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

Molekylær epidemiologi blant pasienter med multiresistent tuberkulose i Tigray, Etiopia

Tuberculosis (TB), which is caused by closely related Mycobacterium tuberculosis complex (MTBC) species, is an ancient human disease that gravely affects millions of people every year. TB is a preventable and treatable infectious disease. The continuing emergence and spread of multidrug-resistant tuberculosis (MDR-TB ) threaten the global TB control efforts. TB is the first killer among infectious diseases worldwide. According to the WHO report, there were an estimated 10.0 million incident cases, 1.4 million TB deaths, with more than 95% of these deaths in developing countries in 2019. Ethiopia is among the three high TB, TB/HIV, and MDR-TB burden countries. In 2019 in Ethiopia, there were 157,000 new TB cases, 1,400 MDR/RR-TB cases and 23,800 death from TB. This thesis aimed to describe the molecular epidemiology of multidrugresistant Mycobacterium tuberculosis among pulmonary TB patients in Tigray Region, Ethiopia. Three hundred sputum samples were collected from six hospitals of the Tigray Region between July 2018 and August 2019. The 227 samples culture positive for MTBC were subjected to drug susceptibility test to 1st- and 2nd- line anti-TB drugs using line probe assay. Among the 227 positive cultures, 74 samples were sequenced using whole-genome sequencing (WGS). WGS analysis showed diversified Mycobacterium tuberculosis genotypes circulating in the region, with L4 as the predominant genotype. The overall proportion of MDR-TB was high. The high proportion of MDR-TB among new and previously treated patients is alarming and calls for an urgent intervention to improve patient management. The high proportion of MDR-TB among newly diagnosed cases and the high level of recent transmission index indicates an ongoing transmission, which suggests the need for an enhanced TB control program performance to interrupt transmission. The study highlighted the usefulness of mutations at rpoB, katG, embB, rpsL, pncA, ethA, gyrA and rrs genes as a molecular marker for the rapid detection of resistance to RIF, INH, ETB, SM, PZA, ETH, FLQs and injectable 2nd-line anti-TB drugs, respectively. Besides the canonical mutations, a significant number of disputed rpoB mutations were also reported. Overall, the regional TB control program should be strengthened to detect and provide appropriate early treatment and follow-up for drug-resistant TB (DR-TB) cases. Abiding by the five WHOrecommended priority actions for DR-TB management is necessary to reduce the current high MDR-TB burden in the study region. Periodic surveillance of drug-resistance conferring mutations, early diagnosis and treatment of TB, and scaling up of drug susceptibility testing facilities to prevent and control the transmission of DR-TB in the community is recommended.Tuberkulose (TB) forårsakes av nært beslektede arter innen Mycobacterium tuberculosiskomplekset (MTBC), og er en eldgammel, alvorlig sykdom hos mennesker som rammer millioner hvert år. TB er en smittsom sykdom som kan forebygges og behandles, men fremveksten og spredningen av multiresistent tuberkulose (MDR-TB) truer den globale bekjempelsesinnsatsen. TB er den smittsomme sykdommen som gir størst antall dødsfall i verden. WHO anslår at det i 2019 var anslagsvis 10,0 millioner tilfeller, 1,4 millioner TB dødsfall, med mer enn 95% av disse dødsfallene i utviklingsland. Etiopia er blant de tre land som er mest belastet, med høye tall av TB, TB / HIV og MDR-TB. I Etiopia var det i 2019 157.000 nye TB-tilfeller, 1400 MDR tilfeller og 23 800 dødsfall fra TB. Denne doktorgradens overordnede mål var å beskrive den molekylære epidemiologien til sjukdom forårsaket av multiresistent Mycobacterium tuberculosis blant lungepasienter i Tigray-regionen, Etiopia. Tre hundre sputumprøver ble samlet inn fra seks sykehus i Tigray-regionen mellom juli 2018 og august 2019. Av disse ble de 227 prøvene som var positive for MTBC, undersøkt med en følsomhetstest mot 1. og 2. linje anti-TB medisiner ved bruk av Line Probe Assay. Av de 227 positive kulturene ble 74 prøver sekvensert ved bruk av helgenomsekvensering (WGS). WGS-analysene viste at forskjellige MTBC-genotyper som sirkulerte i regionen, med L4 som den dominerende genotypen. Den høye andelen MDR-TB blant nye og tidligere behandlede pasienter er alarmerende og stiller store krav til en forbedret pasienthåndtering. Den høye andelen MDR-TB blant nylig diagnostiserte tilfeller og det høye nivået av nylig overførte infeksjoner indikerer en pågående overføring, og antyder behovet for en forbedret ytelse av TB-kontrollprogrammet for å avbryte overføringen. Studien fremhevet nytten av mutasjoner ved rpoB, katG, embB, rpsL, pncA, ethA, gyrA og rrs gener som en molekylær markør for rask påvisning av resistens mot RIF, INH, ETB, SM, PZA, ETH, FLQ og injiserbare andrelinje anti-TB medisiner. Samlet sett bør det regionale TB-kontrollprogrammet styrkes for å oppdage og gi tilpasset passende behandling og oppfølging av TB-tilfeller. Å identifisere TB-kontrollprogrammets begrensninger i regionen, og følge de fem WHO-anbefalte prioriterte tiltakene for styring av DRTB, er nødvendig for å redusere den nåværende høye MDR-TB-belastningen i studieområdet. Det anbefales periodisk overvåking av mutasjoner som gir antibiotikaresistens, tidlig diagnose og behandling av TB, og oppskalering av fasiliteter for testing av isolater for antibiotikafølsomhet for å forhindre og kontrollere overføring av DR-TB i samfunnet.Mekelle Universit

Current Trends In The Laboratory Diagnosis Of Tuberculosis

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First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains

Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future.Institute for Public Health and the Environment (RIVM), European Centre for Diseases Prevention and Control (ECDC

Tuberculosis in Children: Diagnosis and Epidemiology

Globally, an estimated one-million new tuberculosis (TB) cases occurred in children in 2014. For a long time, research of TB in children has been neglected. Most research and surveillance of TB is performed in adults, and the resulting lack of evidence in children is a major barrier for implementation of rational control strategies for children, including diagnosis. More research on TB in children is of importance as children are more susceptible to developing severe extrapulmonary TB, children require different approaches to both diagnosis and treatment and paediatric TB reflects the ongoing transmission of TB in the population. This research gap on the epidemiology of tuberculosis in children, especially in high burden countries, should be addressed in order to better understand the dynamics of TB transmission in both adults and children. Accurate data are the basis for establishment of effective control strategies. This thesis aims to assess the diagnostic role of microscopic observation drug susceptibility (MODS) and mycobacterial blood culture for diagnosis of TB in children as well as to present the epidemiological characteristics of paediatric TB in northern Vietnam with regard to drug resistance and genotypes of Mycobacterium tuberculosis (MTB), the causative agent of TB, isolated from them. MODS is a low cost non-commercial liquid culture assay to detect MTB by microscopy. MODS was compared with conventional assays including Ziehl-Neelsen smear (ZN) and Löwenstein-Jensen culture (LJ) in a study conducted from 2009 to 2010 at the National Hospital for Paediatrics, a general paediatric hospital, in Hanoi, Vietnam. In suspected paediatric TB cases, the MODS test was shown to be significantly more sensitive than both smear (46.0% vs. 8.8%) and LJ (46.0% vs. 38.9%), and significantly faster than LJ with a median time difference of 28 days in favour of MODS (7 days vs. 35 days). The findings suggest that MODS is a rapid low-cost diagnostic tool for TB diagnosis in the paediatric population. The additional yield of mycobacterial blood culture was assessed in comparison to routine detection methods for TB diagnosis in children in two hospitals in Vietnam. The findings show that mycobacterial blood culture detected an additional six TB cases of which 5 cases were negative with other tests and in the remaining case no other tests were done. All six cases were susceptible to rifampicin and isoniazid. The overall performance of TB blood culture was poor as compared to routine culture with regard to detection rate (2.9%, 16/554 vs. 16.6%, 92/554) and turnaround time (26 days vs. 14 days). The incremental cost for adding one additional TB case is substantial. Therefore, addition of mycobacterial blood culture into routine diagnostics has limited utility in resource limited settings. To assess the molecular epidemiology of paediatric TB in northern Vietnam, a collection of 125 MTB isolates from children with TB admitted to NHP during 2009 to 2013 was analysed. Drug susceptibility testing results from 121 isolates and genotypes from 120 isolates were generated. The phenotypic drug susceptibility testing showed that 20.7% was resistant to isoniazid (25/121), 3.3% resistant to rifampicin (4/121), 28.1% resistant to streptomycin (34/121) and 2.5% resistant to ethambutol (1/121). There were 4 cases with multidrug resistant TB. The high frequency of resistance to isoniazid and streptomycin are consistent with data from adults in Vietnam, suggesting the ongoing transmission of drug resistant MTB in the community. MIRU typing patterns showed that the Beijing genotype was predominant in this population (63.3%, 76/120), which is in agreement with various prior studies in adults in Vietnam. These findings provide more evidence to support the hypothesis of the epidemic spread of the Beijing genotype in Vietnam. In this study, an association between Beijing genotype and drug resistance to streptomycin and isoniazid was observed. The number of MDR isolates was too small to draw conclusions regarding association of MDR and Beijing genotype. Collectively, these results demonstrate that liquid culture can improve the yield of TB diagnosis in Vietnam and mycobacterial blood culture should not be routinely performed for paediatric cases. The molecular epidemiology study also showed that the Beijing genotype is the predominant lineage among actively transmitted strains in Vietnam and that it is associated with both isoniazid and streptomycin resistance. Paediatric TB remains a significant cause of morbidity and mortality in Vietnamese children and sustained political and social commitment from all stakeholders, including governments, funders, academics and the medical community will be needed to improve diagnosis, treatment and prevention of TB in children globally

Molecular epidemiology of bovine tuberculosis in Tanzania

A study on molecular epidemiology of bovine tuberculosis in man and cattle in Tanzania was carried with two components. The first component was based on field investigation of tuberculosis in cattle and man in Arusha region, in the north and in the Usangu Plains in the Southern Highlands of Tanzania. The second component involved laboratory analysis of mycobacterialstrains acquired from field study by both conventional and molecular biology techniques.In field work, a total of 6383 cattle were tuberculin tested, and 911 (14.3%) were classified as reactors. 841 of 6383 cattle examined were destine for slaughter and 225 (26.8%) were found to have visible lesions. A total of 1719 pooled lymph node samples collected from slaughter cattle in the study area (Arusha n=1068 and the Usangu Plains n=651) were cultured and 4.0% yielded mycobacteria. 80 of the samples from the Usangu Plains came from cattle classified as reactors (Table 3.9), while samples from Arusha had no accompanying tuberculin test results. Among the isolates 72.6% were classified as M. bovis and the rest as atypical mycobacteria. Of the 805 milk samples cultured (14% were from reactor cattle), only two (0.3%) yielded M. bovis, the remaining 36 isolates were atypical mycobacteria (Table 3.10). Its only two isolates of atypical mycobacteria which came from reactor cattle.Regarding human specimens, a total of 53 lymph node biopsies were submitted for culture and 21 (39.6%) were positive for mycobacteria. Six isolates were identified as M. bovis, and the remaining 15 were M. tuberculosis. Of 96 sputum samples which were collected, mycobacteria species were recovered from 23 but only one (4.3%) was classified as M. bovis. Sixteen (69.1%) isolates were identified as M. tuberculosis, and the rest were atypical mycobacteria. Epidemiological data revealed that M. bovis was more prevalent in people with cattle contact than in other occupations (Table 3.13)The IS986 and mtpAQ multiplex PCR developed in the course of this study was able to differentiate M. bovis from M. tuberculosis. DNA fingerprinting of all the strains cultured was carried out using restriction fragment length polymorphism (RFLP) and spoligotyping techniques. The copy number of IS986 amongst strains of M. bovis from cattle ranged from one to six, while those from man had five to 15. There was similarity of DNA fingerprints among some of the strains from cattle and man as determined by the three typing techniques (Figures 6.2, 6.5 and 6.9). M. tuberculosis strains were found to belong to three clusters by IS986 RFLP, with one cluster containing over 60% of the strains.Intersegment PCR, a molecular typing technique developed in the current study was able to differentiate strains but the results were influenced by the concentration of template DNA. A DNA fragment apparently found only in M. bovis and absent in M. tuberculosis and other mycobacteria was identified by the RAPD PCR techniques. This fragment was cloned, sequenced and its DNA sequence was found to match a M. tuberculosis cosmid, which also matched rfbE gene of Yersinia enterocolitica. Specificity testing revealed hybridization to M. tuberculosis as well.The findings of the above studies have showed the existence of M. bovis infection in man and cattle in Tanzania. The study has also shown the zoonotic importance of infection in the two populations which necessitates a veterinary/medical approach to the control of the disease in Tanzania. Furthermore, it has been shown that molecular biology techniques are essential epidemiological tools in studies of zoonotic conditions such as tuberculosis. The study was unable to find a specific DNA element for M. bovis. This observation concurs with others which have found 100% homogeneity between species of the M. tuberculosis complex

EPIDEMIOLOGY OF HUMAN AND BOVINE TUBERCULOSIS IN THE FEDERAL CAPITAL TERRITORY AND KADUNA STATE OF NIGERIA

Merged with duplicate record (10026.1/1976) on 03.01.2017 by CS (TIS)The epidemiology of bovine and human tuberculosis (TB) was studied in the Federal Capital Territory and Kaduna state of Nigeria using four diagnostic methods; tuberculin test, culture and acid-fast stain of milk, animal (cattle) tissue and human sputum. Two PCR-based molecular techniques (Spoligotyping and Variable Number Tandem Repeat) were used to identify the species and strains of the isolates, while IS61 10-RFLP molecular method was optimised and applied on few samples to deten-nine the efficacy of the method. Of the 967 lactating cows from 57 herds tested for TB, 14.6%, 4% and 81.4% were positive, inconclusive and negative reactors respectively. Tuberculin test also showed that mycobacterial infection was prevalent iii the two management systems studied (nomadic and semi-nomadic), but the effect of management on the prevalence of infection was not significant. However, age was found to play a significant role in the prevalence infection where more positive cases were observed among the older age groups. It was also observed that control policy is either not in place or inadequately implemented in the study area. Of the 156 milk samples collected, 12.6% and 23% were culture and acid-fast positive respectively, while out of the 250 tissue samples 17.3% and 20% were culture and acid-fast positivc respectively. Thii s findiInIIg confirmed a definite relationship between the disease in live and slaughtered cattle. Comparing the three diagnostic methods in 4 detecting mycobacterial infection in cattle, the smear method was found to have detected more positive cases than the tuberculin and culture tests. Of the 900 suspected human TB patients investigated, 27% and 21 A% were culture and acid-fast positive respectively. This trend of high prevalence of TB among human patients in the area is similar to the trend observed among cattle populations; thus indicating a relationship between the disease in human and infection in cattle. In addition, a significant difference in the prevalence of the disease was observed between male and female patients with more positive cases observed among male patients. The prevalence of the disease was aslso found to be significantly higher in patients who did not have BCG vaccination in the past than those who had. It was also observed that the disease was higher in patients who consume raw milk and milk products. The supporting questionnaire survey among herdsmen, abattoir managers and patients further points that there is high possibility of transmitting the disease from cattle to humans. By DNA fingerprinting, strains of M. bovis, M. tuberculosis and M. qtýicanum were identified in cattle and humans respectively; thus indicating a typical animal-to-human and human-to-animal transmissions respectively. Combining the two molecular techniques in this study has vastly improved the level of discrimination of the isolates where of the 71 isolates typed, 49 pattems were produced by the two methods combined together, instead of only 23 and 41 types by spoligotyping and VNTR typing respectively. Of the 21 strains of M. mberculosis obtained in this study, only 5 strains have been descnbed previously in the international databases searched, out of which only 2 of them have been descnbed previously in Nigeria. The result in this study has valuable epidemiological and public health significance and calls for prompt and decisive action fron-i the govemment of Nigena towards controlling this deadly discase in both humans and animals

Testimonial of Professional Contributions in the Biotechnology Field (1991-2019). Pulmonary Infectious Agents Streptococcus pneumoniae and Mycobacterium tuberculosis

Relatório elaborado nos termos do Despacho n.º 20/2010 para obtenção do Grau de Mestre em Biotecnologia por Licenciados “Pré-Bolonha”Pulmonary infectious diseases, like pneumonia and tuberculosis, have been pervasive throughout the world for centuries; they kill millions of people annually worldwide and pose an increased threat when associated with antibiotic resistance and viral co-infections such as influenza and, more recently, Covid-19. This professional activity report summarizes some of my work in the last three decades, using biotechnology to type, characterize or detect two major bacterial infectious agents, Streptococcus pneumoniae and Mycobacterium tuberculosis. Strain typing techniques, like Pulsed Field Gel Electrophoresis and Penicillin Binding Protein patterns, were used to identify Streptococcus pneumoniae clones from different geographic areas in the early-1990s, showing strong evidence of clonal dissemination locally and across the globe, from Spain to Iceland and to the United States. In the mid-1990s, an in vivo expression technology system based on a promoter-trap was constructed to enable the identification of Mycobacterium tuberculosis genes upregulated in human macrophages, through selection for antibiotic resistance. This work led to the identification of eight genes likely relevant for Mycobacterium tuberculosis virulence. Several were later confirmed to be required for infection or survival in the host. A single-step molecular diagnostic real-time PCR assay for the detection of multidrug resistant Mycobacterium tuberculosis was commercialized in the late 2000s, with great impact in the detection of tuberculosis, especially in developing countries. The mechanism of the assay is presented here as published by its inventors, as well as with my role in the industry, from the development of processes for production and quality control, to regulation-compliant distribution, troubleshooting and development of improvements.As doenças infeciosas pulmonares, como a pneumonia e a tuberculose, têm tido, durante séculos uma prevalência mundial significativa, matando milhões de pessoas anualmente e representando uma ameaça crescente quando associadas à resistência a antibióticos ou coinfeções virais, como a gripe e, recentemente, o Covid-19. Este relatório de atividade profissional resume parte do meu trabalho nas últimas três décadas, usando técnicas de biotecnologia para identificar, caracterizar ou detetar dois importantes agentes infeciosos de origem bacteriana, Streptococcus pneumoniae e Mycobacterium tuberculosis. Técnicas de identificação de estirpes, como eletroforese tipo Pulsed Field e padrões de proteínas com afinidade à penicilina, foram usadas para identificar clones de Streptococcus pneumoniae de diferentes áreas geográficas no início da década de 90, mostrando forte evidência de disseminação, não só a nível local, mas também através do globo, nomeadamente, de Espanha para a Islândia e Estados Unidos. Em meados da década de 90, um sistema de expressão in vivo foi construído para permitir a identificação de genes de Mycobacterium tuberculosis com expressão elevada em macrófagos humanos, através de seleção por resistência a antibióticos. Este trabalho levou à identificação de oito genes com probabilidade de serem relevantes para a virulência de Mycobacterium tuberculosis; vários posteriormente confirmados como necessários para a infeção ou sobrevivência no hospedeiro. Mais recentemente, foi comercializado um teste de real-time PCR para diagnóstico molecular de Mycobacterium tuberculosis com multirresistência a antibióticos, com grande impacto na deteção da tuberculose, principalmente em certos países em desenvolvimento. O mecanismo de deteção é apresentado aqui conforme publicado pelos seus inventores, bem como o meu papel na indústria de diagnósticos moleculares, desde o desenvolvimento de processos de produção e controle de qualidade, até a distribuição em conformidade com os respetivos regulamentos, passando por resolução de problemas e desenvolvimento de melhorias

Tuberculosis: Epidemiology and Diagnosis

Despite the discovery of the tubercle bacillus more than a hundred years ago, and all the advances in our knowledge of the disease since then, tuberculosis still remains one of the major health problems facing mankind, particularly in developing countries. About one third of the World’s population is infected with M. tuberculosis. It is estimated that currently there are about 9 million new cases of tuberculosis with 3 million deaths worldwide. More people die of tuberculosis than any other infectious disease. Death from tuberculosis comprises 25% of all avoidable deaths in developing countries. Ninety five per cent of tuberculosis cases and 98% of tuberculosis deaths are in developing countries and 75% of tuberculosis cases are in the economically productive age group1. Geographically, the regions with the highest prevalence and infection rates are the eastern fringe of Asia, the Indian subcontinent, the South eastern part of Africa, South-east Europe, Central America and the Western part of the South America. The WHO has declared a global emergency in 1993 with respect to reemerging menace of tuberculosis