Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

Abstract

BackgroundMycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system.Methodology/Principal FindingsWe sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes.ConclusionsThis is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity.

Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity

“…Notably, all previously published L5 genomes, clustered inside L5.1 (Comas et al. 2010; Winglee et al. 2016; Zhu et al.…”

“…The alignment files were subjected to local realignment and deduplication using the Genome Analysis Toolkit (GATK) (McKenna et al. 2010) and Picard (Winglee et al. 2016).…”

The most frequent Mycobacterium tuberculosis complex families in mali (2006–2016) based on spoligotyping

“…This seems to be high and is in line with the global increase of primary DR in Mali. [19] In a separate study, 2.9% of newly infected TB patients had resistance to rifampicin after screened by Xpert MTB/RIF. [20] This rate should be taken seriously by the Mali National TB Program to plan further actions to avoid uncontrolled spread of drug-resistant strains in the country.…”

Mycobacterium tuberculosisComplex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition

“…Today, the advent of next generation sequencing has provided the first collection of genomic data from M. africanum and animal-adapted species (de la Fuente et al 2015; Winglee et al 2016). Thus, studies covering the whole MTBC are now possible.…”