Bead-captured Mycobacterium tuberculosis for next-generation sequencing diagnosis of uncultured tuberculosis

Use of uncoated magnetic beads to capture Mycobacterium smegmatis and Mycobacterium avium paratuberculosis prior detection by mycobacteriophage D29 and real-time-PCR

Uncoated tosyl-activated magnetic beads were evaluated to capture Mycobacterium smegmatis and Mycobacterium avium subspecies paratuberculosis (MAP) from spiked feces, milk, and urine. Centrifugation and uncoated magnetic beads recovered more than 99% and 93%, respectively, of 1.68 × 10⁷ CFU/mL, 1.68 × 10⁶ CFU/mL and 1.68 × 10⁵ CFU/mL M. smegmatis cells resuspended in phosphate buffer saline. The use of magnetic beads was more efficient to concentrate cells from 1.68 × 10⁴ CFU/mL of M. smegmatis than centrifugation. Likewise, the F57-qPCR detection of MAP cells was different whether they were recovered by beads or centrifugation; cycle threshold (Ct) was lower (p < 0.05) for the detection of MAP cells recovered by beads than centrifugation, indicative of greater recovery. Magnetic separation of MAP cells from milk, urine, and feces specimens was demonstrated by detection of F57 and IS900 sequences. Beads captured no less than 10⁹ CFU/mL from feces and no less than 10⁴ CFU/mL from milk and urine suspensions. In another detection strategy, M. smegmatis coupled to magnetic beads were infected by mycobacteriophage D29. Plaque forming units were observed after 24 h of incubation from urine samples containing 2 × 10⁵ and 2 × 10³ CFU/mL M. smegmatis. The results of this study provide a promising tool for diagnosis of tuberculosis and Johne's disease.

Molecular detection of Mycobacterium tuberculosis sensu stricto in the soil of Niger

Mycobacterium tuberculosis (MTB) complex is comprising of pathogenic mycobacteria responsible for human and animal tuberculosis, a major public health problem in Niger. Although infected individuals are paramount sources of contamination, nevertheless alternative, neglected sources may play some role in minority forms of the infection. Accordingly, we investigated the presence of Mycobacterium tuberculosis complex in soil samples in Niger. A total of 103 soil samples were collected in six different areas in Niger in October and November 2018 and April and May 2020 from residential areas of tuberculosis patients. Screening PCR targeting M. tuberculosis complex CRISPR-Csm4 and Xpert MTB/RIF Ultra assay were applied to detect the M. tuberculosis complex. M. tuberculosis DNA was positively detected in five of 103 (5/103; 4.8%) soil samples (Dosso: one sample, Zinder: one sample and Niamey: three samples) using the CRISPR-Csm4 system. CRISPR-Csm4 gene sequence identified four M. tuberculosis sensu stricto (may be lineages 1, 3 or 4) and one M. tuberculosis L2 lineage (Beijing). Moreover, the five positive samples were confirmed by Xpert MTB/RIF Ultra assay as rifampicin-susceptible M. tuberculosis complex strains. However, culture remained negative after 42 days. In this study, we announced for the first time the presence of M. tuberculosis sensu stricto in the soil of Niger. Moreover, these detected lineages were identical to the dominant M. tuberculosis lineages in patients. The presence of common lineages of M. tuberculosis between the soil and human highlight the risk of transmission from the soil to human.