title: Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing.
abstract: BACKGROUND
  Studies conducted on Mycobacterium spp. isolated from human patients indicate that sequencing of a 711 bp portion of the rpoB gene can be useful in assigning a species identity, particularly for members of the Mycobacterium avium complex (MAC). Given that MAC are important pathogens in livestock, companion animals, and zoo/exotic animals, we were interested in evaluating the use of rpoB sequencing for identification of Mycobacterium isolates of veterinary origin.
  
  
  RESULTS
  A total of 386 isolates, collected over 2008 - June 2011 from 378 animals (amphibians, reptiles, birds, and mammals) underwent PCR and sequencing of a ~ 711 bp portion of the rpoB gene; 310 isolates (80%) were identified to the species level based on similarity at ≥ 98% with a reference sequence. The remaining 76 isolates (20%) displayed < 98% similarity with reference sequences and were assigned to a clade based on their location in a neighbor-joining tree containing reference sequences. For a subset of 236 isolates that received both 16S rRNA and rpoB sequencing, 167 (70%) displayed a similar species/clade assignation for both sequencing methods. For the remaining 69 isolates, species/clade identities were different with each sequencing method. Mycobacterium avium subsp. hominissuis was the species most frequently isolated from specimens from pigs, cervids, companion animals, cattle, and exotic/zoo animals.
  
  
  CONCLUSIONS
  rpoB sequencing proved useful in identifying Mycobacterium isolates of veterinary origin to clade, species, or subspecies levels, particularly for assemblages (such as the MAC) where 16S rRNA sequencing alone is not adequate to demarcate these taxa. rpoB sequencing can represent a cost-effective identification tool suitable for routine use in the veterinary diagnostic laboratory.
authors: Mycobacteria and Brucella Section, National Veterinary Services Laboratories, USDA-APHIS, 1920 Dayton Ave, Ames, IA 50010, USA. James.A.Higgins@aphis.usda.gov
authors: James
authors: J
authors: Higgins
authors: Patrick
authors: P
authors: Camp
authors: David
authors: D
authors: Farrell
authors: Doris
authors: D
authors: Bravo
authors: Mateja
authors: M
authors: Pate
authors: Suelee
authors: S
authors: Robbe-Austerman
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000382:microbiology*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000662:veterinary*; D009161:Mycobacterium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D009164:Mycobacterium Infections / Q000382:microbiology / Q000662:veterinary*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit