Development of a New Oligonucleotide Array to Identify Staphylococcal Strains at Species Level

Overview

Journal J Clin Microbiol

Specialty Microbiology

Date 2005 Aug 6

PMID 16081895

Citations 10

Authors

Philippe Giammarinaro

Sabine Leroy

Jean-Paul Chacornac

Julien Delmas

Regine Talon

Affiliations

Soon will be listed here.

Abstract

The genus Staphylococcus is made up of 36 validated species which contain strains that are pathogenic, saprophytic, or used as starter cultures for the food industry. An oligonucleotide array targeting the manganese-dependent superoxide dismutase (sodA) gene was developed to overcome the drawbacks of the conventional methods of identification. Divergences of the sodA gene were used to design oligonucleotide probes, and we showed that each of the 36 species had a characteristic pattern of hybridization. To evaluate the array, we analyzed 38 clinical and 38 food or food plant Staphylococcus isolates identified by the phenotype-based system VITEK 2 (bioMérieux). This commercial kit failed to identify 8 (21%) of the clinical isolates and 32 (84%) of the food and food plant isolates. In contrast, the oligonucleotide array we designed provided an accurate and rapid method for the identification of staphylococcal strains, isolated from clinical, environmental, or food samples, at species level.

Citing Articles

Biopolymer production by halotolerant bacteria isolated from Caatinga biome.

Parada-Pinilla M, Ferreira M, Roncallo J, Santos S, Melo I, Assef A Braz J Microbiol. 2021; 52(2):547-559.

PMID: 33491139 PMC: 8105489. DOI: 10.1007/s42770-021-00426-1.

Universal Probe Library based real-time PCR for rapid detection of bacterial pathogens from positive blood culture bottles.

Zhu L, Shen D, Zhou Q, Liu C, Li Z, Fang X World J Microbiol Biotechnol. 2013; 30(3):967-75.

PMID: 24122126 DOI: 10.1007/s11274-013-1515-x.

fbl gene as a species-specific target for Staphylococcus lugdunensis identification.

Chatzigeorgiou K, Siafakas N, Petinaki E, Zerva L J Clin Lab Anal. 2010; 24(2):119-22.

PMID: 20333760 PMC: 6647709. DOI: 10.1002/jcla.20352.

Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Dubois D, Leyssene D, Chacornac J, Kostrzewa M, Schmit P, Talon R J Clin Microbiol. 2009; 48(3):941-5.

PMID: 20032251 PMC: 2832446. DOI: 10.1128/JCM.00413-09.

A pentaplex PCR assay for the rapid detection of methicillin-resistant Staphylococcus aureus and Panton-Valentine Leucocidin.

Al-Talib H, Yean Yean C, Al-Khateeb A, Hassan H, Banga Singh K, Al-Jashamy K BMC Microbiol. 2009; 9:113.

PMID: 19476638 PMC: 2700277. DOI: 10.1186/1471-2180-9-113.

References

Rudi K, Skulberg O, Skulberg R, Jakobsen K . Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol. 2000; 66(9):4004-11. PMC: 92251. DOI: 10.1128/AEM.66.9.4004-4011.2000. View

Schena M, Shalon D, Heller R, Chai A, Brown P, Davis R . Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A. 1996; 93(20):10614-9. PMC: 38202. DOI: 10.1073/pnas.93.20.10614. View

Yugueros J, Temprano A, Berzal B, Sanchez M, Hernanz C, Luengo J . Glyceraldehyde-3-phosphate dehydrogenase-encoding gene as a useful taxonomic tool for Staphylococcus spp. J Clin Microbiol. 2000; 38(12):4351-5. PMC: 87604. DOI: 10.1128/JCM.38.12.4351-4355.2000. View

Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S . Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997; 35(4):907-14. PMC: 229700. DOI: 10.1128/jcm.35.4.907-914.1997. View

Euzeby J . List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol. 1997; 47(2):590-2. DOI: 10.1099/00207713-47-2-590. View

Takahashi T, Kaneko M, Mori Y, Tsuji M, Kikuchi N, HIRAMUNE T . Phylogenetic analyses of Staphylococcus based on the 16S rDNA sequence and assignment of clinical isolates from animals. J Vet Med Sci. 1997; 59(9):775-83. DOI: 10.1292/jvms.59.775. View

Forsman P, Alatossava T . Identification of staphylococcal and streptococcal causes of bovine mastitis using 16S-23S rRNA spacer regions. Microbiology (Reading). 1997; 143 ( Pt 11):3491-3500. DOI: 10.1099/00221287-143-11-3491. View

Goh S, Santucci Z, Kloos W, Faltyn M, George C, Driedger D . Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization. J Clin Microbiol. 1997; 35(12):3116-21. PMC: 230133. DOI: 10.1128/jcm.35.12.3116-3121.1997. View

Vannuffel P, Heusterspreute M, Bouyer M, Vandercam B, Philippe M, Gala J . Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species. Res Microbiol. 1999; 150(2):129-41. DOI: 10.1016/s0923-2508(99)80030-8. View

10.

Takahashi T, Satoh I, Kikuchi N . Phylogenetic relationships of 38 taxa of the genus Staphylococcus based on 16S rRNA gene sequence analysis. Int J Syst Bacteriol. 1999; 49 Pt 2:725-8. DOI: 10.1099/00207713-49-2-725. View

11.

Tao H, Bausch C, Richmond C, Blattner F, Conway T . Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol. 1999; 181(20):6425-40. PMC: 103779. DOI: 10.1128/JB.181.20.6425-6440.1999. View

12.

Becker K, Harmsen D, Mellmann A, Meier C, Schumann P, Peters G . Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol. 2004; 42(11):4988-95. PMC: 525259. DOI: 10.1128/JCM.42.11.4988-4995.2004. View

13.

Behr T, Koob C, Schedl M, Mehlen A, Meier H, Knopp D . A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization. Syst Appl Microbiol. 2001; 23(4):563-72. DOI: 10.1016/s0723-2020(00)80031-4. View

14.

Rossi F, Tofalo R, Torriani S, Suzzi G . Identification by 16S-23S rDNA intergenic region amplification, genotypic and phenotypic clustering of Staphylococcus xylosus strains from dry sausages. J Appl Microbiol. 2001; 90(3):365-71. DOI: 10.1046/j.1365-2672.2001.01254.x. View

15.

Martineau F, Picard F, Ke D, Paradis S, Roy P, Ouellette M . Development of a PCR assay for identification of staphylococci at genus and species levels. J Clin Microbiol. 2001; 39(7):2541-7. PMC: 88182. DOI: 10.1128/JCM.39.7.2541-2547.2001. View

16.

Barriere C, Bruckner R, Talon R . Characterization of the single superoxide dismutase of Staphylococcus xylosus. Appl Environ Microbiol. 2001; 67(9):4096-104. PMC: 93135. DOI: 10.1128/AEM.67.9.4096-4104.2001. View

17.

Barriere C, Talon R . Characterization of catalase and superoxide dismutase in Staphylococcus carnosus 833 strain. J Appl Microbiol. 2001; 91(3):514-9. DOI: 10.1046/j.1365-2672.2001.01411.x. View

18.

Hamels S, Gala J, Dufour S, Vannuffel P, Zammatteo N, Remacle J . Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance. Biotechniques. 2002; 31(6):1364-6, 1368, 1370-2. DOI: 10.2144/01316md04. View

19.

Le Novere N . MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics. 2001; 17(12):1226-7. DOI: 10.1093/bioinformatics/17.12.1226. View

20.

Poyart C, Quesne G, Boumaila C, Trieu-Cuot P . Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J Clin Microbiol. 2001; 39(12):4296-301. PMC: 88539. DOI: 10.1128/JCM.39.12.4296-4301.2001. View