The prevalence of nontuberculous mycobacteria (NTM) has increased in tuberculosis (TB)-suspected clinical samples. These bacteria are now recognized as important emerging pathogens, which affect both immunocompetent and immunocompromised individuals. The aim of this study was to evaluate the frequency of NTM in clinical samples and to efficacy of genomic loci as targets for detection of NTM species. This cross-sectional study was performed on 8166 clinical samples to determine the presence of NTM species from April 2013 to December 2015. The phenotypic methods were applied for preliminary NTM identification. The PCR-RFLP assay of heat shock protein-65 (hsp-65) gene and multilocus sequence analysis based on 16S-23S internal transcribes spacer (ITS), rpoB, and 16S rRNA genes were applied for species identification. In a total of 520 isolates from TB-suspected cases, 61 samples (11.7%) were identified as NTM. Overall, Mycobacterium (M.) fortuitum (63.9%) was the most frequently encountered species, followed by M. kansasii (9.8%), M. simiae (9.8%), M. abscessus (6.7%), M. gordonae (4.9%), M. flavescens (3.3%), and M. setense (1.6%). Moreover, sequencing of 16S rRNA and rpoB genes could identify all NTM species. In conclusion, we showed that the samples were infected by six NTM species, and M. fortuitum was the most frequent NTM strain. Based on the findings, 16S rRNA and rpoB genes were superior to ITS gene in identification of NTM species.
Keywords: multilocus sequence analysis; nontuberculous mycobacteria.