Whole genome sequencing for the management of drug-resistant TB in low income high TB burden settings: Challenges and implications

What is New in the Diagnosis of Childhood Tuberculosis?

The fact that almost half of the 1 million cases of childhood tuberculosis (TB) globally remain undiagnosed jeopardizes the TB elimination goal. Fortunately, there are new advances in this field which have the potential to bridge this diagnostic gap. Advances in imaging include computer assisted interpretation of chest X-rays (CXRs), point of care ultrasound (POCUS) and faster and superior computed tomography/ magnetic resonance imaging (CT/ MRI) protocols. The urine lipoarabinomannan test has proved to be a good point of care test for diagnosing TB in Human immunodeficiency virus (HIV) infected children. Stool and nasopharyngeal aspirates are emerging as acceptable alternatives for gastric lavage and induced sputum for diagnosing intrathoracic tuberculosis. Xpert MTB/RIF Ultra has improved sensitivity compared to Xpert MTB/RIF for diagnosing both pulmonary/ extrapulmonary TB. Xpert XDR is another commercially available accurate point of care test for detecting resistance to drugs other than rifampicin in smear positive samples. Other molecular methods including new line probe assays, pyrosequencing, whole genome sequencing, and targeted next generation sequencing are extremely promising but not available commercially at present. The C-Tb skin test is an acceptable alternative to the tuberculin skin test and interferon gamma release assays for diagnosis of latent infection. There is an urgent need to incorporate some of these advances in the existing diagnostic algorithms of childhood TB.

Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field

The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.

Variants associated with Bedaquiline (BDQ) resistance identified in Rv0678 and efflux pump genes in Mycobacterium tuberculosis isolates from BDQ naïve TB patients in Pakistan

Background

Mutations in the Rv0678, pepQ and atpE genes of Mycobacterium tuberculosis (MTB) have been reported to be associated with reduced antimycobacterial susceptibility to bedaquiline (BDQ). Resistance conferring mutations in treatment naïve MTB strains is likely to have implications for BDQ based new drug regimen that aim to shorten treatment duration. We therefore investigated the genetic basis of resistance to BDQ in MTB clinical isolates from BDQ naïve TB patients from Pakistan. In addition, mutations in genes associated with efflux pumps were investigated as an alternate mechanism of resistance.

Methods

Based on convenience sampling, we studied 48 MTB clinical isolates from BDQ naïve TB patients. These isolates (from our strain bank) included 38 MDR/pre-XDR/XDR (10 BDQ resistant, 8 BDQ intermediate and 20 BDQ susceptible) and 10 pan drug susceptible MTB isolates. All strains were subjected to whole genome sequencing and genomes were analysed to identify variants in Rv0678, pepQ, atpE, Rv1979c, mmpLS and mmpL5 and drug resistance associated efflux pump genes.

Results

Of the BDQ resistant and intermediate strains 44% (8/18) had variants in Rv0678 including; two reported mutations S63R/G, six previously unreported variants; L40F, R50Q and R107C and three frameshift mutations; G25fs, D64fs and D109fs.

Variants in efflux pumps; Rv1273c (G462K), Rv0507c (R426H) and Rv1634c (E198R) were found to be present in drug resistant isolates including BDQ resistant and intermediate isolates. E198R in efflux pump gene Rv1634c was the most frequently occurring variant in BDQ resistant and intermediate isolates (n = 10).

Conclusion

We found RAVs in Rv0678 to be commonly associated with BDQ resistance. Further confirmation of the role of variants in efflux pump genes in resistance is required so that they may be incorporated in genome-based diagnostics for drug resistant MTB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02475-4.

The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible

Whole-genome sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity, and transmission dynamics of Mycobacterium tuberculosis. Implementation of WGS in public health microbiology laboratories is impeded by a lack of user-friendly, automated, and semiautomated pipelines. We present the COMBAT-TB Workbench, a modular, easy-to-install application that provides a web-based environment for Mycobacterium tuberculosis bioinformatics. The COMBAT-TB Workbench is built using two main software components: the IRIDA platform for its web-based user interface and data management capabilities and the Galaxy bioinformatics workflow platform for workflow execution. These components are combined into a single easy-to-install application using Docker container technology. We implemented two workflows, for M. tuberculosis sample analysis and phylogeny, in Galaxy. Building our workflows involved updating some Galaxy tools (Trimmomatic, snippy, and snp-sites) and writing new Galaxy tools (snp-dists, TB-Profiler, tb_variant_filter, and TB Variant Report). The irida-wf-ga2xml tool was updated to be able to work with recent versions of Galaxy and was further developed into IRIDA plugins for both workflows. In the case of the M. tuberculosis sample analysis, an interface was added to update the metadata stored for each sequence sample with results gleaned from the Galaxy workflow output. Data can be loaded into the COMBAT-TB Workbench via the web interface or via the command line IRIDA uploader tool. The COMBAT-TB Workbench application deploys IRIDA, the COMBAT-TB IRIDA plugins, the MariaDB database, and Galaxy using Docker containers (https://github.com/COMBAT-TB/irida-galaxy-deploy).

IMPORTANCE While the reduction in the cost of WGS is making sequencing more affordable in lower- and middle-income countries (LMICs), public health laboratories in these countries seldom have access to bioinformaticians and system support engineers adept at using the Linux command line and complex bioinformatics software. The COMBAT-TB Workbench provides an open-source, modular, easy-to-deploy and -use environment for managing and analyzing M. tuberculosis WGS data and thereby makes WGS usable in practice in the LMIC context.

Estimating tuberculosis drug resistance amplification rates in high-burden settings

Background

Antimicrobial resistance develops following the accrual of mutations in the bacterial genome, and may variably impact organism fitness and hence, transmission risk. Classical representation of tuberculosis (TB) dynamics using a single or two strain (DS/MDR-TB) model typically does not capture elements of this important aspect of TB epidemiology. To understand and estimate the likelihood of resistance spreading in high drug-resistant TB incidence settings, we used epidemiological data to develop a mathematical model of Mycobacterium tuberculosis (Mtb) transmission.

Methods

A four-strain (drug-susceptible (DS), isoniazid mono-resistant (INH-R), rifampicin mono-resistant (RIF-R) and multidrug-resistant (MDR)) compartmental deterministic Mtb transmission model was developed to explore the progression from DS- to MDR-TB in The Philippines and Viet Nam. The models were calibrated using data from national tuberculosis prevalence (NTP) surveys and drug resistance surveys (DRS). An adaptive Metropolis algorithm was used to estimate the risks of drug resistance amplification among unsuccessfully treated individuals.

Results

The estimated proportion of INH-R amplification among failing treatments was 0.84 (95% CI 0.79–0.89) for The Philippines and 0.77 (95% CI 0.71–0.84) for Viet Nam. The proportion of RIF-R amplification among failing treatments was 0.05 (95% CI 0.04–0.07) for The Philippines and 0.011 (95% CI 0.010–0.012) for Viet Nam.

Conclusion

The risk of resistance amplification due to treatment failure for INH was dramatically higher than RIF. We observed RIF-R strains were more likely to be transmitted than acquired through amplification, while both mechanisms of acquisition were important contributors in the case of INH-R. These findings highlight the complexity of drug resistance dynamics in high-incidence settings, and emphasize the importance of prioritizing testing algorithms which allow for early detection of INH-R.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07067-1.

Discordant line probe genotypic testing vs culture-based drug susceptibility phenotypic testing in TB endemic KwaZulu-Natal: Impact on bedside clinical decision making

The recommendations for Mycobacterium tuberculosis drug susceptibility testing include both phenotypic and genotypic methods. This concurrent use of differing testing platforms has created an emerging challenge of discordant results, creating a diagnostic dilemma for the laboratorians as well as attending clinicians. We undertook a retrospective study to determine the prevalence of discordant results between the MTBDRplus line probe assay and solid culture-based drug susceptibility testing for rifampicin and isoniazid. The analysis was conducted for the period January 2013 and December 2015 at the Inkosi Albert Luthuli Central Hospital. Rifampicin and isoniazid resistance testing data were "paired" on 8273 isolates for culture-based drug susceptibility testing and line probe assay. The latter method showed high sensitivity and specificity of 93% and 95% respectively for isoniazid testing. For rifampicin testing, sensitivity and specificity were 95% and 75%. Overall, discordance was 14.6% for rifampicin and 7.2% for isoniazid. This report is not intended to determine superiority of one method over another. It is merely to show that discordance does exist between different methods of testing. Given the burden of HIV and Tuberculosis in Sub-Saharan Africa, these findings have clinical significance and huge public health implications. Clinicians should understand the limitations of phenotypic testing methods.

Current and future treatments for tuberculosis

Guidelines on the treatment of tuberculosis (TB) have essentially remained the same for the past 35 years, but are now starting to change. Ongoing clinical trials will hopefully transform the landscape for treatment of drug sensitive TB, drug resistant TB, and latent TB infection. Multiple trials are evaluating novel agents, repurposed agents, adjunctive host directed therapies, and novel treatment strategies that will increase the probability of success of future clinical trials. Guidelines for HIV-TB co-infection treatment continue to be updated and drug resistance testing has been revolutionized in recent years with the shift from phenotypic to genotypic testing and the concomitant increased speed of results. These coming changes are long overdue and are sorely needed to address the vast disparities in global TB incidence rates. TB is currently the leading cause of death globally from a single infectious agent, but the work of many researchers and the contributions of many patients in clinical trials will reduce the substantial global morbidity and mortality of the disease.

One Health approach in the prevention and control of mycobacterial infections in Tanzania: lessons learnt and future perspectives

BACKGROUND

One Health (OH) is an integrated approach, formed inclusive of using multiple disciplines to attain optimal health for humans, animals, and the environment. The increasing proximity between humans, livestock, and wildlife, and its role in the transmission dynamics of mycobacterial infections, necessitates an OH approach in the surveillance of zoonotic diseases. The challenge remains as humans, livestock, and wildlife share resources and interact at various interfaces. Therefore, this review explores the potential of the OH approach to understand the impact of mycobacterial infections in Tanzania in terms of lessons learnt and future perspectives.

MATERIALS AND METHODS

Available literature on OH and mycobacterial infections in Tanzania was searched in PubMed, Google Scholar, and Web of Science. Articles on mycobacterial infections in Tanzania, published between 1997 to 2017, were retrieved to explore the information on OH and mycobacterial infections.

MAIN BODY

The studies conducted in Tanzania had have reported a wide diversity of mycobacterial species in humans and animals, which necessitates an OH approach in surveillance of diseases for better control of infectious agents and to safeguard the health of humans and animals. The close proximity between humans and animals increases the chances of inter-specific transmission of infectious pathogens, including drug-resistant mycobacteria. In an era where HIV co-infection is also the case, opportunistic infection by environmental non-tuberculous mycobacteria (NTM), commonly known as mycobacteria other than tuberculosis (MOTT) may further exacerbate the impact of drug resistance. NTM from various sources have greatest potential for diverse strains among which are resistant strains due to continued evolutional changes.

CONCLUSION

A collaborative interdisciplinary approach among professionals could help in solving the threats posed by mycobacterial infections to public health, particularly by the spread of drug-resistant strains.

Whole genome sequencing for drug-resistant tuberculosis management in South Africa: What gaps would this address and what are the challenges to implementation?

Global control of tuberculosis (TB) has been seriously impacted by the emergence and transmission of its drug-resistant forms. Delayed detection and incomplete characterisation of drug-resistant tuberculosis (DR-TB) contributes to morbidity and mortality, and to ongoing transmission of drug-resistant strains. Current culture-based and molecular diagnostic tools for TB present numerous disadvantages that could potentially lead to misdiagnosis, inappropriate treatment initiation and the amplification of drug resistance. The detection of drug-resistant tuberculosis (DR-TB) in South Africa relies on molecular diagnostic assays such as the Xpert MTB/RIF and line probe assays (MTBDRplus and MTBDRsl). However, these molecular assays are limited to detecting resistance to only a few first-line and second-line drugs. It is for this reason that next-generation sequencing (NGS) and bioinformatics pipelines have been developed for rapid detection of M. tuberculosis drug resistance, with the added advantage that sequence data could also have public health applications through understanding transmission patterns. This review highlights some of the challenges that are currently hampering the diagnosis and control of DR-TB in a high burden setting of the KwaZulu-Natal (KZN) province in South Africa. Shortfalls of current diagnostic techniques for DR-TB are discussed in detail and we also propose how these might be overcome with an accurate and rapid NGS system.

Whole genomic sequencing as a tool for diagnosis of drug and multidrug-resistance tuberculosis in an endemic region in Mexico

Background

Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico.

Methods

WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized.

Findings

Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively. Lastly, four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition.

Conclusions

The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug- and multidrug-resistant tuberculosis.

Role and value of whole genome sequencing in studying tuberculosis transmission

BACKGROUND

Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations.

OBJECTIVES

To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission.

SOURCES

A total of 69 peer-reviewed publications identified in Pubmed database.

CONTENT

Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles.

IMPLICATIONS

WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.