title: Geographical differences associated with single-nucleotide polymorphisms (SNPs) in nine gene targets among resistant clinical isolates of Mycobacterium tuberculosis.
abstract: Alternative diagnostic methods, such as sequence-based techniques, are necessary for increasing the proportion of tuberculosis cases tested for drug resistance. Despite the abundance of data on drug resistance, isolates can display phenotypic resistance but lack any distinguishable markers. Furthermore, because resistance-conferring mutations develop under antibiotic pressure, different drug regimens could favor unique single-nucleotide polymorphisms (SNPs) in different geographical regions. A total of 407 isolates were collected from four geographical regions with a high prevalence of drug-resistant tuberculosis (India, Moldova, the Philippines, and South Africa). The "hot spot" or promoter sequences of nine genes (rpoB, gyrA, gyrB, katG, inhA promoter, ahpC promoter, eis promoter, rrs, and tlyA) associated with resistance to four types of antibiotics (rifampin, isoniazid, fluoroquinolones, and aminoglycosides) were analyzed for markers. Four genes contributed largely to resistance (rpoB, gyrA, rrs, and katG), two genes contributed moderately to resistance (the eis and inhA promoters), and three genes contributed little or no resistance (gyrB, tlyA, and the ahpC promoter) in clinical isolates. Several geographical differences were found, including a double mutation in rpoB found in 37.1% of isolates from South Africa, the C→T mutation at position -12 of the eis promoter found exclusively in 60.6% of isolates from Moldova, and the G→A mutation at position -46 of the ahpC promoter found only in India. These differences in polymorphism frequencies emphasize the uniqueness of isolates found in different geographical regions. The inclusion of several genes provided a moderate increase in sensitivity, and elimination of the examination of other genes might increase efficiency.
authors.affiliation: University of Hawaii, Honolulu, Hawaii, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: Hoshide
authors.forename: Lishi
authors.initials: L
authors.lastname: Qian
authors.forename: Camilla
authors.initials: C
authors.lastname: Rodrigues
authors.forename: Rob
authors.initials: R
authors.lastname: Warren
authors.forename: Tommie
authors.initials: T
authors.lastname: Victor
authors.forename: Henry B
authors.initials: HB
authors.lastname: Evasco
authors.forename: Thelma
authors.initials: T
authors.lastname: Tupasi
authors.forename: Valeriu
authors.initials: V
authors.lastname: Crudu
authors.forename: James T
authors.initials: JT
authors.lastname: Douglas
mesh_terms: D000904:Antibiotics, Antitubercular / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D007194:India; D008826:Microbial Sensitivity Tests / Q000379:methods; D008966:Moldova; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics*; D010679:Philippines; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D013019:South Africa; D014376:Tuberculosis / Q000188:drug therapy / Q000382:microbiology; D018088:Tuberculosis, Multidrug-Resistant / Q000235:genetics*
chemical_list: D000904:Antibiotics, Antitubercular; D001426:Bacterial Proteins; D004269:DNA, Bacterial