Phylogeny and identification of Nocardia species on the basis of multilocus sequence analysis

L. R. McTaggart, S. E. Richardson, M. Witkowska, Sean Xiang Zhang

Research output: Contribution to journalArticle

Abstract

Nocardia species identification is difficult due to a complex and rapidly changing taxonomy, the failure of 16S rRNA and cellular fatty acid analysis to discriminate many species, and the unreliability of biochemical testing. Here, Nocardia species identification was achieved through multilocus sequence analysis (MLSA) of gyrase B of the β subunit of DNA topoisomerase (gyrB), 16S rRNA (16S), subunit A of SecA preprotein translocase (secA1), the 65-kDa heat shock protein (hsp65), and RNA polymerase (rpoB) applied to 190 clinical, 36 type, and 11 reference strains. Phylogenetic analysis resolved 30 sequence clusters with high (>85%) bootstrap support. Since most clusters contained a single type strain and the analysis corroborated current knowledge of Nocardia taxonomy, the sequence clusters were equated with species clusters and MLSA was deemed appropriate for species identification. By comparison, single-locus analysis was inadequate because it failed to resolve species clusters, partly due to the presence of foreign alleles in 22.1% of isolates. While MLSA identified the species of the majority (71.3%) of strains, it also identified clusters that may correspond to new species. The correlation of the identities by MLSA with those determined on the basis of microscopic examination, biochemical testing, and fatty acid analysis was 95%; however, MLSA was more discriminatory. Nocardia cyriacigeorgica (21.58%) and N. farcinica (14.74%) were the most frequently encountered species among clinical isolates. In summary, five-locus MLSA is a reliable method of elucidating taxonomic data to inform Nocardia species identification; however, three-locus (gyrB-16S-secA1) or four-locus (gyrB-16S-secA1-hsp65) MLSA was nearly as reliable, correctly identifying 98.5% and 99.5% of isolates, respectively, and would be more feasible for routine use in a clinical reference microbiology laboratory.

Original languageEnglish (US)
Pages (from-to)4525-4533
Number of pages9
JournalJournal of Clinical Microbiology
Volume48
Issue number12
DOIs
StatePublished - Dec 2010
Externally publishedYes

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Multilocus Sequence Typing
Nocardia
Phylogeny
Fatty Acids
Type I DNA Topoisomerase
DNA-Directed RNA Polymerases
Heat-Shock Proteins
Microbiology
Alleles

ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Phylogeny and identification of Nocardia species on the basis of multilocus sequence analysis. / McTaggart, L. R.; Richardson, S. E.; Witkowska, M.; Zhang, Sean Xiang.

In: Journal of Clinical Microbiology, Vol. 48, No. 12, 12.2010, p. 4525-4533.

Research output: Contribution to journalArticle

McTaggart, L. R. ; Richardson, S. E. ; Witkowska, M. ; Zhang, Sean Xiang. / Phylogeny and identification of Nocardia species on the basis of multilocus sequence analysis. In: Journal of Clinical Microbiology. 2010 ; Vol. 48, No. 12. pp. 4525-4533.
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