The tuberculosis research group is engaged in multiple projects that include improving the TB situation in urban slums, scaling up of the detection and control of pulmonary TB in various prisons, surveillance of MDR and XDR-TB, diagnosis of childhood TB, improving detection and management of TB cases in urban areas by developing a social enterprise model, the implementation of GeneXpert in different programme settings, development and evaluation of rapid tools for detecting anti-TB drug resistance, study of metagenomics of lung flora among tuberculosis patients, Xpert ultra-assay using stool specimens for diagnosis of pulmonary tuberculosis among children, evaluation of OMNIgene Sputum as a sputum stabilizer, detection of biomarkers for diagnosis and monitoring of anti-TB treatment etc. The 25-member laboratory staff runs more than 6,500 TB detection tests and 1,500 drug susceptibility tests each year.
In collaboration with the Mérieux Foundation, we are currently evaluating the QuantiFERON-TB Gold Plus (QFT-Plus) and Heparin-binding haemagglutinin (HBHA) assay as a supportive tool for monitoring anti-tuberculosis treatment efficacy. We also worked on the molecular epidemiology of tuberculosis to understand the transmission dynamics of both drug-susceptible and resistant TB among prisoners by implementing an automated high-throughput MIRU-VNTR approach, spoligotyping, and whole genome sequencing.
Technological strengths
For ongoing research projects, we currently apply various technological approaches that include rapid culture using the automated BACTEC-MGIT-960 system and conventional culture on Lowenstein Jensen (L-J) slants, susceptibility testing by L-J proportion method, BACTEC MGIT 960 SIRE assay, Xpert MTB/RIF assay, GenoType MTBDRplus and MTBDRsl assays, TREK Sensititre MYCOTB assay, rapid D29 mycobacteriophage qPCR assay, and TaqMan microfluidic assay. We also conduct PCR-based diagnosis and deletion analysis for the identification of Mycobacterium species, spoligotyping, MIRU-VNTR typing, whole genome analysis for genotyping and transmission analysis of tuberculosis, rapid immunological diagnostic tests of pulmonary tuberculosis, laboratory diagnosis of pediatric tuberculosis, detection of latent tuberculosis by QuantiFERON -TB Gold Plus and T-SPOT TB test, etc.
Main results obtained on specific topics
Xpert Ultra assay on stool specimens for TB diagnosis among children
Diagnostic performance of Xpert Ultra was assessed for the diagnosis of child TB using stool as an alternative to pulmonary specimens. The study findings revealed that Xpert Ultra on stool specimens showed better sensitivity and yield compared to Xpert for diagnosis of PTB among children.
Evaluation of QuantiFERON-TB Gold Plus (QFT-Plus) and Heparin-binding haemagglutinin (HBHA) for monitoring anti-TB treatment
In this study, we enrolled and followed up drug-sensitive and multi-drug resistant TB (MDR-TB) patients. We have collected blood and sputum specimens from each subject at different time points. We performed QFT-P and HBHA assays, and preliminary data showed that HBHA assay could be an effective blood-based biomarker for monitoring anti-TB treatment efficacy.
Determining the role of serum drug concentration in predicting the treatment outcome of MDR-TB
We have investigated the treatment outcome of severe forms of TB in patients by measuring the serum drug concentration at different time points during the course of treatment. We have completed the enrolment and follow-up of the patients from a selected health care facility.
Control of TB transmission inside the largest prison of Bangladesh
Since 2005, we have been conducting several studies in the Dhaka Central Jail, the largest prison in Bangladesh. During the first two years of the study, we showed, by MIRU typing, that multiple clusters are present. Thanks to our active screening inside the prison and at its entry point, TB transmission inside this setting has decreased significantly, as reflected by the fewer clusters found in the biological samples in the last two years.
Drug-resistant TB surveillance in Bangladesh
Preliminary data from our surveillance reveals that 3% of the primary TB cases have multi-drug resistant (MDR) TB and more than 13% of the retreatment cases have MDR TB.
Discordance among second-line DST methods: We evaluated 87 Mycobacterium tuberculosis isolates for concordance of susceptibility results across six methods
The L-J proportion method, MGIT 960 SIRE AST, Gene/Xpert MTB/RIF, GenoType MTBDRplus line probe assay, MycoTB MIC plate, and a laboratory-developed mycobacteriophage quantitative PCR (qPCR)-based method. Most isolates (80%) were multidrug-resistant. For isoniazid (INH), we found complete concordance among all the above methods used to determine drug susceptibility or resistance in 82% of the isolates, whereas for rifampin (RIF), ethambutol (EMB), and streptomycin (STR), such complete concordance was observed in 77%, 50%, and 51% of isolates, respectively (P<0.05 for INH or RIF versus EMB or STR).
The discrepancies of EMB and STR stemmed largely from diminished concordance of the MGIT EMB results (kappa coefficient range, 0.26 to 0.30) and the L-J STR result (kappa range, 0.35 to 0.45) versus other methods. Phage qPCR and the MycoTB MIC plate were the only methods that yielded second-line susceptibilities and revealed significant quantitative correlations for all drugs except cycloserine, as well as moderate to excellent kappa coefficients for all drugs except for para-aminosalicylic acid. In summary, the performance of M. tuberculosis susceptibility testing differs by platform and by drug. Laboratories should carefully consider these factors before choosing one methodology, particularly in settings where EMB and STR results are clinically important.
Molecular epidemiology of TB rural Bangladesh
Epidemiological studies using a combination of conventional and molecular methods were performed in rural and urban population of Bangladesh. Deletion analysis, spoligotyping and variable number tandem repeats of mycobacterial interspersed repetitive units (VNTR-MIRU) typing were used. In two studies (rural Matlab and greater Mymensingh district), EAI lineage was most prevalent (27.04% and 25% respectively) and Beijing genotype was second most-predominant (7.38% and 16% respectively).
In another study, conducted in the tertiary TB referral hospital, the Beijing genotype was most predominant (19%). Deletion analysis also showed approximately 65% of isolates are ancestral (TbD1 intact) the remaining 35% are modern-type (TbD1 deleted) in rural areas, whereas in urban areas 69 % are modern and 31% are ancestral type. The other genotypes include T1, CAS, LAM, MANU, etc. are also available in Bangladesh. The rate of recent transmission was estimated to be 6.5% to 31% among different studies and the results indicate that in Bangladesh TB is caused primarily by reactivation of latent infection rather than re-infection.