A rare case of isoniazid mono-resistant tuberculosis presenting as cardiac tamponade along with an anterior mediastinal mass in a 15-year-old immunocompetent patient

ABSTRACT

A 15-year-old boy presented with a sudden onset of breathlessness for 7 days, gradual loss of weight of 17.6 lbs over the last month and progressive hoarseness of voice for 7 months. The contrast-enhanced computed tomography (CECT) scan revealed a heterogeneously enhancing lesion in the anterior mediastinum with multiple discrete lymph nodes in the cervical and mediastinal locations. The GeneXpert MTB/RIF assay performed on the CT-guided biopsy of the mass was negative, but the culture for Mycobacterium tuberculosis was positive at 7 weeks of incubation. There was a suboptimal radiological response after 6 months of treatment. First-line drug susceptibility testing (DST) performed by line probe assay (LPA) on the positive culture detected high-level resistance to isoniazid. The treatment was modified as per DST results to which the patient responded well.

Non-tuberculous mycobacteria hybridisation profiles in the GenoType MTBDRplus assay: experience from a diagnostic routine of a high-throughput laboratory

Introduction. Disease caused by non-tuberculous mycobacteria (NTM) is an emergent problem. Because NTM pulmonary disease and tuberculosis (TB) have similar clinical presentations, many cases of NTM may be misdiagnosed as TB before laboratory identification of the NTM species.Hypothesis/Gap Statement. Clinical laboratories should always perform differentiation between Mycobacterium tuberculosis complex (MTBC) and NTM to guide patients' correct treatment.Aim. To describe the characteristics and to identify mycobacterial isolates presumptively classified as MTBC by macroscopic characteristics in culture media that tested negative in GenoType MTBDRplus.Methodology. All cultures from February 2019 to December 2021 showing MTBC macroscopic characteristics were processed by GenoType MTBDRplus. MTBC-negative cultures underwent species identification by immunochromatography, line probe assays and PRA-hsp65. Patients' data were obtained from Brazilian surveillance systems.Results. Only 479 (3.1%) of 15 696 isolates presumptively identified as MTBC were not confirmed by GenoType MTBDRplus and were then subjected to identification. A total of 344 isolates were shown to be NTM, of which 309 (64.5%) and 35 (7.3%) were identified to the species and genus levels, respectively. Of the 204 NTM isolates with MTBC characteristics, the most frequent species were M. fortuitum (n=52, 25.5%), M. abscessus complex (MABC; n=27, 13.2%) and M. avium complex (MAC; n=26, 12.7%). Regarding the GenoType MTBDRplus results from NTM isolates, there were diverse hybridisation profiles with rpoB gene's different wild-type (WT) probes. Seventy-six (16.1%) of the 473 patients were classified as having NTM disease, the most frequent being MAC (n=15, 19.7%), MABC (n=13, 17.1%), M. kansasii (n=10, 13.2%) and M. fortuitum (n=6, 7.9%).Conclusion. Because the signs and symptoms of pulmonary TB are similar to those of pulmonary mycobacteriosis and treatment regimens for TB and NTM are different, identifying the disease-causing species is paramount to indicate the correct management. Thus, in the laboratory routine, when an isolate presumptively classified as MTBC is MTBC-negative, it is still essential to perform subsequent identification.

Pulmonary tuberculosis and multidrug-resistant Mycobacterium tuberculosis in northwestern Ethiopia: a hospital-based cross-sectional study among presumptive pulmonary tuberculosis patients

Introduction

Border areas are important sites for disseminating Mycobacterium tuberculosis among individuals living in such areas. This study examined patients with suspected pulmonary tuberculosis (PTB) visiting the Abrihajira and Metema hospitals in northwest Ethiopia to investigate the prevalence of rifampicin-resistant Mycobacterium tuberculosis (RR-MTB), multidrug-resistant Mycobacterium tuberculosis (MDR-MTB), and risk factors related to Mycobacterium tuberculosis infection.

Methods

A hospital-based cross-sectional study was conducted from February to August 2021 among 314 PTB presumptive patients. Xpert MTB/RIF and line probe assays (LPA) were used to process sputum samples. Data were imported into the Epi-Data 3.1 program and exported to Statistical Package for the Social Sciences (SPSS) version 20.0 (SPSS, Chicago, IL, United States) to conduct the analysis. A logistic regression analysis was used to investigate the relationship between the dependent and independent variables. A value of p of <0.05 denoted statistical significance.

Results

Of the total (314) PTB presumptive patients who participated in this study, 178 (56.69%) were men, and 165 (52.5%) were from 25 to 50 years of age with a median age of 35.00 (inter-quartile: 25-45 years). Among all patients, 12.7% had PTB by Gene Xpert and 7/314 (2.23%) were resistant to rifampicin. Among patients enrolled, 4/314 (1.27%) had MDR-MTB (resistant to RIF and INH) by LPA. Regarding the risk factors assessed, primary level of education, sputum production, night sweating, respiratory disorder, contact history of TB, history of MDR-MTB infection, history of alcohol use, and cigarette smoking showed statistical significance with the prevalence of PTB (p ≤ 0.05).

Discussion

This study observed a high prevalence of PTB, RR-MTB, and MDR-MTB compared with many other previous studies conducted in Ethiopia. Among the assessed risk factors that could be associated with the prevalence of PTB, eight were statistically significant. This prevalence, resistance, and statistically significant variables are the evidence to which more emphasis should be given to the country's border areas.

Molecular characterization of genetic mutations with fitness loss in pulmonary tuberculosis patients associated with HIV co-infection in Northwest Amhara, Ethiopia

Objectives

Molecular approaches to identifying resistance-conferring mutations suggest a revolution in the field of tuberculosis. The aim of the study was to determine the association between resistance-conferring mutations with fitness loss in Mycobacterium tuberculosis clinical isolates and HIV co-infection in the Amhara region of Ethiopia.

Methods

A laboratory-based cross-sectional study was conducted between September 2022 and June 2023. A line probe assay was performed on 146 culture-positive clinical isolates. Logistic regression analysis was used to measure the strength of the association between the drug-resistance-conferring mutations with fitness loss in M. tuberculosis isolates and tuberculosis/HIV co-infection. A p-value ⩽ 0.05 was considered statistically significant.

Results

A total of 11 distinct mutations at four genetic loci among 19 resistant isolates were detected. The frequency of rifampicin, isoniazid, and fluoroquinolones resistance-conferring mutations was identified in 12 (8.2%), 17 (11.6%), and 2 (1.4%) of the isolates, respectively. The most prominent specific mutations were S450L (5/9, 55.6%), S315T (11/11, 100%), C-15T (4/4, 100%), and D94G (1/1, 100%). Double mutations were observed in 10 (52.6%) multidrug-resistant tuberculosis isolates; the most common were detected in both the rpoB and katG genes (8/10, 80.0%). The HIV-co-infected tuberculosis patients carried a higher proportion of low fitness of non-rpoB S450L variants than those tuberculosis patients without HIV (80.0% vs 14.3%) and showed a significant association (cOR = 0.042, 95% CI: 0.002-0.877, p = 0.041), but not with the low fitness of non-katG S315T variants (cOR = 3.00, 95% CI: 0.348-25.870, p = 0.318).

Conclusion

This study provides valuable information on the genetic variants with fitness loss associated with HIV co-infection, but requires further whole-genome-based mutation analysis.

To Test or Not? Xpert MTB/RIF as an Alternative to Smear Microscopy to Guide Line Probe Assay Testing for Drug-Resistant Tuberculosis

Xpert MTB/RIF (Xpert) revolutionized tuberculosis (TB) diagnosis. Laboratory decision making on whether widely-used reflex drug susceptibility assays (MTBDRplus, first-line resistance; MTBDRsl, second-line) are conducted is based on smear status, with smear-negative specimens often excluded. We performed receiver operator characteristic (ROC) curve analyses using bacterial load information (smear microscopy grade, Xpert-generated semi-quantitation categories and minimum cycle threshold [CTmin] values) from Xpert rifampicin-resistant sputum for the prediction of downstream line probe assay results as "likely non-actionable" (no resistance or susceptible results generated). We evaluated actionable-to-non-actionable result ratios and pay-offs with missed resistance versus LPAs done universally. Smear-negatives were more likely than smear-positive specimens to generate a non-actionable MTBDRplus (23% [133/559] versus 4% [15/381]) or MTBDRsl (39% [220/559] versus 12% [47/381]) result. However, excluding smear-negatives would result in missed rapid diagnoses (e.g., only 49% [264/537] of LPA-diagnosable isoniazid resistance would be detected if smear-negatives were omitted). Testing smear-negatives with a semi-quantitation category ≥ "medium" had a high ratio of actionable-to-non-actionable results (12.8 or a 4-fold improvement versus testing all using MTBDRplus, 4.5 or 3-fold improvement for MTBDRsl), which would still capture 64% (168/264) and 77% (34/44) of LPA-detectable smear-negative resistance, respectively. Use of CTmins permitted optimization of this ratio with higher specificity for non-actionable results but decreased resistance detected. Xpert quantitative information permits identification of a smear-negative subset in whom the payoffs of the ratio of actionable-to-non-actionable LPA results with missed resistance may prove acceptable to laboratories, depending on context. Our findings permit the rational expansion of direct DST to certain smear-negative sputum specimens.

Analysis of Discordance between Genotypic and Phenotypic Assays for Rifampicin-Resistant Mycobacterium tuberculosis Isolated from Healthcare Facilities in Mthatha

The study sought to determine the rate of discordant results between genotypic and phenotypic tests for the diagnosis of drug-resistant tuberculosis (DR-TB). Sputum samples and cultured isolates from suspected DR-TB patients were, respectively, analyzed for Mycobacterium tuberculosis by Xpert^® MTB/RIF (Cepheid, Sunnyvale, CA, USA) and line probe assays (LPA) (Hain, Nehren, Germany). Discrepant rifampicin (RMP)-resistant results were confirmed using BACTEC MGIT960 (BD, New York, NY, USA). Of the 224 RMP-resistant results obtained by Xpert MTB/RIF, 5.4% were susceptible to RMP by LPA. MGIT960 showed a 75% agreement with LPA. The discrepancy was attributed to either heteroresistance or DNA contamination during LPA testing in 58.3% of cases. In 25% of the samples showing agreement in RMP resistance between Xpert MTB/RIF and MGIT960, the discrepancy was attributed to laboratory errors causing false RMP susceptible results with LPA. In 16.7% of the cases, the discrepancy was attributed to false RMP susceptible results with Xpert MTB/RIF. Out of the 224 isolates, susceptibility to isoniazid (INH) by LPA was performed in 73.7% RMP-resistant isolates, of which, 80.6% were resistant. All RMP-resistant isolates by Xpert MTB/RIF were confirmed in 98.5% by LPA if TB isolates were resistant to INH, but were only confirmed in 81.3% if TB isolates were susceptible to INH (p < 0.001). In conclusion, laboratory errors should be considered when investigating discordant results.

Genotype MTBDRsl version 2 and phenotypic drug resistance detection of Mycobacterium tuberculosis for fluoroquinolones and aminoglycosides

Background

Information on genotypic with comparison of phenotypic drug sensitivity test of anti-tuberculosis (TB) has been reported in several studies, which have variable results. The present study aimed to assess the Genotype MTBDRsl version 2.0/Line probe assay (LPA) for the detection of fluoroquinolones (FQ) and aminoglycosides (AMGs) resistance mutations among drug-resistant Mycobacterium TB (MTB) strains and also to compare the patterns of genotypic mutations of gyrA/B, rrs, and eis with mycobacteria growth indicator tube (MGIT 960).

Methods

A total of 1416 samples were subjected to Genotype MTBDRsl version 2.0 assay. One hundred and twenty sputum smear positive MTB isolates and 37 sputum smear negative MTB isolates confirmed multiple drug resistance resistant to FQ and AMG by the Genotype MTBDRsl version 2.0 were subjected to phenotypic drug susceptibility testing (DST) were analyzed.

Results

The association sensitivity, specificity, positive predictive value, negative predictive value, and accuracy for the resistance detection between MGIT (DST) and the Genotype MTBDRsl version 2.0 assay was significant (P < 0.01) of moxifloxacin (MFX) concentration. Sensitivity and specificity value for kanamycin (KAN) resistance was 76% and 89%; 47% and 94% for capreomycin (CAP); and 60% and 76% for low-level KAN, respectively.

Conclusion

Our results indicate that MFX (0.25and 1 μg/mL), KAN (2.5 μg/mL), and CAP (2.5 μg/mL) significantly (P < 0.01) and support the World Health Organization guidance to test FQ and AMG by genotypic test.

Molecular Identification of Non-tuberculous Mycobacteria in Suspected Tuberculosis Cases in Central India

Introduction Mycobacterium tuberculosis complex (MTBC), the primary cause of tuberculosis (TB), must be accurately identified to implement effective patient management and control strategies. Non-tuberculous mycobacteria (NTM) in suspected TB cases can result in erroneous diagnoses and needless treatment. Objective The study aimed to identify NTM in patients suspected of TB at a tertiary care hospital in central India using molecular methods. Methods This prospective study enrolled 400 suspected pulmonary and extra-pulmonary TB patients. Patients between the age of two to 90 years, of either gender, new and previously treated cases, Culture positive, patients with immune-compromised status, patients not responding to ATT, HIV positive and negative, and willing to give consent were included in the study. Liquid culture via the Mycobacterial growth indicator tube (MGIT) system was used to culture mycobacteria from clinical samples. The SD Bioline Ag MPT64 Test (Standard Diagnostics, South Korea) and in-house multiplex-PCR (mPCR) were used to differentiate between Mycobacterium tuberculosis complex and NTM species for the molecular identification of NTM GenoType® Mycobacterium Common Mycobacteria (CM) assay kit (HAIN Life Science, Nehren, Germany) was used following the manufacturer's protocol. Results Only 59/400 (14.7%) of the samples produced a positive result in MGIT culture, indicating the presence of mycobacteria, and 85.25% of the remaining 341 samples were negative for mycobacterial growth. Further investigation of these 59 cultures with mPCR and SD Bioline Ag MPT64 test showed that 12 (20.33%) cultures were determined to be NTM, while the remaining 47 (79.67%) were identified as MTBC. Genotype characterization with GenoType® mycobacterium CM assay kit revealed that five of the 12 NTM isolates (41.67%) showed patterns that were consistent with Mycobacterium (M.) fortuitum, three (25%) showed patterns that were consistent with M. abscessus, and four (33.33%) showed patterns that were consistent with M. tuberculosis. Conclusion These results emphasize the value of molecular methods for precisely identifying mycobacterial species, particularly in suspected TB cases. The high prevalence of NTM in positive cultures emphasizes the significance of differentiating between MTBC and NTM to prevent misdiagnosis and ensure proper care. Understanding the epidemiology and clinical significance of these organisms in central India is made possible by the identification of particular NTM species.

Comparison of xpert MTB/RIF assay, line probe assay, and culture in diagnosis of pulmonary tuberculosis on bronchoscopic specimen

Background

In patients unable to expectorate good quality sputum or with minimal to none sputum production, bronchoscopic specimens may be collected. The objective of the study is to determine the use of Xpert MTB/RIF assay and line probe assay (LPA) in the diagnosis of pulmonary TB (PTB) using specimens collected by bronchoscopy in a tertiary care center.

Methods

Bronchoscopy specimens received in the TB laboratory were processed by microscopy, Xpert MTB/RIF assay, LPA, and mycobacteria growth indicator tube (MGIT) culture. Results of MGIT culture are considered gold standard.

Results

Of the 173 specimens tested, MTB was detected in 48 (27.74%) samples by any of the above methods. Positivity in bronchoalveolar lavage was 31.4% (44/140) and in bronchial wash was 12.1% (4/33). Detection by microscopy, Xpert assay, and culture was 20 (11.56%), 45 (26.01%), and 38 (21.96%), respectively. Culture detected MTB in three additional specimens compared to Xpert assay. Xpert assay detected MTB in 45 (26%) specimens which include 10 specimens which were negative by culture. LPA detected MTB in 18 (90%) out of 20 smear-positive specimens. RIF resistance was detected in 20 (41.7%) specimens by Xpert and/or MGIT culture drug susceptibility testing (DST). Isoniazid (INH) resistance was detected in 19 specimens by LPA and MGIT culture DST.

Conclusion

Bronchoscopy can provide alternative respiratory specimens for diagnosing PTB in patients with difficulty to expectorate sputum. The utility of Xpert MTB/RIF as a rapid, sensitive, and specific test should always be supplemented with culture in difficult-to-obtain and precious respiratory specimens. LPA plays an important role in rapid detection of INH monoresistance.

GenoType MTBDRsl for detection of second-line drugs and ethambutol resistance in multidrug-resistant Mycobacterium tuberculosis isolates at a high-throughput laboratory

We assessed the performance of MTBDRsl for detection of resistance to fluoroquinolones, aminoglycosides/cyclic peptides, and ethambutol compared to BACTEC MGIT 960 by subjecting simultaneously to both tests 385 phenotypically multidrug-resistant-Mycobacterium tuberculosis isolates from Sao Paulo, Brazil. Discordances were resolved by Sanger sequencing. MTBDRsl correctly detected 99.7% of the multidrug-resistant isolates, 87.8% of the pre-XDR, and 73.9% of the XDR. The assay showed sensitivity of 86.4%, 100%, 85.2% and 76.4% for fluoroquinolones, amikacin/kanamycin, capreomycin and ethambutol, respectively. Specificity was 100% for fluoroquinolones and aminoglycosides/cyclic peptides, and 93.6% for ethambutol. Most fluoroquinolone-discordances were due to mutations in genome regions not targeted by the MTBDRsl v. 1.0: gyrA_H70R and gyrB_R446C, D461N, D449V, and N488D. Capreomycin-resistant isolates with wild-type rrs results on MTBDRsl presented tlyA mutations. MTBDRsl presented good performance for detecting resistance to second-line drugs and ethambutol in clinical isolates. In our setting, multidrug-resistant. isolates presented mutations not targeted by the molecular assay.

MTBDRplus and MTBDRsl for simultaneous diagnosis of gastrointestinal tuberculosis and detection of first-line and second-line drug resistance

BACKGROUND AND AIM

Emergence of drug resistance, especially to second-line drugs, hampers tuberculosis elimination efforts. The present study aimed to evaluate MTBDRplus and MTBDRsl assays for detecting first-line and second-line drug resistance, respectively, in gastrointestinal tuberculosis (GITB).

METHODS

Thirty ileocecal biopsy specimens, processed in the Department of Microbiology between 2012 and 2022, that showed growth of Mycobacterium tuberculosis on culture were included in the study. DNA, extracted from culture, was subjected to MTBDRplus and MTBDRsl (Hain Lifescience GmbH, Nehren, Germany), following manufacturer's instructions. Their performance was compared against phenotypic drug susceptibility testing (pDST) and gene sequencing.

RESULTS

Out of the 30 specimens, 4 (13.33%) were mono-isoniazid resistant, 4 (13.33%) were multidrug resistant (MDR), 2 (6.67%) were pre-extensively drug resistant (pre-XDR), and 2 (6.67%) were mono-fluoroquinolone resistant. The results were 100% concordant with pDST and gene sequencing.

CONCLUSIONS

In the wake of growing drug resistance in all forms of extrapulmonary tuberculosis, including GITB, MTBDRplus and MTBDRsl are reliable tools for screening of resistance to both first-line and second-line drugs.

Profile and Frequency of Mutations Conferring Drug-Resistant Tuberculosis in the Central, Southeastern and Eastern Ethiopia

Purpose

Advances in molecular tools that assess genes harboring drug resistance mutations have greatly improved the detection and treatment of drug-resistant tuberculosis (DR-TB). This study was conducted to determine the frequency and type of mutations that are responsible for resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolones (FLQs) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis (MTB) isolates obtained from culture-positive pulmonary tuberculosis (TB) patients in the central, southeastern and eastern Ethiopia.

Patients and Methods

In total, 224 stored culture-positive MTB isolates from pulmonary TB patients referred to Adama and Harar regional TB laboratories between August 2018 and January 2019 were assessed for mutations conferring RIF, INH, FLQs and SLIDs resistance using GenoType^®MTBDRplus (MTBDRplus) and GenoType^®MTBDRsl (MTBDRsl).

Results

RIF, INH, FLQs and SLIDs resistance-conferring mutations were identified in 88/224 (39.3%), 85/224 (38.0%), 7/77 (9.1%), and 3/77% (3.9%) of MTB isolates, respectively. Mutation codons rpoB S531L (59.1%) for RIF, katG S315T (96.5%) for INH, gyrA A90V (42.1%) for FLQs and WT1 rrs (100%) for SLIDs were observed in the majority of the isolates tested. Over a 10th of rpoB mutations detected in the current study were unknown.

Conclusion

In this study, the most common mutations conferring drug resistance to RIF, INH, FLQs were identified. However, a significant proportion of RIF-resistant isolates manifested unknown rpoB mutations. Similarly, although few in number, all SLID-resistant isolates had unknown rrs mutations. To further elucidate the entire spectrum of mutations, tool such as whole-genome sequencing is imperative. Furthermore, the expansion of molecular drug susceptibility testing services is critical for tailoring patient treatment and preventing disease transmission.

Drug-Resistant (DR) Tubercular Pleural Effusion: A Rare Case

Tuberculosis (TB) is one of the most common infectious diseases in developing countries throughout the world. According to the WHO, there has been a rise in the number of cases of drug-resistant (DR) TB in recent times. Tubercular pleural effusion is challenging to diagnose given the low bacillary load and frequently negative stains for acid-fast bacilli (AFB) on Ziehl-Neelsen (ZN) staining. We present a case of successful diagnosis and management of primary extra-pulmonary multidrug-resistant (MDR) tubercular pleural effusion after being misdiagnosed from outside as drug-sensitive extra-pulmonary TB. Initial tests revealed exudative effusion with raised adenosine deaminase (ADA) levels, therefore the patient was started on conventional anti-tubercular therapy with isoniazid (H), rifampicin (R), pyrazinamide (Z), and ethambutol (E), but the patient did not improve in spite of regular treatment for two months, which warranted further investigations. Therefore Xpert® MTB/R assay (Cepheid Inc., Sunnyvale, USA), line probe assay (LPA), and drug sensitivity testing (DST) of the pleural fluid were sent, which were suggestive of R- and H-resistant tubercular effusion. The patient was started on an oral bedaquiline-containing regimen as per the WHO guidelines and the patient showed considerable improvement on follow up.

Comparative Performance of Line Probe Assay and GeneXpert in the Detection of Rifampicin Monoresistance in a TB-Endemic African Country

Rapid, accurate and reliable assays are required for timely detection of drug-resistant tuberculosis and early initiation of second-line TB treatment as well as to minimize transmission of resistant strains. This study assessed diagnostic performance characteristics of two rapid molecular assays, line probe assay (LPA) and GeneXpert (MTB/RIF), in the detection rifampicin monoresistance using the phenotypic proportion method on Lowenstein−Jensen media as the gold standard. This study involved a total of 357 isolates, 74 rifampicin-resistant and 283 rifampicin-susceptible, collected at the Central Tuberculosis Reference Laboratory (CTRL) in Dar es Salaam, Tanzania, between 2016 and 2019. Sensitivity, specificity and positive and negative predictive values were used to assess the performance characteristics of the two assays while kappa coefficient was used to determine agreement of test results. The receiver operating curve (ROC) was used to determine the discriminatory ability of the test in distinguishing resistant and susceptible TB isolates. Our results showed that GeneXpert had sensitivity, specificity and positive and negative predictive values of 93.2, 82.7, 58.5 and 97.9%, respectively; the corresponding performance for LPA was 86.5, 97.5, 90.1 and 96.5%, respectively. Compared with conventional phenotypic DST results, GeneXpert had a moderate agreement (kappa 0.621, p < 0.001), while LPA had high agreement (0.853, p < 0.001). LPA showed an accuracy of 95.2% compared to GeneXpert’s 84.9%. ROC curve depicted the ability of the tests to distinguish rifampicin-sensitive and rifampicin-resistant strains to be 87.9% for GeneXpert and 92.0% for LPA. Our results indicate the superiority of LPA over GeneXpert regarding detection of rifampicin monoresistance. However, logistic challenges such as longer turnaround time and need for skilled laboratory personnel may limit its use.

Standardization of a stool concentration method for Mycobacterium tuberculosis detection in the pediatric population

Background

The inability of young children to expectorate sputum and paucibacillary status of Mycobacterium tuberculosis (MTB) increases its diagnostic complexity. In this study, we aimed to standardize a stool concentration method for the detection of MTB and its drug resistance by line probe assay (LPA).

Methods

The stool from 10 healthy children spiked with H37Rv in five different dilutions (1:1, 1:10, 1:100, 1:1000, and 1:10,000), and stool from 10 confirmed TB and 54 clinically diagnosed TB children were subjected to an in-house stool concentration protocol. All the processed filtrates were subjected to smear microscopy, solid culture, Xpert ultra testing, and LPA.

Results

Of 10 control samples, growth was seen in four samples (neat 1:1). In smear microscopy, bacilli could be seen in eight samples (1:1 and 1:10). Xpert ultra testing could detect MTB in eight samples in all dilutions with different loads. LPA could detect MTB in all samples and dilutions. In microbiologically confirmed children, seven out of 10 stool samples tested were positive. Out of 54 children with clinically diagnosed TB, 4 (7.4%) could be confirmed by microbiological diagnosis.

Conclusion

The protocol standardized in this study proves to be better working in the molecular detection of MTB.

Explorative Analysis of Treatment Outcomes of Levofloxacin- and Moxifloxacin-Based Regimens and Outcome Predictors in Ethiopian MDR-TB Patients: A Prospective Observational Cohort Study

Purpose/Background

Although Ethiopia is among the thirty high multi-drug resistant tuberculosis (MDR-TB) burden countries in the world, comparative therapeutic efficacy of moxifloxacin and levofloxacin has not been explored, particularly in MDR-TB patients. We therefore aimed to prospectively compare clinical outcomes and determine potential predictors of the outcomes among patients on moxifloxacin or levofloxacin-based MDR-TB drug regimens.

Methods

We analyzed clinical parameters and laboratory data of eighty MDR-TB patients on moxifloxacin- or levofloxacin-based regimens. The clinical outcomes were compared using the Kaplan–Meier survival functions and the outcome definitions of the 2013 World Health Organization. Monthly sputum culture conversions and a molecular line probe assay results were also assessed. Observed outcomes and patient-related variables between the two groups were compared using chi-square, Wilcoxon Rank and Fisher exact tests. We also determined the potential predictors influencing treatment outcomes of moxifloxacin and levofloxacin using Cox proportional hazard model.

Results

The levofloxacin-based treatment group had a lower failure rate and adverse drug events as well as better treatment success than the moxifloxacin-based group. Overall treatment success was 65%. Disaggregating the data revealed that 53.8% were cured, 11.2% completed treatment, 10.0% died, 11.2% failed, and 13.8% were lost-to-follow-up. The line probe assay result showed that 11.3% of the clinical isolates were resistant to fluoroquinolones and 3.8% were resistant to both fluoroquinolones and injectable anti-TB agents. Treatment regimen type, culture conversion rate, alcohol use, cavity lesion, serum levels of creatinine and alanine aminotransferase were independent predictors of treatment outcome.

Conclusion

The levofloxacin-based regimen group has a better overall treatment success than the moxifloxacin-based group among MDR-TB patients. Clinical parameters and substance use history of the patients influenced treatment outcomes. We recommend further broader clinical studies to substantiate our findings as an input to review MDR-TB treatment guidelines.

Whole-Genome Sequencing to Identify Missed Rifampicin and Isoniazid Resistance Among Tuberculosis Isolates-Chennai, India, 2013-2016

India has a high burden of drug-resistant tuberculosis (DR TB) and many cases go undetected by current drug susceptibility tests (DSTs). This study was conducted to identify rifampicin (RIF) and isoniazid (INH) resistance associated genetic mutations undetected by current clinical diagnostics amongst persons with DR TB in Chennai, India. Retrospectively stored 166 DR TB isolates during 2013–2016 were retrieved and cultured in Löwenstein-Jensen medium. Whole genome sequencing (WGS) and MGIT DST for RIF and INH were performed. Discordant genotypic and phenotypic sensitivity results were repeated for confirmation and the discrepant results considered final. Further, drug resistance-conferring mutations identified through WGS were analyzed for their presence as targets in current WHO-recommended molecular diagnostics. WGS detected additional mutations for rifampicin and isoniazid resistance than WHO-endorsed line probe assays. For RIF, WGS was able to identify an additional 10% (15/146) of rpoB mutant isolates associated with borderline rifampicin resistance compared to MGIT DST. WGS could detect additional DR TB cases than commercially available and WHO-endorsed molecular DST tests. WGS results reiterate the importance of the recent WHO revised critical concentrations of current MGIT DST to detect low-level resistance to rifampicin. WGS may help inform effective treatment selection for persons at risk of, or diagnosed with, DR TB.

Drug Resistance Pattern of M. tuberculosis Complex in Oromia Region of Ethiopia

Purpose

Multidrug resistant tuberculosis is an emerging problem in many parts of the world. The aim of this study was to determine the drug resistance pattern of Mycobacterium tuberculosis complex in Oromia Region of Ethiopia.

Patients and Methods

A cross-sectional study was conducted from Jan 2017 to June 2018 on 450 pulmonary tuberculosis patients who visited health facilities in nine administrative zones of Oromia Region. Socio-demographic characteristics and relevant clinical information were obtained using a structured questionnaire. Line Probe Assay for first and second line drugs was used to assess the pattern of drug resistance. SPSS version 20 was used for statistical analysis.

Results

Median age was 26 years and 240 (53.3%) patients were males. About 24% of them were previously treated for tuberculosis. Thirty-four (7.6%) were HIV co-infected. Line Probe Assay interpretable results were obtained for 387 isolates. Thirty (7.8%) were resistant to rifampicin and isoniazid and thus were multidrug resistant isolates. Among the multidrug resistant samples, three were found to be extensively drug resistant and one was pre-extensively drug resistant. Previous treatment history (AOR 9.94 (95% CI 3.73–26.51), P < 0.001) and nutritional status below normal (AOR 3.15 (95% CI 1.13–8.81), P < 0.029) were found to be associated with multidrug resistance. The chi-square tests have shown that there was a significant difference between the BCG vaccinated and the non-vaccinated in developing multidrug resistant tuberculosis at P = 0.027.

Conclusion

The proportion of multidrug resistance is above the WHO estimate for the country, Ethiopia, and the fact that some zones were at risk of transmission of extensively drug resistant tuberculosis warrant great attention of the control program holders even though it has to be verified through the conventional method.

Pulmonary Mycobacterium abscessus and response to treatment in an outpatient setting: Case series

Pulmonary disease due to Mycobacterium abscessus (Mab) has become an increasing cause of health concern, particularly among individuals infected with nontuberculous mycobacteria. Since Mab is intrinsically resistant to many antibiotics, it is very challenging to treat patients with symptomatic disease. In this case series, we report four patients with symptomatic pulmonary Mab who had prior history of antituberculosis treatment intake and declared cured at the end of treatment. The current episode was confirmed to be due to Mab infection by molecular and clinical diagnosis and received species specific-antibiotics therapy. All were periodically monitored for the sputum smear and culture conversions throughout the treatment period. The clinical course was variable though all received similar antibiotic regimen and showed varied treatment outcomes. The time of diagnosis and the treatment outcome indicate that a better understanding of host-pathogen interactions is essential for the successful treatment of pulmonary Mab infection.

Analysis of drug resistance and mutation profiles in Mycobacterium tuberculosis isolates in a surveillance site in Beijing, China

Objective

This study analyzed drug resistance and mutations profiles in Mycobacterium tuberculosis isolates in a surveillance site in Huairou District, Beijing, China.

Methods

The proportion method was used to assess drug resistance profiles for four first-line and seven second-line anti-tuberculosis (TB) drugs. Molecular line probe assays were used for the rapid detection of resistance to rifampicin (RIF) and isoniazid (INH).

Results

Among 235 strains of M. tuberculosis, 79 (33.6%) isolates were resistant to one or more drugs. The isolates included 18 monoresistant (7.7%), 19 polyresistant (8.1%), 28 RIF-resistant (11.9%), 24 multidrug-resistant (MDR) (10.2%), 7 pre-extensively drug-resistant (XDR, 3.0%), and 2 XDR strains (0.9%). A higher rate of MDR-TB was detected among previously treated patients than among patients with newly diagnosed TB (34.5% vs. 6.8%). The majority (62.5%) of RIF-resistant isolates exhibited a mutation at S531L in the DNA-dependent RNA polymerase gene. Meanwhile, 62.9% of INH-resistant isolates carried a mutation at S315T1 in the katG gene.

Conclusion

Our results confirmed the high rate of drug-resistant TB, especially MDR-TB, in Huairou District, Beijing, China. Therefore, detailed drug testing is crucial in the evaluation of MDR-TB treatment.

Accuracy of molecular drug susceptibility testing amongst tuberculosis patients in Karakalpakstan, Uzbekistan

OBJECTIVES

In this retrospective study, we evaluated the diagnostic accuracy of molecular tests (MT) for the detection of DR-TB, compared to the gold standard liquid-based drug susceptibility testing (DST) in Karakalpakstan.

METHODS

A total of 6670 specimens received in the Republican TB No 1 Hospital Laboratory of Karakalpakstan between January and July 2017 from new and retreatment patients were analysed. Samples were tested using Xpert MTB/RIF and line probe assays (LPA) for the detection of mutations associated with resistance. The sensitivity and specificity of MTs were calculated relative to results based on DST.

RESULTS

The accuracy of MT for detection of rifampicin resistance was high, with sensitivity and specificity over 98%. However, we observed reduced sensitivity of LPA for detection of resistance; 86% for isoniazid (95% CI 82-90%), 86% for fluoroquinolones (95% CI 68-96%), 70% for capreomycin (95% CI 46-88%) and 23% for kanamycin (95% CI 13-35%).

CONCLUSIONS

We show that MTs are a useful tool for rapid and safe diagnosis of DR-TB; however, clinicians should be aware of their limitations. Although detection of rifampicin resistance was highly accurate, our data suggest that resistance mutations circulating in the Republic of Karakalpakstan for other drugs were not detected by the methods used here. This merits further investigation.

Mycobacterium chelonae bacteraemia in a patient with myasthenia gravis receiving long-term steroid therapy

Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms found in soil and water. Infections caused by NTM are increasing with conditions ranging from harmless colonization to invasive infections, the latter being more common in immunocompromised hosts. In this report, we present a case of bacteraemia caused by Mycobacterium chelonae, a rapidly growing NTM belonging to Class IV in the Runyon classification, in a 71-year-old male with ocular myasthenia gravis undergoing treatment with oral prednisolone. Gram staining of these organisms from blood culture can be easily overlooked or confused with diptheroids. Detection of Gram-positive bacilli should prompt Ziehl–Neelsen staining to distinguish diphtheroids from rapidly growing mycobacteria in immunosuppressed patients. In addition, speciation and antimicrobial susceptibility testing are of paramount importance in such cases as there is considerable variation in the resistance patterns between different species of NTM. Line probe assay provides a rapid and reliable method for identification of NTM to the species level, which can guide treatment with appropriate antibiotics. This case report highlights the importance of early detection of such cases so as to optimize management and improve patient outcomes.

Identification of Nontuberculous Mycobacteria from Clinical Isolates and Specimens using AdvanSure Mycobacteria GenoBlot Assay

The aim of this study was to evaluate the clinical performance of AdvanSure GenoBlot assay using nontuberculous mycobacteria (NTM) isolates and clinical specimens. A total of 136 NTM isolates and 176 clinical specimens were used in this study. AdvanSure Mycobacteria GenoBlot assay was performed according to the manufacturer's instructions. We compared the results with those of 16S rRNA and rpoB genes sequencing. Out of the 136 NTM isolates, 111 (81.6%) were correctly identified to the species level using the GenoBlot assay. The final concordance rate was 89.7% (122/136), including 11 Mycobacterium genus positive control (GPC) results for uncommon NTM. The most common NTM, M. avium, M. fortuitum, M. gordonae, M. intracellulare, M. chelonae, M. abscessus, and M. kansasii, were correctly identified using the GenoBlot assay. For 176 organisms in clinical specimens, 117 were identified to the species level, including single species for 111 specimens and two species for 6 specimens. The final detection and identification rates for clinical specimens were 94.9% and 66.5%, respectively. The AdvanSure GenoBlot assay performs well in identifying the most common NTM, and would be useful in a clinical laboratory.

Association Between the Phenotype and Genotype of Isoniazid Resistance Among Mycobacterium tuberculosis Isolates in Thailand

Purpose

The emergence of isoniazid-resistant tuberculosis (HR-TB) is a global public health problem, causing treatment failure and high mortality rates. This study aimed to determine the minimal inhibitory concentration (MIC) of isoniazid and detect the gene mutation in HR-TB and any association between the level of isoniazid resistance and gene mutation.

Methods

We collected 74 clinical HR-TB isolates from two tertiary-care centers in Thailand. MICs were established using broth macrodilution. A line probe assay (LPA) was used to detect gene mutations that confer resistance to isoniazid, rifampicin, aminoglycosides, and fluoroquinolones.

Results

Sixty-one (82.4%) isolates were monoresistant to isoniazid and 44 (72.1%) were highly resistant to isoniazid. From the clinical isolates, the range of isoniazid MICs was 0.4–16 μg/mL. The katG S315T gene mutation was the prominent mutation in both isoniazid-monoresistant TB (70.5%) and multidrug-resistant TB (72.7%) isolates. The positive predictive value (PPV) of katG was 100% in detecting high levels of isoniazid resistance. The PPV of the inhA mutation was 93.8% in detecting low levels of isoniazid resistance. Five isolates (6.8%) exhibited low-level phenotypic resistance, whereas an LPA failed to detect an isoniazid gene mutation. Our study found one HR-TB isolate with a gyrA fluoroquinolone-resistant gene mutation.

Conclusion

Most HR-TB isolates had high isoniazid-resistance levels associated with the katG gene mutation. High-dose isoniazid should be used with caution in patients with HR-TB. Early detection of drug resistance by genotypic assay can help determine an appropriate regimen.

Evaluation of rapid diagnostic tests and assessment of risk factors in drug-resistant pulmonary tuberculosis

Background:

Early diagnosis and treatment of drug-resistant tuberculosis (TB) is crucial to halt the spread of drug resistance in the community.

Aim:

The aim of the study was to compare rapid diagnostic tests (GeneXpert and line probe assay, LPA) with conventional liquid culture for the diagnosis of drug-resistant TB and to assess the risk factors for it.

Method:

This cross-sectional study recruited 229 multidrug-resistant TB suspects who were sputum smear positive. They were evaluated by the rapid diagnostic tests and sensitivity, specificity, positive predictive value and negative predictive value were calculated for drug resistance detection as compared to liquid culture drug susceptibility testing. The risk factors for the development of drug resistance were also assessed and the P value of < 0.05 was considered significant.

Results:

In the final comparison, 193 samples were included. The sensitivity and specificity of GeneXpert for detection of drug resistance (rifampicin) was 100% (95% confidence interval, CI: 88.8–100%) and 99.4% (95% CI: 96.6–99.9%), respectively. Whereas sensitivity and specificity of LPA was 94.3% (95% CI: 80.8–99.3%) and 100% (95% CI: 97.7–100%), respectively. Only three discordant samples were observed. Defaulting to antitubercular therapy, contact with resistant TB, and disseminated disease were found to be significant risk factors for the development of drug-resistant TB with high statistical significance (P value < 0.05).

Conclusion:

Both rapid diagnostic tests have very high sensitivity and specificity for detection of drug resistance in sputum smear positive with the advantage of short turn-around time. Defaulting to antitubercular therapy, contact with resistant TB, and disseminated disease are significant risk factors for drug resistance.

Accuracy of genotype MTBDRplus line probe assay in patients with tuberculous pleural effusion: comparison with clinical and culture based diagnosis

Background: Pleural tuberculosis (TB) diagnosis is challenging due to paucibacillary disease. Diagnostic accuracy of GenoType MTBDRplus Line Probe Assay (MTBDRplus) has been evaluated in this study for pleural TB diagnosis.Objective: To evaluate diagnostic accuracy of MTBDRplus for pleural TB diagnosis compared to clinical and microbiological diagnosis.Methods: This prospective study was conducted at the Aga Khan University, Pakistan. Pleural fluid from 203 suspected pleural TB patients was collected and tested for smear, culture and MTBDRplus. Diagnostic accuracy of MTBDRplus was determined using clinical diagnosis and culture as the gold standard.Results: Out of 203 TB suspect patients, MTBDRplus, culture and smear were positive in 14 (6. 9%), 27 (13.3%) and 4 (1.9%) cases, respectively. A total of 106/203 patients (27 culture positive and 79 culture negative) successfully completed TB treatment. Considering clinical diagnosis as gold standard, sensitivity of MTBDRplus was 13.2%; 95% CI (7.4-21.2%) and specificity was 100%; 95% CI (96.1-100%). The sensitivity and specificity of MTBDRplus in culture positive samples were 44.4%; 95% CI (25.5-64.7%) and 98.9%; 95% CI (95.9-99.9%), respectively. Excluding indeterminate results, MTBDRplus accurately detected isoniazid sensitivity in 5/6 and rifampicin sensitivity in 6/6 cases.Conclusion: MTBDRplus had a low sensitivity of 13.2% in clinically diagnosed and 44% in culture-confirmed pleural TB patients and therefore could not be included in most diagnostic algorithms. Due to a higher sensitivity than smear, MTBDRplus may have a role in tuberculous pleural effusion diagnosis if it is positive pending culture results and pleural biopsy.

Efficacy Of Line Probe Assay In Detection Of Drug-Resistant Pulmonary Tuberculosis In Comparison With GeneXpert And Phenotypic Methods In Iran And Genetic Analysis Of Isolates By MIRU-VNTR

Background

Successful treatment of tuberculosis depends on early diagnosis and use of appropriate drug susceptibility testing in a timely manner. In the present study, LPA efficacy was assayed in detection and drug susceptibility testing of pulmonary tuberculosis in comparison to available methods in Iran and phylogenetic analyses of isolated cases carried out by MIRU-VNTR.

Methods

This study was conducted at the Tehran Regional Reference Laboratory for Tuberculosis. All sputum specimens were subjected to smear, culture, and drug susceptibility testing (DST), GeneXpert, and LPA. Finally, 15-locus-based MIRU-VNTR was used for molecular genotyping.

Results

From a total of 920 sputum specimens, 6.08% (n=56) were identified as MTBC by culture, 6.8% (n=63) by GeneXpert, and 6.5% (n=60) by LPA. Phenotype DST and LPA methods confirmed the resistance of 4 and 14 specimens to rifampin (RIF) and isoniazid (INH); two cases were considered as multidrug-resistant (MDR). Using GeneXpert, four cases were identified as RIF-resistant. Based on LPA results, inhA and katG mutations were detected in 100% and 21.4% of INH-resistant cases, respectively. All 56 culture positive Mycobacterium tuberculosis isolates were placed in 29 different clusters using MIRU-VNTR genotyping. Two MDR-TB, 2 RIF mono-resistant, and 12 INH mono-resistant cases were placed in different clusters.

Conclusion

LPA is an appropriate method for early detection and accurate diagnosis of TB and drug-resistant cases that makes it possible to distinguish INH mono-resistant cases from MDR cases in Iran.

Detection of Second Line Drug Resistance among Drug Resistant Mycobacterium Tuberculosis Isolates in Botswana

The emergence and transmission of multidrug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis (M.tb) strains is a threat to global tuberculosis (TB) control. The early detection of drug resistance is critical for patient management. The aim of this study was to determine the proportion of isolates with additional second-line resistance among rifampicin and isoniazid resistant and MDR-TB isolates. A total of 66 M.tb isolates received at the National Tuberculosis Reference Laboratory between March 2012 and October 2013 with resistance to isoniazid, rifampicin or both were analyzed in this study. The genotypes of the M.tb isolates were determined by spoligotyping and second-line drug susceptibility testing was done using the Hain Genotype MTBDRsl line probe assay version 2.0. The treatment outcomes were defined according to the Botswana national and World Health Organization (WHO) guidelines. Of the 57 isolates analyzed, 33 (58%) were MDR-TB, 4 (7%) were additionally resistant to flouroquinolones and 3 (5%) were resistant to both fluoroquinolones and second-line injectable drugs. The most common fluoroquinolone resistance-conferring mutation detected was gyrA A90V. All XDR-TB cases remained smear or culture positive throughout the treatment. Our study findings indicate the importance of monitoring drug resistant TB cases to ensure rapid detection of second-line drug resistance.

Feasibility of Direct Sputum Molecular Testing for Drug Resistance as Part of Tuberculosis Clinical Trials Eligibility Screening

A rapid diagnosis of drug-resistant tuberculosis (TB) is critical for early initiation of effective therapy. Molecular testing with line probe assays (MTBDRplus and MTBDRsl) on culture isolates has been available for some time and significantly reduces the time to diagnosis of drug resistance. However, routine use of this test directly on sputum is less common. As part of enrollment screening procedures for tuberculosis clinical trials conducted in Hanoi, Vietnam, we evaluated the feasibility and performance of line probe assay (LPA) testing directly on sputum samples from 315 participants with no prior history of TB treatment. Test performance characteristics for the detection of rifampin (RIF) and isoniazid (INH) drug resistance as compared to culture-based drug susceptibility testing (DST) reference standard were calculated. LPA demonstrated high sensitivity and specificity for the diagnosis of drug resistance. Scaling up molecular testing on sputum as part of time-sensitive clinical trial screening procedures in high TB burden settings is feasible and will reduce both time to initiation of appropriate therapy and the risk of late exclusions due to microbiologic ineligibility.

Molecular characterization of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Khartoum, Sudan

Background

The aim of this study was to characterize the drug resistance profile, and the specific lineages of Mycobacterium tuberculosis (MTB) strains isolated from patients with pulmonary TB in the state of Khartoum in Sudan.

Methods

Consecutive sputum samples and clinical data were collected from 406 smear-positive TB patients with pulmonary TB in 2007-2009. The samples were cultured, and drug susceptibility testing (DST) was performed using the proportion method (PM) on solid Löwenstein-Jensen medium, and species were identified using biochemical methods at the National Reference Laboratory (NRL) in Khartoum. Extracted deoxyribonucleic acid from a total of 120, 60 suspected multidrug-resistant isolates (MDR), and 60 non-MDR isolates were subsequently sent to the WHO supranational reference laboratory (SRL) in Stockholm at the Public Health Agency of Sweden, for confirmation of the drug resistance profile, examinations by line probe assay (LPA), and molecular epidemiology analysis with Spoligotyping.

Results

LPA results correlated 100% for non-MDR and 62% for the suspected MDR strains when compared to the DST results obtained by PM at the NRL. Two strains were initially using the PM identified as MDR-TB but later shown by Hain GenoType Mycobacterium CM/AS to belong Mycobacterium avium complex (Mycobacterium intracelluare). These two strains were excluded from the study material for further analysis. The remaining 58 MDR strains were analyzed using LPA, and 36 strains were confirmed as MDR, 10 as rifampicin monoresistant, and eight as isoniazid-monoresistant. Spoligotyping for all the 118 MTB isolates revealed a total of 115 patterns in which four patterns represented major clusters with a total of 108 (91%) of the strains. The CAS1_Delhi/family was the predominant type and detected in 62 isolates (52%), of which 26 were MDR and 36 were susceptible. It was followed by H3/family with 19 (16%) strains, and 11 Latin American Mediterranean3/family, 16 T2/T1, and two strains each of the Beijing and S lineage.

Conclusion

Comparison of DST results obtained using PM and LPA showed 100% agreement for the non-MDR strains but only 62% for the MDR strains. Taking in consideration the time, risk of contamination and the cost of labour to identify MDR TB, the LPA have clear advantages in early detection of MDRTB than the PM. Additionally in this study material Spoligotyping revealed the CAS1 Delhi as the most predominant family. We could not see no major difference in lineages between MDR and non-MDR strains.

Robustness of the Line Probe Assay for the Rapid Diagnosis and Characterization of Mutations in Extensively Drug-Resistant Tuberculosis

Introduction: Extensively drug-resistant tuberculosis (XDRTB) is a public health concern. We evaluated the diagnostic accuracy of Genotype^® MTBDRsl for detection of resistance to fluoroquinolones (FQs) and second-line injectable drugs (SLIDs) and characterized mutations seen. Materials and Methods: MTBDRsl was carried out either directly on sputum samples or indirectly on culture isolates (n = 100) from known multidrug-resistant tuberculosis (MDRTB) patients from July 2015 to September 2017. Diagnostic accuracy for the detection of resistance to FQs and SLIDs was calculated in comparison with conventional culture-based drug susceptibility testing. Mutations at the gyrA and rrs loci, as well as discrepant phenotypic and genotypic results, were studied. A subset of isolates underwent pyrosequencing. Results: Out of 100 MDRTB samples/isolates tested, 59% were pre-XDRTB and 7% were XDRTB. The sensitivity and specificity for the detection of resistance to FQs were 96.6% [95% confidence interval (CI): 88.3-99.6] and 80% [95% CI: 64.4-90.9] and those for SLIDs were 70% [95% CI: 34.8-93.3] and 100% [95% CI: 95.9-100]. The most frequent mutations were the absence of wild type 3 with corresponding mutation 3c (20/66) at the gyrA locus, and absence of wild type 1 and corresponding mutation 1 (6/7) at the rrs locus. The absence of a wt2 band with a corresponding mutation at the gyrA locus was seen in four of eight patients with discrepant genotypic and phenotypic results for FQ resistance. All isolates tested by pyrosequencing (n = 5) were concordant with the line probe assay for FQ resistance with identical mutations (D94G) and four of five isolates were concordant with SLIDs with identical mutations (A1401G). Conclusion: The MTBDRsl is a useful test for accurate diagnosis of XDRTB and may help to tailor therapy.

Genetic characterization of Mycobacterium tuberculosis complex isolates circulating in Abuja, Nigeria

Objective

Nigeria ranks fourth among the high tuberculosis (TB) burden countries. This study describes the prevalence of drug resistance and the genetic diversity of Mycobacterium tuberculosis in Abuja’s Federal Capital Territory.

Materials and methods

Two hundred and seventy-eight consecutive sputum samples were collected from adults with presumptive TB during 2013–2014. DNA was extracted from Löwenstein–Jensen cultures and analyzed for the identification of nontuberculous mycobacteria species, detection of drug resistance with line probe assays, and high-throughput spacer oligonucleotide typing (spoligotyping) using microbead-based hybridization.

Results

Two hundred and two cultures were positive for M. tuberculosis complex, 24 negative, 38 contaminated, and 15 positive for nontuberculous mycobacteria. Five (2.5%) M. tuberculosis complex isolates were resistant to rifampicin (RIF) and isoniazid (multidrug resistant), nine (4.5%) to RIF alone, and 15 (7.4%) to isoniazid alone; two RIF-resistant isolates were also resistant to fluoroquinolones and ethambutol, and one multidrug resistant isolate was also resistant to ethambutol. Among the 180 isolates with spoligotyping results, 164 (91.1%) were classified as lineage 4 (Euro-American), 13 (7.2%) as lineage 5 (West African 1), two (1.1%) as lineage 2 (East Asia), and one (0.6%) as lineage 6 (West African 2). One hundred and fifty-six (86.7%) isolates were grouped in 17 clusters (2–108 isolates/cluster), of which 108 (60.0%) were grouped as L4.6.2/Cameroon (spoligotype international type 61).

Conclusion

The description of drug resistance prevalence and genetic diversity of M. tuberculosis in this study may be useful for improving TB control in Nigeria.

Evaluation of the GenoType MTBDRplus and MTBDRsl for the detection of drug-resistant Mycobacterium tuberculosis on isolates from Beijing, China

Background

The incidence of tuberculosis (TB), especially multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB), continues to increase alarmingly worldwide. Molecular line probe assays (LPAs) are endorsed by the World Health Organization for the fast detection of MDR-TB and XDR-TB. The aim of this study was to evaluate the performance of LPAs in China.

Methods

We analyzed MDR-TB and XDR-TB in 96 isolates from Beijing by using culture-based drug susceptibility testing (DST) and LPAs to compare the detection rate of the two methods.

Results

Compared to phenotypic DST, the GenoType^® MTBDRplus and MTBDRsl, respectively, showed a sensitivity of 98.7% and a specificity of 88.9% for detection of rifampicin resistance, 82.1% and 94.4% for isoniazid, 89.7% and 94.4% for levofloxacin, 60.0% and 98.7% for amikacin/capreomycin, and 57.5% and 98.2% for ethambutol. The sensitivity and specificity of LPAs, respectively, were 80.8% and 100% for MDR-TB and 50.0% and 97.6% for XDR-TB. Mutations in codon S531L of the rpoB gene and S315T1 of the KatG gene were dominated in MDR-TB strains. The most frequently observed mutations were in codon A90V of the gyrA gene, A1401G of the rrs gene, and M306V of the embB gene, according to the MTBDRsl results.

Conclusion

Our study showed that, in combination with phenotypic DST, application of the LPAs might be an efficient and reliable supplementary DST assay for rapid susceptibility screening of MDR-TB and XDR-TB. Using LPAs in countries with high MDR/XDR burden allows for appropriate and timely treatment, which will reduce transmission rates and morbidity, and improve treatment outcomes in patients.

Evaluation of Genotype MTBDRplus and MTBDRsl Assays for Rapid Detection of Drug Resistance in Extensively Drug-Resistant Mycobacterium tuberculosis Isolates in Pakistan

Pakistan ranks 5th among the world's highest tuberculosis (TB) burden countries alongside the 6th among countries with the highest burden of drug-resistant TB, including multi-drug resistant (MDR)-TB. Methods for rapid and reliable drug susceptibility testing (DST) are prerequisite for the prompt institution of effective anti-TB treatment. The aim of this study was to evaluate the efficiency of Genotype MTBDRplus and MTBDRsl assays for the detection of MDR and (pre-) extensively drug-resistant (XDR-TB) isolates in Pakistan. The study included 47 pre-XDR and 6 XDR-TB isolates, recovered from 53 patients from Pakistan. Conventional DST was performed using the standard 1% proportion method on the Löwenstein-Jensen medium. For molecular determination of drug resistance, GenoType MTBDRplus and GenoType MTBDRsl assays (Hain Lifescience, Germany) were used. To evaluate discrepancies between conventional and molecular DST results, mutation profiling was performed by amplifying and sequencing seven genetic loci, i.e., katG, inhA, and mabA-inhA promoter, rpoB, gyrA, embB, rrs. The sensitivity of Genotype MTBDRplus was 71.7% for isoniazid (INH) and 79.2% for rifampicin (RIF). Sequence analysis revealed non-synonymous mutations in 93.3 and 27.3% of isolates phenotypically resistant to INH and RIF, respectively, albeit susceptible when tested by GenoType MTBDRplus. GenoType MTBDRsl had a sensitivity of 73.6, 64.7, 20, 25, and 100% for the detection of fluoroquinolones, ethambutol, kanamycin, amikacin, and capreomycin resistance, respectively. Upon sequencing, mutations were detected in 20, 77.8%, and all isolates phenotypically resistant to aminoglycosides, ethambutol, and fluoroquinolones, respectively, yet declared as susceptible with GenoType MTBDRsl. Low sensitivities seriously impede the large-scale application of the Genotype MTBDRplus and MTBDRsl assays. Unless further optimized, the currently available line-probe assays should rather be auxiliary to the conventional, phenotype-based methods in the detection of MDR- and XDR-TB in Pakistan.

Pyrosequencing method for sensitive detection of HBV drug resistance mutations

Hepatitis B (HBV) drug resistance assay is important for guiding therapy after the development of virologic breakthrough for patients receiving nucleoside/-tide analog therapy. However, the existing genotyping tools are either costly or lack sensitivity to detect mixed genotypes, and an improved method of resistant mutation detection is needed. An assay protocol for clinical application using pyrosequencing method was developed, capable of detecting all known validated HBV polymerase gene mutations that impart resistance to lamivudine, adefovir, tenofovir, and entecavir. Sixty-eight serum samples with known HBV resistance genotypes, previously tested with either Sanger sequencing assay or commercial line probe assay, were used for validation. Where there were discrepancies between the two methods, clonal sequencing by Sanger's method was used for confirmation. The modified pyrosequencing method accurately identified all the cloned polymerase genotypes and was able to distinguish as little as 5% of the mutant populations. This assay can be performed on serum sample with HBV DNA as low as 13.5 IU/mL. The cost per test was less than existing commercial assay. HBV drug resistance pyrosequencing assay was accurate, more sensitive and cheaper compared with the existing methods. It can detect minor populations of drug-resistant clones earlier, before the drug resistant clones become dominant, allowing the opportunity for an earlier change of therapy.

Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping

Use of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-line Mycobacterium tuberculosis resistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728 M. tuberculosis complex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777 M. tuberculosis complex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively (P = 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made.

Drug-resistant Spinal Tuberculosis

Drug-resistant spinal tuberculosis (TB) is an emerging health problem in both developing and developed countries. In this review article, we aim to define management protocols for suspicion, diagnosis, and treatment of such patients. Spinal TB is a deep-seated paucibacillary lesion, and the demonstration of acid-fast bacilli on Ziehl-Neelsen staining is possible only in 10%-30% of cases. Drug resistance is suspected in patients showing the failure of clinicoradiological improvement or appearance of a fresh lesion of osteoarticular TB while on anti tubercular therapy (ATT) for a minimum period of 5 months. The conventional culture of Mycobacterium tuberculosis remains the gold standard for both bacteriological diagnosis and drug sensitivity testing (DST); however, the high turn around time of 2-6 weeks for detection with added 3 weeks for DST is a major limitation. To overcome this problem, rapid culture methods and molecular methods have been introduced. From a public health perspective, reducing the period between diagnosis and treatment initiation has direct benefits for both the patient and the community. For all patients of drug-resistant spinal TB, a complete Drug-O-Gram should be prepared which includes details of all drugs, their doses, and duration. Patients with confirmed multidrug-resistant TB strains should receive a regimen with at least five effective drugs, including pyrazinamide and one injectable. Patients with resistance to additional antitubercular drugs should receive individualized ATT as per their DST results.

Detection of Mycobacterium tuberculosis pncA Mutations by the Nipro Genoscholar PZA-TB II Assay Compared to Conventional Sequencing

Pyrazinamide (PZA) is a standard component of first-line treatment regimens for Mycobacterium tuberculosis and is included in treatment regimens for drug-resistant M. tuberculosis whenever possible. Therefore, it is imperative that susceptibility to PZA be assessed reliably prior to the initiation of therapy. Currently available growth-based PZA susceptibility tests are time-consuming, and results can be inconsistent. Molecular tests have been developed for most first-line antituberculosis drugs; however, a commercial molecular test is not yet available for rapid detection of PZA resistance. Recently, a line probe assay, the Nipro Genoscholar PZA-TB II assay, was developed for the detection of mutations within the pncA gene, including the promoter region, that are likely to lead to PZA resistance. The sensitivity and specificity of this assay were evaluated by two independent laboratories, using a combined total of 249 strains with mutations in pncA or its promoter and 21 strains with wild-type pncA Overall, the assay showed good sensitivity (93.2% [95% confidence interval, 89.3 to 95.8%]) and moderate specificity (91.2% [95% confidence interval, 77.0 to 97.0%]) for the identification of M. tuberculosis strains predicted to be resistant to PZA on the basis of the presence of mutations (excluding known PZA-susceptible mutations) in the pncA coding region or promoter. The assay shows promise for the molecular prediction of PZA resistance.

GenoType MTBDRplus assay for screening and characterization of isoniazid and rifampicin resistance-associated mutations in multidrug-resistant Mycobacterium tuberculosis from India

Multidrug resistant tuberculosis (MDR-TB) is rising and the World Health Organization has recommended the line probe assay (LPA) for screening. In this study we assess LPA at a tertiary care centre from North India in 1758 samples from suspected MDR-TB cases. All smear-positive and/or Mycobacterium tuberculosis culture confirmed cases (n = 1170) were subjected to the GenoType-MTBDR assay. Amongst these the majority were retreatment cases, smear-positive at diagnosis (n = 637). An MDR prevalence of 7·8% was observed with the highest cases reported amongst MDR contacts (33·3%). The most common rifampicin resistance encoding mutation seen overall and in individual patient groups was H531L (53·3%). A higher prevalence of H526D mutation was observed in retreatment cases, smear-positive at 4 months of anti-tubercular therapy vs other patient groups (P = 0·052). The most common mutation encoding isoniazid resistance was S315T1 in the katG (79·9%) and C-15T in the inhA gene (91·1%). Thirty rifampicin and nine isoniazid resistant isolates had wild type gene deletion but no detectable mutation by LPA. Although LPA is a practical and rapid screening method for most mutations expected to result in MDR-TB, we observed that it only detects the known major mutations in specific genes. Such studies can provide the knowledge required to formulate customized strips based on prevalent mutations in our region and in specific patient groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

To the best of our knowledge this is the largest study evaluating the GenoType-MTBDR line probe assay from India. We have studied the prevalence of mutations encoding rifampicin and isoniazid resistance in different patient groups based on criteria for multidrug resistance (MDR) suspicion. The translational impact of this study is in the design of customized country- or region-wise line probe assay strips. The identification of a few mutations in particular patient groups and the detection of wild type deletion mutants with no observable mutations both point toward the need for such customization enabling us to combat the rising trend of MDR tuberculosis.

Utility of Second-Generation Line Probe Assay (Hain MTBDRplus) Directly on 2-Month Sputum Specimens for Monitoring Tuberculosis Treatment Response

The utility of a line probe assay (Genotype MTBDRplus) performed directly on 2-month sputa to monitor tuberculosis treatment response is unknown. We assessed if direct testing of 2-month sputa with MTBDRplus can predict 2-month culture conversion and long-term treatment outcome. Xpert MTB/RIF-confirmed rifampin-susceptible tuberculosis cases were recruited at tuberculosis diagnosis and followed up at 2 and 5 to 6 months. MTBDRplus was performed directly on 2-month sputa and on all positive cultured isolates at 2 and 5 to 6 months. We also investigated the association of a positive direct MTBDRplus at 2 months with subsequent unsuccessful tuberculosis treatment outcome (failure/death during treatment or subsequent disease recurrence). A total of 279 patients (62% of whom were HIV-1 coinfected) were recruited. Direct MTBDRplus at 2 months had a sensitivity of 78% (95% confidence interval [CI], 65 to 87) and specificity of 80% (95% CI, 74 to 84) to predict culture positivity at 2 months with a high negative predictive value of 93% (95% CI, 89 to 96). Inconclusive genotypic susceptibility results for both rifampin and isoniazid were seen in 26% of MTBDRplus tests performed directly on sputum. Compared to a reference of MTBDRplus performed on positive cultures, the false-positive resistance rate for direct testing of MTBDRplus on sputa was 4% for rifampin and 2% for isoniazid. While a positive 2-month smear was not significantly associated with an unsuccessful treatment outcome (adjusted odds ratio [aOR], 2.69; 95% CI, 0.88 to 8.21), a positive direct MTBDRplus at 2 months was associated with an unsuccessful outcome (aOR 2.87; 95% CI, 1.11 to 7.42). There is moderate utility of direct 2-month MTBDRplus to predict culture conversion at 2 months and also to predict an unfavorable outcome.

Evaluation of the GenoType MTBDRsl Version 2.0 Assay for Second-Line Drug Resistance Detection of Mycobacterium tuberculosis Isolates in South Africa

Early detection of resistance to second-line antituberculosis drugs is important for the management of multidrug-resistant tuberculosis (MDR-TB). The GenoType MTBDRsl version 2.0 (VER 2.0) line probe assay has been redesigned for molecular detection of resistance-conferring mutations of fluoroquinolones (FLQ) (gyrA and gyrB genes) and second-line injectable drugs (SLID) (rrs and eis genes). The study evaluated the diagnostic performance of the GenoType MTBDRsl VER 2.0 assay for the detection of second-line drug resistance compared with phenotypic drug susceptibility testing (DST), using the Bactec MGIT 960 system on Mycobacterium tuberculosis complex isolates from South Africa. A total of 268 repository isolates collected between 2012 and 2014, which were rifampin monoresistant or MDR based on DST, were selected. MTBDRsl VER 2.0 testing was performed on these isolates and the results analyzed. The MTBDRsl VER 2.0 sensitivity and specificity indices for culture isolates were the following: FLQ, 100% (95% confidence interval [CI] 95.8 to 100%) and 98.9% (95% CI, 96.1 to 99.9%); SLID, 89.2% (95% CI, 79.1 to 95.6%) and 98.5% (95% CI, 95.7 to 99.7%). The sensitivity and specificity observed for individual SLID were the following: amikacin, 93.8% (95% CI, 79.2 to 99.2%) and 98.5% (95% CI, 95.5 to 99.7%); kanamycin, 89.2% (95% CI, 79.1 to 95.6%) and 98.5% (95% CI, 95.5 to 99.7%); and capreomycin, 86.2% (95% CI, 68.3 to 96.1%) and 95.9% (95% CI, 92.2 to 98.2%). An interoperator reproducibility of 100% and an overall interlaboratory performance of 93% to 96% were found. The overall improvement in sensitivity and specificity with excellent reproducibility makes the GenoType MTBDRsl VER 2.0 a highly suitable tool for rapid screening of clinical isolates for second-line drug resistance for use in high-burden TB/HIV settings.

Diagnostic performance of automated liquid culture and molecular line probe assay in smear-negative pulmonary tuberculosis

The diagnosis of smear-negative pulmonary tuberculosis (PTB) is particularly challenging, and automated liquid culture and molecular line probe assays (LPA) may prove particularly useful. The objective of our study was to evaluate the diagnostic potential of automated liquid culture (ALC) technology and commercial LPA in sputum smear-negative PTB suspects. Spot sputum samples were collected from 145 chest-symptomatic smear-negative patients and subjected to ALC, direct drug susceptibility test (DST) testing and LPA, as per manufacturers' instructions. A diagnostic yield of 26.2% was observed among sputum smear-negative TB suspects with 47.4% of the culture isolates being either INH- and/or rifampicin-resistant. Complete agreement was observed between the results of ALC assay and LPA except for two isolates which demonstrated sensitivity to INH and rifampicin at direct DST but were rifampicin-resistant in LPA. Two novel mutations were also detected among the multidrug isolates by LPA. In view of the diagnostic challenges associated with the diagnosis of TB in sputum smear-negative patients, our study demonstrates the applicability of ALC and LPA in establishing diagnostic evidence of TB.

Detection of multi-drug resistance & characterization of mutations in Mycobacterium tuberculosis isolates from North- Eastern States of India using GenoType MTBDRplus assay

BACKGROUND & OBJECTIVES

Information on drug resistance tuberculosis is sparse from North-East (N-E) States of India. We undertook this study to detect multi-drug resistant tuberculosis (MDR-TB) among MDR-TB suspects, and common mutations among MDR-TB cases using GenoType MTBDRplus.

METHODS

All MDR suspect patients deposited sputum samples to peripheral designated microscopy centres (DMC) in North-East States. The district TB officers (DTOs) facilitated the transport of samples collected during January 2012 to August 2012 to our laboratory. The line probe assay to detect common mutations in the rpoB gene for rifampicin (RIF) and katG and inhA genes for isoniazid (INH), respectively was performed on 339 samples or cultures.

RESULTS

A total of 553 sputum samples from MDR suspects were received of which, 181 (32.7%) isolates were found to be multi-drug resistant. Missing WT8 along with mutation in codon S531L was commonest pattern for rifampicin resistant isolates (65.1%) and missing WT along with mutations in codon S315T1 of katG gene was commonest pattern for isoniazid resistant isolates (86.2%). Average turn-around time for dispatch of LPA result to these States from cultures and samples was 23.4 and 5.2 days, respectively. INTERPRETATIONS & CONCLUSIONS: The MDR-TB among MDR-TB suspects in North-Eastern States of India was found to be 32.7 per cent. The common mutations obtained for RIF and INH in the region were mostly similar to those reported earlier.

Effects of storage and viral load on hepatitis C viral genotyping

Hepatitis C virus (HCV) genotyping is important for determining the treatment protocol for hepatitis C patients. Since amplified material from the Roche HCV Monitor kit is compatible with the Innogenetics INNO-LiPA HCV II kit (line probe assay), amplicons from the Monitor assay can be used to identify the HCV genotype. The Monitor package insert recommends using amplicons within a 7-day period (at 4 degrees C) following amplification. It was hypothesized that storage of amplicons for 4 weeks and longer (at -20 degrees C) would not affect the sensitivity of the genotyping assay. After denaturation, amplicons from two genotypes were stored for 7-386 days prior to performing the genotyping assay. Storage of amplicons did not hamper the ability to identify the genotype. Additionally, the sensitivity of the assay was evaluated by analyzing five genotypes with low viral loads. HCV genotypes were detected most consistently at viral levels of 10,000 copies/mL. In conclusion, the Innogenetics genotyping assay can use stored amplicons, thus reducing the cost of the assay by avoiding additional PCR reactions. Determining the sensitivity of this assay facilitates the efficient use of this test by incorporating a sensitivity cutoff of >or=10,000 copies/mL.