Identification of different subtypes of rapid growing Atypical Mycobacterium from water and soil sources: Using PCR-RFLP using hsp65 and rRNA 16s–23s genes

Mohammad Varahram, Parissa Farnia, Shima Saif, Mehran Marashian, Poopak Farnia, Jaladein Ghanavi, Ali Akbar Velayati
2016 International Journal of Mycobacteriology  
Available online xxxx Keywords: Iran Mycobacterium fortuitum RGM Soil Water A B S T R A C T Objective/Background: Nontuberculosis mycobacteria (NTM) are a diverse group of microorganisms that cause a variety of diseases in humans including skin, respiratory, and gastrointestinal tract infection. Generally, NTM are classified into two categories: rapid (<7 days) and slow growing (>7 days). In this study, we aimed to investigate NTM frequency and prevalence in environmental samples. Additionally,
more » ... we tried to identify various subtypes of isolated rapid growing mycobacteria (RGM). Methods: Through a prospective descriptive cross-sectional study, water and soil samples were gathered from four neighboring towns around Tehran, the capital of Iran, at different geographic directions. Every 100 m 2 of the studied areas gave one sample containing 6 g of soil in 3-5 cm depth deposited in 50 mL sterile water as sampling media. After digestion and decontamination, DNA from culture-positive specimens (RGM) were extracted using phenol-chloroform methods. Then the molecular identification of species and subspecies were performed using 16s-23s rRNA and hsp65 gene. Results: In total, 341 RGM were found, out of which 322 (94.4%) were identified and 20 (5.8%) could not be identified. The most frequent RGM was, Mycobacterium fortuitum (72; 22%), Mycobacterium senegalense (58; 17.7%), Mycobacterium parafortuitum (44; 13.4%) and Mycobacterium conceptionense type 1 (24; 7.2%), and Mycobacterium cheloni type 1 (20; 6.0%). As shown in Table 1 , M. fortuitum had more subtypes (8), and the frequency of subtypes 1 (27.7%), 4 (16.6%), and 5 (13.8%) were higher. Among subtypes of M. senegalense, subtype 1 had a higher frequency (70.4%) in comparison to subtype 2 (29.5%). M. cheloni had just one subtype. http://dx.
doi:10.1016/j.ijmyco.2016.09.057 pmid:28043561 fatcat:7sgkzfgdtrdiras7w3ftci5wbi