rpoB sequence-based identification of Mycobacterium avium complex species

Microbiology (Reading). 2008 Dec;154(Pt 12):3715-3723. doi: 10.1099/mic.0.2008/020164-0.

Abstract

The Mycobacterium avium complex (MAC) comprises slowly growing mycobacteria responsible for opportunistic infections and zoonoses. The ability to speciate MAC isolates in the clinical microbiology laboratory is critical for determining the organism implicated in clinical disease and for epidemiological investigation of the source of infection. Investigation of a 711 bp variable fragment of rpoB flanked by the Myco-F/Myco-R primers found a 0.7-5.1 % divergence among MAC reference strains, with Mycobacterium chimaera and Mycobacterium intracellulare being the most closely related. Using a 0.7 % divergence cut-off, 83 % of 100 clinical isolates, which had been previously identified by phenotypic characteristics and 16S-23S rDNA intergenic spacer (ITS) probing, were identified as M. avium, 8 % as M. intracellulare and 2 % as M. chimaera. The uniqueness of seven isolates, exhibiting < 99.3 % rpoB sequence similarity with MAC reference strains, was confirmed by 16S rDNA, ITS and hsp65 sequencing and phylogenetic analyses. Partial rpoB gene sequencing using the Myco-F/Myco-R primers permits one-step identification of MAC isolates at the species level and the detection of potentially novel MAC species.

Publication types

  • Evaluation Study

MeSH terms

  • Animals
  • Bacterial Proteins / genetics
  • Bacterial Typing Techniques*
  • Chaperonin 60
  • Chaperonins / genetics
  • DNA, Ribosomal Spacer / analysis
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics
  • Humans
  • Molecular Sequence Data
  • Mycobacterium avium Complex / classification*
  • Mycobacterium avium Complex / enzymology
  • Mycobacterium avium Complex / genetics
  • Mycobacterium avium-intracellulare Infection / microbiology
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA*
  • Species Specificity

Substances

  • Bacterial Proteins
  • Chaperonin 60
  • DNA, Ribosomal Spacer
  • RNA, Ribosomal, 16S
  • heat-shock protein 65, Mycobacterium
  • DNA-Directed RNA Polymerases
  • RNA polymerase beta subunit
  • Chaperonins

Associated data

  • GENBANK/EF521900
  • GENBANK/EF521905
  • GENBANK/EF521906
  • GENBANK/EF521907
  • GENBANK/EF521908
  • GENBANK/EF521910
  • GENBANK/EF521911
  • GENBANK/EF584432
  • GENBANK/EF584433
  • GENBANK/EF584434
  • GENBANK/EF584435
  • GENBANK/EF584444
  • GENBANK/EF584445