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.

Uptake of the lateral flow urine LAM test in Europe and Central Asia.

INTRODUCTION: Since 2015 (updated in 2019), the WHO has recommended to include the commercial lateral flow urine lipoarabinomannan TB test (LF-LAM), AlereLAM, in the diagnostic toolkit for severely ill people living with HIV.METHODS: To assess the current use and barriers to the implementation of the test, we conducted an electronic survey among national focal points and managers of TB and HIV programmes in the 53 Member States of the WHO European Region and a European network of clinicians working in TB and HIV medicine.RESULTS: In all, 45 individual responses (37 countries) were received from programme managers and focal points and 17 responses (14 countries) from clinicians. Only eight countries reported adopting LF-LAM policies, with only four currently using the AlereLAM (Armenia, Belarus, Ukraine and Uzbekistan). The most commonly reported barriers to implementing the test were the small number of eligible patients (with HIV-TB co-infections), the test not being included in the TB or HIV programme´s mandate and lack of budget allocation.CONCLUSION: Consistent with findings from high TB burden countries in Africa and Asia, the survey demonstrated that uptake of AlereLAM is almost non-existent. Addressing the identified barriers and the intrinsic limitations of the test could help to increase the use of the test.

TB management in the European Union/European Economic Area: a multi-centre survey.

BACKGROUND: Essential TB care in the European Union/European Economic Area (EU/EEA) comprises 21 standards for the diagnosis, treatment and prevention of TB that constitute the European Union Standards for Tuberculosis Care (ESTC).METHODS: In 2017, we conducted an audit on TB management and infection control measures against the ESTC standards. TB reference centres in five EU/EEA countries were purposely selected to represent the heterogeneous European TB burden and examine geographic variability.RESULTS: Data from 122 patients, diagnosed between 2012 and 2015 with multidrug-resistant TB (n = 49), extensively drug-resistant TB (XDR-TB) (n = 11), pre-XDR-TB (n = 29) and drug-susceptible TB (n = 33), showed that TB diagnosis and treatment practices were in general in agreement with the ESTC.CONCLUSION: Overall, TB management and infection control practices were in agreement with the ESTC in the selected EU/EEA reference centres. Areas for improvement include strengthening of integrated care services and further implementation of patient-centred approaches.

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.

Defining a migrant-inclusive tuberculosis research agenda to end TB.

BACKGROUND: Pillar 3 of the End TB Strategy calls for the promotion of research and innovation at the country level to facilitate improved implementation of existing and novel interventions to end tuberculosis (TB). In an era of increasing cross-border migration, there is a specific need to integrate migration-related issues into national TB research agendas. The objective of the present review is to provide a conceptual framework to guide countries in the development and operationalization of a migrant-inclusive TB research agenda. METHODS: We conducted a literature review, complemented by expert opinion and the previous articles in this State of the Art series, to identify important themes central to migration-related TB. We categorized these themes into a framework for a migration-inclusive global TB research agenda across a comprehensive spectrum of research. We developed this conceptual framework taking into account: 1) the biomedical, social and structural determinants of TB; 2) the epidemiologic impact of the migration pathway; and 3) the feasibility of various types of research based on a country's capacity. DISCUSSION: The conceptual framework presented here is based on the key principle that migrants are not inherently different from other populations in terms of susceptibility to known TB determinants, but that they often have exacerbated or additional risks related to their country of origin and the migration process, which must be accounted for in developing comprehensive TB prevention and care strategies. A migrant-inclusive research agenda should systematically consider this wider context to have the highest impact.

Cross-border outbreak of extensively drug-resistant tuberculosis linked to a university in Romania.

Extensively drug-resistant (XDR) tuberculosis (TB) poses a threat to public health due to its complicated, expensive and often unsuccessful treatment. A cluster of three XDR TB cases was detected among foreign medical students of a Romanian university. The contact investigations included tuberculin skin testing or interferon gamma release assay, chest X-ray, sputum smear microscopy, culture, drug susceptibility testing, genotyping and whole-genome sequencing (WGS), and were addressed to students, personnel of the university, family members or other close contacts of the cases. These investigations increased the total number of cases to seven. All confirmed cases shared a very similar WGS profile. Two more cases were epidemiologically linked, but no laboratory confirmation exists. Despite all the efforts done, the source of the outbreak was not identified, but the transmission was controlled. The investigation was conducted by a team including epidemiologists and microbiologists from five countries (Finland, Israel, Romania, Sweden and the UK) and from the European Centre for Disease Prevention and Control. Our report shows how countries can collaborate to control the spread of XDR TB by exchanging information about cases and their contacts to enable identification of additional cases and transmission and to perform the source investigation.

Time-and-motion tool for the assessment of working time in tuberculosis laboratories: a multicentre study.

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.

Tuberculosis in migrants in low-incidence countries: epidemiology and intervention entry points.

As tuberculosis (TB) rates continue to decline in native populations in most low TB incidence countries, the proportion of TB patients born outside their country of residence ('foreign-born') increases. Some low-incidence countries have experienced a substantial increase in TB rates related to recent increases in the number of asylum seekers and other migrants from TB-endemic countries. However, average TB rates among the foreign-born in low-incidence countries declined moderately in 2009-2015. TB in foreign-born individuals is commonly the result of reactivation of latent infection with Mycobacterium tuberculosis acquired outside the host country. Transmission is generally low in low-incidence countries, and transmission from migrants to the native population is often modest. Variations in levels and trends in TB notifications among the foreign-born are likely explained by differences and fluctuations in the number and profile of migrants, as well as by variations in TB control, health and social policies in the host countries. To optimise TB care and prevention in migrants from endemic to low-incidence countries, we propose a framework for identifying possible TB care and prevention interventions before, during and after migration. Universal access to high-quality care along the entire migration pathway is critical. Screening for active TB and latent tuberculous infection should be tailored to the TB epidemiology, adapted to the needs of specific migrant groups and linked to treatment. Ultimately, the long-term TB elimination goal can be reached only if global health and socio-economic inequalities are dramatically reduced. Low-incidence countries, most of which are among the wealthiest nations, need to contribute through international assistance.

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.

Tuberculosis infection control in health facilities in Lithuania: lessons learnt from a capacity support project.

Tuberculosis (TB) infection control (IC) is key in controlling TB transmission in health facilities in Lithuania. This article presents a project that aimed at supporting health care facilities in Lithuania in implementing TB-IC. The project consisted of 1) facility TB-IC assessments, 2) development of facility TB-IC plans, 3) TB-IC training and 4) site visits. We assessed the impact of these activities through a self-assessment questionnaire. The project resulted in limited improvements. Most progress was seen in administrative and managerial activities. Possible reasons for the limited improvements are challenges with funding and the lack of supportive legislation and a national TB-IC plan.

La lutte contre l'infection tuberculeuse (TB-IC) est la clé du contrôle de la transmission de la TB dans les structures de santé de Lituanie. Cet article présente un projet qui a visé à soutenir les structures de soins de santé de Lituanie dans la mise en œuvre de la TB-IC. Le projet a consisté en : 1) l'évaluation des structures de TB-IC, 2) l'élaboration de plans pour ces structures de TB-IC, 3) la formation à la TB-IC et 4) visites de sites. Nous avons évalué l'impact de ces activités par un questionnaire d'autoévaluation. Le projet a abouti à des améliorations limitées. Les progrès les plus importants ont été vus dans les activités d'administration et de gestion. Les raisons possibles de ces améliorations limitées sont des problèmes relatifs au financement et au manque de soutien légal, ainsi qu'à l'absence d'un plan national de TB-IC.

El control de la infección tuberculosa (TB-IC) constituye una medida fundamental en el control de la transmisión de la TB en los establecimientos de salud en Lituania. En el presente artículo se describe un proyecto encaminado a prestar apoyo a los establecimientos sanitarios en la ejecución de las normas de la TB-IC. El proyecto comportaba las siguientes medidas: 1) la evaluación del TB-IC en las instituciones; 2) la elaboración de planes de TB-IC en los establecimientos; 3) la capacitación en esta esfera; y 4) las visitas a los centros. Se examinó la repercusión de estas intervenciones mediante un cuestionario de autoevaluación. Con el proyecto se alcanzaron mejoras de un alcance limitado. La mayor parte del progreso se observó en las actividades administrativas y de gestión. Entre las posibles razones de este resultado modesto se cuentan las dificultades de financiamiento, la falta de una legislación de apoyo y de un plan nacional de TB-IC.

Strengthening TB infection control in specialized health facilities in Romania--using a participatory approach.

INTRODUCTION: In 2012, the tuberculosis (TB) notification rate among Romanian TB facility doctors and nurses was 7.2 times higher than in the general population. This indicates that transmission is ongoing inside TB facilities and that TB infection control measures are insufficient. To help prevent nosocomial TB transmission a project was implemented that aimed at providing nationwide tailor-made technical assistance in TB infection control (TB-IC) in TB treatment facilities, including the development of TB infection control plans. The objective of the present article is to describe the implementation of the project and to discuss successes and challenges. STUDY DESIGN: The project was an implementation study using two methods of evaluation: (1) a cross sectional questionnaire study; and (2) collection of information, during the training, on challenges related to infection control and to the project implementation. METHODS: The project team developed a TB facility infection control (TB-IC) plan template, together with the Romanian experts. The template was discussed and agreed upon with the experts at a meeting and thereafter distributed by email to all TB facilities. Afterwards, a training of trainers (TOT) seminar was organized which included the provision of information about different training methods, as well as information about TB-IC. The TOT was followed by training for key TB-IC providers. Information about use of the TB-IC template was gathered through a self-administered questionnaire sent to all participants of the expert meeting and the training (42 people). Additionally, non-systematized discussions were held on broader challenges in TB-IC implementation during the training. RESULTS: Within the project 42 key TB-IC service providers were trained in TB-IC, including 9 who were trained at a TOT seminar. The trainees were specialists working at the national level, such as country TB coordinators, or at the TB facility level: TB doctors, epidemiologists, laboratory specialists and maintenance engineers. Out of 42 key TB-IC service providers who were trained, only eighteen responded to the questionnaire (no reminders were sent). Out of these, 14 had used the TB-IC plan template after the project team disseminated it to them by email. The remaining four TB-IC service providers indicated that they were planning to use the template to develop or update their facility TB-IC plans. Related to the use of TB-IC plan template, the following broader challenges in TB-IC were identified: a lack of authority of the individuals responsible for TB-IC to implement the TB-IC measures, lack of training among facility epidemiologists on TB, underdeveloped system for reporting TB in healthcare workers, difficulties with triage of the TB suspects, and poor facility infrastructure hampering implementation of TB-IC measures. DISCUSSION: Implementing TB-IC plans in Romanian health care facilities proved to be challenging, mainly due to the fact that the national infection control plan for TB was not yet adopted at the time of project implementation, and therefore there was neither a regulatory framework to support TB facility-IC planning nor any related budget allocations for the implementation of the facilities' TB-IC plans. Nonetheless, most respondents who answered the questionnaire (18 of 42 responded) indicated that they had started using the TB-IC plan template, which represents a full package of infection control measures that, when implemented effectively and in its entirety, may be expected to reduce nosocomial transmission. The study's limitations are: very low survey response rate, thus there is a likelihood of responder bias.

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.

The European Union and European Economic Area (EU/EEA) tuberculosis (TB) surveillance system collects detailed information on resistance to TB drugs. Using this information, we provide an overview of the current TB drug resistance situation and trends in the EU/EEA by performing a descriptive analysis, including analysis of treatment outcomes, of the TB cases reported between January 2007 and December 2012. The percentages of TB cases with different drug resistance patterns have been stable with about 90% of the new laboratory-confirmed cases pan-susceptible, 6% monodrug-resistant, 2% polydrug-resistant, 2% multidrug drug-resistant (MDR) TB - excluding extensively drugresistant (XDR) TB -, and 0.2% XDR-TB. In previously treated laboratory-confirmed TB cases, the percentage with MDR-TB excluding XDR-TB declined until 2010 to 16% and remained stable thereafter. During the study period, the percentages of cases with monodrug- and polydrug-resistant TB remained constant at about 8% and 2% whereas the percentage of XDR-TB cases increased slightly to 2.6%. Treatment outcome results for all cases have been stable with overall 77.9% of the pan-susceptible cases, 69.6% of the monoresistant cases, 68.2% of the polyresistant cases, 32.2% of the MDR-TB cases (excluding XDR-TB), and 19.1% of the XDR-TB cases treated successfully. The treatment success rate target for new pulmonary culture-positive MDR-TB cases of 70% has not been reached. In addition, drug resistance surveillance can be improved by more complete reporting of drug susceptibility results and treatment outcome.