Multiple-genome comparison reveals new loci for Mycobacterium species identification.
To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus Mycobacterium, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of Corynebacterineae (18 from the Mycobacterium genus, 7 from the Corynebacterium genus, 1 each from the Nocardia and Rhodococcus genera). Our study revealed 26 informative loci for species identification in Mycobacterium. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified, rpoBC, dnaK, and hsp65 were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified dnaK locus is more discriminatory and more robust than the widely used hsp65 locus. The length-variable rpoBC locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the rpoBC, dnaK, and hsp65 loci is a robust tool for accurate identification of Mycobacterium species.
Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd., Gainesville, FL 32611, USA. dai.jian.li@ufl.edu
Jianli
J
Dai
Yuansha
Y
Chen
Susan
S
Dean
J Glenn
JG
Morris
Max
M
Salfinger
Judith A
JA
Johnson
D001426:Bacterial Proteins / Q000235:genetics; D001431:Bacteriological Techniques / Q000379:methods*; D018834:Chaperonin 60 / Q000235:genetics; D019295:Computational Biology; D003352:Corynebacterium / Q000145:classification / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D016680:Genome, Bacterial; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics*; D009164:Mycobacterium Infections / Q000175:diagnosis* / Q000382:microbiology*; D009615:Nocardia / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D012240:Rhodococcus / Q000145:classification / Q000235:genetics; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D018834:Chaperonin 60; D018840:HSP70 Heat-Shock Proteins; C074119:heat-shock protein 65, Mycobacterium; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit