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Journal of Clinical Microbiology, December 2005, p. 5983-5991, Vol. 43, No. 12
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.12.5983-5991.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Identification of 43 Streptococcus Species by Pyrosequencing Analysis of the rnpB Gene

Åsa Innings,1 Margareta Krabbe,2,{dagger} Måns Ullberg,1 and Björn Herrmann1*

Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden,1 Biotage AB, Kungsgatan 76, SE-753 18 Uppsala, Sweden2

Received 4 May 2005/ Returned for modification 11 July 2005/ Accepted 13 September 2005

Pyrosequencing technology was evaluated for identification of species within the Streptococcus genus. Two variable regions in the rnpB gene, which encodes the RNA subunit of endonuclease P, were sequenced in two reactions. Of 43 species, all could be identified to the species level except strains of the species pairs Streptococcus anginosus/S. constellatus and S. infantis/S. peroris. A total of 113 blood culture isolates were identified by pyrosequencing analysis of partial rnpB sequences. All but eight isolates could be unambiguously assigned to a specific species when the first 30 nucleotides of the two regions were compared to an rnpB database comprising 107 streptococcal strains. Principal coordinate analysis of sequence variation of strains from viridans group streptococci resulted in species-specific clusters for the mitis and the salivarius groups but not for the anginosus group. The identification capacity of pyrosequencing was compared to the biochemical test systems VITEK 2 and Rapid ID 32 Strep. The concordance between pyrosequencing and VITEK 2 was 75%, and for Rapid ID 32 Strep the corresponding figure was 77%. Isolates with discrepant identifications in the three methods were subjected to entire rnpB DNA sequence analysis that confirmed the identifications by pyrosequencing. In conclusion, pyrosequencing analysis of the rnpB gene can reliably identify Streptococcus species with high resolution.

* Corresponding author. Mailing address: Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden. Phone: 46 18 6113952. Fax: 46 18 559157. E-mail: bjorn.herrmann{at}medsci.uu.se.

{dagger} Present address: Biology Education Centre, Uppsala University, Box 592, SE-751 24 Uppsala, Sweden.

Journal of Clinical Microbiology, December 2005, p. 5983-5991, Vol. 43, No. 12
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.12.5983-5991.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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