| Salmonella spp.(Salmonella)is an important zoonotic pathogen and food-borne pathogen,which is a huge hazard to the poultry breeding industry and human health.It was found that there were many serotypes of Salmonella,and different serotypes had different pathogenicity to chickens.At present,there are few systematic analyses on the serotype and antimicrobial resistance of Salmonella from chickens in different years and regions.Therefore,studying the serotype distribution and antibacterial resistance trend of Salmonella from chickens was helpful to provide a scientific basis for Salmonella epidemiology and the use of antibacterial agents in my country.In recent years,the rapid development of bioinformatics technology has provided technical support for the analysis of bacterial Whole Genome Sequence(WGS),especially in the serotyping,antimicrobial resistance and molecular typing of Salmonella.The combination of WGS sequencing and bioinformatics technology(WGS sequencing analysis technology)can quickly and easily analyze and obtain results,and has the advantages of strong specificity and high sensitivity,which is expected to become an important research method on epidemic,antibacterial resistance,and molecular typing of Salmonella.Therefore,this paper collected Salmonella from chicken in different areas in China during recent50 years,and analyzed the serotype,antimicrobial resistance and molecular epidemiology of Salmonella by using conventional detection methods and WGS sequencing analysis technology,the results obtained were analysed and compared.The main contents are as follows:Firstly,412 strains of Salmonella from chickens,isolated from 1970 to 2020,were collected from 11provinces(including Bei Jing,Guang Dong and Jiang Su,etc.).After further culturing and identificating,the serotype typing of Salmonella was carried out by plate agglutination and WGS sequencing analysis technology,and the results of the two methods were compared and analyzed.The serotype distribution of Salmonella in different ages and regions was different.Prevalent serotype of Salmonella was S.gallinarum and S.enteritidis before and after 2000,respectively.Dominant serotype was S.enteritidis in 6 regions(including Si Chuan and Bei Jing,etc.),and S.gallinarum in Guang Dong and Jiang Su.The overall coincidence rate was 94.9% between two methods.In addition,the study also conducted a comparative research on the technology of liquid chip typing,and the results showed that the accuracy and reliability of the technology were lower than that of plate agglutination method and WGS sequencing analysis technology.Secondly,antimicrobial resistance of Salmonella,isolated from chickens in different regions in China to 11 kinds of antimicrobial agents during recent 50 years,was studied by broth dilution method and WGS sequencing analysis technology,and the results were analyzed and compared.The results showed that Salmonella had the highest resistance rate to Sulfisoxazole and Ampicillin,but sensitive to meropenem.Different antimicrobial resistance was found for different serotypes of Salmonella.Compared with S.gallinarum,S.enteritidis had higher resistance rate to colistin,amoxicillin/clavulanic acid,tetracycline and trimethoprim-sulfamethoxazole,but lower resistance rate to sulfisoxazole.The resistance of isolates in different ages is different.Except for colistin,the resistance of Salmonella to other 10 antibacterials gradually increased over time.The antimicrobial resistance rates to sulfaisoxazole,tetracycline and Colistin were different for Salmonella from different regions.The overall coincidence rate between the WGS sequencing analysis technology and the micro broth dilution method was 94.1%,the higher consistency was found for the antimicrobial agents with obvious correlation between resistant genes and antimicrobial resistance(sulfonamides,?-lactams and tetracyclines,etc.),while poor consistency was seen for the resistane caused by chromosome mutation(such as colistin)or other reasons.Thirdly,the molecular typing,virulence gene and prophage typing of Salmonella were studied by using WGS sequencing analysis technology,and the data of molecular typing,serotype and drug resistance were analyzed and compared.26 ST types were identified by Multi-locus sequence typing(MLST),and the dominant type was ST11,the relevance was observed between ST types and serotypes or isolation regions of Salmonella.Many virulence genes were found in Salmonella,all strains carried inv A,mgt C and mis L genes.More than half of Salmonella strains carried Prophage 500465-1.Comparative analysis of molecular typing,serotype and antimicrobial resistance data of Salmonella showed that different serotypes of could be divided into different branches and evolution time.S.enteritidis had the earliest evolutionary time,and the same serotypes of Salmonella had a closer relationship.No significant correlation of SNP evolution of Salmonella was observed with the resistance phenotype or virulence genes.In summary,serotypes,antimicrobial resistance and molecular epidemiology of Salmonella from different regions and different ages were studied,and the Pros and cons between conventional methods and WGS sequencing analysis technology were compared and analyzed,which provides data support for epidemiology,antimicrobial resistance and application of WGS sequencing analysis technology of Salmonella isolated from chickens in China. |
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