Epidemiological and genomic analyses of human isolates of Streptococcus suis between 2005 and 2021 in Shenzhen, China

Liyin Ji; Zhigao Chen; Fan Li; Qinghua Hu; Liangcai Xu; Xiangke Duan; Hanguang Wu; Shiqin Xu; Qiongcheng Chen; Shuang Wu; Shuxiang Qiu; Huiqun Lu; Min Jiang; Rui Cai; Yaqun Qiu; Yinghui Li; Xiaolu Shi

doi:10.3389/fmicb.2023.1118056

Epidemiological and genomic analyses of human isolates of Streptococcus suis between 2005 and 2021 in Shenzhen, China

Front Microbiol. 2023 Mar 27:14:1118056. doi: 10.3389/fmicb.2023.1118056. eCollection 2023.

Authors

Liyin Ji¹, Zhigao Chen², Fan Li³, Qinghua Hu², Liangcai Xu⁴, Xiangke Duan², Hanguang Wu³, Shiqin Xu¹, Qiongcheng Chen², Shuang Wu², Shuxiang Qiu⁵, Huiqun Lu⁵, Min Jiang², Rui Cai², Yaqun Qiu², Yinghui Li², Xiaolu Shi^{1

2}

Affiliations

¹ School of Public Health, Shanxi Medical University, Taiyuan, China.
² Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
³ Shenzhen Institute of Quality and Safety Inspection and Research, Shenzhen, China.
⁴ Futian District Center for Disease Control and Prevention, Shenzhen, China.
⁵ School of Public Health, University of South China, Hengyang, China.

Abstract

Streptococcus suis (S. suis) is an important food-borne zoonotic pathogen that causes swine streptococcosis, which threatens human health and brings economic loss to the swine industry. Three-quarters of human S. suis infections are caused by serotype 2. A retrospective analysis of human S. suis cases in Shenzhen, a megacity in China, with high pork consumption, between 2005 and 2021 was conducted to understand its genomic epidemiology, pathogen virulence, and drug resistance characteristics. The epidemiological investigation showed that human cases of S. suis in Shenzhen were mainly associated with people who had been in close contact with raw pork or other swine products. Whole-genome sequence analysis showed that 33 human isolates in Shenzhen were dominated by serotype 2 (75.76%), followed by serotype 14 (24.24%), and the most prevalent sequence types (STs) were ST7 (48.48%) and ST1 (39.40%). ST242 (9.09%) and ST25 (3.03%), which were rarely reported, were also found. Phylogenetic analysis showed that the Shenzhen human isolates had close genetic relatedness to isolates from Guangxi (China), Sichuan (China), and Vietnam. We found a new 82 KB pathogenicity island (PAI) in the serotype 2 isolate that may play a role in sepsis. Similarly, a serotype 14 isolate, containing 78 KB PAI, was isolated from a patient presenting with streptococcal toxic shock syndrome (STSLS) who subsequently died. Multi-drug resistance (MDR) was high in human isolates of S. suis from Shenzhen. Most human isolates were resistant to tetracycline, streptomycin, erythromycin, and clindamycin, and 13 isolates had intermediate resistance to penicillin. In conclusion, swine importation from Guangxi, Sichuan, and Vietnam should be more closely monitored, and the use of antibiotics limited to reduce the potential for antimicrobial resistance (AMR).

Keywords: SNP-based phylogeny; Streptococcus suis; antimicrobial resistance; epidemiology; human; pathogenicity island.