title: Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.
abstract: BACKGROUND
  While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran.
  
  
  METHODS
  A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations.
  
  
  RESULTS
  Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%).
  
  
  CONCLUSIONS
  Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Ali Akbar
authors.initials: AA
authors.lastname: Velayati
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Parissa
authors.initials: P
authors.lastname: Farnia
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Mohadese
authors.initials: M
authors.lastname: Mozafari
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Donya
authors.initials: D
authors.lastname: Malekshahian
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Shima
authors.initials: S
authors.lastname: Seif
authors.affiliation: Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors.forename: Snaz
authors.initials: S
authors.lastname: Rahideh
authors.affiliation: Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois, United States of America.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirsaeidi
mesh_terms: D004777:Environment; D006801:Humans; D007492:Iran / Q000453:epidemiology; D017720:Molecular Epidemiology; D009165:Mycobacterium Infections, Nontuberculous / Q000453:epidemiology* / Q000382:microbiology*; D009170:Nontuberculous Mycobacteria / Q000145:classification / Q000302:isolation & purification*; D015995:Prevalence; D012988:Soil Microbiology; D014871:Water Microbiology