Title: Pathobiology and phylogenomics of M. tuberculosis Beijing and LAM genotypes in Russia

Author: Igor Mokrousov¹

Affiliation: ¹St. Petersburg Pasteur Institute, St. Petersburg, Russia

Abstract:

Background

Mycobacterium tuberculosis sensu stricto is important human pathogen with clonal, hierarchical and heterogeneous population structure. On the phylogenetically large-scale, M. tuberculosis includes phylogenetic lineages, while L1 (Beijing genotype being its most known family) to L4 appear the most global and most significant and their prevalence patterns are different. Ancient/ancestral sublineage of Mycobacterium tuberculosis Beijing genotype is endemic in East Asia and mainly drug susceptible. To our surprise, we recently discovered its highly resistant clonal clusters emerging in Russia. On the global scale, LAM (Latin-American Mediterranean) family is perhaps the second most studied genotype of M. tuberculosis after the Beijing genotype. LAM is prevalent in the Americas, Europe, some parts of Africa. It is second important M. tuberculosis family in Russia. LAM was shown to be associated with multidrug resistance in different settings. LAM population on the vast area of the Northern Eurasia (Russia and neighbors) is overwhelmingly (90-95%) represented by other sublineage RD115/LAM-RUS. Unlike Beijing genotype, LAM has been little studied in terms of virulence, in animal models. Thus we aimed to study virulence and lethality in the murine model of the genetically and clinically distinct strains of the Beijing and LAM family. The Beijing strains represented two clusters within ancestral Beijing sublineage. The LAM strains represented emerging MDR SIT252 and XDR SIT266, diverse, low-prevalent and susceptible SIT264, and mainly resistant and geographically widespread SIT254. The available WGS data were additionally used to investigate possible genetic variation possibly underlying the observed pathogenetic patterns.

Methods

The virulence and lethality were studied in C57BL/6 mouse model. The whole-genome sequencing (WGS) data were submitted to bioinformatics analysis.

Results

Under phylogenetic analysis of the ancient Beijing sublineage (205 genomes from Russia and East Asia), all Russian isolates were drug resistant and formed two clusters. The largest cluster 1071-32 included isolates from different parts of Russia. All had resistance mutations in KatG315/335, RpoB450, RpoC485, EmbB497, RpsL43. The smaller cluster 14717-15 included isolates from Asian Russia; they were phylogenetically close to isolates from Korea. In murine model, the clusters demonstrated contrasting patterns. Low virulent, low lethal Beijing 1071-32-cluster is widespread across former Soviet Union but at low prevalence; multiple resistance mutations likely reduced its fitness and transmissibility. In contrast, highly lethal and hypervirulent Beijing 14717-15-cluster is predominant in Buryatia, Far East (16%), sporadically found beyond it, but not forming clusters of transmission. WGS analysis revealed 69 cluster-specific SNPs, including genes related to immune evasion and mycobacterial adaptation. We term Beijing 14717-15-cluster conditionally transmissible as it is endemically prevalent only in Buryatia.

Analysis of the LAM strains revealed contrasting patterns of drug resistance, virulence and geography. The most virulent and lethal strain was drug susceptible and spread in different places but sporadically. In contrast, the least virulent strain was MDR and it was quite widespread and visible in local collections across Russia.

The reasons underlying our findings for Russian Beijing and LAM strains may also lie in the interplay of the human immune system and the genetic background of this strain. Our analysis highlights that medically relevant research should focus on compact epidemic clusters of the genetically related isolates.

Funding: Russian Science Foundation (grant 19-14-00013).