National Tuberculosis Reference Laboratory Research Articles

History of the establishment of the National Tuberculosis Reference Laboratory in Türkiye

Tüberküloz (TB) çalışan bazı Göğüs Hastalıkları Hastanelerindeki Bakteriyoloji laboratuvarlarının yürüttüğü kültür çalışmalarını standartlaştırmak, tür tanımı ve ilaç duyarlılık testleri gibi ileri testler yapabilmek, metodolojik araştırmalar ve eğitim sağlamak amacıyla ilk kez 1951 yılında Dr. Aral Gürsel tarafından Refik Saydam Hıfzıssıhha Enstitüsü bünyesinde “Tüberküloz Araştırma Laboratuvarı” kurulmuştur. Aral Gürsel laboratuvarın adını daha sonra “Tüberküloz Eğitim ve Araştırma Şubesi” olarak değiştirmiştir. Laboratuvar dönemin ihtiyaçlarına göre gelişmiş ve ismi de bu çerçevede değişikliğe uğramıştır. 1970 yılında ise “Tüberküloz Referans ve Araştırma Şubesi” olarak değiştirilmiştir. Ardından Türkiye genelinde çeşitli iller (Adana Ankara Antalya, Bursa, Çorum, Denizli, Diyarbakır, Elazığ, Erzurum, Eskişehir, İstanbul, İzmir, Kastamonu, Kayseri, Kocaeli, Samsun, Sivas, Trabzon, Van ve Zonguldak)’de 20 adet Bölge TB laboratuvarları kurulmuştur. Standardizasyonun sağlanması amacıyla Bölge TB laboratuvarlarından gönderilen üremiş mikobakteri suşlarının doğrulanması, türlerin belirlenmesi ve ilaç duyarlılık testleri referans laboratuvarında çalışılmaya başlanmıştır. Ayrıca Referans laboratuvarı birçok Göğüs Hastalıkları Hastanelerine TB laboratuvarı kurulmasına da öncülük etmiş ve eğitim sağlamıştır. 2011 yılına kadar Refik Saydam Hıfzıssıhha Merkezi Başkanlığı’na bağlı “Ulusal Tüberküloz Referans Laboratuvarı” (UTRL) olarak mikobakterilerin mikroskopi, kültür, tür tayini ve ilaç duyarlılık testlerinin konvansiyonel ve moleküler yöntemler ile test edilmelerinin yanı sıra, eğitim, denetim, sürveyans ve dış kalite değerlendirme görevlerini sürdürmüştür. AR-GE faaliyetleri için ulusal ve uluslararası işbirliği yapmıştır. Testlerin ülke genelinde standardizasyonu için rehberler hazırlayarak tüm TB laboratuvarlarının kullanımını sağlamıştır. Ülke genelinde Mikobakteri çalışanlarına danışmanlık da yapmaktadır. Bu laboratuvar Hıfzıssıhha Enstitüsü’nün kapatılmasıyla 2011 yılında önce Türkiye Halk Sağlığı Kurumu’na 2017 yılında ise Sağlık Bakanlığı Halk Sağlığı Genel Müdürlüğüne devredilmiştir. UTRL yine aynı isimle görevlerini sürdürmektedir.

Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study

In 2021, an estimated 4800 people developed rifampicin-resistant tuberculosis in Mozambique, 75% of which went undiagnosed. Detailed molecular data on rifampicin-resistant and multidrug-resistant (MDR) tuberculosis are not available. Here, we aimed at gaining precise data on the determinants of rifampicin-resistant and MDR tuberculosis in Mozambique. In this retrospective observational study, we performed whole-genome sequencing of 704 rifampicin-resistant Mycobacterium tuberculosis complex (Mtbc) strains submitted to the National Tuberculosis Reference Laboratory (NTRL) in Maputo, Mozambique, between 2015 and 2021. Phylogenetic strain classification, genomic resistance prediction, and cluster analysis were performed. Between Jan 1, 2015, and July 31, 2021, 2606 Mtbc isolates with an isoniazid or rifampicin resistance were identified in the NTRL biobank, of which, 1483 (56·9%) were from men, 1114 (42·7%) from women, and nine (0·4%) were unknown. Genome-based drug-resistant prediction classified 704 Mtbc strains as rifampicin resistant. 628 (89%) of the 704 Mtbc strains were classified MDR; of those, 146 (23%) were pre-extensively drug resistant (pre-XDR; additional fluoroquinolone resistance), and 24 (4%) extensively drug resistant (XDR; combined fluoroquinolone and bedaquiline resistance). Overall, 61 (9%) of 704 strains revealed resistance to bedaquiline: five (7%) of 76 rifampicin resistant plus bedaquiline resistant, 32 (7%) of 458 MDR plus bedaquiline resistant, and 24 (100%) of 24 XDR. Prevalence of bedaquiline resistance increased from 3% in 2016 to 14% in 2021. The cluster rate (12 single-nucleotide polymorphism threshold) was 42% for rifampicin-resistant strains, 78% for MDR strains, 94% for pre-XDR strains, and 96% for XDR Mtbc strains. 31 (4%) of 704 Mtbc strains, belonging to a diagnostic escape outbreak strain previously described in Eswatini (group_56), had an rpoB Ile491Phe mutation which is not detected by Xpert MTB/RIF (no other rpoB mutation). Of these, 23 (74%) showed additional resistance to bedaquiline, 13 (42%) had bedaquiline and fluoroquinolone resistance, and two (6%) were bedaquiline, fluoroquinolone, and delamanid resistant. Pre-XDR resistance is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance; and the frequency of bedaquiline resistance quadrupled over time and was found even in Mtbc strains without fluoroquinolone resistance. Importantly, strains with Ile491Phe mutation were frequent, accounting for 31% (n=10) of MDR plus bedaquiline-resistant strains and 54% (n=13) of XDR Mtbc strains. Given the current diagnostic algorithms and treatment regimens, both the emergence of rifampicin resistance due to Ile491Phe and bedaquiline resistance might jeopardise MDR tuberculosis prevention and care unless sequencing-based technology is rolled out. The potential cross border spread of diagnostic escape strains needs further investigation. The German Ministry of Health through the Seq_MDRTB-Net project, the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy Precision Medicine in Inflammation and the Research Training Group 2501 TransEvo, the Leibniz Science Campus Evolutionary Medicine of the Lung, and the German Ministry of Education and Research via the German Center for Infection Research.

Xpert MTB/RIF assay among the extra-pulmonary and non-sputum respiratory samples: One year experience at National Tuberculosis Reference Laboratory, Bangladesh

Background: Extra-pulmonary tuberculosis (EPTB) is a diagnostic and therapeutic challenge due to the paucity of suitable rapid diagnostic tools. Objectives: The aim was to assess the frequency of detection of Mycobacterium tuberculosis using Xpert MTB /RIF assay among the extra-pulmonary and non-sputum respiratory samples (NSRS) along with demographic profile, life style variables and proportion of Rifampicin resistant TB among those specimens. Methodology: This cross-sectional retrospective study was conducted at National Tuberculosis Reference Laboratory (NTRL) from January 2018 to December 2018 for period of 1 year. Total 3918 extra-pulmonary and non-sputum respiratory samples from suspected TB patients were enrolled. Detection of Mycobacterium tuberculosis and Rifampicin resistance was performed by Xpert MTB /RIF assay and culture in both liquid and solid media. Results: Among 3918 samples, 3152 were new cases and 766 were previously treated TB cases. A total of 853 (21.77%) MTB were detected by Xpert MTB /RIF assay. Among them, 713 (83.59%) were extra-pulmonary and 140 (16.41%) were non-sputum respiratory samples. Lymph node (LN) aspirates and tissues were the most frequent (37.9 and 9.9%) samples of EPTB. The proportion of RR cases among EPTB was 2.8% and 6.3% among new and previously treated cases. And 2.6% and 11.1% among NSRS new and previously treated cases respectively. Conclusion: This study will give an insight of EPTB and NSRS profile with a view to diagnostic and therapeutic approach in Bangladesh. Bangladesh Journal of Medical Microbiology, January 2023;17(1):21-28

Non-tuberculous mycobacterium isolations from tuberculosis presumptive cases at the National Tuberculosis Reference Laboratory Kenya, 2018–2019

Background: Mycobacterial pathogens are among the top causes of diseases in humans. In Kenya, incidences of Non-Tuberculous Mycobacteria (NTM) species have steadily been on the increase. Most NTMs are resistant to first line treatment of tuberculosis and have a challenge in timely and accurate diagnosis. Misdiagnosis has led to prescribing anti-tuberculosis regimens to patients suffering from NTM. We aimed to determine the most prevalent Non-Tuberculous Mycobacterium in Kenya. Methods: We reviewed records from the National Tuberculosis Reference Laboratory (NTRL) Laboratory information management system (LIMS) between January 2018 and December 2019 for the patients on surveillance. All isolates were cultured in Mycobacterial Growth Indicator Tubes (MGIT) and incubated for detection using BACTEC™ MGIT™ system. Those with negative acid-fast bacilli (AFB) growth and negative for Mycobacterium Tuberculosis Complex Species (MTBC) protein-MPT64 were suggestive of NTM infections, which were sub-cultured in MGIT and characterized using Line Probe Assay (LPA) GenoType® MTBDR CM/AS. Descriptive and bivariate analysis was done. Results: Of the total 24,549 records reviewed, 167(0.7%) were NTM isolates. Males comprised of 74.2% (124/167), and the mean age was 42 years (SD±16), age group 35-44 years had the highest NTM at 26.3% (44/167). Nairobi had 12.6% (21/167), Mombasa 10.8% (18/167), Kilifi and Meru each had 7.8% (13/167). Eleven isolated species comprised of Mycobacterium intracellulare 35.3% (65/167), M. fortuitum at 27% (48/167), and M. scrofulaceum at 10.2% (17/167). Previously treated patients had higher NTM [63.5% (106/167)] than Drug-resistant follow-up patients [26.9% (45/167)]. Coinfection with HIV was at 27.5% (46/167). Conclusion: Previously treated patients should have an additional screening of NTMS, and drug susceptibility testing should be done before initiation of treatment.

Analysis of Mycobacterium tuberculosis Complex Strains Isolated from the Samples of Patients Living in Northern Syria

Tuberculosis causes serious mortality and morbidity worldwide each year. A lot of effort and money is spent for the diagnosis and treatment of tuberculosis all over the world. The importance that countries give to health policies and public health is inversely proportional to the incidence of tuberculosis and multidrug resistant tuberculosis. The aim of our study was to evaluate the resistance profiles of Mycobacterium tuberculosis complex strains which were isolated from sputum samples, collected by World Health Organisation from patients living in the northern region of Syria, where health services were disrupted due to the civil war. According to the protocol signed between the World Health Organization and our hospital; sputum samples taken from tuberculosis patients living in Afrin, Azez and Idlib regions or suspected of being resistant to anti-tuberculosis drugs were studied in our hospital. The cultivation process was performed in our laboratory using Löwenstein Jensen media and MGIT-960 system. The susceptibility tests for primary anti-tuberculosis drugs were performed using MGIT-960 system for M.tuberculosis complex isolates. The isolates identified as MDR/RD-TB (multi-drug-resistant-rifampicin-resistant tuberculosis) were sent to National Tuberculosis Reference Laboratory of Public Health Institution of Türkiye for susceptibility testing to first and second line drugs. Mutation and wild-type determination were studied by "Line Probe Assay (LPA)" method to investigate the susceptibility of the isolates to isoniazid, rifampicin, fluoroquinolone and aminoglycoside/cyclic peptide. The results obtained from the patients were collected and evaluated retrospectively from the records. Growth was observed in 18 samples out of 171 sputum samples from 67 patients; 13 isolates were detected as MDR-TB while one isolate was detected as mono RR-TB. The rate of mono RR-TB was 1.5% and the rate of MDR-TB was 19.4%. MUT3 causing rifampicin resistance was detected in 17.9% of the patients, katG/MUT1 causing isoniazid resistance in 17.9% and WT loss causing aminoglycoside/cyclic peptide resistance were detected in 19.4% of the patients. Neither fluoroquinolone resistance nor a mutation leading to fluoroquinolone resistance was detected in the study. When the sputum samples taken from the patients living in Northern Syria were examined, the frequency of MDR-TB was found to be quite high. MDR-TB, which is an important public health problem, was found at high rates due to the internal turmoil in the region and poor accessibility to health services. Since the gene mutations causing drug resistance with the LPA method differ with the conducted studies, it is important to evaluate the dominant gene mutations for determining the TB treatment strategies in the region.

Validation of GeneXpert using extrapulmonary samples at the National Tuberculosis Reference Laboratory in Lesotho

Validation of GeneXpert using extrapulmonary samples at the National Tuberculosis Reference Laboratory in Lesotho

Multiplex LNA probe-based RAP assay for rapid and highly sensitive detection of rifampicin-resistant Mycobacterium tuberculosis.

The World Health Organization (WHO) Global tuberculosis Report 2021 stated that rifampicin-resistant tuberculosis (RR-TB) remains a major public health threat. However, the in-practice diagnostic techniques for RR-TB have a variety of limitations including longer time, lack of sensitivity, and undetectable low proportion of heterogeneous drug resistance. Here we developed a multiplex LNA probe-based RAP method (MLP-RAP) for more sensitive detection of multiple point mutations of the RR-TB and its heteroresistance. A total of 126 clinical isolates and 78 sputum samples collected from the National Tuberculosis Reference Laboratory, China CDC, were tested by MLP-RAP assay. In parallel, qPCR and Sanger sequencing of nested PCR product assay were also performed for comparison. The sensitivity of the MLP-RAP assay could reach 5 copies/μl using recombinant plasmids, which is 20 times more sensitive than qPCR (100 copies/μl). In addition, the detection ability of rifampicin heteroresistance was 5%. The MLP-RAP assay had low requirements (boiling method) for nucleic acid extraction and the reaction could be completed within 1 h when placed in a fluorescent qPCR instrument. The result of the clinical evaluation showed that the MLP-RAP method could cover codons 516, 526, 531, and 533 with good specificity. 41 out of 78 boiled sputum samples were detected positive by MLP-RAP assay, which was further confirmed by Sanger sequencing of nested PCR product assay, on the contrary, qPCR was able to detect 32 samples only. Compared with Sanger sequencing of nested PCR product assay, both the specificity and sensitivity of the MLP-RAP assay were 100%. MLP-RAP assay can detect RR-TB infection with high sensitivity and specificity, indicating that this assay has the prospect of being applied for rapid and sensitive RR-TB detection in general laboratories where fluorescent qPCR instrument is available.

Policy and programmatic directions for the Lesotho tuberculosis programme: Findings of the national tuberculosis prevalence survey, 2019.

The Kingdom of Lesotho has one of the highest burdens of tuberculosis (TB) in the world. A national TB prevalence survey was conducted to estimate the prevalence of bacteriologically confirmed pulmonary TB disease among those ≥15 years of age in 2019. A multistage cluster-based cross-sectional survey where residents ≥15 years in 54 clusters sampled from across the country were eligible to participate. Survey participants were screened using a symptom screen questionnaire and digital chest X-ray (CXR). Respondents who acknowledged cough of any duration, fever, weight loss, night sweats and/or had any CXR abnormality in the lungs were asked to provide two spot sputum specimens. All sputum testing was conducted at the National TB Reference Laboratory (NTRL), where samples underwent Xpert MTB/RIF Ultra (1st sample) and MGIT culture (2nd sample). HIV counselling and testing was offered to all survey participants. TB cases were those with Mycobacterium tuberculosis complex-positive samples with culture; and where culture was not positive, Xpert MTB/RIF Ultra (Xpert Ultra) was positive with a CXR suggestive of active TB and no current or prior history of TB. A total of 39,902 individuals were enumerated, and of these, 26,857 (67.3%) were eligible to participate; 21,719 (80.9%) participated in the survey of which 8,599 (40%) were males and 13,120 (60%) were females. All 21,719 (100%) survey participants underwent symptom screening and a total of 21,344 participants (98.3%) had a CXR. Of the 7,584 (34.9%) participants who were eligible for sputum examination, 4,190 (55.2%) were eligible by CXR only, 1,455 (19.2%) by symptom screening, 1,630 by both, and 309 by CXR exemption. A total of 6,780 (89.4%) submitted two sputum specimens, and 311 (4.1%) submitted one sample only. From the 21,719 survey participants, HIV counseling and testing was offered to 17,048, and 3,915 (23.0%) were documented as HIV-positive. The survey identified 132 participants with bacteriologically confirmed pulmonary TB thus providing an estimated prevalence of 581 per 100,000 population (95% CI 466-696) for those ≥15 years in 2019. Using the survey results, TB incidence was re-estimated to be 654 per 100,000 (95% CI 406-959), which was comparable to the 2018 TB incidence rate of 611 per 100,000 (95% CI 395-872) reported by the World Health Organization (WHO). The highest TB burden was found in those ≥55 years and among men. The ratio of prevalence to case notification was estimated at 1.22. TB/HIV coinfection was identified in 39 (29.6%) participants. Out of the 1,825 participants who reported a cough, 50% of these participants, mostly men, did not seek care. Those who sought care predominantly went to the public health facilities. The TB prevalence survey results confirmed that burden of TB and TB/HIV coinfection remains very high in Lesotho. Given that TB prevalence remains high, and there is a significant proportion of participants with confirmed TB that did not report TB suggestive symptoms. The National TB Programme will need to update its TB screening and treatment algorithms to achieve the End TB targets. A major focus will need to be placed on finding the "missing cases" i.e., undiagnosed or under-reported TB cases, or ensuring that not only TB symptomatic but also those who do not present with typical TB symptoms are promptly identified to reduce further onward transmission.

Second-line drug resistance markers as proxy indicators of time to sputum culture conversion among second-line drug resistant tuberculosis patients tested in Uganda: A cross-sectional study

Background Increased tuberculosis disease burden arises as a result of low treatment success rates stemming from the emergence of second-line drug resistance. We aimed at determining the usefulness of second-line drug (SLD) resistance markers as proxy indicators of time to sputum culture conversion; a renowned predictor of Tuberculosis treatment outcome, among SLD-resistant tuberculosis (TB) patients tested at the Uganda National TB Reference Laboratory (NTRL). Methods A cross-sectional study was conducted on 72 bacteriologically confirmed SLD resistant TB patients with datasets including culture conversion time and second line probe assay mutation profiles between 01/06/2017 and 31/12/2019. The data were then imported into STATA v15 for descriptive statistical analysis, Univariate cox proportional hazard model analysis and Kaplan-Meier survival curves at a 5% level of significance; p-value ≤0.05. Results Results indicate the median time was achieved at 3 (0–12) months across the studied patients. The rrs G1484T mutation associated with conferring drug resistance to injectable agents was observed to have the shortest median conversion time of 1.5 months, longest by the gryB E540D at 5 months. A single mutation in the gryA gene locus showed higher converted proportions 70.8% (58.9–81.0) than those that had two 8.3% (3.1–17.3) or three 2.7% (0.3–10.0) mutations. Conclusions The studied second-line drug resistance markers had no statistically significant association with the time to sputum culture conversion, although increased drug resistance levels reduced the converted proportions and stressed the need to utilize molecular diagnostics data and other crucial variables to better comprehend proxy indicators of SLD resistant tuberculosis management.

Resistance patterns among drug-resistant tuberculosis patients and trends-over-time analysis of national surveillance data in Gabon, Central Africa

ObjectiveRoutinely generated surveillance data are important for monitoring the effectiveness of MDR-TB control strategies. Incidence of rifampicin-resistant tuberculosis (RR-TB) is a key indicator for monitoring MDR-TB.MethodsIn a longitudinal nationwide retrospective study, 8 years (2014–2021) of sputum samples from presumptively drug-resistant tuberculosis patients from all regions of Gabon were referred to the national tuberculosis reference laboratory. Samples were analysed using GeneXpert MTB/RIF and Genotype MTBDRsl version 2/Line Probe Assay.ResultsOf 3057 sputum samples from presumptive tuberculosis patients, both from local hospital and from referral patients, 334 were RR-TB. The median patient age was 33 years (interquartile range 26–43); one third was newly diagnosed drug-resistant tuberculosis patients; one-third was HIV-positive. The proportion of men with RR-TB was significantly higher than that of women (55% vs 45%; p < 0.0001). Patients aged 25–35 years were most affected (32%; 108/334). The cumulative incidence of RR-TB was 17 (95% CI 15–19)/100,000 population over 8 years. The highest incidences were observed in 2020 and 2021. A total of 281 samples were analysed for second-line drug resistance. The proportions of study participants with MDR-TB, pre-XDR-TB and XDR-TB were 90.7% (255/281), 9% (25/281) and 0.3% (1/281), respectively. The most-common mutations in fluoroquinolones resistance isolates was gyrA double mutation gyrA MUT3B and MUT3C (23%; 4/17). Most (64%; 6/8) second-line injectable drugs resistance isolates were characterised by missing both rrs WT2 and MUT2 banding.ConclusionThe increasing incidence of MDR-TB infection in Gabon is alarming. It is highest in the 25–35 years age category. The incidence of MDR-TB infection in treatment-naïve patients calls for case finding and contact tracing strategy improvement.

Detection of Mycobacterium tuberculosis and rifampicin resistance by Xpert® MTB/RIF assay among presumptive tuberculosis patients in Addis Ababa, Ethiopia from 2014 to 2021

ObjectiveThis study aimed to determine the frequencies and trends of Mycobacterium tuberculosis and rifampicin resistance among presumptive tuberculosis patients in Ethiopia, who were tested using the Xpert MTB/RIF assay between 2014 and 2021. MethodsData were collected retrospectively from patient registries. Laboratory-based data were extracted from the national tuberculosis (TB) referral laboratory database. All patients referred to the National Tuberculosis Reference Laboratory (NTRL) for TB diagnosis from all over the country between March 1, 2014 and September 30, 2021, and tested using the Xpert MTB/RIF assay, were included. The extracted data were entered into a Microsoft Excel sheet and analyzed by Statistical Package for Social Sciences (SPSS) version 23. ResultsAmong a total of 13 772 individuals tested using the Xpert MTB/RIF assay, the majority (8223; 59.7%) were males, and 48.5% (6678) of the individuals were aged between 15 and 39 years. Mycobacterium tuberculosis (MTB) was detected in 17.0% (2347) of the examined individuals. Of the detected MTB cases, nearly 9.9% (233) were rifampicin resistant (RR-TB), while 24 (1.0%) were RR-intermediate. Among all RR-TB cases, more than half (125; 53.6%) were detected in males, and 105 were new TB cases. Extrapulmonary (EPTB) patients had a greater rate of rifampicin resistance (11.0%) than pulmonary (PTB) patients (9.6%). ConclusionThe frequency of TB and RR-TB remains high in the study setting. RR-TB was found to have a statistically significant association with previous anti-TB medication treatment. As a result, improving treatment adherence in recognized instances could assist in preventing MTB and RR-TB cases.

Pre-extensively drug-resistant tuberculosis among multidrug-resistant tuberculosis patients in Ethiopia: a laboratory-based surveillance study

BackgroundThe rise of drug-resistant tuberculosis (DR-TB) has presented a substantial challenge to the national tuberculosis (TB) control program. Understanding the epidemiology of pre-extensively drug-resistant tuberculosis (pre-XDR-TB) could help clinicians to adapt MDR-TB treatment regimens at an earlier stage. This study aimed to assess second-line anti-TB drug resistance among MDR-TB patients in Ethiopia using routine laboratory-based data. MethodsLaboratory-based cross-sectional data were collected from the national TB reference laboratory and seven regional tuberculosis culture laboratories in Ethiopia from July 2019 to March 2022. The required data, such as drug-susceptibility testing (DST) results and sociodemographics, were collected on a structured checklist from laboratory registration books and electronic databases. Data were entered into a Microsoft Excel spreadsheet and analyzed using SPSS version 23. Descriptive statistics were performed to show the distribution and magnitude of drug resistance. ResultsSecond-line drugs (SLDs) susceptibility testing was performed for 644 MDR isolates, of which 19 (3%) were found to be pre-XDR-TB cases. Of the total MDR-TB isolates, 19 (3%) were resistant to at least one fluoroquinolone drug, while 11 (1.7%) were resistant to at least one injectable second-line drug. Of the 644 MDR-TB isolates, 1.9% (5/261) pre-XDR were from new MDR-TB cases, while 3.7% (14/383) were from previously treated MDR-TB patients. The most frequently identified mutations, based on MTBDRsl results, were in codon A90V of the gyrA gene (77.3%) and A1401G of the rrs gene (45.5%). ConclusionThe overall prevalence of pre-XDR-TB in Ethiopia is considerable. The majority of SLD resistance mutations were in the gyrA gene at position A90V. Modern, rapid DST is necessary to enable identification of pre-XDR-TB and XDR-TB in supporting proper regimen administration for patients.

Quality Analysis of Tuberculosis Specimens Transported by Drones versus Ground Transportation

There are many challenges that impact the current referral network for Tuberculosis (TB) sputum specimens in Mozambique. In some cases, health facilities are remote and the road infrastructure is poor and at times impassable, leading to delays in laboratory specimen transportation and long turn-around times for results. Drone transportation is a promising solution to reduce transportation time and improve access to laboratory diagnostics if the sample quality is not compromised during transport. This study evaluated the impact of drone transportation on the quality of TB sputum specimens with suspected Mycobacterium tuberculosis. 156 specimens were collected at five (5) health centers and sent to the Instituto Nacional de Saúde (INS) National TB Reference Laboratory. Specimens were then equally divided into two aliquots; one to be transported on land and the other by air using a drone. Control and study group specimens were processed using the NALC-NaOH method. Agreement between sample and control specimens was acceptable, indicating that drone transportation did not affect the quality of TB specimens. The authors recommend additional studies to validate drone transportation of TB specimens over a longer period of time to give further confidence in the adoption of drone delivery in Mozambique.

Determination of genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Turkey using 15 locus MIRU-VNTR and spoligotyping methods

ABSTRACT Tuberculosis (TB) remains the leading cause of deaths from infectious disease worldwide. Nowadays, the tendency of Mycobacterium tuberculosis complex (MTBC) to spread between continents due to uncontrolled migration movements shows that TB is a global health problem. The number of studies for the detection of MTBC strains’ epidemiological features in areas with TB spread risk using molecular-based methods such as spoligotyping and Mycobacterial Interspersed Repetitive Unit (MIRU) Variable Number Tandem Repeats (VNTR) at the clonal level is insufficient. In this study, it was aimed to determine the phylogenetic relationships of MTBC strains at the species level by spoligotyping and 15 locus MIRU-VNTR (MIRU-VNTR15) molecular methods of 96 multidrug-resistant (MDR) MTBC strains isolated from sputum samples of patients with a preliminary diagnosis of pulmonary TB or suspected contact history those sent to National Tuberculosis Reference Laboratory from the centers that are members of the Tuberculosis Laboratory Surveillance Network. The phylogenetic relationship between 96 MDR-TB strains was investigated with the combination of bead-based spoligotyping and MIRU-VNTR15 methods on the MAGPIX® Milliplex Map device. In this study, it was determined that the T1 family is more common in our country and LAM7-TUR family is less common than the Beijing family unlike other studies. It was determined that the strains in the same cluster had different locus profiles, and there was no transmission from the same clone in the clonal typing we performed with spoligotyping and MIRU-VNTR15.

PERFORMANCE OF XPERT MTB/RIF ULTRA AND GENOTYPE MTBDRPLUS ASSAY IN THE DIAGNOSIS OF DRUG-RESISTANT TB IN TIRANA, ALBANIA

TYPE: Late Breaking Abstract TOPIC: Chest Infections PURPOSE: In a low resource setting, the tuberculosis (TB) culture may pose a problem for case detection and initiation of second-line treatment due to both financial restraints and technical challenges. There is a need for rapid, reliable and easily accessible tools for diagnosis of drug resistant TB. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF Ultra and MTBDRplus Assay. METHODS: A systematic random sampling procedure was used to select sputum samples from a pool of samples received at the National TB Reference Laboratory for TB diagnosis between January to December 2021. Fifty-three smear positive sputum samples were subjected to testing by GeneXpert MTB/RIF Ultra, MTBDRplus Assay, BACTEC MGIT Culture and drug susceptibility testing (DST). Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the two assays compared to DST as a reference standard. RESULTS: For diagnosis of rifampicin resistance, GeneXpert MTB/RIF Ultra had a sensitivity, specificity, positive predictive value, and negative predictive value of 66.7, 100, 100 and 98.1% respectively while MTBDRplus assay had 100, 100, 100 and 100%. For diagnosis of isoniazid resistance, MTBDRplus assay had a sensitivity, specificity, positive predictive value, and negative predictive value of 87.5, 100, 100, and 97.8% compared to DST. CONCLUSIONS: MTBDRplus assay shows a slightly better performance characteristic to GeneXpert MTB/RIF Ultra, regarding detection of rifampicin resistance. CLINICAL IMPLICATIONS: MTBDRplus assay may represent an alternative to culture with regards to detection of both rifampicin and isoniazid resistance in smear positive samples. DISCLOSURE: No significant relationships. KEYWORD: drug resistant tuberculosis

Experience on the first national anti-TB drug resistance survey (DRS) in Timor-Leste

BackgroundA national drug resistance survey (DRS) was implemented for the first time in Timor-Leste (TL) in 2019. The primary objective of the survey was to assess the prevalence of drug resistance among new and previously treated pulmonary TB patients in the country.MethodsThis nation-wide cross-sectional survey was conducted in 2019 targeting all new and previously treated sputum smear-positive pulmonary TB patients. Sputum samples were submitted to the National TB Reference Laboratory for confirmation of TB and to determine resistance to rifampicin by Xpert MTB/RIF. Culture was performed on solid media, and culture isolates of confirmed TB cases were shipped to the WHO Supranational TB Reference Laboratory in Chennai, India for whole genome sequencing (WGS). Survey summary statistics, data cross-tabulations and analysis of potential risk factors of rifampicin-resistant TB (RR-TB) were conducted using R statistical software (version 3.5.2).ResultsA total of 953 sputum-smear positive patients were enrolled, of which 917 were confirmed as positive for TB by either Xpert MTB/RIF or culture. An electronic web-based system was used for entry and storage of the data. Rifampicin resistance was detected among 0.6% (95% CI 0.2–1.3) of new cases and 2.7% (95% CI 0.5- 8.2) of previously treated cases. WGS was conducted for validation purposes on 65 randomly selected isolates (29% of RR-TB (2/7) and 7% of RS-TB (63/910) by Xpert MTB/RIF or pDST). The original test results agreed with the WGS validation results for 62/64 isolates (97%).ConclusionThe prevalence of RR-TB in Timor-Leste is relatively low compared to the estimated proportions of RR-TB in the WHO South-East Asia Region (2.5% [95% CI 1.9–3.3] among new cases and 14% [95% CI 7.7–21] among previously treated cases). The rapid sputum collection and transportation mechanism implemented in the survey demonstrates its feasibility in low resource settings and should be replicated for routinely transporting TB specimens from microscopy labs to GeneXpert sites. Establishment of in-country capacity for rapid molecular diagnostics for both first- and second-line DST is an immediate need for achieving universal drug susceptibility testing (DST) to guide appropriate patient management.

Statistical Investigation of High Culture Contamination Rates in Mycobacteriology Laboratory

BackgroundCulture of Mycobacterium tuberculosis remains the gold standard in mycobacteriology laboratories, constrained by the very high risk of contamination; therefore, contamination rate is an important key performance indicator (KPI) for laboratory monitoring and evaluation processes.AimThis study aimed to investigate the factors that contribute to elevated contamination rates in the Sudan National Tuberculosis Reference Laboratory.MethodA laboratory-based retrospective study was applied; a TB culture register-book was carefully reviewed and data from 2 January 2019 to 31 December 2019 were entered, cleaned, and analyzed using IBM SPSS 20. A multivariate logistic regression model was performed to examine two dependent variables, the massive contamination, and the single tube contamination against predictors of reason for cultivation, type of specimen, experiment team, and the quarter of cultivation.ResultsIt has been found that in 2019 contamination rates were frequently higher; the highest rates were recorded in January and November, 28.2 and 25.2%, respectively. August is an exception with an accepted contamination rate of 4.6%. Of 1,149 specimens requested for culture, 945 (82.2%) samples were eligible to be included in multivariate logistic regression analysis. The team conducting the experiment was significantly associated with a high single tube contamination p value 0.007; adjusted odds ratio AOR 3.570 (1.415–9.005). The correlation between the single tube contamination and the massive contamination is significant; p value 0.01.ConclusionThe study concludes that high culture contamination is the greatest risk to the quality of laboratory service and can end in either the loss of specimens or delay in the decisions of initiating patient treatment. In addition, the low quality or incompleteness of data increases the uncertainty and undermines the measurement of key performance indicators.

Epidemiological and laboratory characteristics of multidrug-resistant tuberculosis patients in Bhutan, 2015-2019

Bhutan is no exception to the rising global threat of drug resistance tuberculosis (TB), particularly multidrug-resistant (MDR) TB. Although drug resistance surveillance has been carried out in Bhutan since 2010, limited analysis reports are available. Therefore, we looked at data from 2015-2019 to understand patient characteristics. To obtain data for MDR-TB from the past 5 years, we looked at manual registers and laboratory worksheets for all samples received at National TB Reference Laboratory. Epidemiological factors and laboratory variables were analyzed using descriptive statistics. Among 304 patients with MDR-TB, 85.20% (n=259) are new cases with no previous history of treatment. Those aged 16-25 years from both genders are affected more (46.05%, n=140) than other age groups. The majority (94.62%, n=264) of rifampicin resistance was found in the MUT 3 rpoB gene. For Isoniazid, 97.13% (n=271) resistance was seen in the MUT1 band of the katG gene. A high number of MDR-TB cases among new patients and little variation in the resistance band pattern over 5 years could indicate uncontrolled ongoing transmission. Whole-genome sequencing for the samples is required to further understand the epidemiology of the resistance pattern.

Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year\u2019s review

BackgroundSecond-line drug resistance (SLD) among tuberculosis (TB) patients is a serious emerging challenge towards global control of the disease. We characterized SLD-resistance conferring-mutations among TB patients with rifampicin and/or isoniazid (RIF and/or INH) drug-resistance tested at the Uganda National TB Reference Laboratory (NTRL) between June 2017 and December 2019.MethodsThis was a descriptive cross-sectional secondary data analysis of 20,508 M. tuberculosis isolates of new and previously treated patients’ resistant to RIF and/or INH. DNA strips with valid results to characterise the SLD resistance using the commercial Line Probe Assay Genotype MTBDRsl Version 2.0 Assay (Hain Life Science, Nehren, Germany) were reviewed. Data were analysed with STATAv15 using cross-tabulation for frequency and proportions of known resistance-conferring mutations to injectable agents (IA) and fluoroquinolones (FQ).ResultsAmong the eligible participants, 12,993/20,508 (63.4%) were male and median (IQR) age 32 (24–43). A total of 576/20,508 (2.8%) of the M. tuberculosis isolates from participants had resistance to RIF and/or INH. These included; 102/576 (17.7%) single drug-resistant and 474/576 (82.3%) multidrug-resistant (MDR) strains. Only 102 patients had test results for FQ of whom 70/102 (68.6%) and 01/102 (0.98%) had resistance-conferring mutations in the gyrA locus and gyrB locus respectively. Among patients with FQ resistance, gyrAD94G 42.6% (30.0–55.9) and gyrA A90V 41.1% (28.6–54.3) mutations were most observed. Only one mutation, E540D was detected in the gyrB locus. A total of 26 patients had resistance-conferring mutations to IA in whom, 20/26 77.0% (56.4–91.0) had A1401G mutation in the rrs gene locus.ConclusionsOur study reveals a high proportion of mutations known to confer high-level fluoroquinolone drug-resistance among patients with rifampicin and/or isoniazid drug resistance. Utilizing routinely generated laboratory data from existing molecular diagnostic methods may aid real-time surveillance of emerging tuberculosis drug-resistance in resource-limited settings.

Genetic diversity of nontuberculous mycobacteria among symptomatic tuberculosis negative patients in Kenya.

Non-Tuberculous Mycobacteria (NTM) transmission to humans occurs through inhalation of dust particles or vaporized water containing NTM leading to pulmonary manifestations. NTM infections are often misdiagnosed for tuberculosis (TB) due to their similar clinical and radiological manifestations. We, therefore, performed a species-level identification of NTM in symptomatic TB negative patients through sequencing of the hsp65 gene. We conducted a cross-sectional study at the National Tuberculosis Reference Laboratory in the period between January to November 2020. One hundred and sixty-six mycobacterial culture-positive samples that tested negative for TB using capilia underwent Polymerase Chain Reaction targeting the hsp65 gene. Isolates showing a band with gel electrophoresis at 441 bp position were sequenced using Sanger technology. Geneious software was used to analyze the obtained sequences, and the National Center for Biotechnology Information gene database identified NTM species for each isolate. A phylogenetic tree was constructed from the DNA sequences and evolutionary distances computed using the general time-reversible method. Pearson chi-square was used to determine the association between NTM infection and participants' characteristics. Our study identified 43 different NTM species. The dominant NTM belonged to Mycobacterium avium complex 37 (31%). Slow-growing NTM were the majority at 86 (71%) while rapid-growing NTM were 36 (29%). A significant association (P<0.05) was observed for regions and age, while patient type had a weak likelihood of NTM infection. Our study characterized the diversity of NTM in Kenya for the first time and showed that species belonging to M. Avium Complex are the most prevalent in the country.