Comparing Genomic Characteristics of Streptococcus pyogenes Associated with Invasiveness over a 20-year Period in Korea
2
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
Background: Few studies have investigated the invasiveness of Streptococcus pyogenes based on whole-genome sequencing (WGS). Using WGS, we determined the genomic features associated with invasiveness of S. pyogenes strains in Korea. Methods: Forty-five S. pyogenes strains from 1997, 2006, and 2017, including common emm types, were selected from the repository at Gyeongsang National University Hospital in Korea. In addition, 48 S. pyogenes strains were randomly selected depending on their invasiveness between 1997 and 2017 to evaluate the genetic evolution and the associations between invasiveness and genetic profiles. Using WGS datasets, we conducted virulence-associated DNA sequence determination, emm genotyping, multi-locus sequence typing (MLST), and superantigen gene profiling. Results: In total, 87 strains were included in this study. There were no significant differences in the genomic features throughout the study periods. Four genes, csn1, ispE, nisK, and citC, were detected only in invasive strains. There was a significant association between invasiveness and emm cluster type A-C3, including, emm1.0, emm1.18, emm1.3, and emm1.76 (P<0.05). The predominant emm1 lineage belonged to ST28. There were no associations between invasiveness and superantigen gene profiles. Conclusions: This is the first study using WGS datasets of S. pyogenes strains collected between 1997 and 2017 in Korea. Streptococcal invasiveness is associated with the presence of csn1, ispE, nisK, and citC. The emm1 lineage and ST28 clone are explicitly associated with invasiveness, whereas genomic features remained stable over the 20-year period.
Abstract
Background: Few studies have investigated the invasiveness of Streptococcus pyogenes based on whole-genome sequencing (WGS). Using WGS, we determined the genomic features associated with invasiveness of S. pyogenes strains in Korea. Methods: Forty-five S. pyogenes strains from 1997, 2006, and 2017, including common emm types, were selected from the repository at Gyeongsang National University Hospital in Korea. In addition, 48 S. pyogenes strains were randomly selected depending on their invasiveness between 1997 and 2017 to evaluate the genetic evolution and the associations between invasiveness and genetic profiles. Using WGS datasets, we conducted virulence-associated DNA sequence determination, emm genotyping, multi-locus sequence typing (MLST), and superantigen gene profiling. Results: In total, 87 strains were included in this study. There were no significant differences in the genomic features throughout the study periods. Four genes, csn1, ispE, nisK, and citC, were detected only in invasive strains. There was a significant association between invasiveness and emm cluster type A-C3, including, emm1.0, emm1.18, emm1.3, and emm1.76 (P<0.05). The predominant emm1 lineage belonged to ST28. There were no associations between invasiveness and superantigen gene profiles. Conclusions: This is the first study using WGS datasets of S. pyogenes strains collected between 1997 and 2017 in Korea. Streptococcal invasiveness is associated with the presence of csn1, ispE, nisK, and citC. The emm1 lineage and ST28 clone are explicitly associated with invasiveness, whereas genomic features remained stable over the 20-year period.
참고문헌 (34)
- Stevens DL, "Severe group A streptococcal infections associated with a toxic shock-like syndrome and scarlet fever toxin A", N Engl J Med, 321, pp.1~7 (1989)
- Carapetis JR, "The global burden of group A streptococcal diseases", Lancet Infect Dis, 5, pp.685~694 (2005)
- Enright, "Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone", Infect Immun, 69, pp.2416~2427 (2001)
- Luca AV, "Pulsed field gel electrophoresis of group A streptococci", Methods Mol Biol, 1301, pp.129~138 (2015)
- Lewis T, "High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak", J Hosp Infect, 75, pp.37~41 (2010)
- Schuchat A, "Active bacterial core surveillance of the emerging infections program network", Emerg Infect Dis, 7, pp.92~99 (2001)
- Hyatt D, "Prodigal : prokaryotic gene recognition and translation initiation site identification", BMC Bioinformatics, 11, pp.1~11 (2010)
- Chun J, "Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae", Proc Natl Acad Sci U S A, 106, pp.15442~15447 (2009)
- Tanizawa Y, "DFAST : a flexible prokaryotic genome annotation pipeline for faster genome publication", Bioinformatics, 34, pp.1037~1039 (2018)
- Takashi Takahashi, "Epidemiological Study of Erythromycin-Resistant Streptococcus pyogenes From Korea and Japan by emm Genotyping and Multilocus Sequence Typing", Annals of Laboratory Medicine, 36(1), pp.9~14 (2016), 대한진단검사의학회
- 김선주, "Molecular Epidemiological Features and Antibiotic Susceptibility Patterns of Streptococcus dysgalactiae subsp. equisimilis Isolates from Korea and Japan", Annals of Laboratory Medicine, 38(3), pp.212~219 (2018), 대한진단검사의학회[DOI]
- Tamayo E, "Streptococcus pyogenes pneumonia in adults : clinical presentation and molecular characterization of isolates 2006-2015", PLoS One, 11, pp.e0152640~ (2016)
- Sakai T, "Pleural empyema and streptococcal toxic shock syndrome due to Streptococcus pyogenes in a healthy Spanish traveler in Japan", IDCases, 9, pp.85~88 (2017)
- Takashi Takahashi, "Clonal Distribution of Clindamycin-Resistant Erythromycin-Susceptible (CRES) <italic>Streptococcus agalactiae<", italic> in Korea Based on Whole Genome Sequences, 2020, pp.40(5), 370~381[DOI]
- Larsen MV, "Multilocus sequence typing of total-genome-sequenced bacteria", J Clin Microbiol, 50, pp.1355~1361 (2012)
- Nascimento M, "PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods", Bioinformatics, 33, pp.128~129 (2017)
- Steer AC, "Global emm type distribution of group A streptococci : systematic review and implications for vaccine development", Lancet Infect Dis, 9, pp.611~616 (2009)
- Luca-Harari B, "Clinical and microbiological characteristics of severe Streptococcus pyogenes disease in Europe", J Clin Microbiol, 47, pp.1155~1165 (2009)
- Ekelund K, "Variations in emm type among group A streptococcal isolates causing invasive or noninvasive infections in a nationwide study", J Clin Microbiol, 43, pp.3101~3109 (2005)
- Enright MC, "Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus", J Clin Microbiol, 38, pp.1008~1015 (2000)
- Feil EJ, "eBURST : inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data", J Bacteriol, 186, pp.1518~1530 (2004)
- Le Rhun A, "CRISPR-Cas in Streptococcus pyogenes", RNA Biol, 16, pp.380~389 (2019)
- Nozawa T, "CRISPR inhibition of prophage acquisition in Streptococcus pyogenes", PLoS One, 6, pp.e19543~ (2011)
- Heuston S, "Isoprenoid biosynthesis in bacterial pathogens", Microbiology(Reading), 158, pp.1389~1401 (2012)
- Voynova NE, "Staphylococcus aureus mevalonate kinase : isolation and characterization of an enzyme of the isoprenoid biosynthetic pathway", J Bacteriol, 186, pp.61~67 (2004)
- Bekal S, "Purification of Leuconostoc mesenteroides citrate lyase and cloning and characterization of the citCDEFG gene cluster", J Bacteriol, 180, pp.647~654 (1998)
- Kawada-Matsuo M, "Two-component systems involved in susceptibility to nisin A in Streptococcus pyogenes", Appl Environ Microbiol, 82, pp.5930~5939 (2016)
- Quadri LE, "Regulation of antimicrobial peptide production by autoinducer-mediated quorum sensing in lactic acid bacteria", Antonie Van Leeuwenhoek, 82, pp.133~145 (2002)
- Hu J, "Citrate lyase CitE in Mycobacterium tuberculosis contributes to mycobacterial survival under hypoxic conditions", PLoS One, 15, pp.e0230786~ (2020)
- Weeks CR, "Nucleotide sequence of the type A streptococcal exotoxin(erythrogenic toxin)gene from Streptococcus pyogenes bacteriophage T12", Infect Immun, 52, pp.144~150 (1986)
- Yu CE, "Molecular epidemiologic analysis of the type A streptococcal exotoxin(erythrogenic toxin)gene(speA)in clinical Streptococcus pyogenes strains", Infect Immun, 57, pp.3715~3719 (1989)
- Shibasaki T, "Microbial proline 4-hydroxylase screening and gene cloning", Appl Environ Microbiol, 65, pp.4028~4031 (1999)
- Mori H, "Detection of novel proline 3-hydroxylase activities in Streptomyces and Bacillus spp. by regio- and streospecific hydroxylation of L-proline", Appl Environ Microbiol, 62, pp.1903~1907 (1996)
- Park HJ, "How sequence populations persist inside bacterial genomes", Genetics, 217, pp.iyab027~ (2021)