Identification of region of difference and H37Rv-related deletion in Mycobacterium tuberculosis complex by structural variant detection and genome assembly

Understanding the epidemiology and pathogenesis of Mycobacterium tuberculosis with non-redundant pangenome of epidemic strains in China

Tuberculosis is a major public health threat resulting in more than one million lives lost every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China including 344 Lineage 2 strains, 69 Lineage 4 strains, six Lineage 3 strains, and one Lineage 1 strain. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 are core genes. However, due to 99,694 interruptions in 2,447 coding genes, we can only confidently confirm 1,651 of these genes are translated in all samples. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structural variations, mostly small indels. Assuming a proportion of these interruptions are artifacts, the number of active core genes would still be much lower than 3,438. We further described differential evolutionary patterns of genes under the influences of selective pressure, population structure and purifying selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations are concentrated in 1,310 genes. Genes involved in cell wall biogenesis are under the strongest selective pressure, while the biological process of disruption of host organelles indicates the direction of the most intensive positive selection. This study provides a comprehensive view on the genetic diversity and evolutionary patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.

Analysis of complete genomes of Mycobacterium tuberculosis sublineage 2.1 (Proto-Beijing) revealed the presence of three pe_pgrs3-pe_pgrs4-like genes

Mycobacterium tuberculosis Complex (MTBC), the etiological agent of tuberculosis (TB), demonstrates considerable genotypic diversity with distinct geographic distributions and variable virulence profiles. The pe-ppe gene family is especially noteworthy for its extensive variability and roles in host immune response modulation and virulence enhancement. We sequenced an Mtb genotype L2.1 isolate from Chiangrai, Northern Thailand, using second and third-generation sequencing technologies. Comparative genomic analysis with two additional L2.1 isolates and two L2.2.AA3 (Asia Ancestral 3 Beijing) isolates revealed significant pe-ppe gene variations. Notably, all L2.1 isolates harbored three copies of pe_pgrs3-pe_pgrs4-like genes (pe_pgrs3*, pe_pgrs4*, and pe_pgrs4), different from L2.2.AA3 and H37Rv strains. Additionally, ppe53 was duplicated in all but H37Rv, and ppe50 was deleted in L2.1 isolates, contrasting with an extended ppe50 in an L2.2 isolate (Mtb 18b), which contains an additional SVP motif. Complete deletion of ppe66 and loss of wag22 were observed in L2.1 isolates. These findings highlight the high structural variability of the pe-ppe gene family, emphasizing its complex roles in Mtb-host immune interactions. This genetic complexity offers potentially critical insights into mycobacterial pathogenesis, with significant implications for vaccine development and diagnostics.

Mycobacterium tuberculosis protein Rv2652c enhances intracellular survival by inhibiting host immune responses

BACKGROUNDS

Mycobacterium tuberculosis (Mtb), the pathogen responsible for tuberculosis, secretes a multitude of proteins that modulate the host's immune response to ensure its own persistence. The region of difference (RD) genes encoding proteins play key roles in TB immunity and pathogenesis. Nevertheless, the roles of the majority of RD-encoded proteins remain to be elucidated.

OBJECTS

To elucidate the role of Rv2652c located in RD13 in Mtb on bacterial growth, bacterial survival, and host immune response.

METHODS

We constructed the strain MS_Rv2652c which over-expresses Mtb RD-encoding protein Rv2652c in M. smegmatis (MS), and compared it with the wild strain in the bacterial growth, bacterial survival, virulence of Rv2652c, and determined the effect of MS_Rv2652c on host immune response in macrophages.

RESULTS

Rv2652c protein is located at cell wall of MS_Rv2652c strain and also an integral component of the Mtb H37Rv cell wall. Rv2652c can enhance the resistance of recombinant MS to various stressors. Moreover, Rv2652c inhibits host proinflammatory responses via modulation of the NF-κB pathway, thereby promoting Mtb survival in vitro and in vivo.

CONCLUSION

Our data suggest that cell wall protein Rv2652c plays an important role in creating a favorable environment for bacterial survival by modulating host signals and could be established as a potential TB drug target.

Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia

Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti-TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti-TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein-Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline-resistant strains (2/3), and other mutations also found in phenotypically drug-sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin-resistant TB. Using Mykrobe and TB-Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro-American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo-Oceanic; 5%). This work underlines the requirement to increase the representation of genotype-phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.

An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more pairwise SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.

Whole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers

Introduction

Mycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members.

Methods

Isolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference.

Results

M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification.

Conclusion

The present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.