS of Campylobacter from different chicken farms and different sources were different.At different rearing stages,although the average IS of Campylobacter decreased in 11 weeks,the IS trend of Cjejuni increased,while those of C.coli decreased.Cjejuni isolates had 3 nearly complete IS,and C.coli has 12 complete IS.Prophage analysis found that the proportion of C.jejuni containing complete prophage sequence(4.65%)was lower than that of C.coli(16.13%).The situation of the prophage of Campylobacter genome from different chicken farms and different sources were different.At different rearing stages,the number of prophage contained in C.jejuni showed an increasing trend;while those of C.coli revealed a decreasing trend.There are 4 complete prophage sequences of Campylobactery of which were all CJIE1-like prophage fragments of C.jejuni after blast comparison.Analysis of transposon showed that the Campylobacter genome sequence contained 383 transposon sequences,which were all from the Tn3 family.Among them,there are 125 transposons of C.jejuni,and 158 transposons of C.coli.TnBth1,TnBth2,TnBth3 are present in all Campylobacter.The average number of transposon sequences in chicken farm A(8)was higher than those in chicken farm B(6).At different rearing stages,the number of transposon sequences contained in C.jejuni revealed a stable trend,while that of C.coli showed an increasing trend.The transposon of Campylobacter from chicken and the environment were slightly different. |
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