Search

Here, we report the development and key features of the first external quality assessment (EQA) scheme for Mycobacterium tuberculosis whole-genome sequencing (WGS). The results of four rounds (2017 to 2020) of implementation within the European tuberculosis reference laboratories network (ERLTB-Net-2) are presented and discussed. EQA panels comprising 10 genomic DNAs were distributed to ERLTB-Net 2 laboratories volunteering to participate in this exercise. Since 2018, five FASTQ files were added to better assess the dry WGS processes, and in 2020, three of the five files were replaced by synthetic files (providing additional flexibility for the mutations included in the panels). Ten National tuberculosis reference laboratories participated in all four EQA rounds, and seven participated in at least one. High-confidence resistance mutations were correctly identified by all laboratories, but challenges remained with respect to the identification of mixed loci and interpretation of rare mutations. M. tuberculosis genotyping and clustering analysis was >90% accurate for pure samples with the main challenges being related to the analysis of mixed genotypes and DNA FASTQ files. The development and implementation of this WGS EQA scheme has contributed to the continuous improvement in performance of participating laboratories in M. tuberculosis WGS and data analysis. This scheme can serve as a model of comprehensive quality assessment for M. tuberculosis WGS that can be replicated in different settings worldwide. IMPORTANCE The wider availability of whole-genome sequencing (WGS) coupled to new developments in bioinformatic tools and databases to interpret Mycobacterium tuberculosis complex WGS data has accelerated the adoption of this method for the routine prediction of antimycobacterial drug resistance and genotyping, thus necessitating the establishment of a comprehensive external quality control system. Here, we report 4 years of development and results from such a panel.

Background Tackling tuberculosis (TB) requires testing and treatment latent tuberculosis in high-risk groups. The aim of this study was to estimate the predictive values of the tuberculin skin test (TST) and interferon gamma release assays (IGRAs) for development of active TB . Method A cohort of migrants and contacts of active TB patients were prospectively recruited in clinics, the community and primary care. Each participant received three tests (Quantiferon Gold In-Tube [QFT-GIT], TSPOT.TB and TST). A positive TST was reported using three thresholds: 5mm (TST5), 10mm (TST10), and 5mm in BCG-naïve or 15mm in vaccinated (TST15). Participants were followed for a median of 2.9 years. Incident TB cases were identified by national TB databases, telephone interview, and medical note review. Outcomes were ratio of incidence rate ratios and predictive values for TB development. Findings Ninety-seven (1.0%) of 9,610 participants developed active TB (77 of 6,380 with results for all 3 tests). In all tests, TB incidence was very low in test-negatives (1.2-1.6 per 1000 per year). Incidence rates in test-positives were highest for T-SPOT.TB (13.2, 95%CI: (9.9,17.4)), TST15 (11.1 (8.3,14.6)) and QFT-GIT (10.1 (7.4,13.4)). Positive results for these tests were significantly more predictive of progression than TST10 and TST5. However, TST5 identified a higher proportion of progressors than TST10, TST15, T-SPOT.TB and QFT-GIT. Interpretation IGRA-based or TST15 strategies appear most suited for screening. Although TST5 and TST10 detect more TB cases, they also classify more individuals who are unlikely to develop TB as testpositive. Funding source: National Institute for Health Research Health Technology Assessment Programme 08-68-01.

SETTING: Implementation of novel diagnostic assays in tuberculosis (TB) laboratory diagnosis requires effective management of time and resources. OBJECTIVE: To further develop and assess at multiple centres a time-and-motion (T&M) tool as an objective means for recording the actual time spent on running laboratory assays. DESIGN: Multicentre prospective study conducted in six European Union (EU) reference TB laboratories. RESULTS: A total of 1060 specimens were tested using four laboratory assays. The number of specimens per batch varied from one to 60; a total of 64 recordings were performed. Theoretical hands-on times per specimen (TTPS) in h:min:s for Xpert® MTB/RIF, mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping, Ziehl-Neelsen staining and manual fluorescence microscopy were respectively 00:33:02 ± 00:12:32, 00:13:34 ± 00:03:11, 00:09:54 ± 00:00:53 and 00:06:23 ± 00:01:36. Variations between laboratories were predominantly linked to the time spent on reporting and administrative procedures. Processing specimens in batches could help save time in highly automated assays (e.g., line-probe) (TTPS 00:14:00 vs. 00:09:45 for batches comprising 7 and 31 specimens, respectively). CONCLUSIONS: The T&M tool can be considered a universal and objective methodology contributing to workload assessment in TB diagnostic laboratories. Comparison of workload between laboratories could help laboratory managers justify their resource and personnel needs for the implementation of novel, time-saving, cost-effective technologies, as well as identify areas for improvement.

OBJECTIVES: We conducted a systematic review to determine the diagnostic accuracy of Whole Genome Sequencing (WGS) of M. tuberculosis for the detection of resistance to first and second line anti-tuberculosis (TB) drugs. METHODS: The study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A total of 20 publications were included. The sensitivity, specificity, PPV and NPV of WGS using phenotypic Drug Susceptibility Testing (DST) methods as a gold standard were determined. RESULTS: Anti-TB agents tested included all first line drugs, a variety of reserve drugs, as well as new drugs. Polymorphisms in a total of 53 genes were tested for associations with drug resistance. Pooled sensitivity and specificity values for detection of resistance to selected first line drugs were 0.98 (95% CI, 0.93 to 0.98) and 0.98 (95% CI, 0.98 to 1.00) for rifampicin and 0.97 (95% CI, 0.94 to 0.99) and 0.93 (95% CI 0.91 to 0.96) for isoniazid, respectively. Due to high heterogeneity in studies' design, lack of data, knowledge of resistance mechanisms and clarity on exclusion of phylogenetic markers, there was a significant variation in analytical performance of WGS for the remaining first-line, reserved drugs and new drugs. CONCLUSIONS: WGS could be considered a promising alternative to existing phenotypic and molecular DST methods for rifampicin and isoniazid pending standardization of analytical pipelines. To ensure clinical relevance of WGS for detection of M. tuberculosis complex drug resistance, future studies should include information on clinical outcomes.

Background External quality assurance (EQA) systems are essential to ensure accurate diagnosis of TB and drug-resistant TB. The implementation of EQA through organising regular EQA rounds and identification of training needs is one of the key activities of the European TB reference laboratory network (ERLTB-Net). The aim of this study was to analyse the results of the EQA rounds in a systematic manner and to identify potential benefits as well as common problems encountered by the participants. Methods The ERLTB-Net developed seven EQA modules to test laboratories’ proficiency for TB detection and drug susceptibility testing using both conventional and rapid molecular tools. All National TB Reference laboratories in the European Union and European Economic Area (EU/EEA) Member States were invited to participate in the EQA scheme. Results A total of 32 National TB Reference laboratories participated in six EQA rounds conducted in 2010–2014. The participation rate ranged from 52.9% - 94.1% over different modules and rounds. Overall, laboratories demonstrated very good proficiency proving their ability to diagnose TB and drug-resistant TB with high accuracy in a timely manner. A small number of laboratories encountered problems with identification of specific Non-tuberculous Mycobacteria (NTMs) (N = 5) and drug susceptibility testing to Pyrazinamide, Amikacin, Capreomycin, and Ethambutol (N = 4). Conclusions The European TB Reference laboratories showed a steady and high level of performance in the six EQA rounds. A network such as ERLTB-Net can be instrumental in developing and implementing EQA and in establishing collaboration between laboratories to improve the diagnosis of TB in the EU/EEA.

Objective and Methods: A long-term observational study was conducted in Samara, Russia to assess the survival and risk factors for death of a cohort of non-multidrug resistant tuberculosis (non-MDRTB) and multidrug resistant tuberculosis (MDRTB) civilian and prison patients and a civilian extensive drug-resistant tuberculosis (XDRTB) cohort. Results: MDRTB and XDRTB rates of 54.8% and 11.1% were identified in the region. Half (50%) of MDRTB patients and the majority of non-MDRTB patients (71%) were still alive at 5 years. Over half (58%) of the patients died within two years of establishing a diagnosis of XDRTB. In the multivariate analysis, retreatment (HR = 1.61, 95%CI 1.04, 2.49) and MDRTB (HR = 1.67, 95%CI 1.17, 2.39) were significantly associated with death within the non-MDR/MDRTB cohort. The effect of age on survival was relatively small (HR = 1.01, 95%CI 1.00, 1.02). No specific factor affected survival of XDRTB patients although median survival time for HIV-infected versus HIV-negative patients from this group was shorter (185 versus 496 days). The majority of MDRTB and XDRTB strains (84% and 92% respectively) strains belonged to the Beijing family. Mutations in the rpoB (codon 531 in 81/92; 88.8%), katG (mutation S315T in 91/92, 98.9%) and inhA genes accounted for most rifampin and isoniazid resistance respectively, mutations in the QRDR region of gyrA for most fluroquinolone resistance (68/92; 73.5%). Conclusions: Alarmingly high rates of XDRTB exist. Previous TB treatment cycles and MDR were significant risk factors for mortality. XDRTB patients survival is short especially for HIV-infected patients. Beijing family strains comprise the majority of drug-resistant strains. © 2011 Balabanova et al.

Objective: To analyse the feasibility, cost and performance of rapid tuberculosis (TB) molecular and culture systems, in a high multidrug-resistant TB (MDR TB) middle-income region (Samara, Russia) and provide evidence for WHO policy change. Methods: Performance and cost evaluation was conducted to compare the BACTEC™ MGIT™ 960 system for culture and drug susceptibility testing (DST) and molecular systems for TB diagnosis, resistance to isoniazid and rifampin, and MDR TB identification compared to conventional Lowenstein-Jensen culture assays. Findings: 698 consecutive patients (2487 sputum samples) with risk factors for drug-resistant tuberculosis were recruited. Overall M. tuberculosis complex culture positivity rates were 31.6% (787/2487) in MGIT and 27.1% (675/2487) in LJ (90.5% and 83.2% for smear-positive specimens). In total, 809 cultures of M. tuberculosis complex were isolated by any method. Median time to detection was 14 days for MGIT and 36 days for LJ (10 and 33 days for smear positive specimens) and indirect DST in MGIT took 9 days compared to 21 days on LJ. There was good concordance between DST on LJ and MGIT (96.8% for rifampin and 95.6% for isoniazid). Both molecular hybridization assay results correlated well with MGIT DST results, although molecular assays generally yielded higher rates of resistance (by approximately 3% for both isoniazid and rifampin). Conclusion: With effective planning and logistics, the MGIT 960 and molecular based methodologies can be successfully introduced into a reference laboratory setting in a middle incidence country. High rates of MDR TB in the Russian Federation make the introduction of such assays particularly useful. © 2009 Balabanova et al.

Background Russia is one of 22 high burden tuberculosis (TB) countries. Identifying individuals, particularly health care workers (HCWs) with latent tuberculosis infection (LTBI), and determining the rate of infection, can assist TB control through chemoprophylaxis and improving institutional cross-infection strategies. The objective of the study was to estimate the prevalence and determine the relative risks and risk factors for infection, within a vertically organised TB service in a country with universal bacille Calmette-Guérin (BCG) vaccination. Methods and Findings We conducted a cross-sectional study to assess the prevalence of and risk factors for LTBI among unexposed students, minimally exposed medical students, primary care health providers, and TB hospital health providers in Samara, Russian Federation. We used a novel in vitro assay (for gamma-interferon [IFN-γ]) release to establish LTBI and a questionnaire to address risk factors. LTBI was seen in 40.8% (107/262) of staff and was significantly higher in doctors and nurses (39.1% [90/230]) than in students (8.7% [32/368]) (relative risk [RR] 4.5; 95% confidence interval [CI] 3.1–6.5) and in TB service versus primary health doctors and nurses: respectively 46.9% (45/96) versus 29.3% (34/116) (RR 1.6; 95% CI 1.1–2.3). There was a gradient of LTBI, proportional to exposure, in medical students, primary health care providers, and TB doctors: respectively, 10.1% (24/238), 25.5% (14/55), and 55% (22/40). LTBI was also high in TB laboratory workers: 11/18 (61.1%). Conclusions IFN-γ assays have a useful role in screening HCWs with a high risk of LTBI and who are BCG vaccinated. TB HCWs were at significantly higher risk of having LTBI. Larger cohort studies are needed to evaluate the individual risks of active TB development in positive individuals and the effectiveness of preventive therapy based on IFN-γ test results., Gamma-interferon assays were used in a cross-sectional study of Russian health care workers and found high rates of latent tuberculosis infection., Editors' Summary Background. Tuberculosis (TB) is a very common and life-threatening infection caused by a bacterium, Mycobacterium tuberculosis, which is carried by about a third of the world's population. Many people who are infected do not develop the symptoms of disease; this is called “latent infection.” However, it is important to detect latent infection among people in high-risk communities, in order to prevent infected people from developing active disease, and therefore also reduce the spread of TB within the community. 22 countries account for 80% of the world's active TB, and Russia is one of these. Health care workers are particularly at risk for developing active TB disease in Russia, but the extent of latent infection is not known. In order to design appropriate measures for controlling TB in Russia, it is important to know how common latent infection is among health care workers, as well as other members of the community. Why Was This Study Done? The researchers here had been studying the spread of tuberculosis in Samara City in southeastern Russia, where the rate of TB disease among health care workers was very high; in 2004 the number of TB cases among health care workers on TB wards was over ten times that in the general population. There was also no information available on the rates of latent TB infection among health care workers in Samara City. The researchers therefore wanted to work out what proportion of health care workers in Samara City had latent TB infection, and particularly to compare groups whom they thought would be at different levels of risk (students, clinicians outside of TB wards, clinicians on TB wards, etc.). Finally, the researchers also wanted to use a new test for detecting latent TB infection. The traditional test for detecting TB infection (tuberculin skin test) is not very reliable among people who have received the Bacillus Calmette-Guérin (BCG) vaccination against TB earlier in life, as is the case in Russia. In this study a new test was therefore used, based on measuring the immune response to two proteins produced by M. tuberculosis, which are not present in the BCG vaccine strain. What Did the Researchers Do and Find? In this study the researchers tested health care workers from all the TB clinics in Samara City, as well as other clinical staff and students, for latent tuberculosis. In total, 630 people had blood samples taken for testing. A questionnaire was also used to collect information on possible risk factors for TB. As expected, the rate of latent TB infection was highest among clinical staff working in the TB clinics, 47% of whom were infected with M. tuberculosis. This compared to a 10% infection rate among medical students and 29% infection rate among primary care health workers. The differences in infection rate between medical students, primary care health workers, and TB clinic staff were statistically significant and reflected progressively increasing exposure to TB. Among primary care health workers, past exposure to TB was a risk factor for having latent TB infection. What Do These Findings Mean? This study showed that there was a high rate of latent TB infection among health care workers in Samara City and that infection is increasingly likely among people with either past or present exposure to TB. The results suggest that further research should be carried out to test whether mass screening for latent infection, followed by treatment, will reduce the rate of active TB disease among health care workers and also prevent further spread of TB. There are concerns that widespread treatment of latent infection may not be completely effective due to the relatively high prevalence of drug-resistant TB strains and any new initiatives would therefore need to be carefully evaluated. Additional Information. Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040055. The Stop TB Partnership has been set up to eliminate TB as a public health problem; its site provides data and resources about TB in each of the 22 most-affected countries, including Russia Tuberculosis minisite from the World Health Organization, providing data on tuberculosis worldwide, details of the Stop TB strategy, as well as fact sheets and current guidelines The US Centers for Disease Control has a tuberculosis minisite, including a fact sheet on latent TB Information from the US Centers for Disease Control about the QuantiFERON-TB Gold test, used to test for latent TB infection in this study

Reliable laboratory diagnosis of tuberculosis (TB), including laboratory biomarkers of cure, remains a challenge. In our study we evaluated the performance of a Propidium Monoazide (PMA) assay for the detection of viable TB bacilli in sputum specimens during anti-TB chemotherapy and its potential use as a TB biomarker.The study was conducted at three centres on 1937 sputum specimens from 310 adult bacteriologically confirmed pulmonary TB patients obtained before commencing anti-TB treatment and at regular intervals afterwards. Performance of the PMA assay was assessed using various readout assays with bacteriology culture results and time to positivity on liquid media used as reference standards.Treatment of sputum with N-acetyl-cysteine was found to be fully compatible with the PMA assay. Good sensitivity and specificity (97.5% and 70.7–80.0%) for detection of live TB bacilli was achieved using the Xpert® MTB/RIF test as a readout assay. Tentative Ct and ΔCt thresholds for the Xpert® MTB/RIF system were proposed. Good correlation (r = 0.61) between Ct values and time to positivity of TB cultures on liquid media was demonstrated.The PMA method has potential in monitoring bacterial load in sputum specimens and so may have a role as a biomarker of cure in TB treatment. Reliable laboratory diagnosis of tuberculosis (TB), including laboratory biomarkers of cure, remains a challenge. In our study we evaluated the performance of a Propidium Monoazide (PMA) assay for the detection of viable TB bacilli in sputum specimens during anti-TB chemotherapy and its potential use as a TB biomarker. The study was conducted at three centres on 1937 sputum specimens from 310 adult bacteriologically confirmed pulmonary TB patients obtained before commencing anti-TB treatment and at regular intervals afterwards. Performance of the PMA assay was assessed using various readout assays with bacteriology culture results and time to positivity on liquid media used as reference standards. Treatment of sputum with N-acetyl-cysteine was found to be fully compatible with the PMA assay. Good sensitivity and specificity (97.5% and 70.7-80.0%) for detection of live TB bacilli was achieved using the Xpert® MTB/RIF test as a readout assay. Tentative Ct and ΔCt thresholds for the Xpert® MTB/RIF system were proposed. Good correlation (r = 0.61) between Ct values and time to positivity of TB cultures on liquid media was demonstrated. The PMA method has potential in monitoring bacterial load in sputum specimens and so may have a role as a biomarker of cure in TB treatment.