Investigation of the Rv3065, Rv2942, Rv1258c, Rv1410c, and Rv2459 efflux pump genes expression among multidrug-resistant Mycobacterium tuberculosis clinical isolates

The catalogue of Mycobacterium tuberculosis mutations associated with drug resistance to 12 drugs in China from a nationwide survey: a genomic analysis

BACKGROUND

WHO issued the first edition catalogue of Mycobacterium tuberculosis complex (MTBC) mutations associated with drug resistance in 2021. However, country-specific issues might lead to arising complex and additional drug-resistant mutations. We aimed to fully reflect the characteristics of drug resistance mutations in China.

METHODS

We analysed MTBC isolates from the nationwide drug-resistant tuberculosis surveillance with 70 counties in 31 provinces, municipalities, and autonomous regions in China. Three types of MYCOTB plates were used to perform drug susceptibility testing for 12 antibiotics (rifampicin, isoniazid, ethambutol, levofloxacin, moxifloxacin, amikacin, kanamycin, ethionamide, clofazimine, linezolid, delamanid, and bedaquiline). Mutations were divided into five groups according to their odds ratios, positive predictive values, false discovery rate-corrected p values, and 95% CIs: (1) associated with resistance; (2) associated with resistance-interim; (3) uncertain significance; (4) not associated with resistance-interim; and (5) not associated with resistance. The Wilcoxon rank-sum and Kruskal-Wallis tests were used to quantify the association between mutations and minimum inhibitory concentrations (MICs). Our dataset was compared with the first edition of the WHO catalogue.

FINDINGS

We analysed 10 146 MTBC isolates, of which 9071 (89·4%) isolates were included in the final analysis. 744 (8·2%) isolates were resistant to rifampicin and 1339 (14·8%) to isoniazid. 208 (1·9%) of 11 065 mutations were classified as associated with resistance or associated with resistance-interim. 33 (97·1%) of 34 mutations in group 1 and 92 (52·9%) of 174 in group 2 also appeared in groups 1 or 2 of the WHO catalogue. Of 81 indel mutations in group 2, 15 (18·5%) were in the WHO catalogue. The newly discovered mutation gyrA_Ala288Asp was associated with levofloxacin resistance. MIC values for rifampicin, isoniazid, moxifloxacin, and levofloxacin corresponding to resistance mutations in group 1 were significantly different (p<0·0001), and 12 high-level resistance mutations were detected. 61 mutations in group 3 occurred as solo in at least five phenotypically susceptible isolates, but with MIC values moderately higher than other susceptible isolates. Among 945 phenotypically resistant but genotypically susceptible isolates, 433 (45·8%) were mutated for at least one efflux pump gene.

INTERPRETATION

Our analysis reflects the complexity of drug resistance mutations in China and suggests that indel mutations, efflux pump genes, protein structure, and MICs should be fully considered in the WHO catalogue, especially in countries with a high tuberculosis burden.

FUNDING

National Key Research and Development Program of China and the Science and Technology Major Project of Tibetan Autonomous Region of China.

Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis

The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.

EfpA is required for regrowth of Mycobacterium tuberculosis following isoniazid exposure

Efflux of antibiotics is an important survival strategy in bacteria. Mycobacterium tuberculosis has approximately sixty efflux pumps, but little is known about the role of each pump or the substrates they efflux. The putative efflux pump, EfpA, is a member of the major facilitator superfamily and has been shown to be essential by saturation transposon mutagenesis studies. It has been implicated in the efflux of isoniazid (INH), which is a first-line drug used to treat tuberculosis (TB). This is supported by evidence from transcriptional profiling showing that efpA is induced in response to INH exposure. However, its roles in the physiology and adaptation of M. tuberculosis to antibiotics have yet to be determined. In this study, we describe the repression of efpA in M. tuberculosis, using CRISPR interference (CRISPRi) to knockdown the expression of this essential gene and the direct effect of this on the ability of M. tuberculosis to survive exposure to INH over a 45-day time course. We determined that wild-type levels of efpA were required for recovery of M. tuberculosis following INH exposure and that, after 45 days of INH exposure, only a few viable colonies were recoverable from efpA-repressed M. tuberculosis. We conclude that EfpA is required for recovery of M. tuberculosis following INH exposure, which could reduce the efficacy of INH in vivo, and that EfpA may have a role in the development of resistance during drug therapy.

Overexpression of efflux pump genes is one of the mechanisms causing drug resistance in Mycobacterium tuberculosis

IMPORTANCE

Gene mutations cannot explain all drug resistance of Mycobacterium tuberculosis, and the overexpression of efflux pump genes is considered another important cause of drug resistance. A total of 46 clinical isolates were included in this study to analyze the overexpression of efflux pump genes in different resistant types of strains. The results showed that overexpression of efflux pump genes did not occur in sensitive strains. There was no significant trend in the overexpression of efflux pump genes before and after one-half of MIC drug induction. By adding the efflux pump inhibitor verapamil, we can observe the decrease of MIC of some drug-resistant strains. At the same time, this study ensured the reliability of calculating the relative expression level of efflux pump genes by screening reference genes and using two reference genes for the normalization of quantitative PCR. Therefore, this study confirms that the overexpression of efflux pump genes plays an important role in the drug resistance of clinical isolates of Mycobacterium tuberculosis.

Transcriptional regulation and drug resistance in Mycobacterium tuberculosis

Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.

Rescue of susceptibility to second-line drugs in resistant clinical isolates of Mycobacterium tuberculosis

Aim: Antibiotic resistance is one of the biggest threats to global health, and this study aimed better understand how the efflux pumps are related to this process in tuberculosis clinical isolates. Results: The combination of antibiotics plus efflux pumps (EP) inhibitors was able to restore the susceptibility of clinical isolates in 100% of aminoglycosides resistance and 33.3% of the fluoroquinolones resistance. The relative expression of EP genes in pre-extensively drug-resistant isolates showed an increase of up to 1000-times. Conclusion: The rescue of susceptibility in the presence of EP inhibitors, the increased of activity and expression of the EP genes alert that the inhibition of EP can reduce the selection of resistant strains and improve treatment.