Identification of Staphylococcus spp. using (GTG)5-PCR fingerprinting

Systematic and Applied Microbiology

Volumn 33, Issue 8, 2010, Pages 451-456

  Švec, Pavel ^a   Pantů̊ček, Roman ^a   Petráš, Petr ^b   Sedláček, Ivo ^a   Nováková, Dana ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

^b NATIONAL INSTITUTE OF PUBLIC HEALTH   (Czech Republic)

Author keywords

(GTG)5 PCR; Identification; Rep PCR; RpoB gene sequencing; Staphylococcus; Taxonomy

Indexed keywords

PRIMER DNA; RNA POLYMERASE BETA SUBUNIT;

ANALYTIC METHOD; ARTICLE; BACTERIUM IDENTIFICATION; CZECH REPUBLIC; DNA FINGERPRINTING; GENE CLUSTER; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STAPHYLOCOCCUS; STAPHYLOCOCCUS CAPRAE; STAPHYLOCOCCUS EQUORUM; STAPHYLOCOCCUS PISCIFERMENTANS; STAPHYLOCOCCUS SAPROPHYTICUS; STAPHYLOCOCCUS SCIURI; STAPHYLOCOCCUS XYLOSUS; TAXONOMY;

ANIMALS; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN SUBUNITS; STAPHYLOCOCCAL INFECTIONS; STAPHYLOCOCCUS;

STAPHYLOCOCCUS; STAPHYLOCOCCUS CAPRAE; STAPHYLOCOCCUS EQUORUM; STAPHYLOCOCCUS PISCIFERMENTANS; STAPHYLOCOCCUS SAPROPHYTICUS; STAPHYLOCOCCUS SCIURI; STAPHYLOCOCCUS XYLOSUS;

EID: 78649715194     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2010.09.004     Document Type: Article

References (37)

1. Abolmaaty A., El-Shemy M.G., Khallaf M.F., Levin R.E. Effect of lysing methods and their variables on the yield of Escherichia coli O157: H7 DNA and its PCR amplification. J. Microbiol. Methods 1998, 34:133-141.
2. Burr M.D., Pepper I.L. Variability in presence-absence scoring of AP PCR fingerprints affects computer matching of bacterial isolates. J. Microbiol. Methods 1997, 29:63-68.
3. 5-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans. Int. J. Food Microbiol. 2008, 125:79-90.
4. Del Vecchio V., Petroziello J., Gress M., McCleskey F., Melcher G., Crouch H., Lupski J. Molecular genotyping of methicillin-resistant Staphylococcus aureus via fluorophore-enhanced repetitive-sequence PCR. J. Clin. Microbiol. 1995, 33:2141-2144.
5. Deplano A., Schuermans A., Van Eldere J., Witte W., Meugnier H., Etienne J., Grundmann H., Jonas D., Noordhoek G.T., Dijkstra J., van Belkum A., van Leeuwen W., Tassios P.T., Legakis N.J., van der Zee A., Bergmans A., Blanc D.S., Tenover F.C., Cookson B.C., O'Neil G., Struelens M.J. Multicenter evaluation of epidemiological typing of methicillin-resistant Staphylococcus aureus strains by repetitive-element PCR analysis. J. Clin. Microbiol. 2000, 38:3527-3533. The European Study Group on Epidemiological Markers of the ESCMID.
6. Gevers D., Huys G., Swings J. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 2001, 205:31-36.
7. Grisold A.J., Zarfel G., Hoenigl M., Krziwanek K., Feierl G., Masoud L., Leitner E., Wagner-Eibel U., Badura A., Marth E. Occurrence and genotyping using automated repetitive-sequence-based PCR of methicillin-resistant Staphylococcus aureus ST398 in Southeast Austria. Diagn. Microbiol. Infect. Dis. 2010, 66:217-221.
8. Healy M., Huong J., Bittner T., Lising M., Frye S., Raza S., Schrock R., Manry J., Renwick A., Nieto R., Woods C., Versalovic J., Lupski J.R. Microbial DNA typing by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 2005, 43:199-207.
9. Huys G., Cnockaert M., Nemec A., Dijkshoorn L., Brisse S., Vaneechoutte M., Swings J. Repetitive-DNA-element PCR fingerprinting and antibiotic resistance of pan-European multi-resistant Acinetobacter baumannii clone III strains. J. Med. Microbiol. 2005, 54:851-856.
10. Iacumin L., Comi G., Cantoni C., Cocolin L. Molecular and technological characterization of Staphylococcus xylosus isolated from naturally fermented Italian sausages by RAPD, rep-PCR and Sau-PCR analysis. Meat Sci. 2006, 74:281-288.
11. Ishii S., Sadowsky M.J. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ. Microbiol. 2009, 11:733-740.
12. Kang H.P., Dunne W.M. Stability of repetitive-sequence PCR patterns with respect to culture age and subculture frequency. J. Clin. Microbiol. 2003, 41:2694-2696.
13. Koreňová J., Lopašovská J., Kuchta T. Biofilm forming bacterial contaminants in small and medium-sized ewes' milk and meat processing enterprises in Slovakia. J. Food Nutr. Res. 2009, 48:115-120.
14. Lanoot B., Vancanneyt M., Dawyndt P., Cnockaert M., Zhang J.L., Huang Y., Liu Z.H., Swings J. BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus. Syst. Appl. Microbiol. 2004, 27:84-92.
15. Meacham K.J., Zhang L., Foxman B., Bauer R.J., Marrs C.F. Evaluation of genotyping large numbers of Escherichia coli isolates by enterobacterial repetitive intergenic consensus-PCR. J. Clin. Microbiol. 2003, 41:5224-5226.
16. Meintanis C., Chalkou K.I., Kormas K.A., Lymperopoulou D.S., Katsifas E.A., Hatzinikolaou D.G., Karagouni A.D. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus. Lett. Appl. Microbiol. 2008, 46:395-401.
17. Mellmann A., Becker K., von Eiff C., Keckevoet U., Schumann P., Harmsen D. Sequencing and staphylococci identification. Emerg. Inf. Dis. 2006, 12:333-336.
18. Nascimento J.dos S., Giambiagi-deMarval M., de Oliveira S.S., Ceotto H., dos Santos K.R.N., Bastos M.do C.de F. Genomic fingerprinting of bacteriocin-producer strains of Staphylococcus aureus. Res. Microbiol. 2005, 156:837-842.
19. Rantsiou K., Iacumin L., Cantoni C., Comi G., Cocolin L. Ecology and characterization by molecular methods of Staphylococcus species isolated from fresh sausages. Int. J. Food. Microbiol. 2005, 97:277-284.
20. Ross T.L., Merz W.G., Farkosh A., Carroll K.C. Comparison of an automated repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for analysis of outbreaks of methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 2005, 43:5642-5647.
21. Sasaki T., Kikuchi K., Tanaka Y., Takahashi N., Kamata S., Hiramatsu K. Reclassification of phenotypically identified Staphylococcus intermedius strains. J. Clin. Microbiol. 2007, 45:2770-2778.
22. Shutt C.K., Pounder J.I., Page S.R., Schaecher B.J., Woods G.L. Clinical evaluation of the DiversiLab microbial typing system using repetitive-sequence-based PCR for characterization of Staphylococcus aureus strains. J. Clin. Microbiol. 2005, 43:1187-1192.
23. Schleifer K.H., Bell J.A. Genus I. Staphylococcus Rosenbach 1884, 18AL (Nom. Cons. Opin. 17 Jud. Comm. 1958, 153.). Bergey's Manual of Systematic Bacteriology, The Firmicutes, 2009, vol. 3:392-421. Springer, New York.
24. Snelling A., Gerner-Smidt P., Hawkey P., Heritage J., Parnell P., Porter C., Bodenham A., Inglis T. Validation of use of whole-cell repetitive extragenic palindromic sequence-based PCR (REP-PCR) for typing strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and application of the method to the investigation of a hospital outbreak. J. Clin. Microbiol. 1996, 34:1193-1202.
25. Štěpán J., Pantůček R., Doškař J. Molecular diagnostics of clinically important staphylococci. Folia Microbiol. 2004, 49:353-386.
26. 5-PCR for identification of Enterococcus spp. FEMS Microbiol. Lett. 2005, 247:59-63.
27. 5-PCR for rapid identification of Streptococcus mutans. Anton. Leeuw. Int. J. G. 2008, 94:573-579.
28. te Witt R., Kanhai V., van Leeuwen W.B. Comparison of the DiversiLab™ system, pulsed-field gel electrophoresis and multi-locus sequence typing for the characterization of epidemic reference MRSA strains. J. Microbiol. Methods 2009, 77:130-133.
29. Trevino M., Martinez-Lamas L., Romero-Jung P.A., Giraldez J.M., Alvarez-Escudero J., Regueiro B.J. Endemic linezolid-resistant Staphylococcus epidermidis in a critical care unit. Eur. J. Clin. Microbiol. Infect. Dis. 2009, 28:527-533.
30. van Belkum A., Bax R., Peerbooms P., Goessens W.H.F., Vanleeuwen N., Quint W.G.V. Comparison of phage typing and DNA fingerprinting by polymerase chain reaction for discrimination of methicillin-resistant Staphylococcus aureus strains. J. Clin. Microbiol. 1993, 31:798-803.
31. van Belkum A., Tassios P.T., Dijkshoorn L., Haeggman S., Cookson B., Fry N.K., Fussing V., Green J., Feil E., Gerner-Smidt P., Brisse S., Struelens M. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 2007, 13:1-46.
32. van der Zee A., Verbakel H., van Zon J.C., Frenay I., van Belkum A., Peeters M., Buiting A., Bergmans A. Molecular genotyping of Staphylococcus aureus strains: comparison of repetitive element sequence-based PCR with various typing methods and isolation of a novel epidemicity marker. J. Clin. Microbiol. 1999, 37:342-349.
33. Versalovic J., Schneider M., de Bruijn F.J., Lupski J.R. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 1994, 5:25-40.
34. Versalovic J., Lupski J.R. Interspersed repetitive sequences in bacterial genomes. Bacterial Genomes: Physical Structure and Analysis 1999, 38-48. Kluwer Academic Publishers, Norwell, MA. 2nd ed. F.J. De Bruijn, J.R. Lupski, G.M. Weinstock (Eds.).
35. Wieser M., Busse H.J. Rapid identification of Staphylococcus epidermidis. Int. J. Syst. Evol. Microbiol. 2000, 50:1087-1093.
36. Wilson L.A., Sharp P.M. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: evolution and implications for ERIC-PCR. Mol. Biol. Evol. 2006, 23:1156-1168.
37. Zhong Z., Chai T., Duan H., Miao Z., Li X., Yao M., Yuan W., Wang W., Li Q., Zucker B.-A., Schlenker G. REP-PCR tracking of the origin and spread of airborne Staphylococcus aureus in and around chicken house. Indoor Air 2009, 19:511-516.