Comparative analysis on the identification of global Salmonella based on average nucleotide identity and 16S rDNA technology
10.13602/j.cnki.jcls.2024.05.10
- VernacularTitle: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
- Author:
Miaomiao HUA
1
;
Xiaoli CAO
;
Jincao HU
;
Han SHEN
Author Information
1. 江苏大学医学院附属鼓楼医院检验科,南京 210008
- Keywords:
Salmonella;
identification;
subspecies;
serovar;
average nucleotide identity;
16S rDNA
- From:
Chinese Journal of Clinical Laboratory Science
2024;42(5):363-369
- CountryChina
- Language:Chinese
-
Abstract:
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 2 306 genomes,1 767 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 2 276 strains(98.7%)of Salmonella could be assigned to 2-5 subspecies.When the threshold was 97%,all 2 306 strains(100%)of Salmonella could be assigned to a specific subspecies.Based on the analysis of 16S rDNA,only 1 072 strains(46.5%)of Salmonella were identified,of which 95.2%(1 021/1 072)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.
