Early and accurate diagnosis and rigorous clinical and microbiological monitoring of multidrug-resistant tuberculosis (MDR-TB) treatment can curb morbidity and mortality. While others are still under evaluation, the World Health Organization has recommended few novel molecular methods for MDR-TB diagnosis only. We present current molecular methods for diagnosis and monitoring of MDR-TB treatment in TB-endemic settings. A systematic meta-narrative review was conducted according to the RAMESES recommendations. Electronic databases were searched for relevant articles published in English language from January 2013 to June 2018. Based on predefined criteria, two independent reviewers extracted the key messages from relevant articles. Disagreement between them was resolved through discussion and the involvement of a third reviewer, if needed. Key messages were synthesized to create the meta-narratives for method's accuracy, drug-susceptibility capability, and laboratory infrastructure required. We included 33 articles out of 1213 records retrieved, of which 16 (48%) and 12 (36%) were conducted in high- and low-TB-endemic settings, respectively. Xpert^® MTB/RIF, GenoType MTBDRplus, GenoType MTBDRsl, FlouroType™ MTBDR, TB TaqMan^® array card, and DNA sequencers can accurately guide effective treatment regimens. Molecular bacterial load assay quantifies mycobactericidal impact of these regimens. Although they present inherent advantages compared to the current standard of care, they carry important limitations to implementation and/or scale-up. Therefore, considerable effort must now be directed to implementation and health systems research to maximize these forecasted benefits for individual patient's health outcomes.

Background: Effective control of tuberculosis is achieved by early diagnosis and drug susceptibility testing for initiation of appropriate treatment. The performance of crystal violet decolorization assay (CVDA) for susceptibility testing of Mycobacterium tuberculosis to isoniazid (INH) and rifampicin (RIF) was compared in a multicenter study. Methods: Seventy-two M. tuberculosis isolates were tested in two phases by CVDA. Results: In Phase I, the specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and agreement for INH were 100%, respectively. Specificity, sensitivity, PPV, NPV, and agreement for RIF were 98.2%, 100%, 94.1%, 100%, and 98.6%, respectively. In Phase II, specificity, sensitivity, PPV, NPV, and agreement were 98%, 100%, 95.4%, 100%, and 98.6% for INH, respectively. Specificity, sensitivity, PPV, NPV, and agreement for RIF were 96.3%, 88.2%, 88.2%, 96.3%, and 94.4%, respectively. Results in the study were obtained on average 10.9 ± 3.1 days in Phase I and 9.8 ± 2.2 days in Phase II. Conclusion: CVDA can be performed for drug susceptibility testing in developed and developing countries. In addition, further studies with larger sample size are needed for evaluation of this method.

Background: The prevalence of multidrug-resistant-tuberculosis (MDR-TB) among new and previously treated cases is increasing worldwide as well as in India. Rapid detection of MDR-TB allows the establishment of an effective treatment regimen; minimizes the risk of further resistance, and limits the spread of drug-resistant strains. Early diagnosis of MDR-TB is the need of the hour in high-TB burden countries like India, and GenotypeMTBDRplus is quite sensitive and specific in determining the molecular resistance in drugs such as rifampicin and isoniazid. Methods: The present study was done for molecular detection of rifampicin and isoniazid resistance and resistance patterns among MDR-TB suspects and comparison of resistance patterns among new and previously treated cases by GenoType^® MTBDRplus Line Probe Assay. A total of 1268 sputum samples of MDR-TB suspects were subjected to fluorescent microscopy. Fluorescent microscopy positive samples were subjected to GenoType^® MTBDRplus (HAIN Lifescience) assay. Results: MDR-TB was detected 11.02%, 20.03% in new and previously treated cases. Among MDR-TB patients S531 L was the most common mutation detected in rpoB gene; 71.43% in new, and 72.17% in previously treated cases. S315T1 was the most common mutation noted in katG gene; 100% in new and 81.74% in previously treated. While in hA gene, it was C15T (7.8%) among previously treated cases. Conclusion: MDR-TB has high prevalence in the western part of Uttar Pradesh, India. Previously treated cases have even more high rate of MDR-TB than new TB cases. The most dominant gene mutations associated with resistance to INH and RIF were observed in codon 315 of the katG gene and codon 531 of the rpoB gene. While comparing the mutation patterns by Genotype MTBDRplus assay, previously treated cases showed more diversity of mutations and had greater number of unknown mutations.

Background: In spite of the fact that the standard test for nitrate reductase activity is negative for Mycobacterium avium, it can grow in a defined minimal medium with either nitrate (NO₃) or nitrite (NO₂) as sole nitrogen sources. Methods: NO₃-and NO₂-reductase activities were measured in soluble and membrane fractions of aerobically grown cells of M. avium and those grown aerobically and shifted to anaerobiosis. Results: NO₃- and NO₂-reductase activities were only detected in the membrane fractions and the two enzyme activities were significantly reduced if cells were grown aerobically in the presence of ammonia (NH₄). The NO₂-reductase activity of membrane fractions was 2-fold higher than that of NO₃-reductase consistent with the fact that NO₃-reductase activity of M. avium cannot be detected if measured by nitrite formation. Membrane fractions of M. avium cells grown 1 week aerobically and then 2 weeks under anaerobic conditions had NO₃-and NO₂-reductase activities. Conclusion: The results are consistent with the presence of assimilatory NO₃-and NO₂-reductase activities in cells of M. avium grown under aerobic conditions. Further, the data suggest that a shift to anaerobic conditions results in the appearance of ammonium-insensitive NO₃-and NO₂-reductase activities; quite possibly that function in a dissimilatory role (redox balancing).

Background: Nucleic acid amplification techniques have become important machineries in the diagnosis of several diseases in clinical laboratories. Polymerase chain reaction (PCR) contamination/amplicon contamination leading to false positivity remains a major concern in these laboratories. Prevention of these contaminations in establishing these molecular biology laboratories has been very crucial over the years. Although closed system PCRs have substantial reduction in the PCR contamination rates, the conventional probe-based hybridization methods continue to show occurrence of contamination for various reasons. The study involved checking the crucial parameters as well as the probable candidates of causing the contamination at a high-burden setting. Bringing out the most effective interventions in controlling the PCR contaminations for future endeavors stood as priority. The study explored the efficacies of different sets of interventions contributed to the process of reducing the contaminants. Methods: The detection of the contaminating PCR products or amplicons or contaminating organism is done by the genotype MTBDR plus V2 kits (Hains Life Sciences) based on DNA strip technology. Results: The pre- and post-cleaning as well as cleaning of the working surfaces was able to bring down the mean contamination percentage by 36.5%. The combined effect of cleaning the work surfaces, the automated pipetting devices, and the AC machines was able to bring down the mean contamination percentage to 53.5% reducing the contamination rate nearly to 94.6%. Conclusion: Regularly cleaning the work surfaces, the automated pipetting devices, the PCR machine, and the AC machines along with it filters and exposure of UV rays significantly lowers down the mean contamination percentage.

Background: Studying DNA methylation changes in disease condition provides the basis of disease pathogenesis or host immune response to infection. Evidences suggest that pathogen-mediated DNA methylation changes influences the expression pattern of genes contributing to disease condition to avert host immune response. Hence, we attempted to study the association between tubercle bacilli-mediated global DNA methylation changes in children with tuberculosis (TB) disease and healthy controls. Methods: Forty-three children diagnosed with TB and 33 healthy children were enrolled in this study. ELISA-based global DNA methylation quantification was performed to measure the changes in percentage of global genomic DNA methylation level. Results: Highly significant difference in global DNA methylation level was found between cases and controls and median global DNA methylation level was 6.25% (interquartile range [IQR] 2.5%–10%) in cases and 25% (IQR, 12.5%–25%) in controls (P < 0.001). Significant difference was found in GeneXpert-positive cases (P < 0.01). Receiver operating curve analysis showed that area under curve 0.81 for the total study population and 0.76 for GeneXpert-positive cases. Conclusion: The results show the significant difference in global DNA methylation level in children with TB disease that can serve as a potential biomarker in early diagnosis of TB disease. Measuring global DNA methylation level, however, not an accurate or sensitive diagnostic method but evaluating active demethylation at genome-wide level can be used to monitor disease progression and treatment efficacy.

Background: Tuberculosis (TB) is one of the biggest problems of global health, at present. Bacillus–Calmette–Guérin is the only vaccine available against this disease. It protects only against the severe forms of TB in the childhood, which is a challenge in the search of new vaccine candidates. Taking into account the protective history of Mycobacterium “habana” against experimental TB, we proposed to provide the elements that support the use of M. “habana” TMC 5135 as a vaccine candidate against TB by infection studies in murine macrophages cell cultures. Methods: The production of microbicidal compounds dependent on oxygen metabolism as nitric oxide and hydrogen peroxide by murine peritoneal macrophages was detected. The invasive and toxigenic capacity of M. “habana” to infect this cell type was also evaluated through the quantification of intracellular alive bacillus and 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide assay, respectively. Results: The results suggest that M. “habana” TMC 5135 is able to persist into peritoneal macrophages, to resist the effectors mechanisms of respiratory burst, and to keep the viability of the target cell. The demonstration of these effector mechanisms and the survival capacity of M. “habana” in this niche are relevant aspects of this research assuring the continuity of this candidate to next phases of preclinical development. Conclusion: The present investigation contributes to the characterization of the infection by this mycobacteria in its main target cells of innate immunity and it suggest future investigations to evaluate the activation of effector mechanisms of the innate immunity against this candidate.

Background: In Sub-Saharan Africa, HIV endemic has substantially contributed to the increasing tuberculosis (TB) incidence. The joint effect of the HIV and TB pestilences has confronted the feeble systems of healthcare in resource-limited countries. Methods: The aim of this study was to determine the pathological attributes, outcomes of TB treatment, and the contributing factors of unsuccessful results among TB/HIV patients. A retrospective cohort study of all confirmed adult TB/HIV coinfected hospitalized patients with drug-resistant TB reported for the treatment in two different hospitals from 2010 to 2016 in Eastern Cape, South Africa. Cox proportional hazard model was used in identifying the predictors of unsuccessful treatment. Results: Unsuccessful treatment outcomes among TB/HIV coinfected patients with treatment category were (95% confidence interval [CI]: 0.988–1.318) age, smoking (1.047; 95% CI: 0.892–1.229), pregnancy (1.940; 95% CI: 0.793–4.743), CD 4+ count (1.163; 95% CI: 0.993–1.361), and patients with comorbidity diseases such as diabetes, liver diseases, renal failure, hepatitis, and silicosis were all significantly associated with unsuccessful treatment. The preantiretroviral treatment (ART) females appear to have significantly better survival than pre-ART males. Conclusion: The study showed that the unsuccessful treatment outcomes among TB/HIV coinfected patients were slightly below the WHO target. The key predictors of unsuccessful TB treatment outcomes among the TB/HIV coinfected patients were associated with pregnancy, productive age group, gender, contraception, and comorbidity diseases.

Background: The use of imaging techniques is important for prompt diagnosis and treatment of atypical mycobacterial infections; it also reduces the burden of these infections. The purpose of the present study was to determine the association between computed tomography (CT) scan findings of pulmonary infection caused by atypical mycobacteria and bacillus count in sputum samples. Methods: This cross-sectional, observational, comparative study included 50 consecutive patients with pulmonary infection caused by atypical mycobacteria, who were hospitalized in Masih-Daneshvari Hospital of Tehran, Iran during 2012–2017. The association between CT scan findings of pulmonary infection caused by atypical mycobacteria and bacillus count in sputum samples was determined in these patients. Results: The results demonstrated that the presence of nodules smaller than 5 mm in diameter, consolidation, bronchiectasis, and pleural thickening were related to bacillus count in sputum samples (P < 0.05). Conclusion: Some CT scan findings, such as nodule diameter smaller than 5 mm, consolidation, bronchiectasis, and pleural thickening, may be indicators of atypical mycobacterial infection. Increased number of involved lobes with bronchiectasis can promote early diagnosis in patients with higher smear and culture grading.

Background: Antimicrobial resistance (AMR) has rendered certain species of Mycobacterium difficult to treat clinically, particularly the nontuberculous Mycobacterium, Mycobacterium abscessus, in patients with cystic fibrosis (CF). Such patients are treated with several nonantibiotic medicines, which may have antimicrobial properties. Given the growing burden of AMR in M. abscessus, it is importtant to investigate the antimicrobial activity of all medicines used in the treatment of such patients. It was, therefore, the aim of this study to examine the antimicrobial activity of 10 nonantibiotic medicines used commonly in the treatment of CF. Methods: Antibiotic susceptibility studies were performed on human clinical isolates of M. abscessus (n = 16) including 11 smooth isolates, four rough isolates and one Reference isolate (NCTC 13031), against the following 10 nonantibiotic medicines:-aspirin (850 ug/ml), chlorphenamine (400 ug/ml), Creon (4000 international units/ml), cyclizine (50 mg/ml), DNase (1 μg/ml), hypertonic saline (NaCl) 7% (w/v), ibuprofen (44.4 mg/ml), lansoprazole (300 ug/ml), paracetamol (10 mg/ml), and prednisolone (500 ug/ml). Results: Of the 10 nonantibiotic drugs investigated, inhibition of M. abscessus was noted with chlorphenamine (400 ug/ml), cyclizine (50 mg/ml), ibuprofen (44.4 mg/ml) and lansoprazole (300 ug/ml), with no activity associated with aspirin (850 ug/ml), Creon (4000 international units/ml), DNase (1 μg/ml), hypertonic saline (NaCl) 7% (w/v), paracetamol (10 mg/ml), and prednisolone (500 ug/ml). The minimum inhibitory concentration (MIC) of cyclizine to M. abscessus (n = 6) ranged from 8.0 to 12.5 ug/ml, with a mean MIC, MIC₅₀, and MIC₉₀of 10.6, 10.0 and 12.5 ug/ml, respectively. Conclusion: This study identified that chlorphenamine, cyclizine, ibuprofen, and lansoprazole have in vitro antimycobacterial activity against clinical M. abscessus, isolated from patients with CF. Further studies should now examine potential antimicrobial synergy between these compounds and common conventional antimycobacterial antibiotics, including the macrolides and fluoroquinolones, to decide how best to exploit such positive interactions to reduce AMR burden and improve treatment regimens.

Background: Pulmonary tuberculosis (PTB) remains major public health problem over the world. Cities witnessing religious event throughout of the year like Kerbala/Iraq require great efforts to minimize the incidence of deadly communicable diseases like TB. The aim of this study is to model the monthly incidence rates of PTB cases in Kerbala/Iraq. Methods: This is a retrospective study in which records of confirmed PTB patients whom they referred to the chest and respiratory illnesses center of Holy Kerbala governorate were obtained. Monthly registered new smear-positive PTB cases from January 2010 to December 2016 were analyzed. Seasonal autoregressive integrated moving average (SARIMA), SARIMA-exponential smoothing method (ETS), SARIMA-neural network autoregressive, and SARIMA-adaptive neuro-fuzzy inference system (SARIMA-ANFIS) were used for forecasting monthly incidence rate of TB in Kerbala, Iraq. Mean absolute percentage error, root mean square error, and mean absolute square error were used to compare the models, and Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to selected best model. Results: The trend of PTB incidence showed a seasonal characteristic, with peaks in spring and winter. Predicted estimates using all models proposed to forecast the number of PTB cases from 2016 to 2018 showed that the PTB cases indicated marginal decrease trends and best forecasted in SARIMA-ANFIS model (the lower AIC and BIC values, 712.69 and 731.05, respectively). Conclusion: Seasonal characteristic of PTB incidence was observed with peaks during spring and winter. Forecasting of PTB incidence between the period 2016 and 2018 showed marginal decrease trends, and the best forecasting model was SARIMA-ANFIS model.

Background: The current research aims to isolate pyruvate kinase (Pyk) gene from Mycobacterium tuberculosis and expression of the gene (Rv1617) to obtain a purified enzyme. The enzyme activity and secondary structural features were assessed through biochemical assays and circular dichroism (CD) spectroscopy, respectively. Methods: The Pyk-encoding gene from the complete genome of M. tuberculosis was cloned, sequenced, and expressed in Escherichia coli BL21 (DE3). The enzyme was purified by nickel-nitrilotriacetic acid affinity chromatography and enzyme activity was determined by a lactose dehydrogenase-coupled assay system. Further, far ultraviolet CD spectra of the enzyme and the substrate bound enzyme were analyzed using a Jasco J712 spectrophotometer. Results: A single protein with an approximate molecular mass of 54 kDa was purified and a specific activity of 5.31 units/mg was determined from purified M. tuberculosis Pyk. The activity of the enzyme indicating a protein is defined by separate domain for each catalytic function. The secondary structure analysis of CD spectra of the recombinant Pyk has revealed a content of 17% α-helix, 34% β-sheet, and 49% turns in the enzyme. Conclusion: The growing evidence has impacted M. tuberculosis central carbon metabolism as a key determinant of the survival and pathogenicity in the host. The purified Pyk was observed to have increased enzyme activity in all steps of purification. Retention of Pyk activity indicates a possible catalytic role for the lower part of the glycolytic pathway. The overall results of the spectra obtained from the CD suggest that the substrate phosphoenolpyruvate and adenosine diphosphate binding to the enzyme can cause conformational changes resulting in the exposure or shielding of residues susceptible to modification.

Background: Appearance of Mycobacterium tuberculosis (MTB) in the sputum of a tuberculosis (TB)/human immunodeficiency virus (HIV) co-infected patient under treatment may indicate either failure or new infection. This study aims to evaluate whether TB treatment failure among TB/HIV co-infected patients is a real failure. Methods: A prospective cohort study was conducted among 566 TB/HIV co-infected patients who started TB treatment in 12 townships in the upper Myanmar. Among the 566 participants, 16 (2.8%) resulted in treatment failure. We performed a molecular study using mycobacterial interspersed repetitive-unit-variable number of tandem repeat (MIRU-VNTR) genotyping for them. The MIRU-VNTR profiles were analyzed using the web server, MIRU-VNTRplus. All data were entered into EpiData version 3.1 and analyzed using R version 3.4.3. Results: Among 16 failure patients, seven had incomplete laboratory results. Of the nine remaining patients, nobody had exactly the same MIRU-VNTR pattern between the initial and final isolates. Four patients had persistent East-African Indian (EAI) lineages and one each had persistent Beijing lineage, changing from EAI to Beijing, from Beijing to EAI, NEW-1 to Beijing, and NEW-1 to X strains. Female patients have significantly larger genetic difference between MTB of the paired isolates than male patients (t-test, P = 0.04). Conclusion: Thus, in our study patients, infection of multiple MTB strains is a possible cause of TB treatment failure. Explanation for the association between gender and distance of genotypes from the initial to subsequent MTB infection needs further studies.

Background: Gene polymorphisms have been associated with drug-induced liver injury (DILI). This study aimed to elucidate the association between polymorphisms of NAT2, CYP2E1, GSTT1, GSTM1, and HLA genes with isoniazid plasma concentration and DILI. Methods: This study was a prospective cohort study recruiting adult newly diagnosed tuberculosis (TB) patients who met the inclusion criteria from the Public Health Centers in Yogyakarta and Lampung. Defined single-nucleotide polymorphisms were rs1799929, rs1799930, rs1799931, rs1801280, and rs1041983 of NAT2; rs2031920, rs8192775, and rs2515641 of CYP2E1; rs1041981, rs1063355, and rs6906021 of HLA. GSTT1 and GSTM1 were defined as GSTT1, GSTM1, and GSTT1 deletion and GSTM1 deletion. The DNA was taken from the patient saliva. Data of anti-TB drug plasma concentration on the weeks 4–8 of treatment were retrieved from the patients' medical report. Statistical analysis was performed using Chi-square test, Student's t-test, and multinomial logistic regression. Results: Over the 207 patients, up to 1.9% of them experienced DILI. The percentage of slow acetylators of NAT2 was 69.5%. Patients with extensive acetylator phenotype did not experience DILI (odds ratio [OR]: 0.46; 95% confidence interval [CI]: 0.23–0.94). The G carriership of HLA rs1063355 could protect the patients from the DILI (OR: 0.39; 95% CI: 0.14–0.9). Furthermore, the C carriership of HLA rs1041981 can protect the patients from DILI (OR: 0.38; 95% CI: 0.15–0.50). The genotype of HLA-DQB*0302 significantly affects the isoniazid concentration. Conclusion: The NAT2 genotype was significantly associated with DILI. Furthermore, the absence of G carriership of HLA-DQA*0102 could protect the patients from DILI without being associated with an effect on the isoniazid concentration.

Adolescent is a high-risk population for developing tuberculosis (TB) disease, unfortunately adolescence TB remains to be neglected. Clinical manifestations of TB are usually chronic and nonspecific that could be mimicking other disease. Unrecognized TB disease will lead to misdiagnosis, delayed, and inappropriate management. A 15-year-old female adolescent, admitted to the hospital due to severe anemia, loss of body weight accompanied with recurrent fever and tend to be easily tired. She was through investigation for hematology disorder with normal results. She was studying in a Muslim boarding school with overcrowded environment. History of contact with TB patient was unclear. Tuberculosis diagnosed based on positive genXpert result, detected sensitive to rifampicin Mycobacterium tuberculosis although acid-fast bacilli sputum smear and culture yielded results were negative. Worsening of the chest X-ray were obtained, initially showed infiltrate of the lung and then revealed bronchogenic spread. Lymph nodes enlargement of the neck-proven TB from fine-needle aspiration biopsy. Anti-TB drugs were started, and after the treatment, there were clinical improvement. TB among adolescents against many unique challenges such as difficulty in case detection, wider potential transmissions and problem on adherence; hence, this age group should be identified as a primary issue in the community.

Leprosy or Hansen's disease is a chronic infectious granulomatous disease with varied presentation, especially in the setting of lepra reactions. We report two such atypical presentations each of Type I and Type II Lepra reactions; the first being an elderly male presenting with fever, while the second case being of a young boy being evaluated for cervical lymphadenitis.