Identification of a Novel Nucleic Acid Target for the Rapid and Specific Detection of Mycobacterium Simiae Using Comparative Genomic Analysis.

BACKGROUND

Mycobacterium simiae (M. simiae) is a non-tuberculous mycobacterium (NTM) that closely resembles Mycobacterium tuberculosis (M. tuberculosis) in clinical and biochemical characteristics, notably its niacin-positive phenotype. This similarity frequently leads to misdiagnosis and inappropriate treatment with first-line anti-tuberculosis drugs, to which M. simiae is frequently resistant. Current diagnostic methods are expensive or need complex equipment, highlighting the urgent need for a rapid, specific, and accessible molecular target to identify M. simiae accurately.

METHODS

In this study, a modified genome comparison method was applied to the complete reference genome of M. simiae (AP022568.1) in order to identify a putative species-specific nucleotide sequence. A conventional PCR assay was designed to amplify a 168-bp fragment within this target, designated MST601 (M. simiae Target, 601 bp). The analytical sensitivity [Limit of Detection (LOD)] was determined using serial dilutions of genomic DNA. The pilot evaluation of the assay was assessed using 10 well-characterized clinical isolates of M. simiae.

RESULTS

The MST601-PCR assay demonstrated high analytical sensitivity, with a limit of detection of ~10 fg (≈2 genome equivalents per reaction) of M. simiae genomic DNA. No cross-reactivity among the tested species was observed with any of the 10 non-target mycobacterial species tested. The assay successfully amplified the target sequence from all 10 clinical isolates. Sequencing of the amplicons revealed ≥99% identity to reference M. simiae strains in the GenBank database, validating the assay's accuracy.

CONCLUSION

A species-specific nucleic acid target, MST601, facilitating the rapid and accurate detection of M. simiae via conventional PCR was presented. This assay provides a low-cost and accessible option for diagnostic laboratories.