Quadruple-first line drug resistance in Mycobacterium tuberculosis in Vietnam: What can we learn from genes?

Multi-drug resistance and compensatory mutations in Mycobacterium tuberculosis in Vietnam

BACKGROUND

Vietnam is a hotspot for the emergence and spread of multidrug-resistant Mycobacterium tuberculosis. This study aimed to perform a retrospective study on the compensatory evolution in multidrug-resistant M. tuberculosis strains and the association with drug-resistant mutations and M. tuberculosis genotypes.

METHODS

Hundred and seventy-three strains resistant to rifampicin (n = 126) and/or isoniazid (n = 170) (multidrug-resistant = 123) were selected according to different drug-resistant patterns and genotypes. The genes/promoter regions including rpoA, rpoB, rpoC, katG, inhA, inhA promoter, ahpC, ahpC promoter, gyrA, gyrB, and rrs were sequenced for each strain.

RESULTS

Frequency of rifampicin- and isoniazid-resistant mutations in multidrug-resistant strains was 99.2% and 97.0%, respectively. Mutations associated with low -high levels of drug resistance with low- or no-fitness costs compared to the wild type, including rpoB_Ser450Leu, katG_Ser315Thr, inhA-15(A-T), gyrA_Asp94Gly, and rrs_A1401GA, accounted for 46.3%, 76.4%, 16.2%, 8.9%, and 11.4%, respectively, in the multidrug-resistant strains. Beijing and Euro-American genotype strains were associated with high-level drug-resistant mutations, rpoB_Ser450Leu, katG_Ser315Thr, and gyrA_Asp94Gly, while East African-Indian genotype strains were associated with low to high-level drug-resistant mutations, rpoB_His445Asp, rpoB_His445Tyr, inhA-15(C-T) and rrs_A1401G. Multidrug-resistant strains (19.5%) harboured compensatory mutations linked to rifampicin resistance in rpoA, rpoB, or rpoC. Notably, the frequency of compensatory mutations in Beijing genotypes was significantly higher than in East African-Indian genotypes (21.1% vs. 3.3%, OR = 7.7; 95% CI = 1.0 to 61.2, p = 0.03). The proportion of multidrug-resistant strains with rpoB_Ser450Leu mutations carrying rpoA-rpoC mutations was higher than that of strains with other rpoB mutations (OR = 5.4; 95% CI = 1.4 to 21.1, p = 0.02) and was associated with Beijing strains. Only 1.2% (2/170) isoniazid-resistant strains carried aphC-52(C-T) mutation in the promoter region of the ahpC gene, which was hypothesised to be the compensatory mutation in isoniazid-resistant strains. Meanwhile, 11 isoniazid-resistant strains carried a katG mutation combined with either inhA-8(T-C) or inhA-15(A-T) mutations and were associated with East African-Indian strains.

CONCLUSIONS

Mutations associated with high levels of drug resistance without/with low fitness costs (rpoB_Ser450Leu and katG_Ser315Thr) along with compensatory mutations linked to rifampicin resistance were strongly associated with multidrug-resistant M. tuberculosis Beijing strains in Vietnam.

Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions

Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.

Host-pathogen relationship in retreated tuberculosis with major rifampicin resistance-conferring mutations

Introduction

It is assumed that host defense systems eliminating the pathogen and regulating tissue damage make a strong impact on the outcome of tuberculosis (TB) disease and that these processes are affected by rifampicin (RIF) resistance-conferring mutations of Mycobacterium tuberculosis (Mtb). However, the host responses to the pathogen harboring different mutations have not been studied comprehensively in clinical settings. We analyzed clinico-epidemiological factors and blood transcriptomic signatures associated with major rpoB mutations conferring RIF resistance in a cohort study.

Methods

Demographic data were collected from 295 active pulmonary TB patients with treatment history in Hanoi, Vietnam. When recruited, drug resistance-conferring mutations and lineage-specific variations were identified using whole-genome sequencing of clinical Mtb isolates. Before starting retreatment, total RNA was extracted from the whole blood of HIV-negative patients infected with Mtb that carried either the rpoB H445Y or rpoB S450L mutation, and the total RNA was subjected to RNA sequencing after age-gender matching. The individual RNA expression levels in the blood sample set were also measured using real-time RT-PCR. Logistic and linear regression models were used to assess possible associations.

Results

In our cohort, rpoB S450L and rpoB H445Y were major RIF resistance-conferring mutations [32/87 (36.8%) and 15/87 (17.2%), respectively]. H445Y was enriched in the ancient Beijing genotype and was associated with nonsynonymous mutations of Rv1830 that has been reported to regulate antibiotic resilience. H445Y was also more frequently observed in genetically clustered strains and in samples from patients who had received more than one TB treatment episode. According to the RNA sequencing, gene sets involved in the interferon-γ and-α pathways were downregulated in H445Y compared with S450L. The qRT-PCR analysis also confirmed the low expression levels of interferon-inducible genes, including BATF2 and SERPING1, in the H445Y group, particularly in patients with extensive lesions on chest X-ray.

Discussion

Our study results showed that rpoB mutations as well as Mtb sublineage with additional genetic variants may have significant effects on host response. These findings strengthen the rationale for investigation of host-pathogen interactions to develop countermeasures against epidemics of drug-resistant TB.

Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam

Drug-resistant tuberculosis (TB) is a serious global problem, and pathogen factors involved in the transmission of isoniazid (INH)-resistant TB have not been fully investigated. We performed whole genome sequencing of 332 clinical Mycobacterium tuberculosis (Mtb) isolates collected from patients newly diagnosed with smear-positive pulmonary TB in Hanoi, Vietnam. Using a bacterial genome-wide approach based on linear mixed models, we investigated the associations between 31-bp k-mers and clustered strains harboring katG-S315T, a major INH-resistance mutation in the present cohort and in the second panel previously published in South Africa. Five statistically significant genes, namely, PPE18/19, gid, emrB, Rv1588c, and pncA, were shared by the two panels. We further identified variants of the genes responsible for these k-mers, which are relevant to the spread of INH-resistant strains. Phylogenetic convergence test showed that variants relevant to PPE46/47-like chimeric genes were significantly associated with the same phenotype in Hanoi. The associations were further confirmed after adjustment for the confounders. These findings suggest that genomic variations of the pathogen facilitate the expansion of INH-resistance TB, at least in part, and our study provides a new insight into the mechanisms by which drug-resistant Mtb maintains fitness and spreads in Asia and Africa.

Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review

Drug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations.

Resistance of Mycobacterium tuberculosis strains to Rifampicin: A systematic review and meta-analysis

Introduction

Antitubercular drug resistance strain is a horrifying barrier to effective TB treatment and prevention. The present study aimed to determine the prevalence and geographical distribution of rifampicin-resistance M. tuberculosis (MTB) strains.

Methods

We searched two electronic databases, PubMed and EMBASE, until 26 March 2017 and updated our search on 27 April 2018 and accessed all prevalence studies of MTB strain and their drug susceptibility patterns to rifampicin. The pooled prevalence estimate was determined using random effects model.

Results

We identified 23 studies satisfying the inclusion criteria. The proportion of rifampicin resistance strains was diverged depending on the type of strains, country and Regions. The pooled estimate of rifampicin-resistance strains of MTB for the included studies was 4% (95% CI: 3–5%). In subgroup analysis based on World Health Organization (WHO) Regions, the pooled estimate of rifampicin-resistance strains of MTB was 11% (95% CI: 9–13%) with the Western Pacific Region 24%, Europian Region 10%, South-East Asian Region 6%, African Region 3% and Region of American 1%. Beijing family was the most dominant strain resistance to rifampicin with pooled prevalence of 14% (95% CI: 10–18%). The pooled prevalence of other families, i.e. EAI, T, CAS, MANU, Haarlem, LAM and Ural, was ≤2% for each.

Conclusion

High burden of rifampicin resistance MTB strains was identified in the Western Pacific Region. Of these, Beijing family was predominantly resistance to rifampicin in Western Pacific Region and South-East Asian Region and also spread to European Region and Region of American.

Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis

At present, the successful transmission of drug-resistant Mycobacterium tuberculosis, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, in human populations, threatens tuberculosis control worldwide. Differently from many other bacteria, M. tuberculosis drug resistance is acquired mainly through mutations in specific drug resistance-associated genes. The panel of mutations is highly diverse, but depends on the affected gene and M. tuberculosis genetic background. The variety of genetic profiles observed in drug-resistant clinical isolates underlines different evolutionary trajectories towards multiple drug resistance, although some mutation patterns are prominent. This review discusses the intrinsic processes that may influence drug resistance evolution in M. tuberculosis, such as mutation rate, drug resistance-associated mutations, fitness cost, compensatory mutations and epistasis. This knowledge should help to better predict the risk of emergence of highly resistant M. tuberculosis strains and to develop new tools and strategies to limit the development and spread of MDR and XDR strains.