Alireza Neshani

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.

Loop-mediated isothermal amplification is a promising candidate for the rapid detection of Mycobacterium tuberculosis. However, the high potential for carry-over contamination is the main obstacle to its routine use. Here, a closed tube LAMP was intended for the visual detection of Mtb to compare turbidimetric and two more favorable colorimetric methods using calcein and hydroxy naphthol blue (HNB). Additionally, a less studied dye (i.e., eriochrome black T (EBT)) was optimized in detail in the reaction for the first time. Mtb purified DNA and 30 clinical specimens were used to respectively determine the analytical and diagnostic sensitivities of each method. The turbidimetric method resulted in the best analytical sensitivity (100 fg DNA/reaction), diagnostic sensitivity and specificity (100%), and time-to-positivity of the test (15 min). However, this method is highly prone to subjective error in reading the results. Moreover, HNB-, calcein-, and EBT-LAMP could respectively detect 100 fg, 1 pg, and 1 pg DNA/reaction (the analytical sensitivities) in 30, 15, and 30 min, while the diagnostic sensitivity and specificity were respectively 93.3% and 100% for them all. Interestingly, EBT-LAMP showed the lowest potential for subjective error in reading the results. This report helps judiciously choose the most appropriate visual method, taking a step forward toward the field applicability of LAMP for the detection of Mtb, particularly in resource-limited settings.