Analysis of Mycobacterium africanum in the last 17 years in Aragon identifies a specific location of IS6110 in Lineage 6

Abstract

The purpose of this study was to increase our knowledge about Mycobacterium africanum and report the incidence and characteristics of tuberculosis (TB) due to their lineages in Aragon, Spain, over the period 2003–2019. The study includes all the cases in our region, where all the M. tuberculosis complex isolates are systematically characterised. We detected 31 cases of M. africanum among 2598 cases of TB in the period studied. TB caused by M. africanum is rare (1.19%) in our population, and it affects mainly men of economically productive age coming from West African countries. Among the isolates, Lineage (L) 6 was more frequent than L5. The genotyping of these strains identified five clusters and 13 strains with a unique pattern. The isolates’ characterisation identified a copy of IS6110 within the moaX gene, which turned out to be specific for L6. It will allow the differentiation of this lineage from the rest of MTBC with a simple PCR reaction. It remains to be established whether this polymorphism may limit M. africanum transmission. Furthermore, a mutation in the mutT2 promoter was found as specific for L6 strains, which could be related to the high variability found for L6 compared to L5.

In-depth Analysis of IS6110 Genomic Variability in the Mycobacterium tuberculosis Complex

“…Furthermore, we studied several strains whose IS 6110 locations were known as result of our previous studies. For the second approach, we studied IS 6110 in specific locations defined for different families, including Haarlem, LAM, S, and L6 strains ( Reyes et al, 2012 ; Comín et al, 2021 ) to determine its inter- and intra-strain variability using a sample collection. In addition, CAS_DELHI and T strains were included to study the IS copy located in the DR region.…”

“…To extend the study to other MTBC families and to more strains, we relied on the specific IS 6110 locations for Haarlem, LAM, S, and L6 strains detailed in other publications ( Reyes et al, 2012 ; Comín et al, 2021 ). For the hot spot DR location, we included additional T and CAS_DELHI isolates.…”

“…A recent work ( Comín et al, 2021 ) determined that 100% of the L6 strains have a copy of IS 6110 in the moaX gene (3,709,622, −). We analysed five copies for this position, all presenting the wild-type genotype.…”

“…The first was the study of all the IS 6110 copies present in the same strain to determine whether they had an identical sequence. For the second approach, a sample collection was used to study IS 6110 copies in different MTBC families for which the location had been previously published ( Reyes et al, 2012 ; Comín et al, 2021 ) to elucidate how conserved IS 6110 is among families for the same location.…”

Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches

“…Phylogenetically, this places L5 closer to the human-adapted MTBC and L6 closer to the animal-adapted strains ( Gagneux 2018 ). Recent studies have further classified L5 based on the presence and absence of RD711 ( Ates et al, 2018 ; Coscolla et al, 2021 ; Comín et al, 2021 ).…”