Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets.
The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis. With the recent availability of genome sequences for strains of the M. tuberculosis complex, novel PCR-based M. tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs). This paper describes the identification of seven VNTR loci in M. tuberculosis H37Rv, the copy number of which varies in other strains of the M. tuberculosis complex. Six of these VNTRs were applied to a panel of 100 different M. bovis isolates, and their discrimination and correlation with spoligotyping and an established set of ETRs were assessed. The number of alleles varied from three to seven at the novel VNTR loci, which differed markedly in their discrimination index. There was positive correlation between spoligotyping, ETR- and VNTR-typing. VNTR-PCR discriminates well between M. bovis strains. Thirty-three allele profiles were identified by the novel VNTRs, 22 for the ETRs and 29 for spoligotyping. When VNTR- and ETR-typing results were combined, a total of 51 different profiles were identified. Digital nomenclature and databasing were intuitive. VNTRs were located both in intergenic regions and annotated ORFs, including PPE (novel glycine-asparigine-rich) proteins, a proposed source of antigenic variation, where VNTRs potentially code repeating amino acid motifs. VNTR-PCR is a valuable tool for strain typing and for the study of the global molecular epidemiology of the M. tuberculosis complex. The novel VNTR targets identified in this study should additionally increase the power of this approach.
Skuce
Robin A
RA
Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1.
McCorry
Thomas P
TP
The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2.
McCarroll
Julie F
JF
Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1.
Roring
Solvig M M
SMM
The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2.
Scott
Alistair N
AN
The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2.
Brittain
David
D
Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1.
Hughes
Stephen L
SL
Veterinary Laboratories Agency, Department for Environment, Food and Rural Affairs, Weybridge, Surrey KT15 3NB, UK3.
Hewinson
R Glyn
RG
Veterinary Laboratories Agency, Department for Environment, Food and Rural Affairs, Weybridge, Surrey KT15 3NB, UK3.
Neill
Sydney D
SD
The Queen's University of Belfast, Department of Veterinary Science, Stormont, Belfast BT4 3SD, UK2.|Veterinary Sciences Division, Department of Agriculture and Rural Development, Stormont, Belfast BT4 3SD, UK1.
D000483:Alleles; D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D002417:Cattle; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D030561:Databases, Nucleic Acid; D018598:Minisatellite Repeats; D009163:Mycobacterium bovis / Q000145:classification* / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*
D004269:DNA, Bacterial