Whole-Genome Analysis of Mycobacterium tuberculosis from Patients with Tuberculous Spondylitis, Russia

Whole genome sequencing of drug resistance Mycobacterium tuberculosis from extra-pulmonary sites

This study aimed to determinate characteristics of drug resistance Mycobacterium tuberculosis from patients with extra-pulmonary tuberculosis (EPTB). Patients were retrospectively studied from January 2020 to December 2021. All the isolates were cultured, tested drug susceptibility, and detected the gene mutation using whole genome sequencing. The correlations of whole genome sequencing, pattern of DR, patients' distribution, and transmission were analyzed. 111 DR-EPTB isolates included pre-XDR-TB (53.2%), MDR-TB (29.7%), and poly-DR-TB (12.6%). The resistant drugs were INH followed by RFP and SM. The genotypes of 111 strains were lineage 2 and lineage 4. KatG_p.Ser315Thr was main gene mutation for resistance to INH; rpsL_p.Lys43Arg for SM, rpoB_p.Ser450Leu for rifampicin, embB_p.Met306Val for ethambutol, gyrA_p.Asp94Gly for FQs, and pncA_p.Thr76Pro for PZA. The residence was a significant risk factor for cluster transmission by patients and phenotypic DR types of strains for lineage 2 transmission. In the local area of southwest China INH, rifampicin and SM were main drugs in patients with DR-EPTB. KatG_p.Ser315, rpoB_p.Ser450Leu, and rpsL_p.Lys43Arg were main gene mutations. Phenotypic DR types and residence were main risk of transmission.

Resistance patterns and transmission of mono- and polyresistant TB: clinical impact of WGS

Objectives

Rapidly diagnosing drug-resistant TB is crucial for improving treatment and transmission control. WGS is becoming increasingly accessible and has added value to the diagnosis and treatment of TB. The aim of the study was to perform WGS to determine the rate of false-positive results of phenotypic drug susceptibility testing (pDST) and characterize the molecular mechanisms of resistance and transmission of mono- and polyresistant Mycobacterium (M.) tuberculosis.

Methods

WGS was performed on 53 monoresistant and 25 polyresistant M. tuberculosis isolates characterized by pDST. Sequencing data were bioinformatically processed to infer mutations encoding resistance and determine the origin of resistance and phylogenetic relationship between isolates studied.

Results

The data showed the variable sensitivity and specificity of WGS in comparison with pDST as the gold standard: isoniazid 92.7% and 92.3%; streptomycin 41.9% and 100.0%; pyrazinamide 15% and 94.8%; and ethambutol 75.0% and 98.6%, respectively. We found novel mutations encoding resistance to streptomycin (in gidB) and pyrazinamide (in kefB). Most isolates belonged to lineage 4 (80.1%) and the overall clustering rate was 11.5%. We observed lineage-specific gene variations encoding resistance to streptomycin and pyrazinamide.

Conclusions

This study highlights the clinical potential of WGS in ruling out false-positive drug resistance following phenotypic or genetic drug testing, and recommend this technology together with the WHO catalogue in designing an optimal individualized treatment regimen and preventing the development of MDR TB. Our results suggest that resistance is primarily developed through spontaneous mutations or selective pressure.

Population structure of Mycobacterium tuberculosis from referral clinics in Western Siberia, Russia: Before and during the Covid-19 pandemic

The dramatic change in global health imposed by the Covid-19 pandemic has also impacted TB control. The TB incidence decreased dramatically not because of the improved situation but due to undertesting, reduced resources, and ultimately, substantially reduced detection rate. We hypothesized that multiple and partly counteracting factors could influence changes in the local Mycobacterium tuberculosis population. To test this hypothesis, we analyzed M. tuberculosis isolates collected in Western Siberia, Russia, before and during the Covid-19 pandemic. A total of 269 M. tuberculosis isolates from patients admitted at referral clinics were studied. The pre-pandemic and pandemic collections included 179 and 90 isolates, respectively. Based on genotyping, both pre-pandemic and pandemic samples are heavily dominated by the Beijing genotype isolates (95% and 88%) that were mostly MDR (80 and 68%). The high proportion of MDR isolates is due to the specific features of the studied collections biased towards patients with severe TB admitted at the National referral center in Novosibirsk. While no dramatic change was observed in the M. tuberculosis population structure in the survey area in Western Siberia during the Covid-19 pandemic in 2020–2021 compared to the pre-pandemic collection, still we note a certain decrease of the Beijing genotype and an increase in the proportion and diversity of the non-Beijing isolates. However, the transmissible and MDR Beijing B0/W148 did not increase its prevalence rate during the pandemic. More generally, the high prevalence rate of the Beijing genotype and its strong association with MDR both before and during the pandemic are alarming features of this region in Western Siberia, Russia.

A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China

BACKGROUND

Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis (Mtb). China is the third in top 8 high TB burden countries and Guangxi is one of the high incidence areas in South China. Determine bacterial factors that affected TB incidence rate is a step toward Ending the TB epidemic.

RESULTS

Genomes of M. tuberculosis cultures from a relatively high and low incidence region in Guangxi have been sequenced. 347 of 358(96.9%) were identified as M. tuberculosis. All the strains belong to Lineage 2 and Lineage 4, except for one in Lineage 1. We found that the genetic structure of the M. tuberculosis population in each county varies enormously. Low incidence rate regions have a lower prevalence of Beijing genotypes than other regions. Four isolates which harbored mutT4-48 also had mutT2-58 mutations. It is suggested that strains from the ancestors of modern Beijing lineage is circulating in Guangxi. Strains of modern Beijing lineage (OR=2.04) were more likely to acquire drug resistances than Lineage 4. Most of the lineage differentiation SNPs are related to cell wall biosynthetic pathways.

CONCLUSIONS

These results provided a higher resolution to better understand the history of transmission of M. tuberculosis from/to South China. And the incidence rate of tuberculosis might be affected by bacterial population structure shaped by demographic history. Our findings also support the hypothesis that Modern Beijing lineage originated in South China.

Genomic Variations in Drug Resistant Mycobacterium tuberculosis Strains Collected from Patients with Different Localization of Infection

Mycobacterium tuberculosis is a highly studied pathogen due to public health importance. Despite this, problems like early drug resistance, diagnostics and treatment success prediction are still not fully resolved. Here, we analyze the incidence of point mutations widely used for drug resistance detection in laboratory practice and conduct comparative analysis of whole-genome sequence (WGS) for clinical M. tuberculosis strains collected from patients with pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (XPTB) localization. A total of 72 pulmonary and 73 extrapulmonary microbiologically characterized M. tuberculosis isolates were collected from patients from 2007 to 2014 in Russia. Genomic DNA was used for WGS and obtained data allowed identifying major mutations known to be associated with drug resistance to first-line and second-line antituberculous drugs. In some cases previously described mutations were not identified. Using genome-based phylogenetic analysis we identified M. tuberculosis substrains associated with distinctions in the occurrence in PTB vs. XPTB cases. Phylogenetic analyses did reveal M. tuberculosis genetic substrains associated with TB localization. XPTB was associated with Beijing sublineages Central Asia (Beijing CAO), Central Asia Clade A (Beijing A) and 4.8 groups, while PTB localization was associated with group LAM (4.3). Further, the XPTB strain in some cases showed elevated drug resistance patterns relative to PTB isolates. HIV was significantly associated with the development of XPTB in the Beijing B0/W148 group and among unclustered Beijing isolates.

Differential determinants of virulence in two Mycobacterium tuberculosis Colombian clinical isolates of the LAM09 family

The heterogeneity of the clinical outcome of Mycobacterium tuberculosis (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.

Early ancient sublineages of Mycobacterium tuberculosis Beijing genotype: unexpected clues from phylogenomics of the pathogen and human history

OBJECTIVE

The Mycobacterium tuberculosis Beijing family is an epidemiologically important lineage subdivided into large-scale phylogenetic sublineages: ancient, endemic in East Asia, and global modern. Here, we analysed ancient sublineages of the Beijing genotype in the Omsk region of southwestern Siberia, an intriguing area at the intersection of European Russia, Siberia, and Central Asia.

METHODS

The study included 423 M. tuberculosis strains isolated in 2013-2017 and subjected to drug susceptibility testing, genotyping, and whole genome sequencing.

RESULTS

The Beijing genotype constituted 280 out of 423 strains. Forty Beijing strains belonged to the early ancient sublineage (wild type mutT4-48). Of these, 11 belonged to the 14717-15 MIRU-VNTR cluster and had intact RD181, 29 belonged to the 1071-32 cluster and had the RD181 deletion. Thirty-nine ancient strains were multidrug-resistant (MDR) and 20 pre-extensively drug resistant (XDR)/XDR. Comparison with global data demonstrated that these clones circulate mainly in Asian Russia with certain phylogenetic affinity to strains from Japan, Korea, and northeastern China. The genome-wide analysis revealed 29-37 single nucleotide polymorphism distances between isolates from different Russian regions within these two clusters.

CONCLUSIONS

Based on phylogenetic, phylogeographic, genomic, and historical data, we hypothesize that these two clones or their direct ancestors were probably brought to Russia ∼70 years ago after the Second World War with Japanese prisoners of war and, until recently, were mainly circulating in Siberia and the Far East. Their elevated prevalence in Omsk along with the extremely strong association with not only MDR but also pre-XDR/XDR also observed in other locations highlight their epidemic potential and the need for monitoring and attention from health authorities.