Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area

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.

Tuberculosis surveillance in adolescents: what to learn from European Union/European Economic Area data?

OBJECTIVE: To describe tuberculosis (TB) characteristics in the adolescent 10-19 years age group that is often underrepresented in surveillance and studies despite the high global TB burden estimated for this group.SETTING AND DESIGN: We use the case-based data reported to the European Surveillance System (TESSy) from European Union (EU)/European Economic Area (EEA) countries between 2007 and 2016 to describe notification rates, TB characteristics and treatment outcomes among adolescent TB cases. We also compare TB characteristics in young adolescents (10-14 years) and older adolescents (15-19 years).RESULTS: For the period 2007 to 2016, 705 826 TB cases were reported to TESSy by 29 EU/EEA countries, 38 054 (5.4%) of which were adolescents. The overall EU/EEA notification rate among adolescents was 6.9 per 100 000 population, 3.5 among young adolescents and 10.1 among older adolescents. The two adolescent groups had differences regarding sex distribution, site of disease, sputum smear microscopy positivity, laboratory confirmation and treatment outcome.CONCLUSION: Younger and older adolescents should be analysed as separate groups when studying and reporting TB, particularly to inform better targeting of TB prevention and care interventions in the future, in order to improve outcomes.

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.

Tuberculosis notification rate decreases faster in residents of native origin than in residents of foreign origin in the EU/EEA, 2010 to 2015

To estimate trends in tuberculosis (TB) notification rates by geographical origin, we retrieved surveillance data from 2010 to 2015 for 29 European Union and European Economic Area countries. The TB notification rate decreased at an annual rate of 5.3%. The decrease in notification rate was higher in native residents (7.0%) than in those of foreign origin (3.7%). Targeted screening and facilitated access to care and treatment could help prevent and control TB in migrants.

Second worldwide proficiency study on variable number of tandem repeats typing of Mycobacterium tuberculosis complex

BACKGROUND

The quality of variable number of tandem repeats (VNTR) typing of Mycobacterium tuberculosis was first investigated in 2009 in 37 laboratories worldwide. The results revealed an inter- and intra-laboratory reproducibility of respectively 60% and 72%. These data spurred an improvement in laboratory-specific assays and global standardisation of VNTR typing.

OBJECTIVE

To measure the effects of the technical improvements and increased standardisation, a test panel consisting of 30 M. tuberculosis complex DNA samples was distributed for VNTR typing in 41 participating laboratories from 36 countries.

RESULTS

The inter- and intra-laboratory reproducibility increased overall to respectively 78% and 88%. The 33 laboratories that participated in both the first and second proficiency studies improved their inter- and intra-laboratory reproducibility from 62% and 72% to respectively 79% and 88%. The largest improvement in reproducibility was detected in 10 laboratories that use an in-house polymerase chain reaction technique and perform amplicon sizing using gel electrophoresis. Detailed error analysis revealed a reduction in the number of systematic errors, sample exchange events and non-amplifiable loci.

CONCLUSION

This second worldwide proficiency study indicates a substantial increase in the reproducibility of VNTR typing of M. tuberculosis. This will contribute to a more meaningful interpretation of molecular epidemiological and phylogenetic studies on the M. tuberculosis complex.

Molecular surveillance of multi- and extensively drug-resistant tuberculosis transmission in the European Union from 2003 to 2011

The European Centre for Disease Prevention and Control (ECDC) initiated a project on the molecular surveillance of multi- and extensively drug-resistant tuberculosis (MDR-/XDR-TB) transmission in the European Union (EU) in the period from 2009 to 2011. In total, 2,092 variable number of tandem repeat (VNTR) patterns of MDR-/XDR-TB Mycobacterium tuberculosis isolates were collected, originating from 24 different countries in the period 2003 to 2011. Of the collected VNTR patterns, 45% (n=941) could be assigned to one of the 79 European multiple-country molecular fingerprint clusters and 50% of those (n=470) belonged to one extremely large cluster caused by Beijing strains of one genotype. We conclude that international transmission of MDR-/XDR-TB plays an important role in the EU, especially in the eastern part, and is significantly related to the spread of one strain or clone of the Beijing genotype. Implementation of international cluster investigation in EU countries should reveal underlying factors of transmission, and show how TB control can be improved regarding case finding, contact tracing, infection control and treatment in order to prevent further spread of MDR-/XDR-TB in the EU.

Drug resistance among tuberculosis cases in the European Union and European Economic Area, 2007 to 2012

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Complete republication: Epidemiology of tuberculosis in the EU/EEA in 2010 - Monitoring the progress towards tuberculosis elimination

The 2012 combined tuberculosis (TB) surveillance and monitoring report for the European Union and European Economic Area identifies a mean annual decline in TB notification rate by 4.4% from 2006 to 2010. Culture confirmation for new pulmonary cases and drug susceptibility testing have increased to 65.6% and 70.8%, but remain under their targets of 80% and 100%, respectively. Reporting of treatment outcome and coinfection with human immunodeficiency virus also remain suboptimal. Strengthened control practices are needed to allow progress towards TB elimination.

Epidemiology of tuberculosis in the EU/EEA in 2010 – monitoring the progress towards tuberculosis elimination

The 2012 combined tuberculosis (TB) surveillance and monitoring report for the European Union and European Economic Area identifies a mean annual decline in TB notification rate by 4.4% from 2006 to 2010. Culture confirmation for new pulmonary cases and drug susceptibility testing have increased to 65.6% and 70.8%, but remain under their targets of 80% and 100%, respectively. Reporting of treatment outcome and co-infection with human immunodeficiency virus also remain suboptimal. Strengthened control practices are needed to allow progress towards TB elimination.

Tuberculosis and HIV co-infection in European Union and European Economic Area countries

In order to ensure the availability of resources for tuberculosis (TB) and HIV management and control, it is imperative that countries monitor and plan for co-infection in order to identify, treat and prevent TB-HIV co-infection, thereby reducing TB burden and increasing the years of healthy life of people living with HIV. A systematic review was undertaken to determine the burden of TB-HIV infection in the European Union (EU) and European Economic Area (EEA). Data on the burden of HIV infection in TB patients and risk factors for TB-HIV co-infection in the EU/EEA were extracted from studies that collected information in 1996 and later, regardless of the year of initiation of data collection, and a narrative synthesis presented. The proportion of HIV-co-infected TB patients varied from 0 to 15%. Western and eastern countries had higher levels and increasing trends of infection over time compared with central EU/EEA countries. Groups at higher risk of TB-HIV co-infection were males, young adults, foreign-born persons, the homeless, injecting drug users and prisoners. Further research is needed into the burden and associated risk factors of co-infection in Europe, to help plan effective control measures. Increased HIV testing of TB patients and targeted and informed strategies for control and prevention could help curb the co-infection epidemic.

The burden of TB-HIV in the EU: how much do we know? A survey of surveillance practices and results

Information on the burden of tuberculosis (TB)-HIV co-infection is critical for the planning and evaluation of TB-HIV control and treatment strategies. This study assessed current practices in countries of the European Union (EU) and European Economic Area (EEA) for monitoring HIV co-infection in TB surveillance systems, countries' current co-infection burden and associated clinical practice. An online survey was distributed to all national TB surveillance nominated European Centre for Disease Prevention and Control contact points in the EU/EEA. We received 25 responses from 30 countries (83% response rate). Patients' HIV status was collected in 18 out of the 25 TB surveillance systems, usually via clinician reporting (16 out of 18 surveillance systems). Although most countries recommended routine testing of TB patients for HIV, the proportion actually tested varied from 5% to 90%. The burden of HIV co-infection was found to be elevated in countries with higher levels of HIV testing and higher prevalence of HIV. We suggest that TB-HIV co-infection be monitored in all EU/EEA countries to facilitate the planning and evaluation of TB-HIV control strategies. Strengthening collaboration between TB and HIV clinicians and surveillance departments, and consideration of patient confidentiality restraints would be advantageous. The level of HIV testing in TB patients is low despite national recommendations and testing should be further promoted and monitored.

Marking 15 years of efforts towards a comprehensive European TB surveillance system: the epidemiological situation of TB in the EU/EEA in 2009

Efforts have been ongoing since 1996 to strengthen tuberculosis (TB) surveillance in Europe, starting with the launch of the EuroTB initiative. We present TB surveillance data for the Member States of the European Union (EU) and of the European Economic Area (EEA) for the latest reporting year (2009), highlighting key areas of epidemiological and programmatic focus. Despite a sustained decline of TB notifications at EU/EEA level, several aspects of TB control can still be improved.

Multidrug- and extensively drug-resistant tuberculosis: a persistent problem in the European Union and European Economic Area

Since 2008, the European Centre for Disease Prevention and Control has been collecting data from the European Union (EU) and European Economic Area (EEA) on resistance to first- and second-line drugs against tuberculosis (TB). In 2008, the proportion of multidrug-resistant tuberculosis (MDR TB) was 6.0% of the total case load for 25 countries reporting data. Extensively drug-resistant (XDR TB) reporting has increased since 2007 and was observed in 7.3% of the MDR TB cases in 13 reporting countries. MDR TB remains a threat and XDR TB is now established within the EU/EEA borders.

Analysis of tuberculosis treatment outcomes in the European Union and European Economic Area: efforts needed towards optimal case management and control

An analysis of surveillance data was performed to assess treatment outcomes of patients belonging to selected calendar year cohorts. Twenty-two countries in the European Union (EU) and European Economic Area (EEA) reported treatment outcome monitoring data for culture-confirmed pulmonary tuberculosis (TB) cases reported in 2007. The overall treatment success rate was 73.8% for all culture-confirmed pulmonary cases and 79.5% for new culture-confirmed pulmonary cases. For the cohort of new culture-confirmed TB cases, only three countries achieved the target of 85% success rate. This underachievement appears to be a result of relative high defaulting and unknown outcome information. Case fatality remains high particularly among cases of national origin. This factor appears attributable to advanced age of the national cohort. Treatment outcomes for multidrug-resistant tuberculosis were reported by 15 countries, with a range of 19.8% to 100% treatment success at 24 months. The data underline the urgent need for strengthening treatment outcome monitoring in the EU and EEA in order to ensure an effective programme implementation and case management that will ultimately contribute to TB elimination.

Multidrug- and extensively drug-resistant tuberculosis: a persistent problem in the European Union European Union and European Economic Area

Since 2008, the European Centre for Disease Prevention and Control has been collecting data from the European Union (EU) and European Economic Area (EEA) on resistance to first- and second-line drugs against tuberculosis (TB). In 2008, the proportion of multidrug-resistant tuberculosis (MDR TB) was 6.0% of the total case load for 25 countries reporting data. Extensively drug-resistant (XDR TB) reporting has increased since 2007 and was observed in 7.3% of the MDR TB cases in 13 reporting countries. MDR TB remains a threat and XDR TB is now established within the EU/EEA borders.

Tuberculosis in the EU and EEA/EFTA countries - what is the latest data telling us?

Since 1 January 2008, the European Centre for Disease Prevention and Control (ECDC) and the World Health Organization Regional Office for Europe (WHO/Europe) jointly coordinate the tuberculosis (TB) surveillance activities in Europe. The data collected provides an opportunity for a comprehensive analysis of the TB situation. We aimed at analysing the EU and EEA/EFTA data to identify general TB trends and to provoke some discussion regarding the challenges and needs for monitoring the epidemic.

Molecular characterization of rifampin-resistant isolates of Mycobacterium tuberculosis from Hungary by DNA sequencing and the line probe assay

Two regions of rpoB associated with rifampin resistance were sequenced in 29 rifampin-resistant (determined by the proportion method) isolates of Mycobacterium tuberculosis obtained from patients from three counties in Hungary. Of the 29 resistant strains, 27 had a mutation in either the 81-bp region (26 strains) or the N-terminal region (1 strain), while the other 2 strains had no mutations in either region. The locations and frequencies of the mutations differed from those previously reported. The most common mutation in this study, D516V, was found in 38% of the Hungarian strains, a frequency 2 to 10 times higher than that found in studies from other countries. These same 29 isolates were also evaluated with the Inno-LiPA Rif. TB test (LiPA), a reverse hybridization assay for the rapid detection of rifampin resistance. Although LiPA detected the presence of an rpoB mutation in 26 of the resistant isolates, the type of mutation could not be determined in 4 isolates because the mutations present were not among those included on the LiPA strip. In addition, a silent mutation in one of the rifampin-susceptible control strains was interpreted as rifampin resistant by LiPA. These findings demonstrate the importance of validating this rapid molecular test by comparison with DNA sequence results in each geographic location before incorporating the test into routine diagnostic work.

[Routine direct detection of Mycobacterium tuberculosis with a rapid test of polymerase chain reaction applied to a Hungarian patient population]

The results of the present study, based on 1869 examined clinical specimens of 543 patients, represent the Hungarian parameters of a PCR test. By using the final and resolved results, the clinical sensitivity, specificity, positive and negative predictive values were 83.8%, 99.2%, 95.4% and 97%, respectively for PCR, 63.5%, 100%, 100% and 93.5%, respectively for culture, and 16.2%, 100%, 100% and 86.3%, respectively for Ziehl-Neelsen (ZN) staining. These results are essential to allow Hungarian clinicians to interpret PCR results in accordance with local conditions. The present study has demonstrated a high sensitivity (PCR vs. culture and smear, p < 0.01) and an excellent specificity of PCR. Our results indicate that the majority of M. tuberculosis-positive specimens can be identified rapidly with the test and, because of the high negative predictive value, the PCR test can help to exclude tuberculosis from the differential diagnosis in 24 hours. Moreover, the PCR can detect the presence of M. tuberculosis in 66.6% of ZN-negative and subsequently culture-positive specimens at the time of admission. The results of PCR must be interpreted with extreme caution, and the procedure is recommended only for laboratories, which simultaneously perform culture and microscopy for control of the performance of PCR tests.

Comparison of recoveries of mycobacterium tuberculosis using the automated BACTEC MGIT 960 system, the BACTEC 460 TB system, and Löwenstein-Jensen medium

Using two different liquid media and one conventional solid medium, a total of 57 mycobacterial isolates (Mycobacterium tuberculosis, n = 55; nontuberculous mycobacteria, n = 2) were recovered from 377 clinical specimens. The rates of recovery of M. tuberculosis were 96. 4% with the BACTEC MGIT 960 liquid medium, 92.7% with BACTEC 12B liquid medium, and 81.8% with the Löwenstein-Jensen (LJ) medium. The mean time to detection of M. tuberculosis in smear-positive specimens was 12.6 days for BACTEC MGIT 960 medium, 13.8 days for BACTEC 12B medium, and 20.1 days for LJ medium, and in smear-negative specimens it was 15.8 days for BACTEC MGIT 960 medium, 17.7 days for BACTEC 12B medium, and 42.2 days for LJ medium. The rates of contamination were 3.7, 2.9, and 1.2% for the BACTEC MGIT 960, BACTEC 12B, and LJ media, respectively. In conclusion, the nonradiometric, fully automated 7-ml BACTEC MGIT 960 system can be considered a viable alternative to the semiautomated, radiometric BACTEC 460 TB system.