An insight into the characterization of L2 Beijing multi-drug resistant tuberculosis: Description of resistance-associated-variants and discovery of Modern 7 L2 sublineage

Abstract

Drug-resistant tuberculosis (TB) complicates global efforts toward TB elimination. However, the introduction of new and repurposed drugs— particularly the all-oral BPaL regimen (bedaquiline, pretomanid, and linezolid)—has raised hopes due to its favorable treatment outcomes for multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. Susceptibility to these new drugs may vary depending on the lineage of the Mycobacterium tuberculosis (MTB) strain. Within the framework of a research project investigating the association between potential resistance-associated nucleotide variants and MTB lineages, we used the proprietary pipeline TB-Annotator to analyze 125,000 publicly available Short Read Archive datasets from NCBI.

We identified 65 mutations across 65 clonal complexes of the lineage 2 (L2), that share at least one SNP within a list of 14 genes potentially involved in drug resistance to BPaL. During this large-scale genomic screening, we identified a previously uncharacterized clonal complex of 49 SRAs that did not belong to any previously described ancient or modern L2-sublineages (modern 1 to modern 6). We therefore performed a comparative genomic analysis on a representative set of L2 isolates to fully characterize this group. These 49 SRAs are found in an independent branch of the L2 phylogenetic tree. They share 4 SNPs, including an Ile-to-Leu substitution in the product of fbiD, and are organized into two subclusters, with an intra-sublineage SNP distance of around 150 ± 50 SNPs. We named this novel sublineage L2.2-M7. Further functional validation—through phenotypic drug susceptibility testing and gene replacement—is needed to determine whether this fbiD mutation confers resistance to pretomanid. Global genomic surveillance of this emerging sublineage is warranted to monitor its spread and clinical relevance in the era of new TB treatment regimens.