GyrB polymorphisms accurately assign invasive viridans group streptococcal species

Journal of Clinical Microbiology

Volumn 52, Issue 8, 2014, Pages 2905-2912

  Galloway Peña, Jessica ^a   Sahasrabhojane, Pranoti ^a   Tarrand, Jeffrey ^a   Han, Xiang Y ^a   Shelburne, Samuel A ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING) B; RNA 16S; BACTERIAL DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); HELMINTH DNA; RIBOSOME DNA;

16S GENE; ALPHA HEMOLYTIC STREPTOCOCCUS; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; DATA ANALYSIS; GENETIC POLYMORPHISM; GYRB GENE; INFORMATION STORAGE; MEASUREMENT ACCURACY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SODA GENE; SPECIES IDENTIFICATION; SPECIES INVASION; STREPTOCOCCUS MITIS; STREPTOCOCCUS ORALIS; BACTEREMIA; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR DIAGNOSIS; PROCEDURES; STREPTOCOCCAL INFECTIONS; VALIDATION STUDY;

BACTEREMIA; DNA GYRASE; DNA, BACTERIAL; DNA, HELMINTH; DNA, RIBOSOMAL; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMORPHISM, GENETIC; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; STREPTOCOCCAL INFECTIONS; VIRIDANS STREPTOCOCCI;

EID: 84905251119     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01068-14     Document Type: Article

References (39)

1. Bochud PY, Calandra T, Francioli P. 1994. Bacteremia due to viridans streptococci in neutropenic patients: a review. Am. J. Med. 97:256-264. http://dx.doi.org/10.1016/0002-9343(94)90009-4. (Pubitemid 24284365)
2. Husain E, Whitehead S, Castell A, Thomas EE, Speert DP. 2005. Viridans streptococci bacteremia in children with malignancy: relevance of species identification and penicillin susceptibility. Pediatr. Infect. Dis. J. 24:563-566. http://dx.doi.org/10.1097/01.inf.0000164708.21464.03. (Pubitemid 40847536)
3. Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG. 2009. Assigning strains to bacterial species via the internet. BMC Biol. 7:3. http://dx.doi.org/10.1186/1741-7007-7-3.
4. Han XY, Kamana M, Rolston KV. 2006. Viridans streptococci isolated by culture from blood of cancer patients: clinical and microbiologic analysis of 50 cases. J. Clin. Microbiol. 44:160-165. http://dx.doi.org/10.1128/JCM.44.1.160- 165.2006. (Pubitemid 43100595)
5. Kitten T, Munro CL, Zollar NQ, Lee SP, Patel RD. 2012. Oral streptococcal bacteremia in hospitalized patients: taxonomic identification and clinical characterization. J. Clin. Microbiol. 50:1039-1042. http://dx.doi.org/10.1128/ JCM.06438-11.
6. Shelburne SA, Sahasrabhojane P, Saldana M, Yao H, Su X, Horstmann N, Thompson K, Flores AR. 2014. Streptococcus mitis strains causing severe clinical disease in cancer patients. Emerg. Infect. Dis. 20:762-771. http://dx.doi.org/10.3201/eid2005.130953.
7. Haanperä M, Jalava J, Huovinen P, Meurman O, Rantakokko-Jalava K. 2007. Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of Vitek 2. J. Clin. Microbiol. 45:762-770. http://dx.doi.org/10.1128/JCM.01342-06. (Pubitemid 46427689)
8. Hoshino T, Fujiwara T, Kilian M. 2005. Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J. Clin. Microbiol. 43:6073-6085. http://dx.doi.org/10.1128/JCM.43.12. 6073-6085.2005. (Pubitemid 43100663)
9. Ikryannikova LN, Lapin KN, Malakhova MV, Filimonova AV, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM. 2011. Misidentification of alpha-hemolytic streptococci by routine tests in clinical practice. Infect. Genet. Evol. 11:1709-1715. http://dx.doi.org/10.1016/j.meegid.2011.07.010.
10. Teles C, Smith A, Ramage G, Lang S. 2011. Identification of clinically relevant viridans group streptococci by phenotypic and genotypic analysis. Eur. J. Clin. Microbiol. Infect. Dis. 30:243-250. http://dx.doi.org/10.1007/s10096- 010-1076-y.
11. Woo PC, Teng JL, Wu JK, Leung FP, Tse H, Fung AM, Lau SK, Yuen KY. 2009. Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria. J. Med. Microbiol. 58:1030-1036. http://dx.doi.org/10.1099/jmm.0.008615-0.
12. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2008. GenBank. Nucleic Acids Res. 36:D25-D30. http://dx.doi.org/10.1093/nar/gkm929. (Pubitemid 351149691)
13. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296. http://dx.doi.org/10.1093/nar/gki038. (Pubitemid 40207881)
14. Harmsen D, Rothgänger J, Frosch M, Albert J. 2002. RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Res. 30:416-417. http://dx.doi.org/10.1093/nar/30.1.416. (Pubitemid 34679601)
15. Simmon KE, Croft AC, Petti CA. 2006. Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory. J. Clin. Microbiol. 44:4400-4406. http://dx.doi.org/10. 1128/JCM.01364-06. (Pubitemid 44937071)
16. Woo PC, Teng JL, Yeung JM, Tse H, Lau SK, Yuen KY. 2011. Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB. J. Clin. Microbiol. 49:1799-1809. http://dx.doi.org/10.1128/JCM.02350-10.
17. Drancourt M, Roux V, Fournier PE, Raoult D. 2004. rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J. Clin. Microbiol. 42:497-504. http://dx.doi.org/10.1128/JCM.42.2.497-504.2004. (Pubitemid 38222619)
18. Ip M, Chi F, Chau SS, Hui M, Tang J, Chan PK. 2006. Use of the housekeeping genes, gdh (zwf) and gki, in multilocus sequence typing to differentiate Streptococcus pneumoniae from Streptococcus mitis and Streptococcus oralis. Diagn. Microbiol. Infect. Dis. 56:321-324. http://dx.doi.org/10.1016/j.diagmicrobio.2006.04.013. (Pubitemid 44648595)
19. Kawamura Y, Whiley RA, Shu SE, Ezaki T, Hardie JM. 1999. Genetic approaches to the identification of the mitis group within the genus Streptococcus. Microbiology 145(Pt 9):2605-2613. (Pubitemid 29454379)
20. Konishi I, Hoshino T, Kondo Y, Saito K, Nishiguchi M, Sato K, Fujiwara T. 2009. Phylogenetic analyses and detection of viridans streptococci based on sequences and denaturing gradient gel electrophoresis of the rod shape-determining protein gene. J. Oral Microbiol. 1. http://dx.doi.org/10.3402/ jom.v1i0.2015.
21. Nielsen XC, Justesen US, Dargis R, Kemp M, Christensen JJ. 2009. Identification of clinically relevant nonhemolytic streptococci on the basis of sequence analysis of 16S-23S intergenic spacer region and partial gdh gene. J. Clin. Microbiol. 47: 932-939. http://dx.doi.org/10.1128/JCM.01449-08.
22. Park HK, Yoon JW, Shin JW, Kim JY, Kim W. 2010. rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol. Lett. 305:58-64. http://dx.doi.org/10.1111/j.1574-6968.2010.01913.x.
23. Poyart C, Quesne G, Coulon S, Berche P, Trieu-Cuot P. 1998. Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J. Clin. Microbiol. 36:41-47. (Pubitemid 28047430)
24. Westling K, Julander I, Ljungman P, Vondracek M, Wretlind B, Jalal S. 2008. Identification of species of viridans group streptococci in clinical blood culture isolates by sequence analysis of the RNase PRNAgene, rnpB. J. Infect. 56:204-210. http://dx.doi.org/10.1016/j.jinf.2007.12.006.
25. Do T, Jolley KA, Maiden MC, Gilbert SC, Clark D, Wade WG, Beighton D. 2009. Population structure of Streptococcus oralis. Microbiology 155:2593-2602. http://dx.doi.org/10.1099/mic.0.027284-0.
26. Hakenbeck R, Balmelle N, Weber B, Gardes C, Keck W, de Saizieu A. 2001. Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69:2477-2486. http://dx.doi.org/10. 1128/IAI.69.4.2477-2486.2001. (Pubitemid 32239720)
27. Hanage WP, Fraser C, Spratt BG. 2005. Fuzzy species among recombinogenic bacteria. BMC Biol. 3:6. http://dx.doi.org/10.1186/1741-7007-3-6.
28. Hohwy J, Reinholdt J, Kilian M. 2001. Population dynamics of Streptococcus mitis in its natural habitat. Infect. Immun. 69:6055-6063. http://dx.doi.org/10.1128/IAI.69.10.6055-6063.2001. (Pubitemid 32885165)
29. Kilian M, Poulsen K, Blomqvist T, Håvarstein LS, Bek-Thomsen M, Tettelin H, Sørensen UB. 2008. Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One 3:e2683. http://dx.doi.org/10.1371/ journal.pone.0002683.
30. Whatmore AM, Efstratiou A, Pickerill AP, Broughton K, Woodard G, Sturgeon D, George R, Dowson CG. 2000. Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of "atypical" pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factorencoding genes. Infect. Immun. 68:1374-1382. http://dx.doi.org/10.1128/IAI.68.3.1374-1382.2000. (Pubitemid 30108534)
31. Ikryannikova LN, Filimonova AV, Malakhova MV, Savinova T, Filimonova O, Ilina EN, Dubovickaya VA, Sidorenko SV, Govorun VM. 2013. Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra. Clin. Microbiol. Infect. 19:1066-1071. http://dx.doi.org/10. 1111/1469-0691.12113.
32. Sahasrabhojane P, Galloway-Peña JR, Velazquez L, Saldaña M, Horstmann N, Tarrand J, Shelburne SA. 2014. Species-level assessment of the molecular basis of fluoroquinolone resistance among viridans group streptococci causing bacteraemia in cancer patients. Int. J. Antimicrob. Agents, in press. http://dx.doi.org/10.1016/j.ijantimicag.2014.01.031.
33. Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T. 1995. Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int. J. Syst. Bacteriol. 45:406-408. http://dx.doi.org/10.1099/00207713-45-2-406.
34. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. 1985. Rapid determination of 16S ribosomalRNAsequences for phylogenetic analyses. Proc. Natl. Acad. Sci. U. S. A. 82:6955-6959. http://dx.doi.org/10.1073/pnas.82.20. 6955. (Pubitemid 16209672)
35. Scholz CF, Poulsen K, Kilian M. 2012. Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J. Clin. Microbiol. 50:1968-1973. http://dx.doi.org/10.1128/JCM.00365-12.
36. Maeda Y, Murayama M, Goldsmith CE, Coulter WA, Mason C, Millar BC, Dooley JS, Lowery CJ, Matsuda M, Rendall JC, Elborn JS, Moore JE. 2011. Molecular characterization and phylogenetic analysis of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC and parE gene loci in viridans group streptococci isolated from adult patients with cystic fibrosis. J. Antimicrob. Chemother. 66:476-486. http://dx.doi.org/10.1093/jac/dkq485.
37. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649. http://dx.doi.org/10.1093/bioinformatics/bts199.
38. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 2000. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38:3623-3630.
39. Naveen Kumar V, van der Linden M, Menon T, Nitsche-Schmitz DP. 2014. Viridans and bovis group streptococci that cause infective endocarditis in two regions with contrasting epidemiology. Int. J. Med. Microbiol. 304:262-268. http://dx.doi.org/10.1016/j.ijmm.2013.10.004.