title: Characterization of the genetic diversity of extensively-drug resistant Mycobacterium tuberculosis clinical isolates from pulmonary tuberculosis patients in Peru.
abstract: BACKGROUND
  Peru holds the fourth highest burden of tuberculosis in the Americas. Despite an apparently well-functioning DOTS control program, the prevalence of multidrug resistant tuberculosis (MDR-TB) continues to increase. To worsen this situation, cases of extensively drug resistance tuberculosis (XDR-TB) have been detected. Little information exists about the genetic diversity of drug-susceptible vs. MDR-TB and XDR-TB.
  
  
  METHODS
  Cryopreserved samples of XDR strains from 2007 to 2009 (second semester), were identified and collected. Starting from 227 frozen samples, a total of 142 XDR-TB strains of Mycobacterium tuberculosis complex (MTBC; 1 isolate per patient) were retained for this study. Each strain DNA was analyzed by spoligotyping and the 15-loci Mycobacterial Interspersed Repetitive Unit (MIRU-15).
  
  
  RESULTS
  Among the 142 isolates analyzed, only 2 samples (1.41%) could not be matched to any lineage. The most prevalent sublineage was Haarlem (43.66%), followed by T (27.46%), LAM (16.2%), Beijing (9.15%), and X clade (1.41%). Spoligotype analysis identified clustering for 128/142 (90.1%) isolates vs. 49/142 (34.5%) with MIRUs. Of the samples, 90.85% belonged to retreated patients. The drug resistant profile demonstrated that 62.67% showed resistance to injectable drugs capreomycin (CAP) and kanamycin (KAN) vs. 15.5% to CAP alone and 21.8% to KAN alone. The SIT219/T1 and SIT50/H3 were the most prevalent patterns in our study. The spoligoforest analysis showed that SIT53/T1 was at the origin of many of the T lineage strains as well as a big proportion of Haarlem lineage strains (SIT50/H3, followed by SIT47/H1, SIT49/H3, and SIT2375/H1), as opposed to the SIT1/Beijing strains that did not appear to evolve into minor Beijing sublineages among the XDR-TB strains.
  
  
  CONCLUSIONS
  In contrast with other Latin-American countries where LAM sublineage is the most predominant, we found the Haarlem to be the most common followed by T sublineage among the XDR-TB strains.
authors.affiliation: Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru.
authors.forename: Omar
authors.initials: O
authors.lastname: Cáceres
authors.affiliation: WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.affiliation: Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru.
authors.forename: Carlos
authors.initials: C
authors.lastname: Bartra
authors.affiliation: WHO Supranational TB Reference Laboratory, TB and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France.
authors.forename: David
authors.initials: D
authors.lastname: Couvin
authors.affiliation: Biotechnology and Molecular Biology Laboratory, Instituto Nacional de Salud, Lima, Peru.
authors.forename: Marco
authors.initials: M
authors.lastname: Galarza
authors.affiliation: Mycobacterias National Reference Laboratory, Instituto Nacional de Salud, Lima, Peru.
authors.forename: Luis
authors.initials: L
authors.lastname: Asencios
authors.affiliation: Ministerio de Salud (MINSA), Lima, Peru.
authors.forename: Alberto
authors.initials: A
authors.lastname: Mendoza-Ticona
mesh_terms: D000328:Adult; D000995:Antitubercular Agents / Q000008:administration & dosage / Q000494:pharmacology; D019143:Evolution, Molecular; D054908:Extensively Drug-Resistant Tuberculosis / Q000382:microbiology*; D005260:Female; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D060005:Genotyping Techniques; D006801:Humans; D007267:Injections; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D008297:Male; D008875:Middle Aged; D018598:Minisatellite Repeats / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D010568:Peru; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*
chemical_list: D000995:Antitubercular Agents