A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city

Yi，Qiuwei1; Li，Liqiang2,3; Wang，Heping1; Zhu，Chunqing1; Chen，Yunsheng1; Yang，Liang4; Zheng，Yuejie1; Yang，Yonghong1; Bao，Yanmin1

2024-03-01

10.1016/j.jgar.2024.01.016

Journal of Global Antimicrobial Resistance   影响因子和分区

2213-7165

2213-7173

Objectives: We characterized the population structure and features of clinical Streptococcus pneumoniae isolates associated with invasive pneumococcal disease (IPD) from 2009 to 2017 in a Chinese metropolitan city using a whole-genome sequencing approach. Methods: Seventy-nine pneumococcal strains, including 60 serogroup-19 strains from children enduring IPD from a paediatric hospital in Shenzhen, were subjected to whole-genome sequencing. Population structure was characterized through phylogenetic analysis, sequence typing, serotyping, virulence factor, and antimicrobial drug resistance (AMR) gene profiling, combining the publicly available related WGS data. Clinical demography and antibiotic susceptibility profiles were compared among different populations to emphasize the higher-risk populations. Genetic regions associated with AMR gene mobilization were identified through comparative genomics. Results: These IPD strains mainly belonged to clonal complex 320 (CC320) and were composed of serotypes 19A and 19F. In addition to sporadic possible importation-related isolates (ST320), we identified an independent clade, CC320_SZpop (ST271), that predominantly circulated in Shenzhen and possibly expanded its range. Clinical features and antibiotic susceptibility analysis revealed that CC320_SZpop might manifest much higher pathogenicity and tolerance to β-lactams. Specific virulence factors in Shenzhen isolates of CC320_SZpop were identified. Furthermore, an ca. 40 kb hotspot genomic region enduring frequent recombination was identified, possibly associated with the divergence of S. pneumoniae strains. Conclusion: A novel pneumococcal clade, CC320_SZpop, circulating in Shenzhen and other regions in China, possibly under expansion, was found and deserves more study and surveillance. Our study also emphasizes the importance of continuous genomic surveillance of clinical S. pneumoniae isolates, especially IPD isolates.

CC320 Invasive pneumococcal disease Mobile genetic elements Population genomics Streptococcus pneumoniae

SCI

英语

通讯

2-s2.0-85186522519

Scopus

1.Shenzhen Children's Hospital,Guangdong,China
2.National Clinical Research Center for Infectious Diseases,The Third People's Hospital of Shenzhen,Southern University of Science and Technology,Guangdong Provincial Clinical Research Center for Infectious Diseases (Tuberculosis),Shenzhen Clinical Research Center for Tuberculosis,Shenzhen,China
3.Department of Clinical Laboratory,The Third People's Hospital of Shenzhen,Southern University of Science and Technology,Shenzhen,China
4.Southern University of Science of and Technology,Guangdong,China

Yi，Qiuwei,Li，Liqiang,Wang，Heping,et al. A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city[J]. Journal of Global Antimicrobial Resistance,2024,36:379-388.

Yi，Qiuwei.,Li，Liqiang.,Wang，Heping.,Zhu，Chunqing.,Chen，Yunsheng.,...&Bao，Yanmin.(2024).A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city.Journal of Global Antimicrobial Resistance,36,379-388.

Yi，Qiuwei,et al."A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city".Journal of Global Antimicrobial Resistance 36(2024):379-388.