基于平均核苷酸相似度和16S rDNA技术对全球沙门氏菌的鉴定比对分析

Comparative analysis on the identification of global Salmonella based on average nucleotide identity and 16S rDNA technology

目的评估平均核苷酸相似度(average nucleotide identity,ANI)和16S rDNA技术对沙门氏菌的鉴定能力。方法从GenBank数据库批量下载全球沙门氏菌基因组和相应血清型,以沙门氏菌典型菌株的基因组作为分型菌株。利用fastANI软件,根据默认参数进行ANI分析。使用在线软件SpeciesFinder针对细菌的16S rDNA进行物种和血清型鉴定。结果在下载的2306个基因组中,1767株沙门氏菌存在178种血清型,以鼠伤寒沙门菌323株(18.3%)和肠炎沙门菌300株(17.0%)最为常见。ANI分析显示,以95%为界值时,仅有30株(1.3%)沙门氏菌被分配到1个特定的亚种,其余2276株(98.7%)沙门氏菌均可分配到2~5个亚种;以97%为界值时,2306株(100%)沙门氏菌均可被鉴定到唯一的亚种。基于16S rDNA的分析仅鉴定出1072株(46.5%)沙门氏菌,其中95.2%(1021/1072)的沙门氏菌鉴定的亚种结果与ANI(≥97%)分析鉴定的结果完全一致;与已知的血清型相比,仅有2.4%(19/784)的沙门氏菌与已知的血清型结果一致。结论ANI更适合沙门氏菌的种及亚种鉴定,ANI≥97%可作为沙门氏菌亚种的鉴定标准。16S rDNA技术对于沙门氏菌鉴定的敏感性尚有待提高。

Objective To evaluate the ability of average nucleotide identity(ANI)and 16S rDNA technology on the identification of Salmonella.Methods The genomes and corresponding serovars of global Salmonella were downloaded in batch from the GenBank database.The classical strains of Salmonella were used as typing strains.The ANI analysis was conducted by the fastANI software according to the silent parameters.The species and serovars of Salmonella were identified by their 16S rDNA using the online software SpeciesFinder.Results Among the downloaded 2306 genomes,1767 strains of Salmonella had 178 serovars,with 323 strains(18.3%)of Salmonella Typhimurium and 300 strains(17.0%)of Salmonella Enteritidis being the most common.The ANI analysis showed that with a 95%threshold,only 30 strains(1.3%)of Salmonella were assigned to a specific subspecies,while the remaining 2276 strains(98.7%)of Salmonella could be assigned to 2-5 subspecies.When the threshold was 97%,all 2306 strains(100%)of Salmonella could be assigned to a specific subspecies.Based on the analysis of 16S rDNA,only 1072 strains(46.5%)of Salmonella were identified,of which 95.2%(1021/1072)of Salmonella subspecies were completely consistent with the results of ANI(≥97%)analysis.Only 2.4%(19/784)of Salmonella strains showed consistent results with known serovars.Conclusion ANI is more suitable for the identification of Salmonella species and subspecies,and ANI≥97%can be used as the identification standard for Salmonella subspecies.The sensitivity of 16S rDNA for the identification of Salmonella still needs to be improved.