title: Targeted hybridization of IS6110 fingerprints identifies the W-Beijing Mycobacterium tuberculosis strains among clinical isolates.
abstract: Targeted IS6110-based RFLP genotyping can be applied to rapidly identify specific groups of biomedically/epidemiologically relevant Mycobacterium tuberculosis clinical isolates. One such group is the W-Beijing strain family (also known as Beijing/W), implicated in significant nosocomial and community outbreaks worldwide. Using previously defined criteria, we developed a simple and accurate method to identify members of the W-Beijing family, based on rehybridization of Southern blot membranes used previously in routine IS6110 DNA fingerprint analysis. The hybridization probe constructed ("W-Beijing polyprobe") contains the PCR-amplified fragments specific for three M. tuberculosis chromosomal loci used for the identification of W-Beijing strains. The targets include the dnaA-dnaN and NTF regions and the direct repeat locus. A total of 526 selected clinical isolates (representative of 253 different IS6110-defined strain types) were analyzed using the W-Beijing polyprobe. A total of 148 isolates from this collection were found to be members of the W-Beijing phylogenetic lineage, comprising 106 strains from the W-Beijing family (46 clusters) and 42 related isolates. Rehybridization results were confirmed by computer-assisted analysis. The sensitivity and specificity of this method were estimated at 98.7% and 99.7%, respectively. This study demonstrates that the W-Beijing polyprobe can accurately and reliably discriminate members of the W-Beijing phylogenetic lineage and the W-Beijing family of M. tuberculosis strains.
authors.affiliation: TB Center, Public Health Research Institute, 225 Warren St., Newark, NJ 07103, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Kurepina
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Likhoshvay
authors.forename: Elena
authors.initials: E
authors.lastname: Shashkina
authors.forename: Barun
authors.initials: B
authors.lastname: Mathema
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
authors.forename: Pablo
authors.initials: P
authors.lastname: Bifani
authors.forename: Barry N
authors.initials: BN
authors.lastname: Kreiswirth
mesh_terms: D001483:Base Sequence; D002681:China; D002874:Chromosome Mapping; D016172:DNA Fingerprinting; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D017403:In Situ Hybridization; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods; D015183:Restriction Mapping; D014376:Tuberculosis / Q000175:diagnosis / Q000382:microbiology
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial