Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis.
PopPUNK sequence clustering
Streptococcus mitis
multilocus sequence typing
population diversity
transmission
within-host diversity
Journal
Journal of clinical microbiology
ISSN: 1098-660X
Titre abrégé: J Clin Microbiol
Pays: United States
ID NLM: 7505564
Informations de publication
Date de publication:
26 01 2023
26 01 2023
Historique:
pubmed:
15
12
2022
medline:
31
1
2023
entrez:
14
12
2022
Statut:
ppublish
Résumé
Streptococcus mitis is a common oral commensal and an opportunistic pathogen that causes bacteremia and infective endocarditis; however, the species has received little attention compared to other pathogenic streptococcal species. Effective and easy-to-use molecular typing tools are essential for understanding bacterial population diversity and biology, but schemes specific for S. mitis are not currently available. We therefore developed a multilocus sequence typing (MLST) scheme and defined sequence clusters or lineages of S. mitis using a comprehensive global data set of 322 genomes (148 publicly available and 174 newly sequenced). We used internal 450-bp sequence fragments of seven housekeeping genes (
Identifiants
pubmed: 36515506
doi: 10.1128/jcm.00802-22
pmc: PMC9879099
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0080222Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Department of Health
ID : 16/136/46
Pays : United Kingdom
Organisme : Wellcome Trust (WT)
ID : 218205/Z/19/Z
Organisme : Department of Health
ID : NIHR200652
Pays : United Kingdom
Références
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Genome Res. 2019 Feb;29(2):304-316
pubmed: 30679308
Clin Diagn Lab Immunol. 2005 Oct;12(10):1184-90
pubmed: 16210481
J Dent. 2000 Jan;28(1):45-50
pubmed: 10666961
J Microbiol Methods. 2015 Jun;113:13-5
pubmed: 25818760
PLoS One. 2014 Aug 14;9(8):e104921
pubmed: 25122163
J Med Microbiol. 1995 Jan;42(1):67-72
pubmed: 7739028
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
PLoS Pathog. 2020 Dec 28;16(12):e1008686
pubmed: 33370399
J Clin Microbiol. 2007 Aug;45(8):2392-7
pubmed: 17553974
Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3140-5
pubmed: 9501229
Front Microbiol. 2021 Aug 02;12:687259
pubmed: 34408729
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
Infect Immun. 2001 Oct;69(10):6055-63
pubmed: 11553543
Genome Biol. 2021 Dec 21;22(1):349
pubmed: 34930397
Lancet Infect Dis. 2013 Feb;13(2):137-46
pubmed: 23158499
Infect Immun. 2000 Mar;68(3):1374-82
pubmed: 10678950
Int J Antimicrob Agents. 2014 Jun;43(6):558-62
pubmed: 24721231
Clin Diagn Lab Immunol. 1996 Sep;3(5):517-22
pubmed: 8877128
mBio. 2019 Sep 3;10(5):
pubmed: 31481387
mBio. 2014 Jul 22;5(4):e01490-14
pubmed: 25053789
J Clin Microbiol. 2004 Jun;42(6):2651-7
pubmed: 15184447
Mol Microbiol. 1999 May;32(3):459-70
pubmed: 10320570
Mol Biol Evol. 2013 May;30(5):1224-8
pubmed: 23408797
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Pediatr Infect Dis J. 2005 Jun;24(6):563-6
pubmed: 15933573
Diagn Microbiol Infect Dis. 2015 Apr;81(4):240-5
pubmed: 25616316
Circulation. 2020 Aug 25;142(8):720-730
pubmed: 32580572
Vaccine. 2013 Dec 17;32(1):165-79
pubmed: 24331112
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Microb Genom. 2016 Apr 29;2(4):e000056
pubmed: 28348851
Infect Immun. 2008 May;76(5):1889-96
pubmed: 18316382
Ann Med. 2000 Mar;32(2):107-12
pubmed: 10766401
J Antimicrob Chemother. 1997 Feb;39(2):135-40
pubmed: 9069532
Microbiology (Reading). 1998 Nov;144 ( Pt 11):3049-3060
pubmed: 9846740
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Emerg Infect Dis. 2014 May;20(5):762-71
pubmed: 24750901
Bioinformatics. 2009 Jan 1;25(1):119-20
pubmed: 18990721
J Antimicrob Chemother. 2004 Apr;53(4):631-4
pubmed: 15014065
Nucleic Acids Res. 2012 Aug;40(15):e115
pubmed: 22730293
Arch Intern Med. 2009 Mar 9;169(5):463-73
pubmed: 19273776
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14625-30
pubmed: 11724955
Sci Rep. 2019 Mar 1;9(1):3285
pubmed: 30824850
EBioMedicine. 2019 May;43:338-346
pubmed: 31003929
Front Cell Infect Microbiol. 2017 Feb 28;7:50
pubmed: 28293542
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Clin Microbiol Rev. 1989 Jul;2(3):315-28
pubmed: 2670193
Eur J Clin Microbiol Infect Dis. 2016 Oct;35(10):1615-25
pubmed: 27325438
Nat Commun. 2019 May 22;10(1):2273
pubmed: 31118420
Heart. 2006 Jul;92(7):879-85
pubmed: 16216860
PLoS One. 2008 Jul 16;3(7):e2683
pubmed: 18628950
Mol Biol Evol. 2020 Aug 1;37(8):2450-2460
pubmed: 32167543
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
J Clin Microbiol. 2018 Oct 25;56(11):
pubmed: 30135231
Genome Biol. 2020 Jul 22;21(1):180
pubmed: 32698896
J Clin Microbiol. 1988 Nov;26(11):2465-6
pubmed: 3069867
Wellcome Open Res. 2018 Jul 30;3:93
pubmed: 30345380
Appl Environ Microbiol. 2012 Apr;78(8):3004-9
pubmed: 22307284
Microb Genom. 2017 Sep 4;3(10):e000131
pubmed: 29177089
Wellcome Open Res. 2018 Sep 24;3:124
pubmed: 30345391
Nat Genet. 2013 Jun;45(6):656-63
pubmed: 23644493
Microb Genom. 2016 Nov 30;2(11):e000093
pubmed: 28348833
Oral Microbiol Immunol. 1993 Feb;8(1):1-4
pubmed: 8510978
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Emerg Infect Dis. 2020 Jul;26(7):1538-1541
pubmed: 32568039
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063