Streptococcus suis serotype 9: a rising threat with potential meningitis-inducing capability, population structure, virulence genes, and antimicrobial resistance

Abstract

Streptococcus suis (S. suis) is the principal etiological agent of swine streptococcosis and is an emerging zoonotic pathogen. In recent years, the prevalence of S. suis serotype 9 (SS9) has transitioned from primarily subclinical colonization to invasive disease, accompanied by a continuous increase in isolation rates across multiple countries. However, compared with that of serotype 2 (SS2), our understanding of SS9 remains markedly limited. In this study, we analyzed 7,913 S. suis isolates, among which SS9 was the second most prevalent serotype, accounting for 9.12% (722/7,913), followed by SS2 at 26.9% (2,132/7,913). We also isolated a highly virulent SS9 meningitis-associated strain and performed a comprehensive genomic analysis of 722 SS9 isolates. Population structure analysis revealed substantial genetic diversity within SS9, comprising 168 sequence types (STs) and 23 CCs, with ST16 representing the predominant lineage. The predominance of isolates from the brain and cerebrospinal fluid (37.89%), together with the lack of source-specific phylogenetic clustering, suggests a potential association of SS9 with central nervous system-related infection, particularly meningitis. Bioinformatics analysis revealed significant differences in the distribution of 17 virulence genes between brain-associated and nonbrain-associated isolates, indicating a potential association between these genes and meningitis. The most common antimicrobial resistance genes were tet(O) (54.29%) and erm(B) (62.05%), with 36.98% of the strains carrying both resistance to tetracycline and resistance to MLS_B antibiotics. This study was designed to investigate whether the meningitis-associated pathogenicity of SS9 is related to the enrichment of specific virulence determinants and multidrug resistance-associated genomic features, thereby enhancing our understanding of the pathogenicity and resistance of SS9 and providing important data for improving disease control strategies and public health preparedness.

Keywords

Streptococcus suis serotype 9 / Meningitis / Population structure / Virulence genes / Antimicrobial resistance genes

References

[1] Aarestrup FM, Jorsal SE, Jensen NE. Serological characterization and antimicrobial susceptibility of Streptococcus suis isolates from diagnostic samples in Denmark during 1995 and 1996. Veterinary Microbiology, 1998, 60(1): 59-66.

[2] Albert E, Kis IE, Kiss K, K-Jánosi K, Révész T, Biksi I. Serotype distribution and antimicrobial susceptibility of Streptococcus suis isolates from porcine diagnostic samples in Hungary, 2020-2023. Porcine Health Management, 2025, 11(1. ArticleID: ARTN 3

[3] Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pangenome-wide association studies with Scoary (vol 17, 238, 2016). Genome Biology, 2016, 17. ArticleID: 262

[4] Cucco L, Paniccià M, Massacci FR, Morelli A, Ancora M, Mangone I, Di Pasquale A, Luppi A, Vio D, Cammà C, et al.. New sequence types and antimicrobial drug-resistant strains of Streptococcus suis in diseased pigs, Italy, 2017-2019. Emerging Infectious Diseases, 2022, 28(1): 139-147.

[5] Dando SJ, Mackay-Sim A, Norton R, Currie BJ, St John JA, Ekberg JaK, Batzloff M, Ulett GC, Beacham IR. Pathogens penetrating the central nervous system: Infection pathways and the cellular and molecular mechanisms of invasion. Clinical Microbiology Reviews, 2014, 27(4): 691-726.

[6] Dominguez-Punaro MC, Segura M, Plante MM, Lacouture S, Rivest S, Gottschalk M. Streptococcus suis serotype 2, an important swine and human pathogen, induces strong systemic and cerebral inflammatory responses in a mouse model of infection. The Journal of Immunology, 2007, 179(3): 1842-1854.

[7] Dutkiewicz J, Zajac V, Sroka J, Wasinski B, Cisak E, Sawczyn A, Kloc A, Wójcik-Fatla A. Streptococcus suis: A re-emerging pathogen associated with occupational exposure to pigs or pork products. Part II - Pathogenesis. Ann Agr Env Med, 2018, 25(1): 186-203.

[8] Fittipaldi N, Takamatsu D, Domínguez-Punaro MD, Lecours MP, Montpetit D, Osaki M, Sekizaki T, Gottschalk M. Mutations in the gene encoding the ancillary pilin subunit of the Streptococcus suis srtF cluster result in pili formed by the major subunit only. PLoS ONE, 2010, 5(1. ArticleID: ARTN e8426

[9] Goyette-Desjardins G, Auger JP, Xu J, Segura M, Gottschalk M. Streptococcus suis, an important pig pathogen and emerging zoonotic agent-An update on the worldwide distribution based on serotyping and sequence typing. Emerg Microbes Infec, 2014, 3. ArticleID: e45

[10] Huang JH, Liu X, Chen H, Chen L, Gao XP, Pan ZH, Wang J, Lu CP, Yao HC, Wang LP, et al.. Identification of six novel capsular polysaccharide loci (NCL) from Streptococcus suis multidrug resistant nontypeable strains and the pathogenic characteristic of strains carrying new NCLs. Transboundary and Emerging Diseases, 2019, 66(2): 995-1003.

[11] Ji, L.Y., Chen, Z.G., Li, F., Hu, Q.H., Xu, L.C., Duan, X.K., Wu, H.G., Xu, S.Q., Chen, Q.C., Wu, S., et al., 2023. Epidemiological and genomic analyses of Streptococcus suis human isolates of between 2005 and 2021 in Shenzhen, China. Front Microbiol 14. ARTN 1118056 https://doi.org/10.3389/fmicb.2023.1118056.

[12] Jiang F, Guo JJ, Cheng C, Gu B. Human infection caused by Streptococcus suis serotype 2 in China: Report of two cases and epidemic distribution based on sequence type. BMC Infectious Diseases, 2020.

[13] Kataoka Y, Sugimoto C, Nakazawa M, Morozumi T, Kashiwazaki M. The epidemiological studies of Streptococcus suis infections in Japan from 1987 to 1991.. Journal of Veterinary Medical Science, 1993, 55(4): 623-626.

[14] Kerdsin A, Dejsirilert S, Puangpatra P, Sripakdee S, Chumla K, Boonkerd N, Polwichai P, Tanimura S, Takeuchi D, Nakayama T, et al.. Genotypic profile of Streptococcus suis serotype 2 and clinical features of infection in humans, Thailand. Emerging Infectious Diseases, 2011, 17(5): 835-842.

[15] Kerdsin A, Hatrongjit R, Gottschalk M, Takeuchi D, Hamada S, Akeda Y, Oishi K. Emergence of Streptococcus suis serotype 9 infection in humans. Journal of Microbiology and Immunology, 2017, 50(4): 545-546.

[16] Lachance C, Gottschalk M, Gerber PP, Lemire P, Xu JG, Segura M. Exacerbated Type II Interferon Response drives hypervirulence and toxic shock by an emergent epidemic strain of Streptococcus suis. Infection and Immunity, 2013, 81(6): 1928-1939.

[17] Lacouture S, Olivera YR, Mariela S, Gottschalk M. Distribution and characterization of Streptococcus suis serotypes isolated from January 2015 to June 2020 from diseased pigs in Quebec, Canada. Canadian Journal of Veterinary Research, 2022, 86(1): 78-82

[18] Lai LY, Dai J, Tang HY, Zhang SM, Wu CY, Qiu WC, Lu CP, Yao HC, Fan HJ, Wu ZF. Streptococcus suis serotype 9 strain GZ0565 contains a type VII secretion system putative substrate EsxA that contributes to bacterial virulence and a vanZ-like gene that confers resistance to teicoplanin and dalbavancin in Streptococcus agalactiae. Veterinary Microbiology, 2017, 205: 26-33.

[19] Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J. pyseer: A comprehensive tool for microbial pangenome-wide association studies. Bioinformatics, 2018, 34(24): 4310-4312.

[20] Li Q, Liu HZ, Du DC, Yu YF, Ma CF, Jiao FF, Yao HC, Lu CP, Zhang W. Identification of novel Laminin- and Fibronectin-binding proteins by Far-Western Blot: Capturing the adhesins of Streptococcus suis type 2. Frontiers in Cellular and Infection Microbiology, 2015, 5. ArticleID: 82

[21] Li K, Lacouture S, Lewandowski E, Thibault E, Gantelet H, Gottschalk M, Fittipaldi N. Molecular characterization of Streptococcus suis isolates recovered from diseased pigs in Europe. Veterinary Research, 2024, 55(1. ArticleID: ARTN 117

[22] Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li GW, et al.. The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs. Proceedings of the National Academy of Sciences, 2023, 120(47. ArticleID: ARTN e2307773120

[23] Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics, 2015, 31(22): 3691-3693.

[24] Palmieri C, Varaldo PE, Facinelli B. Streptococcus suis, an emerging drug-resistant animal and human pathogen. Frontiers in Microbiology, 2011, 2. ArticleID: 235

[25] Price MN, Dehal PS, Arkin AP. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS ONE, 2010, 5(3. ArticleID: ARTN e9490

[26] Qian YY, Zhang YH, Yu YF, Li Q, Guo GL, Fu Y, Yao HC, Lu CP, Zhang W. SBP1 is an adhesion-associated factor without the involvement of virulence in Streptococcus suis serotype 2. Microbial Pathogenesis, 2018, 122: 90-97.

[27] Rayanakorn A, Ademi Z, Liew D, Lee LH. Burden of disease and productivity impact of Streptococcus suis infection in Thailand. Plos Neglect Trop D, 2021, 15(1. ArticleID: ARTN e0008985

[28] Roodsant TJ, Van Der Putten BCL, Tamminga SM, Schultsz C, Van Der Ark KCH. Identification of Streptococcus suis putative zoonotic virulence factors: A systematic review and genomic meta-analysis. Virulence, 2021, 12(1): 2787-2797.

[29] Scherrer S, Rosato G, Serrano NS, Stevens MJA, Rademacher F, Schrenzel J, Gottschalk M, Stephan R, Peterhans S. Population structure, genetic diversity and pathotypes of Streptococcus suis isolated during the last 13 years from diseased pigs in Switzerland. Veterinary Research, 2020, 51(1. ArticleID: ARTN 85

[30] Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 2014, 30(14): 2068-2069.

[31] Segers RPaM, Kenter T, De Haan LaM, Jacobs AaC. Characterization of the gene encoding Suilysin from Streptococcus suis and expression in field strains. FEMS Microbiology Letters, 1998, 167(2): 255-261.

[32] Segura M. Streptococcus suis research: Progress and challenges. Pathogens, 2020, 9(9. ArticleID: ARTN 707

[33] Segura M, Fittipaldi N, Calzas C, Gottschalk M. Critical Streptococcus suis virulence factors: Are they all truly critical?. Trends in Microbiology, 2017, 25(7): 586-U294.

[34] Spoerry C, Seele J, Valentin-Weigand P, Baums CG, Von Pawel-Rammingen U. Identification and characterization of IgdE, a novel IgG-degrading protease of Streptococcus suis with unique specificity for porcine IgG. Journal of Biological Chemistry, 2016, 291(15): 7915-7925.

[35] Sui YT, Chen Y, Lv QY, Zheng YL, Kong DC, Jiang H, Huang WH, Ren YH, Liu P, Jiang YQ. Suilyin disrupts the Blood‒Brain Barrier by activating Group III Secretory Phospholipase A2. Life, 2022, 12(6. ArticleID: ARTN 919

[36] Tan C, Liu ML, Li JQ, Jin ML, Bei WC, Chen HC. SsPep contributes to the virulence of Streptococcus suis. Microbial Pathogenesis, 2011, 51(5): 319-324.

[37] Uruén C, Fernandez A, Arnal JL, Del Pozo M, Amoribieta MC, De Blas I, Jurado P, Calvo JH, Gottschalk M, González-Vázquez LD, et al.. Genomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits. Veterinary Research, 2024, 55(1. ArticleID: ARTN 11

[38] Wang J, Dong RR, Zou P, Chen YJ, Li N, Wang Y, Zhang T, Pan XZ. Identification of a novel linear B-cell epitope on the Sao protein of Streptococcus suis serotype 2. Frontiers in Immunology, 2020, 11. ArticleID: 1492

[39] Wang XM, Sun JJ, Bian C, Wang JP, Liang ZJ, Shen YL, Yao HC, Huang JH, Wang LP, Zheng H, et al.. The population structure, antimicrobial resistance, and pathogenicity of Streptococcus suis cps31. Veterinary Microbiology, 2021, 259. ArticleID: 109149

[40] Wertheim HFL, Nguyen HN, Taylor W, Lien TTM, Ngo HT, Nguyen TQ, Nguyen BNT, Nguyen HH, Nguyen HM, Nguyen CT, et al.. Streptococcus suis, an important cause of adult bacterial meningitis in Northern Vietnam. PLoS ONE, 2009, 4(6. ArticleID: ARTN e5973

[41] Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Computational Biology, 2017, 13(6. ArticleID: ARTN e1005595

[42] Ye CY, Bai XM, Zhang J, Jing HQ, Zheng H, Du HM, Cui ZG, Zhang SY, Jin D, Xu YM, et al.. Spread of Streptococcus suis sequence type 7, China. Emerging Infectious Diseases, 2008, 14(5): 787-791.

[43] Yu YF, Qian YY, Du DC, Xu CY, Dai C, Li Q, Liu HZ, Shao J, Wu ZF, Zhang W. SBP2 plays an important role in the virulence changes of different artificial mutants of. Molecular BioSystems, 2016, 12(6): 1948-1962.

[44] Zhang AD, Yang M, Hu P, Wu JY, Chen B, Hua YF, Yu J, Chen HC, Xiao JF, Jin ML. Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics, 2011, 12. ArticleID: 523

[45] Zheng H, Du PC, Qiu XT, Kerdsin A, Roy D, Bai XM, Xu JG, Vela AI, Gottschalk M. Genomic comparisons of serotype 9 strains recovered from diseased pigs in Spain and Canada (vol 49, 1, 2018). Veterinary Research, 2019, 50(1. ArticleID: ARTN 62

[46] Zhu JL, Wang JP, Kang WM, Zhang XY, Kerdsin A, Yao HC, Zheng H, Wu ZF. Streptococcus suis serotype 4: A population with the potential pathogenicity in humans and pigs. Emerg Microbes Infec, 2024, 13(1. ArticleID: Artn 2352435

Funding

National Natural Science Foundation of China(32573362)

RIGHTS & PERMISSIONS

The Author(s)