Analysis of gene characteristics of Streptococcus pneumoniae based on whole-genome sequencing
10.3760/cma.j.cn112309-20240201-00045
- VernacularTitle:基于全基因组测序的肺炎链球菌基因特征分析
- Author:
Xufei ZHANG
1
;
Baohua HE
;
Zhaoyi JIA
;
Haixia ZHANG
;
Hongbin ZHANG
;
Yinqi SUN
;
Qi LI
Author Information
1. 华北理工大学公共卫生学院，唐山 063210
- Publication Type:Journal Article
- Keywords:
Streptococcus pneumoniae;
Whole-genome sequencing;
Virulence genes;
Drug resistance genes;
Multilocus sequence typing
- From:
Chinese Journal of Microbiology and Immunology
2024;44(12):1076-1083
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze 80 strains of Streptococcus pneumoniae by using whole-genome sequencing technology, including serotype characteristics, drug resistance genes, carriage of virulence genes, multilocus sequence typing (MLST), and relatedness between strains. Methods:Whole-genome sequencing was performed on Streptococcus pneumoniae. Serotypes, resistance genes, virulence genes, and sequence typing (ST) were analyzed in conjunction with the CARD database, the NCBI database, the VFDB database, and the PubMLST website. The strains were compared by using KSNP4 based on the analysis of single-nucleotide polymorphisms (SNPs). An evolutionary tree was constructed with the IQ-TREE software and beautified by using EvolView software. Results:Of all 80 Streptococcus pneumoniae strains, serotypes 19F, 19A, 14 and 23F were predominant, 30 strains were from cases of invasive pneumococcal disease (IPD) and 50 strains were from cases of non-invasive pneumococcal disease (NIPD). The virulence genes psaA, nanB, lytA, lytC, and ply were detected in all cases, while cps4 A, cps4 B, and hysA were detected in 98.75% of cases, and nanA was detected in 90.00%, rrgA and rrgB showed statistical differences between IPD and NIPD( P<0.05). The resistance genes patA, patB, tetM, pmrA, PBP1 b, RlmA( II), and ermB were detected in all cases, while PBP1 a was detected in 98.75% of cases. There was a statistically significant difference between IPD and NIPD for mefA and msrD( P<0.05). MLST analysis of 80 strains of bacteria showed that the ST types were mainly ST271, ST320, ST876, ST81, in which seven new ST types were emerged; the phylogenetic tree could be divided into three branches, The dominant ST types of the strains with serotypes 14, 23F, 19F, and 19A were ST876, ST81, ST271, and ST320, respectively. Conclusions:The study finds that the main serotypes of the 80 strains are 19F, 19A, 14 and 23F. The strains have more varieties of virulence genes, resistance genes and high carriage of some genes; rrgA, rrgB and mefA, msrD differ between IPD and NIPD. ST-types are characterised by diversity and new ST-types are constantly emerged. A correlation exists between serotypes and systemic evolution in the phylogenetic analyses, with each serotype contains its own dominant ST-types.
