title: Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran.
abstract: OBJECTIVE
  Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis.
  
  
  METHODS
  A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification.
  
  
  RESULTS
  A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%).
  
  
  CONCLUSIONS
  The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.
authors.affiliation: Microbiology Department, Kurdistan Science and Research Branch, Islamic Azad University, Sanandaj, Iran.
authors.forename: Mahsa
authors.initials: M
authors.lastname: Dastranj
authors.affiliation: Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
authors.forename: Abbas
authors.initials: A
authors.lastname: Farahani
authors.affiliation: Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.
authors.forename: Abdolrazagh
authors.initials: A
authors.lastname: Hashemi Shahraki
authors.affiliation: West Tuberculosis Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Sara
authors.initials: S
authors.lastname: Atashi
authors.affiliation: Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Shirudi Shahid Boulevard, Daneshgah Street, Kermanshah, 67148-69914, Iran.
authors.forename: Parviz
authors.identifier: http://orcid.org/0000-0002-2596-264X
authors.initials: P
authors.lastname: Mohajeri
mesh_terms: D015169:Colony Count, Microbial; D003430:Cross-Sectional Studies; D004269:DNA, Bacterial / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D006801:Humans; D015994:Incidence; D007492:Iran / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D009165:Mycobacterium Infections, Nontuberculous / Q000453:epidemiology / Q000382:microbiology*; D009170:Nontuberculous Mycobacteria / Q000235:genetics* / Q000302:isolation & purification; D010641:Phenotype; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D013183:Sputum / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: clinical samples; molecular identification; non-tuberculous mycobacteria; polymerase chain reaction