Spoligotyping with pncA sequencing strategy conferring the transmission of multidrug-resistant tuberculosis in Egypt Suzan Ismail, Khaled Al Amry, Galal Aggor, Hoida El Naggar, Salah Selim International Journal of Mycobacteriology 2019 8(3):211-217 Background: This study explored the genetic diversity of Mycobacterium tuberculosis isolates in Egypt by spoligotyping in combination with pncA gene sequencing, spoNC. Methods: First, isolates were selected from 400 isolates positive for M. tuberculosis that referred to Central Labs Ministry of Health and then were subjected to the study analyses. Results: Twenty one isolates were found to be multidrug resistant (MDR) and 29 isolates were sensitive for isonizide (INH) and rifampicine (RIF) after testing by phenotypic drug susceptibility testing (DST) and Mycobacteria Growth Indicator Tube (MGIT). Spoligotyping yielded 45 patterns belonging to seven families that previously reported in neighboring countries such as Iraq, Syria, Iran, and Turkey. While four isolates were orphans. Conclusion: Application of spoNC on obtained spoligotype patterns enhances to reduce the clustering rate. Bejing family the predominant (34%) were subdivided by pncA sequence into three sensitive DST pncA wild type, three MDR-DST isolates showing cys14Arg mutation in pncA, two sensitive DST isolates with pncA Gly97Asp mutation, and three sensitive DST pncAVal128Gly mutation. The next most common CASI_DELHI family (16%) were subdivided by pncA sequencing into CASI_DELHI (st 381, MDR) including two pncA silent mutation ser65ser (tcc > tct) and CASI_DELHI (st26, sensitive) which included six pncA (wild-type) results, and Latin-American-Mediterranean 6 family (6%) all had PncA Gly97Asp mutation. We concluded that spoNC provides good snap shot for MDR surveillance and its country origin and performs early identification of outbreaks in Egypt.

A bioinformatics analysis of exosomal microRNAs released following mycobacterial infection Shamila D Alipoor, Ian M Adcock, Gert Folkerts, Johan Garssen, Esmaeil Mortaz International Journal of Mycobacteriology 2019 8(3):218-222 Background: Tuberculosis (TB) still remains a major health threat worldwide. The current TB diagnostics are suboptimal, and there is a high clinical need for identifying novel biomarkers of disease prevalence. Circulating exosomes have been currently attractive as novel biomarkers in a wide range of pathological conditions. Methods: In this study, we performed bioinformatics analysis on the downstream targets of a dysregulated microRNA (miRNA) cluster induced by Bacillus Calmette–Guerin infection of human macrophages to provide greater understanding of their potential roles in disease pathogenesis. Results: Our analysis demonstrated that these dysregulated miRNAs have central roles in the host metabolic and energy pathways. Conclusion: This suggests that the host miRNA network is perturbed by Mycobacterium to re-patterning host metabolism machinery to favor its intracellular survival. The dysregulated miRNAs can be delivered to local and distal cells by exosomes and thereby modulate their function.

Surveillance and characterization of drug-resistant Mycobacterium tuberculosis isolated in a reference hospital from Argentina during 8 years' period Belén Rocío Imperiale, Ángela Beatríz Di Giulio, María Belén Mancino, Martín José Zumárraga, Nora Susana Morcillo International Journal of Mycobacteriology 2019 8(3):223-228 Background: Argentina is considered a country with a middle tuberculosis (TB) incidence. However, according to the last national epidemiological report released in 2018, since 2013, the trends are steadily increasing. The aims of this study were to determine the drug-resistance (DR), multi-DR and extensively DR (MDR/XDR-TB), and rifampicin resistance (RIF-R) burden as a part of the local TB diagnosis (June 2010–August 2018); to detect the mutations associated to isoniazid (INH) and RIF-R and their geographical distribution; and to analyze the lineage relationship among the genetic patterns of the isolates circulating in the community. Methods: Respiratory and extrapulmonary specimens were processed by Ziehl–Neelsen stain and cultured on specific media. Drug-susceptibility testing of isolates was performed by the MGIT 960 and a colorimetric micro-method. Mutations conferring DR were detected by Genotype and DNA sequencing. Results: The study showed a DR-TB prevalence of approximately 20% of the isolated strains, while M/XDR-TB-and particularly RIF-R-affected more than 5.0% of the total amount of cases. DR geographical distribution revealed isolates carrying mutations in the inhA gene promoter region only constrained to three districts where it was also registered two same family relatives' cases with the infrequent rpoB S522 L/Q mutation. The fact that most DR/MDR-TB isolates were not grouped in genetic clusters suggested that these cases may mostly have occurred due to endogenous reactivation rather than recently transmission. Conclusion: According to the obtained results, it would be convenient, in highly MDR-TB suspected individuals, to confirm phenotypically, the INH and RIF susceptibility detected by molecular tests.

Multiple docking analysis and In silico absorption, distribution, metabolism, excretion, and toxicity screening of anti-leprosy phytochemicals and dapsone against dihydropteroate synthase of Mycobacterium leprae Sumit T Halder, Tehseen M Dhorajiwala, Lalit R Samant, International Journal of Mycobacteriology 2019 8(3):229-236 Background: Leprosy is a neglected tropical disease affecting millions of people. The current treatment against leprosy includes various antibacterial drugs of which dapsone is known to bind to dihydropteroate synthase of Mycobacterium leprae. Dapsone is an expensive antibacterial drug with many side effects. A natural alternative for dapsone having less to no side effects and cheaper in production is needed. The three-dimensional protein structure of dihydropteroate synthase of M. leprae is not available. Methods: Protein homology modeling of target protein was carried out, and protein structure validation and energy minimization were performed. Phytochemicals mentioned in literature having anti-leprosy properties were studied for absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties and that which passed ADMET filters were further carried for comparative in silico docking analysis along with dapsone. Preliminary docking analysis was carried using AutoDock Vina, and results obtained were validated using AutoDock 4.2.6 and SwissDock. Results: Neobavaisoflavone was predicted to be ten times safer for administration than dapsone. On performing in silico docking, it was found that neobavaisoflavone has better binding affinity than dapsone and forms a stable protein–ligand complex. Residues GLY.50, THR.88, and VAL.107 play an important role as binding site residues. Conclusion: Further, in vitro and in vivo experimental studies are required to confirm anti-leprosy properties of neobavaisoflavone over drug dapsone.

Expression of mycolic acid in response to stress and association with differential clinical manifestations of tuberculosis Naresh Kumar Sharma, Nisha Rathor, Rajesh Sinha, Shraddha Gupta, Gaurav Tyagi, Kushal Garima, Rakesh Pathak, Pooja Singh, Ashima Jain, Mridula Bose, Mandira Varma-Basil International Journal of Mycobacteriology 2019 8(3):237-243 Background: Extrapulmonary tuberculosis (EPTB), accounting for 10%–20% of all cases of tuberculosis (TB), is known to be determined by host immunity. However, the contribution of bacterial factors to the development of EPTB has not been studied extensively. Mycolic acids are predominant lipids constituting the cell wall of Mycobacterium tuberculosis, and keto-mycolic acid is involved in the synthesis of foamy macrophages that facilitate persistence of mycobacteria. Hence, the present study was performed to gain an insight into variable expression of mycolic acids in clinical isolates of M. tuberculosis under stress. Methods: Pansusceptible clinical isolates of M. tuberculosis from patients with lymph node TB (LNTB) (n = 10) and pulmonary TB (PTB) (n = 10) were subjected to sodium dodecyl sulfate (SDS) stress, and the expression of mycolic acid and its biosynthetic genes was compared. Any bias arising due to the genotype of the clinical isolates was ruled out by performing single-nucleotide polymorphism cluster grouping (SCG), wherein no significant difference was observed between the SCG of LNTB or PTB isolates. Results: The expression of α-mycolic acid during the exposure to SDS was high in 7/10 (70%) LNTB and 6/10 (60%) PTB isolates. Methoxy mycolic acid showed an increased expression in 7/10 (70%) LNTB isolates and 4/10 (40%) PTB isolates. Increased expression of keto-mycolic acid on exposure with SDS was observed in 8/10 (80%) M. tuberculosis LNTB and 3/10 (30%) PTB isolates. Similarly, the mycolic acid synthesis gene, fas, was upregulated more in LNTB isolates than PTB isolates in vitro and ex vivo. SCG 3a was the most common SCG observed in 40% (8/20) of the isolates, followed by SCG 3b in 30% (6/20) of the isolates. There was no significant difference between the SCG of LNTB or PTB isolates. Conclusion: The higher expression of keto-mycolic acid in LNTB as against PTB isolates may indicate better survival in LNTB isolates in the presence of stress.

Survival model analysis of tuberculosis treatment among patients with human immunodeficiency virus coinfection Adeboye Azeez, Ruffin Mutambayi, Akinwumi Odeyemi, James Ndege International Journal of Mycobacteriology 2019 8(3):244-251 Background: Tuberculosis (TB) with human immunodeficiency virus (HIV) coinfection is the highest clinical epidemiology and public health issue. Despite many programs established to tackle the epidemic, TB target controls have not been reached. One of the many factors attributed to the failure in TB treatment is HIV coinfection. The aim of this study is to assess the survival rate of HIV infection among TB patients and the risk factors of death among the TB patients with HIV coinfection during the retro of directly observed treatment, short-course (DOTS) program. Methods: This study is a retrospective cohort conducted to compare the survivorship between TB/HIV patients for 8 months DOTS. Death among TB patients was considered as failures and those defaulted or survived were censored. The Cox proportional-hazards regression and log-linear model were used to establish the hazard ratio (HR) of death for each variable at baseline and estimate the risk factors effect among TB patients. Results: The findings revealed that 50% of death from TB/HIV patients were from HIV coinfection (advanced HR = 2.01, 95% confidence interval = 1.13–3.17). The risk of death was significantly higher in HIV-positive TB patients (P = 0.000) during the extension care phase. TB/HIV-positive patients on antiretroviral therapy have decreased survival rate (log-rank test = 14.88, df = 2, P = 0.0001). The probability of TB patients surviving is significantly decreased in HIV positive with some factors such as age, weight, smoking, and alcohol found significant. Conclusion: The probability of survival in HIV-positive TB patients was significantly lower during the TB treatment. Weight loss, age, alcohol, smoking, and pregnancy were showed to affect the survival probability of TB/HIV patients' coinfection significantly.

An In silico approach to identify potential inhibitors against multiple drug targets of Mycobacterium tuberculosis Satish Kumar, Parameswar Sahu, Lingaraja Jena International Journal of Mycobacteriology 2019 8(3):252-261 Background: The increasing incidence of multidrug-resistant cases of tuberculosis (TB) and difficulty in treating these cases requires an urgent need to find an effective anti-TB drug. There are many phytochemicals with reported antibacterial and antitubercular activities. Instead of targeting only a single target of Mycobacterium tuberculosis (MTB), this study aims to identify phytochemicals targeting multiple drug targets of MTB through subtractive genomic/proteomic approach followed by in silico screening of phytochemicals with reported anti-TB activity. Methods: Of 614 essential genes of MTB reported in database of essential genes, 15 gene products were selected using different bioinformatic resources and tools such as PANTHER, Venny, NCBI, and BLAST. Results: Virtual screening analysis of these selected drug targets against identified 148 phytochemicals revealed that amentoflavone, carpaine, 13'bromo-tiliacorinine, and 2'nortiliacorinine, able to inhibit more than one target of MTB. Conclusion: These selected compounds may be proposed as potential inhibitors of MTB and need to be tested in TB culture studies in vitro to assess their anti-TB activity.

Soluble urokinase-type plasminogen activator receptor as a biomarker of treatment response in childhood tuberculosis Ery Olivianto, Sri Sudarwati, Heda Melinda Nataprawira International Journal of Mycobacteriology 2019 8(3):262-266 Background: Childhood tuberculosis (TB) is a major health problem worldwide, especially in developing countries. In 2015, there are estimated 950,000 cases of childhood TB. Since most TB in children is paucibacillary, this gives rise not only to problem in diagnosing but also in monitoring the response to anti-TB treatment as well. Soluble urokinase-type plasminogen activator receptor (suPAR), a glycosylphosphatidylinositol-linked membrane protein of various cells of immune system, is one of the potential biomarkers to be used in the management of TB. The objective of this study is to study the decrease of serum suPAR level after anti-TB treatment in children with TB and its association with patient characteristics. Methods: We conducted a prospective study on children suspected of having TB due to a history of contact with active TB case and symptoms such as coughing, fever, and enlarged lymph nodes. The diagnosis of TB is established by history, physical examination including anthropometric examination. Tuberculin skin test using PPD RT-23 and interferon-gamma releasing assay with Quantiferon TB-Gold Plus was performed. Chest X-rays were read by two independent radiologists. Microbiological examination was performed using microscopic examination and Xpert MTB/RIF. The level of suPAR before and after anti-TB treatment was examined with the Elisa method. Results: There was no significant difference of serum suPAR levels before and after anti-TB treatment (mean 0.71 [standard deviation 0.585] ng/mL; P = 0.072). There was no association between ages (P = 0.112), nutritional status (P = 0.228), diagnosis of pulmonary or extrapulmonary TB (P = 0.956), and radiological feature (P = 0.810) with serum suPAR levels decrease. Conclusion: There is no suPAR serum level decrease 2 months after treatment with anti-TB and there is no association with age, nutritional status, pulmonary or extrapulmonary TB diagnosis, and radiological feature.

Is pulmonary tuberculosis in pregnant women a problem in Ghana? Observations and lessons from the national tuberculosis prevalence project Nana Yaa Awua-Boateng, Aliyu Mohammed, Leslie Mawuli Aglanu, Godfred Acheampong, John Humphrey Amuasi, Frank Adae Bonsu, Richard Odame Phillips, Ellis Owusu-Dabo International Journal of Mycobacteriology 2019 8(3):267-272 Background: Despite appropriate prevention and control measures, tuberculosis (TB) remains a significant contributor to maternal morbidity and mortality. Diagnosis of the disease in pregnancy is usually challenging, as the symptoms may be attributed to the pregnancy. Little is known about the true burden of the disease and its associated risk factors among pregnant women. This study sought to assess the prevalence of TB among pregnant women and associated sociodemographic characteristics in Ghana. Methods: The study used nationally representative data gathered from the national TB project in 2013. A total of 1747 pregnant women were sampled from 56 randomly selected diagnostic health centers across the ten regions of Ghana. TB was confirmed with Ziehl–Neelsen staining technique using morning sputum samples from pregnant women who reported coughing for more than 2 weeks. We assessed how the observed TB prevalence differed by some sociodemographic characteristics and other factors. We further examined the regional spatial distribution of pregnant women with TB in the country. Results: Up to 11.2% of the pregnant women had a history of cough during pregnancy. Eighteen (1.1%) cases of TB were confirmed among the pregnant women during the 2-year period, with the Eastern region of the country recording the highest (n = 13, 72%), followed by Volta region ( n = 2, 11.1%). No cases were recorded in five regions. The geographical region of residence was the only determinant of TB in pregnancy significantly associated with TB (P = 0.001). Conclusion: Although the burden of TB was found to be low, appropriate control measures have to be put in place to detect the disease during the early stages of pregnancy to safeguard the health of the expectant mother and the unborn child.

A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus sequence typing) using whole-genome sequencing data Michelle Wuzinski, Aneta K Bak, Aaron Petkau, Walter H B. Demczuk, Hafid Soualhine, Meenu Kaushal Sharma International Journal of Mycobacteriology 2019 8(3):273-280 Background:Mycobacterium abscessus is a rapid growing nontuberculous mycobacteria (NTM) and a clinically significant pathogen capable of causing variable infections in humans that are difficult to treat and may require months of therapy/surgical interventions. Like other NTMs, M. abscessus can be associated with outbreaks leading to complex investigations and treatment of affected cases. Typing schemes for bacterial pathogens provide numerous applications; including identifying chain of transmission and tracking genomic evolution, are lacking or limited for many NTMs including M. abscessus. Methods: We extended the existing scheme from PubMLST using whole-genome data for M. abscessus by extracting data for 15 genetic regions within the M. abscessus genome. A total of 168 whole genomes and 11 gene sequences were used to build this scheme (MAB-multilocus sequence typing [MLST]). Results: All seven genes from the PubMLST scheme, namely argH, cya, gnd, murC, pta, purH, and rpoB, were expanded by 10, 14, 13, 10, 13, 10, and 9 alleles, respectively. Another eight novel genes were added including hsp 65, erm(41), arr, rrs, rrl, gyrA, gyrB, and recA with 16, 16, 25, 7, 32, 35, 29, and 15 alleles, respectively, with 85 unique sequence types identified among all isolates. Conclusion: MAB-MLST can provide identification of M. abscessus complex to the subspecies level based on three genes and can provide antimicrobial resistance susceptibility prediction based on results from seven genes. MAB-MLST generated a total of 85 STs, resulting in subtyping of 90 additional isolates that could not be genotyped using PubMLST and yielding results comparable to whole-genome sequencing (WGS). Implementation of a Galaxy-based data analysis tool, MAB-MLST, that simplifies the WGS data and yet maintains a high discriminatory index that can aid in deciphering an outbreak has vast applicability for routine diagnostics.