{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:18:17Z","timestamp":1789172297518,"version":"build-2803163510"},"reference-count":40,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,4,18]],"date-time":"2025-04-18T00:00:00Z","timestamp":1744934400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["32200151"],"award-info":[{"award-number":["32200151"]}]},{"name":"National Natural Science Foundation of China","award":["ZR2022QC043"],"award-info":[{"award-number":["ZR2022QC043"]}]},{"name":"National Natural Science Foundation of China","award":["SDAIT-08-09"],"award-info":[{"award-number":["SDAIT-08-09"]}]},{"name":"National Natural Science Foundation of China","award":["665-1122009"],"award-info":[{"award-number":["665-1122009"]}]},{"name":"Natural Science Foundation of Shandong Province","award":["32200151"],"award-info":[{"award-number":["32200151"]}]},{"name":"Natural Science Foundation of Shandong Province","award":["ZR2022QC043"],"award-info":[{"award-number":["ZR2022QC043"]}]},{"name":"Natural Science Foundation of Shandong Province","award":["SDAIT-08-09"],"award-info":[{"award-number":["SDAIT-08-09"]}]},{"name":"Natural Science Foundation of Shandong Province","award":["665-1122009"],"award-info":[{"award-number":["665-1122009"]}]},{"name":"Position for the Production and Environmental Control of Innovation Team in Pig Industry of Modern Agricultural Technology System in Shandong Province","award":["32200151"],"award-info":[{"award-number":["32200151"]}]},{"name":"Position for the Production and Environmental Control of Innovation Team in Pig Industry of Modern Agricultural Technology System in Shandong Province","award":["ZR2022QC043"],"award-info":[{"award-number":["ZR2022QC043"]}]},{"name":"Position for the Production and Environmental Control of Innovation Team in Pig Industry of Modern Agricultural Technology System in Shandong Province","award":["SDAIT-08-09"],"award-info":[{"award-number":["SDAIT-08-09"]}]},{"name":"Position for the Production and Environmental Control of Innovation Team in Pig Industry of Modern Agricultural Technology System in Shandong Province","award":["665-1122009"],"award-info":[{"award-number":["665-1122009"]}]},{"name":"Research Foundation for Distinguished Scholars of Qingdao Agricultural University","award":["32200151"],"award-info":[{"award-number":["32200151"]}]},{"name":"Research Foundation for Distinguished Scholars of Qingdao Agricultural University","award":["ZR2022QC043"],"award-info":[{"award-number":["ZR2022QC043"]}]},{"name":"Research Foundation for Distinguished Scholars of Qingdao Agricultural University","award":["SDAIT-08-09"],"award-info":[{"award-number":["SDAIT-08-09"]}]},{"name":"Research Foundation for Distinguished Scholars of Qingdao Agricultural University","award":["665-1122009"],"award-info":[{"award-number":["665-1122009"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>(1) Background: S. parasuis is a potential opportunistic zoonotic pathogen that can infect pigs, cattle, and humans, composed of former members of S. suis serotypes 20, 22, and 26. In recent years, unclassified serotypes and a serotype 11 S. parasuis have been discovered. (2) Methods: We characterized two S. parasuis strains (FZ1 and FZ2) isolated from brain samples of paralyzed pigs and examined evolutionary divergence among 22 available S. parasuis and 8 serotype 2 S. suis genomes through whole-genome sequencing and comparative genomic analysis. We compared virulence genes (VGs) and antibiotic resistance genes (ARGs) and analyzed mobile genetic elements (MGEs) in FZ1 and FZ2. (3) Results: Comparative genomics revealed that srtC, ctpV, and sugC may represent key virulence determinants in S. parasuis, although their pathogenic potential appears attenuated compared to serotype 2 S. suis. In addition, S. parasuis exhibited primary resistance to aminoglycosides, macrolides, tetracyclines, and oxazolidinones, while demonstrating heightened susceptibility to oxazolidinone-class antibiotics. Moreover, we found an important association between MGEs and antibiotic resistance in S. parasuis FZ1 and FZ2. (4) Conclusions: This study provides new insights into the genomic and evolutionary characteristics of S. parasuis and provides a new basis for the study of bacterial pathogenesis and drug resistance in the future.<\/jats:p>","DOI":"10.3390\/pathogens14040395","type":"journal-article","created":{"date-parts":[[2025,4,18]],"date-time":"2025-04-18T05:11:16Z","timestamp":1744953076000},"page":"395","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic Characterization of Potential Opportunistic Zoonotic Streptococcus parasuis Isolated in China"],"prefix":"10.3390","volume":"14","author":[{"given":"Gang","family":"Liu","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikang","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kang","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianwen","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juyuan","family":"Hao","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Kong","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajie","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zicheng","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Li","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianjie","family":"Han","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,18]]},"reference":[{"key":"ref_1","first-page":"e45","article-title":"Streptococcus suis, an important pig pathogen and emerging zoonotic agent-an update on the worldwide distribution based on serotyping and sequence typing","volume":"3","author":"Auger","year":"2014","journal-title":"Emerg. Microbes Infect."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1111\/tbed.13725","article-title":"Pan-genome analysis of Streptococcus suis serotype 2 revealed genomic diversity among strains of different virulence","volume":"68","author":"Guo","year":"2021","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Wang, J.P., Yi, X.L., Liang, P.J., Tao, Y.M.H., Wang, Y., Jin, D., Luo, B., Yang, J., and Zheng, H. (2021). Investigation of the Genomic and Pathogenic Features of the Potentially Zoonotic. Pathogens, 10.","DOI":"10.3390\/pathogens10070834"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1292\/jvms.18-0083","article-title":"Development of PCR for identifying Streptococcus parasuis, a close relative of Streptococcus suis","volume":"80","author":"Yamada","year":"2018","journal-title":"J. Vet. Med. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1099\/ijs.0.067116-0","article-title":"Reappraisal of the taxonomy of Streptococcus suis serotypes 20, 22 and 26: Streptococcus parasuis sp. nov","volume":"65","author":"Nomoto","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.vetmic.2008.12.015","article-title":"Characterization of Streptococcus suis isolates from the diseased pigs in China between 2003 and 2007","volume":"137","author":"Wei","year":"2009","journal-title":"Vet. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/j.vetmic.2012.10.028","article-title":"Characterization of Streptococcus suis isolates recovered between 2008 and 2011 from diseased pigs in Qu\u00e9bec, Canada","volume":"162","author":"Gottschalk","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1128\/jcm.27.12.2633-2636.1989","article-title":"Description of 14 new capsular types of Streptococcus suis","volume":"27","author":"Gottschalk","year":"1989","journal-title":"J. Clin. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Qi, K., Yi, X., Wang, M., Wang, J., Sun, H., Liang, P., Xu, J., and Zheng, H. (2023). Streptococcus parasuis, an Emerging Zoonotic Pathogen, Possesses the Capacity to Induce Cerebral Inflammatory Responses. Pathogens, 12.","DOI":"10.3390\/pathogens12040600"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Han, N., Li, J., Wan, P., Pan, Y., Xu, T., Xiong, W., and Zeng, Z. (2023). Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine. Antibiotics, 12.","DOI":"10.3390\/antibiotics12050825"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3233","DOI":"10.1128\/aem.63.8.3233-3241.1997","article-title":"Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients","volume":"63","author":"Heuer","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13742-015-0069-2","article-title":"Erratum: SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler","volume":"4","author":"Luo","year":"2015","journal-title":"GigaScience"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: An information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: Consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"9077","DOI":"10.1093\/nar\/gkab688","article-title":"tRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes","volume":"49","author":"Chan","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An improved algorithm and software for calculating average nucleotide identity","volume":"66","author":"Lee","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: A comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: Faster than PHASTER, better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"D732","DOI":"10.1093\/nar\/gkad935","article-title":"ICEberg 3.0: Functional categorization and analysis of the integrative and conjugative elements in bacteria","volume":"52","author":"Wang","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Chaudhari, N.M., Gupta, V.K., and Dutta, C. (2016). BPGA\u2014An ultra-fast pan-genome analysis pipeline. Sci. Rep., 6.","DOI":"10.1038\/srep24373"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Darling, A.E., Mau, B., and Perna, N.T. (2010). progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0011147"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Guo, G., Wang, Z., Li, Q., Yu, Y., Li, Y., Tan, Z., and Zhang, W. (2022). Genomic characterization of Streptococcus parasuis, a close relative of Streptococcus suis and also a potential opportunistic zoonotic pathogen. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08710-6"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/j.1365-2958.2008.06396.x","article-title":"Sortase-mediated assembly and surface topology of adhesive pneumococcal pili","volume":"70","author":"Nelson","year":"2008","journal-title":"Mol. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1111\/j.1365-2958.2010.07273.x","article-title":"CtpV: A putative copper exporter required for full virulence of Mycobacterium tuberculosis","volume":"77","author":"Ward","year":"2010","journal-title":"Mol. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"21761","DOI":"10.1073\/pnas.1014642108","article-title":"Trehalose-recycling ABC transporter LpqY-SugA-SugB-SugC is essential for virulence of Mycobacterium tuberculosis","volume":"107","author":"Kalscheuer","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Liu, N., Liu, D.P., Li, K.X., Hu, S.N., and He, Z.L. (2022). Pan-Genome Analysis of Reveals Key Factors Influencing Genomic Plasticity. Microbiol. Spectr., 10.","DOI":"10.1128\/spectrum.03117-22"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"West, P.T., Chanin, R.B., and Bhatt, A.S. (2022). From genome structure to function: Insights into structural variation in microbiology. Curr. Opin. Microbiol., 69.","DOI":"10.1016\/j.mib.2022.102192"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/jac\/dkab297","article-title":"Identification of a Streptococcus parasuis isolate co-harbouring the oxazolidinone resistance genes cfr(D) and optrA","volume":"76","author":"Zhu","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"110567","DOI":"10.1016\/j.ecoenv.2020.110567","article-title":"Family livestock waste: An ignored pollutant resource of antibiotic resistance genes","volume":"197","author":"Gu","year":"2020","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s41545-020-0051-0","article-title":"Antibiotic resistance genes from livestock waste: Occurrence, dissemination, and treatment","volume":"3","author":"He","year":"2020","journal-title":"Npj Clean. Water"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/jobm.202100201","article-title":"Antibiotic resistance genes in bacteria: Occurrence, spread, and control","volume":"61","author":"Jian","year":"2021","journal-title":"J. Basic. Microb."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Huang, J.H., Ma, J.L., Shang, K.X., Hu, X., Liang, Y., Li, D.W., Wu, Z.W., Dai, L., Chen, L., and Wang, L.P. (2016). Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in: A Probable Mobile Genetic Elements Reservoir for Other Streptococci. Front. Cell. Infect. Microbiol., 6.","DOI":"10.3389\/fcimb.2016.00118"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/4\/395\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:17:06Z","timestamp":1760030226000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/4\/395"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,18]]},"references-count":40,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["pathogens14040395"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14040395","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,18]]}}}