Tuberculosis

The Foundation initiated research in tuberculosis (TB) in the mid-1990s as a natural progression to then two decades of experience in Leprosy and the shared characteristics of the causative agents. Seminal studies using molecular epidemiology techniques on the ever-expanding problem of multiple drug resistant TB in India and rapid transmission within the community have been studied through basic biomedical and translational research at the Foundation. Since 2015, cutting-edge technologies such as whole genome sequencing, RNA sequencing and gene editing have been applied to bring disease understanding, as well as to develop point-of-care tests for rapid diagnosis and effective treatment. On the prevention side, there is an ongoing focus on implementing principles of airborne infection control for health facilities and the community and in looking at environmental and housing parameters that promote the spread of infection. Advocacy and health system strengthening is considered crucial, especially in the field of disease and operational processes of community care that affect patient help-seeking behaviour. Our belief that attention to non-medical determinants of health like nutrition, environment, housing and education are crucial for the eventual eradication of TB continues to be our guiding principle.


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Some key highlights of our research in this area are

  • Warning of high levels of drug resistant TB in Mumbai and defined mechanisms of rapid acquisition of drug resistance
  • Assessed and assisted airborne infection control activities in the public health system in Mumbai
  • Provided insights into TB patient care pathways and highlighted the need for developing a comprehensive patient care model for holistically managing the treatment of TB patients
  • Contributed to generating sequences and drug resistance data from more than 7000 tuberculosis patient samples that were utilized for developing a global catalogue of drug resistance mutations in tuberculosis, recently endorsed by WHO for clinical use in the management of drug resistant TB
  • Unravelled mechanisms behind TB transmission and its relevance to TB spread at household level. Working on extending these studies to identify novel mechanisms and targets that could be tapped for new drug development
  • Developed a non-invasive sampling method that captures breath of TB patients for diagnosis of TB. Working on applying this technology for diagnosis of paediatric TB, which is a huge problem globally. 70% of the children do not get an appropriate microbiological diagnosis for the correct management of TB.
  • Worked on rapid diagnostics of TB that will help individualized treatment for drug resistant TB patients
  • Working with the Union, GOI and national TB programme for national laboratory strengthening for whole genome sequencing

Projects

  • Principal Investigator

    Dr. Kalpana Sriraman

  • CO-PRINCIPAL INVESTIGATORS

    Dr. Ambreen Shaikh, Dr. Nerges Mistry

  • COLLABORATORS

    1. Dr. Ira Shah (B.J. Wadia Hospital for Children, Mumbai)
    2. Dr. Sushant Mane (J.J. Hospital, Mumbai)
    3. Dr. Vikas Oswal (Vikas Nursing Home, Mumbai)
    4. Dr. Varinder Singh (Kalawati Saran Children’s Hospital, Delhi)

  • Project Team

    Project Co-ordinator: Ms. Ananya Mitra
    Data & Lab Co-ordinator: Ms. Smriti Vaswani
    Research Assistants: Ms. Rosephil Coutinho, Mr. Satyam Tiwari
    Public Health Research Associate: Ms.Vidula Purohit
    On-Site Researchers: Dr. Ramsha Ansari, Mr. Vivek Posture, Mr. Yashwant Jadhav, Ms. Samiksha Dhale
  • FUNDED By:

    Indian Council of Medical Research, Delhi

  • DURATION

    4 years (March 2024- February 2028)

  • BUDGET

    INR 7 crores

  • Status

    Initiated

  • CLINICAL TRIAL REGISTRY INDIA REGISTRATION NUMBER

    CTRI/2024/03/064735, (www.ctri.nic.in)

ABOUT THE PROJECT

Diagnosing pulmonary tuberculosis (TB) in children poses challenges due to the presence of atypical symptoms, nonspecific radiological features, and the difficulty in obtaining sputum samples. Consequently, most children undergo invasive sampling to obtain a confirmatory diagnosis. FMR has developed SMaRT-PCR, an innovative, non-invasive diagnostic method that involves a brief 10-minute sampling using a modified mask coupled with TB-RNA detection using RT-PCR. Initial findings from a pilot study involving children with confirmed TB or other ailments indicate a 75% sensitivity and 95% specificity for TB detection. SMaRT-PCR has now been simplified and refined to detect TB and drug resistance simultaneously without losing sensitivity up to one week from sample collection. The proposed study aims to evaluate the refined SMaRT-PCR's clinical utility in 1200 children aged 1 to 14 having signs and symptoms of TB. We will compare SMaRT-PCR's accuracy with standard methods and evaluate its operational adaptability in urban and rural settings.
The study has three following objectives and will be conducted using a hub-and-spoke model in diverse settings:-

  • Implement and validate the SMaRT-PCR workflow in an urban setting, utilizing hospitals/clinics in Mumbai and Delhi as spokes, with FMR serving as the hub for mask sample processing and RT-PCR testing.
  • Evaluate the adaptability of the SMaRT-PCR workflow to a rural setting through a pilot study.
  • Validate the SMaRT-PCR workflow in 3-4 geographic locations across India.

The primary outcome will be the SMaRT-PCR’s diagnostic accuracy estimated based on:-

  • Comprehensive reference standards for defining confirmed, unconfirmed, and unlikely TB cases.
  • Comparison with CBNAAT/TrueNAT in reference samples.
  • Comparison with sequencing for determining drug resistance.

Furthermore, the operational adaptability of SMaRT-PCR will be assessed using survey tools and focus groups that will capture the perspectives of various stakeholders in implementing SMaRT-PCR workflow in diverse settings in all three objectives. If validated, this indigenously developed technology could improve TB confirmation for children in India and globally, offering a non-invasive alternative to invasive testing and clinical diagnosis.

Media coverages

  • Principal Investigator

    Dr. Ambreen Shaikh

  • PROJECT TEAM

    Ms. Chrismita Hegde

  • FUNDED BY

    Institutional funds

  • DURATION

    1 year

  • BUDGET

    4.29 lakhs

  • Status

    Ongoing

ABOUT THE PROJECT

Tuberculosis (TB) persists as a significant global health concern, affecting an estimated 10 million individuals worldwide in 2023. Delving into the intricate molecular mechanisms employed by Mycobacterium tuberculosis (Mtb) to adapt within the host environment, particularly those governed post-transcriptionally by small noncoding RNA (sRNA), holds promise for developing more efficacious treatment modalities. While the regulatory role of sRNAs in the pathogenesis of enteric bacteria is well-established, their functions within Mtb remain largely unexplored.
Building upon our prior investigations into Mtb's transcriptomic responses during effective treatment, our findings pointed towards a potential significance of MTS2823 in maintaining Mtb's infectious capability. This observation has spurred our current hypothesis that MTS2823 plays a pivotal role in TB infection, with alterations in its expression pattern potentially impacting Mtb's ability to invade new host cells. To put this hypothesis to the test, we propose employing a targeted repression strategy utilizing the CRISPR-dCAS9 technique to elucidate the importance of MTS2823 in Mtb growth and infection in vitro.
By undertaking this study, we aim to shed light on the biological role of MTS2823 in Mtb pathogenesis and establish a toolkit for investigating other regulatory sRNAs within mycobacteria.

SPECIFIC OBJECTIVES

  • Optimize the CRISPRi system for precise repression of sRNA in Mycobacterium tuberculosis.
  • Determine the significance of sRNA MTS2823 for Mtb survival, growth, and in vitro infection within macrophages.
  • Principal Investigator

    Dr. Yatin Dholakia

  • Project Team

    Ms. Laxmi Govekar, Ms. Shaziya M. Saleem, Mr. Nilesh Shahasane

  • Duration

    4 months

  • BUDGET

    INR 600,000

  • Status

    Completed

ABOUT THE PROJECT

In 2020, a study of vitamin D in DRTB cases and contacts was conducted. Estimation of Vitamin D levels was undertaken among cases and household and non-household controls. Active TB / LTBI was ruled out among contacts by symptom screening, chest X-ray and Interferon-Gamma Release Assays (IGRA). Individuals who had low Vitamin D levels were administered oral Vitamin D. No preventive treatment was given to either of the contacts.
Among the 180 HH contacts and 82 NHH contacts enrolled in the study, 65 and 26 respectively were detected to be IGRA positive.
This study was designed to assess the progress of the contacts during this period.

Study Objectives

  • To assess development of active tuberculosis among the contacts.
  • To determine the role IGRA in predicting tuberculosis among contacts.
  • To assess the effect of Vitamin D on development of tuberculosis among contacts.

Methodology

HH and non HH contacts were contacted, written consent was taken and consenting individuals were interviewed using a questionnaire to obtain information regarding TB symptoms, tests and treatment taken during the period. Symptomatic individuals at the time of interview were assessed for active TB. Co-morbidities such as diabetes mellitus, hypertension, history of Covid-19 and HIV were recorded and response to treatment recorded.

KEY FINDINGS/ACHIEVEMENTS

  • Among the 262 contacts (180 household and 82 non-household), 34.73% had latent TB.
  • Of 219 contacts which were interviewed, three (2 household and 1 non-household) developed active TB, with a crude incidence rate of 4.64 per 1000 people.
  • Baseline Vitamin D deficiency was prevalent in 75.3% of contacts (including the three active TB cases).
  • Vitamin D supplementation showed a non-significant trend in reducing TB risk (OR = 0.56), p = 0.492).
  • IGRA status did not significantly predict TB development.

PUBLICATION

  • Dholakia, Y., Govekar, L., & Mistry, N. (2024). Long-term follow-up of contacts of drug-resistant tuberculosis cases in high-burden areas of Mumbai, India. Indian J Tuberc. (Accepted)
  • Principal Investigator

    Dr. Nerges Mistry

  • Co-Investigator

    Dr. Raghuram Rao, Jt. Director, TB Division, MoHFW, GoI

  • Collaborators

    1. Dr. Susmita Chatterjee, The George Institute, Delhi [Costing]
    2. Dr. Sarang Deo, Indian School of Business, Hyderabad [Analysis]
    3. Dr. Nimalan Arinaminpathy, Imperial College, London [Modelling]

  • Project Team

    Dr. Anupam Shukla, Dr. Shilpa Karvande, Ms. Priyanka Borhade, Mr. Pitamber Soren, Ms. Vidula Purohit.

  • Funded by

    Bill and Melinda Gates Foundation

  • Duration

    September 2021-May 2026

  • Budget

    INR 2790 Lakhs (approx.)

  • Status

    Terminated - The project was terminated in October 2023 due to lack of approval from Central TB Division, Government of India for an extended period of time.

ABOUT THE PROJECT

The National Strategic Plan (NSP) for Tuberculosis (TB) Elimination in India 2017-25 included Private Provider Engagement (PPE) as a key strategy for TB elimination. In the last 5 years various TB management interventions have been undertaken by the National TB Elimination Program, Government of India. The present study aims to evaluate the impact of PPSA Intervention under Private Sector Engagement for TB control in the country.

The study is being conducted in five districts which are representative of different levels of implementation of PPE Strategy. The study districts have been selected in consultation between BMGF, FMR, and CTD. A sample size of 250 TB patients per site i.e., a total of 1250 patients would be enrolled and followed up for duration of six months under the study. The study methodology is prospective cohort study and is observational in design. Inclusion criteria for the study include Drug Sensitive - Pulmonary TB patients, new or retreated between 18-70 years of age. Drug Resistant TB Patients and Extra Pulmonary TB patients will be excluded from the study.

The primary objective of study is to determine the level of exposure to PPE strategy of an averagely treated patient in selected five districts in India. It aims to measure the patient level outcomes in terms of enhanced access, correct diagnosis, shorter care pathways, patient retention and adherence as well as relief from excessive costs. It also aims to evaluate the strength of association between different components of the private engagement strategy and successful patient outcomes.

Scoping visits undertaken

Scoping visits were undertaken as part of the preparatory stage in the Madhubani and Pune sites. Madhubani has an active GOI patient-provider support agency (PPSA, since February 2022), which transitioned from the joint effort for elimination of TB (JEET) PPSA. Shortcomings observed with the program included a weak linkage of PPSA with private labs/chemists and lack of capacity-building workshops being organized for the private providers. Scoping visit also highlighted the need for improvement in service delivery from the program's side, as reflected by the district's scarcity of Cartridge based Nucleic Acid Amplification Tests (CB-NAAT) diagnostic cartridges and anti-TB drugs. Scoping in the Pune Municipal Corporation (PMC), a site not having an active PPSA currently, showed considerable efforts from the district TB team to engage and serve private sector patients. GOI PPSA is expected to be functional soon in PMC area.

  • Principal Investigators

    Dr. Nerges Mistry and Dr. Kayzad Nilgiriwala

  • Collaborators

    The Union, Collaboration for Elimination of TB in India, ECHO India, ICMR-National Institute for Research in Tuberculosis (NIRT), Chennai.

  • Project Team

    Dr. Mubin Kazi, Ms. Prajakta Advirkar, Ms. Chrismita Hegde; Dr. Rita Mukhopadhyay, Dr. Pooja Gumaste

  • Funded by

    USAID

  • Duration

    October 2020 – September 2023

  • Budget

    INR 573 lakhs

  • Status

    Terminated

ABOUT THE PROJECT

The project aims at institutional strengthening of TB laboratories in India to accelerate actions for tuberculosis and drug resistant tuberculosis in India, notably drug resistant TB surveillance. The project is funded by USAID and led by the Union along with seven partners including the Foundation for Medical Research (FMR), Mumbai. The Central Tuberculosis Division (CTD) has planned to conduct DR TB surveillance by including whole genome sequencing (WGS) technology for the very first time in the country, towards which FMR is providing technical assistance to the national referral laboratories (NRLs) to apply this modern technology with reliability and quality. WGS of tuberculosis (TB) has been existent in the country since past 3 decades, yet all TB public sector labs are not able to efficiently apply the technology on a regular basis. We provide technical assistance, regular monitoring and assessment of the 5 NRLs in the country along with 30+ intermediate labs mandated to provide clinical TB isolates to their designated NRL. The NIRT Chennai is to lead the surveillance design and efforts.

Key achievements

  • Comprehensive Assessment of WGS Labs and IRLs: The project conducted a thorough assessment of both the whole genome sequencing (WGS) labs and intermediate reference laboratories (IRLs) to evaluate their readiness for conducting drug-resistant tuberculosis (DR TB) surveillance using WGS. The assessment aimed to identify strengths, weaknesses, and areas requiring improvement in the laboratories' capabilities.
  • Identification of Training Needs for the WGS labs: Based on the preparedness assessment, the project identified the specific areas where additional training was necessary for the WGS labs. By recognizing the gaps in their knowledge and skills, the project laid the groundwork for targeted interventions to enhance the capabilities of the labs.
  • Identification of Additional Training Needs for IRLs: As part of the project, an assessment of various IRLs was conducted, revealing that many of these laboratories would require additional training. This finding emphasized the importance of continuous capacity building efforts to improve the IRLs' preparedness and ensure consistency in DR TB surveillance.
  • Hands-on Refresher Training for WGS Labs: The project provided hands-on refresher training to the WGS labs. This training was tailored to address the identified gaps and improve the labs' proficiency in conducting DR TB surveillance using WGS. The hands-on approach ensured that the labs received practical training, enabling them to apply their newly acquired knowledge effectively.
  • Orientation on DR TB Surveillance Protocol: The project conducted orientation sessions for both the WGS labs and IRLs regarding the DR TB surveillance protocol. These orientations were delivered either through on-site presentations during training sessions or online presentations using platforms like ECHO. The goal was to familiarize the labs and IRLs with the established protocol to ensure standardized practices and efficient surveillance.

Overall, the project successfully assessed the preparedness of WGS labs and IRLs for conducting DR TB surveillance using WGS. It provided targeted training, orientation on protocols, and identified areas for improvement in human resource management and competencies. These achievements contribute to building a robust and efficient system for DR TB surveillance, ultimately supporting improved patient care and public health outcomes.

CONFERENCE PRESENTATION

  • Mistry, N. Implementation considerations for drug-resistant tuberculosis sequencing. Invited Talk. Capacity building workshop on use of Next Generation Sequencing for improved surveillance and outbreak investigations of drug-resistant tuberculosis” organized by ICMR-NIRT, Chennai, 14th- 17th December, 2021.
  • Mistry N. Introducing Seq & Treat to enable next-generation TB care. Invited Panelist. Joint Symposium at 50th Union World Conference on Lung Health on “Lighting the path to TB care: Advances in diagnostics” organized by Foundation for Innovative New Diagnostics and New Diagnostics (FIND) Working Group, Hyderabad,30th October 2019.

(A follow-up study to “Evaluation of mask cough aerosol sampling method for diagnosis of pulmonary TB in pediatric patients- A Pilot Study”)

  • Principal Investigators

    Dr. Ambreen Shaikh and Dr. Kalpana Sriraman

  • Project Team

    Ms. Smriti Vaswani

  • Funded by

    National Academy of Sciences, through PEER programme of USAID, USA as Women in Science Mentorship Program for Career Advancement

  • Duration

    March 2022- February 2023

  • Budget

    INR18.7 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

Diagnosis poses a significant hurdle in children with pulmonary TB, as critical microbiological confirmation, including the drug-resistant status required for ensuring proper treatment, is often missing. Children have difficulty in expectorating sputum, and hence invasive methods which require fasting and hospitalization like gastric lavage (GL) are alternatively used to collect samples. Thus, there is an increased impetus for developing and using non-invasive diagnostic methods. We tested a non-invasive sample collection for paediatric pulmonary TB diagnosis in a pilot study and found promising results. The method was termed SMaRT-PCR. This project aims to conduct laboratory-based optimization of SMaRT-PCR workflow to develop drug resistance assay, and point of care collection and improve its scalability for diagnosing pediatric pulmonary TB.

The PEER SEED grant project additionally includes a mentoring component under which junior women researchers at the Foundation are being mentored in:-

  • Presentation skills
  • Writing effective biodata
  • Writing research methods
  • Personality development
  • Team building

KEY ACHIEVEMENTS

  • The refined and improved SMaRT-PCR workflow: -
    • Allows remote sample collection
    • Simple RNA isolation from low-bacterial load samples
    • A single-step, sensitive RT-PCR assay to detect TB and drug resistance at the same time.
  • SMaRT-PCR can be implemented in a hub-and-spoke model for paediatric TB diagnosis, that could provide equitable access to care.

The study findings were disseminated at an event in Mumbai on 18th February 2023, which featured presentations and a panel discussion by national and international paediatric TB experts. It included academicians, clinicians, fellow diagnostic workflow developers, national TB programme officers, and members of the National Technical Expert group. The key outcomes from the discussions were

  • Emphasis on developing and validating child-friendly diagnostics
  • Availability of cafeteria-like test options to clinicians to make a best fit with the patient
  • Focus to be given for concomitant development of infrastructure and personnel for rapid adaptation of newer technologies
  • A provisional patent has been filed towards the technology developed.

PUBLICATION

  • Vaswani, S. & Shaikh, A. (2022). Methods for bioaerosol sampling in tuberculosis and COVID-19: Potential tool for disease diagnosis and assessment of infectivity. J Prev Diagn Treat Strategies Med, 1:209-216.

CONFERENCE PRESENTATION

  • Shaikh A. Oral presentation in panel discussion ‘Presentation Sampling with Mask and Reverse-Transcriptase PCR (SMaRT-PCR workflow)’ at National Conference for fostering partnership to end TB, organized by Deepak Foundation, Vadodra, 18th March 2023.
  • Principal Investigator

    Dr. Kayzad Nilgiriwala

  • Collaborators

    Dr. Anirvan Chatterjee, HaystackAnalytics, Mumbai

  • Project Team

    Ms. Grishma Patel (FMR)
    Dr. Amrutraj Zede, Ms. Sanjana Kuruwa, Ms. Sanchi Shah (HaystackAnalytics)

  • Sponsored by

    HaystackAnalytics, Mumbai

  • Duration

    July 2022 – December 2022

  • Budget

    INR 8.5 lakhs

  • Status

    Completed

ABOUT THE PROJECT

Whole genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) has been demonstrated to reliably replace current methods, which take months to generate a drug resistance profile. Treatment of patients becomes extensively delayed leading to clinical deterioration and death. Direct-from-sputum WGS of MTB DNA can significantly reduce the turn-around-time (TAT) of universal DST from months to days and enable its wider use. This project aims to develop a low-cost method for the enrichment of MTB DNA directly from sputum for WGS as also the determination of the drug susceptibility profile.

  • Principal Investigator

    Dr. Kayzad Nilgiriwala

  • Project Team

    Ms. Tejal Mestry, Ms. Aditee Ashar (Intern)

  • Funded by

    This is a secondary study of CRyPTIC

  • Duration

    June 2022– November 2022

  • Budget

    INR 0.94 lakhs

  • Status

    Completed

ABOUT THE PROJECT

Bedaquiline (BDQ) is a relatively new drug introduced in the treatment of MDR TB, and the presence of clinical TB isolates having high MIC of BDQ in the CRyPTIC repository (BDQ naïve cases) is concerning. In this pilot project, we plan to revive selected clinical TB isolates (drug-susceptible, MDR and XDR) with high MIC of BDQ from the CRyPTIC repository. We will then study the growth kinetics of the revived clinical isolates using Mycobacterial Growth Indicator Tubes (MGIT). A comparison of growth of these isolates (between various drug susceptibility categories) will be performed to understand strain fitness in isolates with high MIC of BDQ.

KEY ACHIEVEMENTS

  • MDR -TB isolates irrespective of their BDQ susceptibility showed a marginally reduced lag phase (~61 h) in comparison to drug susceptible (DS) (~70 h) and pre-extensively drug resistant (pre-XDR) isolates (~68 h)
  • The DS TB isolates irrespective of BDQ susceptibility showed higher stochasticity in the doubling time (31-124 h) as compared to MDR (51-99 h) and pre-XDR (45-93 h) isolates
  • The average revival time for BDQ monoresistant TB isolates was lower (~142 h) than the drug susceptible isolates (~272 h). Also, the average revival time for pre-XDR isolates with BDQ resistance was lower (~132 h) than BDQ susceptible pre-XDR isolates (~320 h)
  • Reduced revival time of DS and pre-XDR isolates with BDQ resistance indicate potential fitness benefit of BDQ resistance in clinical TB isolates
  • Principal Investigator

    Dr. Kalpana Sriraman

  • Collaborators

    Dr Sandeep Gharat, Godrej Industries Pvt. Ltd., Mumbai

  • Project Team

    Ms. Smriti Vaswani, MS. Shalini Sakthivel (FMR)

  • Sponsored by

    Godrej Industries Pvt. Ltd.

  • Duration

    May 2019- June 2022

  • Budget

    INR 8.7 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

The study over three phases evaluated the anti-tubercular activity of a proprietary industrial compound for potential use in TB and MDR-TB treatment. The study in the initial phase established the anti-tubercular activity on drug sensitive and drug resistant strains of TB by rezasurin microtitre assay and agar proportion method. Through this, the minimum inhibitory concentration was defined. Subsequently the study evaluated the kill kinetics and synergism with standard anti-TB drugs for its potential use as a combination therapy with standard anti-TB drugs. The possible mechanism of action was studied by scanning electron microscope. In addition, the study also established the compound’s potential to target and kill intracellular TB bacteria through a macrophage cell line infection model.

OUTCOMES

A patent has been filed as co-inventor along with the study’s sponsor.

  • Principal Investigators

    Dr. Kalpana Sriraman and Dr. Nerges Mistry

  • Collaborators

    1. Dr. Ira Shah, Bai Jerbai Wadia Hospital for Children (BJWHC), Mumbai
    2. Dr. Vikas Oswal, Vikas Nursing Home, Mumbai
    3. Dr. Sushant Mane, JJ Group of Hospitals (JJ Group), Mumbai

  • Project Team

    Dr. Ambreen Shaikh, Ms. Smriti Vaswani, Mr. Nilesh Shahasne (FMR)
    Dr. Vishrutha Karkera (BJWHC); Dr. Sakina Rajagara (JJ Group)

  • Funded by

    Private donation from Mr. N.B. Godrej

  • Duration

    August 2019 - May 2021

  • Budget

    INR 10 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

Diagnosis of TB in children is a major hurdle, with about 70% being denied a microbiological diagnosis. Often invasive techniques are used to collect samples for diagnosis. Hence there is a need to develop a non-invasive collection method to avoid discomfort to children. The study aimed to assess the feasibility of using mask-based cough aerosol collection for the detection of TB in pediatric pulmonary TB cases on a pilot scale. The specific objectives of the study were: a) Investigate the mask specimen for detection of TB bacteria in pulmonary pediatric patients using molecular methods like quantitative real-time PCR (qPCR) and GeneXpert; b) Compare the results obtained from mask sampling with regular sampling method (gastric lavage (GL) and sputum) performed as a part of standard care at the hospital; c) Assess the practical challenges associated with collection of mask specimens.

KEY FINDINGS/ACHIEVEMENTS

~50% of TB pts in our cohort had invasive sample collection for diagnosis

  • This method’s performance was comparable to doing GeneXpert in standard samples like sputum and GL in the same patients
  • Even 6 TB patients who tested negative by GeneXpert were detected as TB patients by this method
  • The method identified sub-clinical TB in one control patient without any symptoms A promising non-invasive tool for paediatric pulmonary TB diagnosis. Further research to improve the technique to adapt to field usage in the process (Link to SMaRT-PCR study)

PUBLICATIONS

  • Shaikh, A., Sriraman, K., Vaswani, S…Mistry, N. (2024). SMaRT-PCR: Sampling with mask and reverse transcriptase PCR, a promising non-invasive diagnostic tool for paediatric pulmonary tuberculosis. Int J Tuber and Lung Dis, 28(4): 189-194. medRxiv preprint doi.org/10.1101/2023.06.17.23291480

CONFERENCE PRESENTATIONS

  • Sriraman, K. New diagnostic approaches to childhood tuberculosis: SMaRT-PCR – A promising non-invasive method. Oral Presentation. India TB Summit 2022 on “Redesigning TB care for equity and access”, organized by Survivors Against TB, 12th March 2022.
  • Sriraman, K. Non-invasive respiratory aerosol sampling using masks for detection of pulmonary tuberculosis in children. Oral presentation. 51st Union World Conference on lung health, “Advancing prevention”, organized by The Union, 20th to 24th October 2020 (Virtual).
  • Principal Investigator

    Dr. Nerges Mistry

  • Co-Investigator

    Dr. Yatin Dholakia, FMR

  • Collaborators

    1. Prof Fawzi Wafaie, Harvard T.H. Chan School of Public Health, USA
    2. Lok Seva Sangam, Mumbai (for field work)

  • Project Team

    Dr. Anupam Shukla, Ms. Prachi Dev, Ms. Lakshmi Govekar, Ms. Niharika Shinde

  • Funded by

    Dubai Harvard Foundation for Medical Research through Harvard Medical School Centre for Global Health Delivery, Dubai

  • Duration

    August 2019 - Febaury 2021

  • Budget

    INR 69.49 lakhs

  • Status

    Completed

ABOUT THE PROJECT

The long duration and high cost of multi-drug resistant TB (MDR-TB) treatment motivate efforts to develop cost-effective preventive and adjunctive therapies including, Vit D supplementation. Vit D confers multi-modal protective approaches to human hosts and encourages better clinical responses.

This project was undertaken to expand the evidence base for the use of Vit D supplementation in the course of treatment of drug resistant TB as well as prevention of disease progression in household contacts exposed to TB infection. This study involved measurement of Vit D levels in both randomly selected DR TB patients within two months of starting treatment and two of their household contacts. The latter was tested to ascertain whether they are latently infected with TB. Additionally, they were evaluated for their food intake and frequency with a focus on intake of micro and macronutrients. The case-control study also assessed TB infection levels amongst household contacts of DR TB patients. This project was designed to provide guidance to support a larger intervention trial of Vit D supplementation for prevention and adjunct treatment of DR TB disease.

KEY FINDINGS/ACHIEVEMENTS

  • Low levels of Vit D were identified as an independent risk factor for active MDR-TB compared to household and non-household controls.
  • There was no association between Vit D status and IGRA positivity, an indicator of sub-clinical TB infection.

PUBLICATIONS

  • Shukla, A., Bromage, S., Dholakia, Y…Mistry, N. et al. (2022). Case-control study of vitamin D status and adult multidrug-resistant pulmonary tuberculosis in Mumbai, India. Int J Tuberc Lung Dis, 26:826-834.
  • Mistry, N.F., Hemler, E.C., Dholakia, Y., Shukla, A., Dev, P., Govekar, L…. Fawzi, W. et al. (2020). Protocol for a case-control study of vitamin D status, adult multidrug-resistant tuberculosis disease and tuberculosis infection in Mumbai, India. BMJ Open,10: 1-8.
  • Principal Investigator

    Dr. Nerges Mistry

  • CRyPTIC Consortium Primary Investigator

    Prof. Derrick Crook, University of Oxford, UK (CRyPTIC website)

  • Collaborators (India Component)

    1. Dr. Camilla Rodrigues, Hinduja Hospital and Research Centre, Mumbai
    2. Prof. Stefan Neimann, German Centre for Infection Research, Borstel, Germany

  • Project Team

    Dr. Kayzad Nilgiriwala, Ms. Grishma Patel, Ms. Tejal Mestry, Mr. Ayan Mandal, Ms. Sanchi Shah, Ms. Prachi Dev, Ms. Vidushi Chitalia, Ms. Akshata Papewar, Ms. Nithya Ganesan, Ms. Nishtha Gala (FMR); Ms. Preeti Kamble, Ms. Utkarsha Surva, Ms. Rukhasar Khot, Ms. Remya Nambiar (Hinduja)

  • Funded by

    Through University of Oxford:
    Phase-1: Bill and Melinda Gates Foundation, Phase-2: The Wellcome Trust

  • Duration

    Febaury 2016 – June 2021

  • Budget

    INR 236 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

As a part of developing contemporary molecular epidemiology capacity, FMR invested early on in developing the whole genome sequencing (WGS) techniques for understanding TB disease transmission and drug resistance. The work led to the publication of one of the first reports on the application for tracking transmission and diagnosis of drug resistance in India. This led to the invitation by the University of Oxford to participate in their multi-country global project CRyPTIC. The aim of the CRyPTIC project was to achieve sufficiently accurate genetic prediction of resistance to 14 anti-tuberculosis drugs from whole genome sequencing to replace slow, cumbersome, culture-based drug susceptibility testing (DST) for Mycobacterium tuberculosis complex (MTBC). This would enable rapid-turnaround near-to-patient assays to revolutionize drug-resistant TB identification and management. In the first phase of the project (CRyPTIC-BMGF), 14-drug microtiter DST was validated for 1,000 isolates from India (FMR and Hinduja Hospital). The second phase of the CRyPTIC project (CRyPTIC-WT) was in continuation of the CRyPTIC-BMGF, which used large-scale global and clade-representative genome sequences (>15,000 isolates sequenced from 27 countries during the project) to build-up on the drug resistance catalogue. India (FMR and Hinduja Hospital) contributed to 6,500 isolates in this project. The project identified genomic variants with precision for improving statistical methods to detect associations between variants and DST, and the predicted resistant variants were validated.

INDIA KEY FINDINGS/ACHIEVEMENTS

  • Largest contribution of TB sequences to the global repository
  • Drug resistance profile and strain lineage determined for all the study isolates.
  • Transmission clusters of Beijing determined in Mumbai Metropolitan Region
  • Demonstrated through local genome analysis the drastic increase of fluoroquinolone drug resistance, as well as emerging bedaquiline (new drug) resistance, which endangers the success of newly endorsed MDR-TB treatment regimens

PUBLICATIONS

  • CRyPTIC Consortium (2024). Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis, reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun, 15(1): 488. Res Sq [Preprint]. rs.3.rs-3378915. doi.org/1021203/rs.3.rs-3378915/v1
  • Sonnenkalb, L., Carter, J. J., Spitaleri, A, et al. (The CRyPTIC Consortium) (2023). Bedaquiline and clofazimine resistance resistance in Mycobacterium tuberculosis: an in vitro and in silico data analysis. Lancet Microbe, 4: e358–368.
  • The CRyPTIC Consortium. (2022). A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics. PLoS Biol, 20: e 3001721. bioRxiv preprint doi:10.1101/2021.09.14.460274
  • The CRyPTIC Consortium. (2022). Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biol, 20: e3001755. bioRxiv preprintdoi:10.1101/2021.09.14.460272
  • Fowler, P.W., Wright, C., Spiers, H. et al. (The CRyPTIC Consortium). A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates. Elife, 11: e75046. bioRxiv preprint doi:10.1101/2021.07.20.453060
  • The CRyPTIC Consortium. (2022). Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.Eur Resp J, 60(4):2200239.
  • Hunt, M., Letcher, B., Malone, K. M., et al. (CRyPTIC consortium) (2022). Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol, 23(1): 147.
  • Walker, T.M., Miotto, P., Köser, C.U. et al. (The CRyPTIC Consortium) (2022). The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A new global standard for molecular diagnostics. Lancet Microbe, 3: 265-273.
  • Yang, Y., Walker, T.M., Kouchaki, S., et al. (CRyPTIC Consortium) (2021). An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction. Brief Bioinform, 22(6): bbab299.
  • Adams, O., Deme, J.C., Parker, J.L,…. et al. (The CRyPTIC Consortium) (2021). Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target. Structure, 29:1
  • Horter, S., Daftary, A., Keam, T.,…Mistry, N. et al. (2021). Person-centred care in tuberculosis. Int J Tuber and Lung Dis, 25: 784-787.
  • The CRyPTIC Consortium, Lachapelle, A.C. (2021). A generalisable approach to drug susceptibility prediction for M. tuberculosis using machine learning and whole-genome sequencing.
  • The CRyPTIC Consortium, Carter, J.J. (2021). Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. bioRxiv preprint doi.org/10.1101/2021.09.14.460353
  • Sonnenkalb, L., Carter, J., Spitaleri,…Nilgiriwala, K., et al. (The CRyPTIC Consortium) (2021). Deciphering bedaquiline and clofazimine resistance in tuberculosis: An evolutionary medicine approach. bioRxiv preprint doi.org/10.1101/2021.03.19.436148
  • Dreyer, V., Mandal, A., Dev, P…. Nilgiriwala, K., et al. (The CRyPTIC Consortium) (2022). High fluoroquinolone resistance proportions among multidrug resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region. Genome Med, 14: 1-16. bioRxiv preprint doi:10.1101/2021.02.02.429364.
  • Kouchaki, S., Yang, Y., Lachapelle, A. et al. (CRyPTIC Consortium) (2020). Multi-label random forest model for tuberculosis drug resistance classification and mutation ranking. Front Microbiol, 11: 667.
  • Wilson, D.J., The CRyPTIC Consortium. (2020). GenomegaMap within-species genome-wide d N/d S estimation from over 10,000 genomes. Mol Biol Evol, 37: 2450-2460
  • Yang, Y., Walker, T.M., Walker, A.S.,… et al. (The CRyPTIC Consortium) (2019). DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis. Bioinformatics, 35: 3240-3249.
  • Kouchaki, S., Yang, Y., Walker, T.M.,… et al. (The CRyPTIC Consortium) (2018). Application of machine learning techniques to tuberculosis drug resistance analysis. Bioinformatics, 35: 2276–2282.
  • Rancoita, P.M.V., Cugnata, F., Gibertoni, Cruz A.L.,… et al. (The CRyPTIC Consortium) (2018). Validating a 14-drug microtiter plate containing bedaquiline and delamanid for large scale research susceptibility testing of Mycobacterium tuberculosis. Antimicrob. Agent Chemother, 62: e00344-18.
  • Sagili, K.D., Muniyandi, M., Nilgiriwala, K.S. et al. (2018). Cost-effectiveness of GeneXpert and LED-FM for diagnosis of pulmonary tuberculosis: A systematic review. PLOS One, 13: e0205233.
  • CRyPTIC Consortium and the 100,000 Genomes Project (2018). Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing: The CRyPTIC Consortium and the 100,000 Genomes Project. N Engl J Med, 379: 1403-1415.

CONFERENCE PRESENTATIONS

  • Nilgiriwala, K. High minimum inhibitory of Bedaquiline naive clinical isolates of Mycobacterium tuberculosis from Mumbai, India. Oral Presentation. UNION/CDC Late-breaker session on “Tuberculosis, TB-HIV and diabetes and lung health”, organized by UNION/CDC, Hyderabad, 2nd November 2019.
  • Mistry N. Harnessing political support and inter-sectoral Co-ordination for TB elimination by 2025. Invited Panelist. Meeting at 50th Union World Conference on Lung Health,organized by Global Coalition Against TB, Hyderabad,31st October 2019.
  • Nilgiriwala, K. Next generation DNA sequencing and its application in TB. Oral Presentation. Meeting on “NGS for DR-TB” organized by Medecins Sans Frontiers, Mumbai, 9th May 2019.
  • Nilgiriwala, K. Application of WGS for Public Health. Oral Presentation. Truth seekers meeting on “Application of WGS for Public Health” Organized by Tata Institute of Social Sciences, Mumbai, 20th July 2017.
  • Mistry, N. Highlighting issues likely to affect application and outcomes of WGS in India for TB control. Oral Presentation. Workshop on “Building capacity for Whole genome sequencing of mycobacterial strains” organized by National Institute for Research in Tuberculosis, Chennai, 19th February 2017.
  • Mistry, N. Insight into Applications of whole shotgun sequencing of M. tuberculosis in the high endemic region of Mumbai. Poster Discussion. 47th Union World Conference on “Lung Health” organized by The Union, Liverpool (UK), 26th -29th October 2016.
  • Principal Investigators

    Dr. Nerges Mistry and Dr. Kalpana Sriraman

  • Collaborator

    Dr. Vikas Oswal, Vikas Nursing Home, Mumbai

  • Project Team

    Dr. Ambreen Shaikh, Ms. Smriti Vaswani, Mr. Nilesh Shahasne

  • Funded by

    Tata Education and Development Trust - India Health Fund Initiative

  • Duration

    February 2017 – August 2020

  • Budget

    INR 192 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

Very little information exists to guide patients on how soon they are rendered non-infectious after beginning their treatment. Through this study we sought to understand the effect of anti-TB treatment on infectiousness (ability to spread to others) of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients and how this knowledge can be used to reduce risk of spreading TB to family members, close contacts and community. Since the tuberculosis bacteria spread through aerosols from breath, it was felt that the bacteria derived from them would be better representatives for studying infectiousness, as opposed to sputum derived bacteria. Using the innovative method of isolation of bacteria from gelatin lined masks, the study was able to not only isolate and identify the live TB bacteria, but also study their pattern of gene regulation related to infectiousness using contemporary molecular methods like RNA sequencing and qRT-PCRs.

KEY FINDINGS/ACHIEVEMENTS

  • Developed a non-invasive mask-based aerosol sampling of breath from TB patients while talking, breathing and coughing.
  • This is the first study to demonstrate the detection of viable TB bacteria through a mask aerosol sampling approach from TB patients even in the absence of productive cough, opening the possibility of a non-invasive and sensitive diagnostic tool for the detection of TB.
  • The study also showed that effective treatment in TB patients induces a significant change in the aerosol-derived bacteria at a molecular level as early as 24 hours of initiation of anti TB treatment, potentially altering its ability to infect new hosts. This emphasizes the need for patients to be started on correct and effective treatment at the earliest.
  • The study also identified 10 key genes that could be used as a biomarker for monitoring treatment efficacy or infectiousness of TB patients,

PUBLICATIONS

  • Shaikh, A., Sriraman K., Vaswani, S, Oswal, V., Mistry, N. (2021). Early phase of effective treatment induces distinct transcriptional changes in Mycobacterium tuberculosis expelled by pulmonary tuberculosis patient. Scientific Reports, 11: 1-13.
  • Shaikh, A., Sriraman, K., Vaswani, S., Oswal, V.& Mistry, N. (2019). Detection of Mycobacterium tuberculosis RNA in bioaerosols from pulmonary tuberculosis patients. Int J Infect Dis, 86:5-11.

CONFERENCE PRESENTATIONS

  • Shaikh, A. Transcriptomic signature of M.tb in response to antibiotics-predictor of treatment response. Oral Presentation. Annual meeting of the RePORT India” organized by RePORT Consortia India, 10th February 2021 (Virtual).
  • Shaikh, A. Transcriptomic profile of aerosolized Mycobacterium tuberculosis from patients during the early phase of drug-sensitive anti-tuberculosis treatment. Oral Presentation. 51st Union World Conference on lung health on “Advancing prevention”, organized by The Union, 20thto 24th October 2020 (Virtual).
  • Shaikh, A. Preliminary comparative microbiome analysis of pulmonary tuberculosis patients: Metatranscriptomics approach. Oral Presentation.TB Science 2019 pre-conference event on “Basic and transitional TB research” organized by International Union against Tuberculosis and Lung Disease, Hyderabad, 30th October 2019.
  • Sriraman, K. Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients during early treatment show differential response in human macrophages in vitro. Oral Presentation. 50th Union World Conference on Lung Health on “Ending the emergency: Science leadership action”, organized by The Union, Hyderabad, 31st October 2019.
  • Shaikh, A. Quantifying Mycobacterium tuberculosis RNA in masks samples of pulmonary tuberculosis patients. Oral Presentation. 49th Union World Conference on “Lung Health”, organized by The Union, The Hague, The Netherlands, 24th - 27th October 2018.
  • Principal Investigators

    Dr. Nerges Mistry and Dr. Kayzad Nilgiriwala

  • Collaborator

    International UNION Against Tuberculosis and Lung Disease (THE UNION) and ECHO India

  • Project Team

    Dr. Shefali Mishra, Ms.Vidushi Chitalia, Mr. Ayan Mandal, Ms. Grishma Patel, Ms. Akshata Papewar and Ms. Nithya Ganesan

  • Funded by

    International UNION Against Tuberculosis and Lung Disease (THE UNION) and ECHO India

  • Duration

    April 2019– September 2021

  • Budget

    INR 8.76Lakhs

  • Status

    Completed

ABOUT THE PROJECT

FMR conducted a hands-on training on whole genome sequencing (WGS) in Sep 2018 in Mumbai towards training in WGS for the 5 national referral laboratory staff in India. Later, in 2019, on-site hand holding was conducted at all the 5 labs individually. In order to prepare the 5 whole genome sequencing (WGS) sites in India to proficiently perform WGS (DNA isolation/library preparation/sequencing using MiSeq) and to analyze the sequence data for prediction of drug resistance and strain lineage, hands-on training was provided at each of the 5 WGS labs individually. In order to support the WGS labs in their continual sequencing efforts and troubleshooting, FMR initiated a virtual interaction with the WGS labs using the ECHO (Extension for Community Healthcare Outcomes) program - FMR ECHO Sahayata Sequencing TB. The ECHO program was initiated in July 2019 and continued till Sep 2021. A new ECHO program under the iDEFEAT TB project has been undertaken since Oct 2021 towards supporting the labs for conducting national level DR TB surveillance using WGS for the first time in the country. This is a hallmark approach for using a virtual platform for training in laboratory-based technologies.

KEY ACHIEVEMENTS

  • The 5 WGS sites in India were prepared for conducting WGS of clinical TB isolates and for interpreting drug resistance and lineage profile using Mykrobe Predictor software.
  • Challenges encountered in conducting and applying WGS in India for considering it in the diagnostic/surveillance workflow were highlighted based on the hand-holding experience.
  • Virtual hand-holding (ECHO) was undertaken for specific problem solving, key demos and interpretation of sequences and reinforcement of quality measures.

CONFERENCE PRESENTATIONS

  • Nilgiriwala, K. Virtual interaction with the Genome Sequencing (WGS) sites in India (for TB). Oral Presentation. 50th Union World Conference on Lung Health a “Post graduate course innovation in action: Application of the ECHO”, organized by The Union and ECHO, Hyderabad, 30th October 2019.
  • Principal Investigators

    Dr. Nerges Mistry and Dr. Kayzad Nilgiriwala

  • Collaborator

    Dr. Timothy Walker, University of Oxford, UK)
    Dr. Zamin Iqbal, European Bioinformatics Institute, UK

  • Project Team

    Ms. Vidushi Chitalia, Mr. Ayan Mandal, Ms. Akshata Papewar, Ms. Nithya Ganesan, Ms. Grishma Patel, Ms. Tejal Mestry

  • Funded by

    NESTA (Through University of Oxford)

  • Duration

    January 2018– December 2018 (Phase I); January 2019 – July 2020 (Phase II)

  • Budget

    INR 4.19 Lakhs (Phase I); INR 12 Lakhs (Phase II)

  • Status

    Completed

ABOUT THE PROJECT

A pilot study aimed to test the feasibility of portable Nanopore sequencing (using MinION – a USB-based portable sequencing device) on DNA isolated from sputum containing Mycobacterium tuberculosis (M.tb) was explored. Nanopore sequencing is a unique, simple to use technology that enables direct, real-time analysis of long DNA or RNA fragments. It has fast turnaround time making it an ideal technology for field use. In this study, Nanopore sequencing of sputum DNA samples was conducted by single plex and by multiplexing of 6-8 samples in one flow cell to check the feasibility of creating a cost-effective point-of-care test for TB.

Subsequently an additional study (Phase II) entitled Rapid diagnosis of TB from sputum DNA (isolation by UBB protocol) using Nanopore sequencing platform was undertaken in which the Ultimate Boiling Buffer (UBB) protocol standardized by Oxford for isolation of Mycobacterium tuberculosis (M.tb) DNA was tested on 30 clinical sputum samples. The lower limit of detection of M.tb in sputum required for prediction of DST and strain lineage was determined. Validation of Nanopore sequencing data was conducted by GeneXpert, Illumina sequencing of sputum & culture DNA, and culture DST. Multiplexing (of up to 5 samples in one flow cell) to design a cost-effective workflow for potential diagnosis of TB from sputum in future was tested

KEY FINDINGS/ACHIEVEMENTS

Phase I

  • A protocol for the isolation of DNA from sputum was standardized.
  • The feasibility of Nanopore sequencing on DNA isolated from sputum in Point of Care (POC) sequencing of M.tb was tested.
  • Nanopore sequencing of samples by multiplexing of samples in one flow cell is feasible but needs further enrichment of M.tb DNA and additional standardization toward its application as a cost-effective test

Phase II

  • The UBB protocol was successfully used for the isolation and enrichment of M.tb DNA from sputum samples, very suitable for Nanopore sequencing. The proportion of the M.tb DNA/reads varied in different sputum grades (1+, 2+ and 3+).
  • The minimum amount of M.tb DNA required in the samples to determine strain lineage and to predict DST profile (for 11 drugs) using Nanopore sequencing was determined for singleplex and multiplex sequencing.
  • Nanopore sequencing of sputum DNA was validated with GeneXpert, Illumina sequencing of sputum & culture and culture DST (UKMYC6 – microtiter plate method) for DST prediction.

PUBLICATIONS

  • Votintseval, A.A., Bradley, P., Pankhurst, L., Loose, M., Del Ojo, E.C., Nilgiriwala, K., Chatterjee, A. et al. (2016). Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples. JCM, 55: 1285-1298.

CONFERENCE PRESENTATIONS

  • Nilgiriwala, K. Diagnosis of tuberculosis by whole genome sequencing of DNA from sputum. Oral Presentation. International Virtual Conference “London Calling: Dedicated to Nanopore DNA/RNA sequencing” organized by Oxford Nanopore Technologies Limited from 17th to 19th June 2020.
  • Nilgiriwala, K. Towards Point-of-Care Diagnosis of Pulmonary Tuberculosis and Drug Susceptibility Testing by Whole Genome Sequencing of DNA Isolated from Sputum. Poster presentation. Conference on “2017 Next Gen Genomics, Biology, Bioinformatics, Technology”, organized by SciGenom Research Foundation, Bhubaneswar, 2nd-4th October 2017.
  • Principal Investigator

    Dr. Nerges Mistry

  • Project Team

    Dr. Rahul Kamble, Ms. Karishma Gupta (Fogarty Fellow)

  • Funded by

    Personal donation from Mr. N. B. Godrej

  • Duration

    January 2016– May 2018

  • Budget

    INR 10 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

The Foundation invested in a survey of health facilities in high-burden TB wards of Mumbai and in the training of the facility staff in adopting infection control (IC) measures. Personal practice, infrastructural and administrative aspects of IC were recorded at these facilities and outcomes were conveyed to the local RNTCP and MCGM. The introduction of germicidal UV lights in in-patient and out-patient care was advocated in both Delhi and Mumbai. This initiative was successfully taken up at scale by the National Institute of TB and Respiratory Diseases, New Delhi, with around 32 units installed in various locations. The staff of NITRD were repeatedly trained in maintenance and measurement of lamp and fixture efficacy. The latter was undertaken with help from CDC, USA expert, a Fogarty Fellow and Mr. Bill Palmer (Aeromed) who supplied and supervised the installation for correctness and safety.

  • Principal Investigator

    Dr. Nerges Mistry

  • Co-Investigator

    Dr. Anirvan Chatterjee

  • Collaborators

    Mumbai TB programme (RNTCP)

  • Project Team

    Dr. Kalpana Sriraman, Dr. Kayzad Nilgiriwala, Ms. Rupali Kekane

  • Funded by

    Science and Engineering Research Board, A Statutory Body under the Department of Science and Technology Government of India

  • Duration

    September 2014– February 2018

  • Budget

    INR 50.49 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

The aim of the study was to examine and validate critical genes associated with the acquisition of multi-drug resistance in longitudinal clinical isolates and in vitro generated resistant strains by quantitative real-time PCR

KEY FINDINGS/ACHIEVEMENTS

  • The study identified five genes associated with drug resistance that were not previously known to be associated with the development of drug resistance
  • Among the five genes identified, the levels of ppsD, a critical gene involved in the production of lipids present on the surface of the bacteria, appeared to reflect treatment response in patients and hence could be considered as a potential biomarker for the prediction of poor treatment response in patients undergoing first-line TB treatment

PUBLICATIONS

  • Sriraman, K.,Kekane, R., Shah, D., Saranath, D. & Mistry, N. (2019). Expression of ppsD a gene involved in synthesis of Mycobacterium tuberculosis virulence factor PDIM, reflects treatment response in pulmonary tuberculosis patients. bioRxiv, 576470.
  • Sriraman,K., Nilgiriwala, K., Saranath, D., Chatterjee, A. & Mistry, N.(2017). Deregulation of genes associated with alternate drug resistance mechanism of Mycobacterium tuberculosis. CurrMicrobiol, 75: 394-400.

CONFERENCE PRESENTATIONS

  • Sriraman K. ppsD –a potential marker for treatment responses in tuberculosis infection. Poster presentation. Keystone Symposia on Molecular & Cellular Biology on “Tuberculosis: Translating Scientific Findings for Clinical and Public Health Impact(X7)”, organized by Keystone Symposia, Canada, 15th - 19th April 2018.
  • Sriraman K. Transcriptional analysis of genes associated with rapid acquisition of multidrug resistance in Mycobacterium tuberculosis. Oral Presentation. 47th Union World Conference on “Lung Health” organized by The Union, Liverpool (UK), on 26th -29th October 2016
  • Sriraman, K. Transcriptional analysis of gene associated with rapid acquisition of MDR in MTB. Oral Presentation. Joint meeting of stakeholders on “Progress and Plans of TB Control Activities in Mumbai” organized by Municipal Corporation of greater Mumbai, Central TB Division and Maharashtra state, Mumbai, 16th August 2016.
  • Principal Investigator

    Dr. Nerges Mistry

  • Collaborators

    Dr. Madhukar Pai, McGill University, Canada & Dr. Nimalan Arinaminpathy, Imperial College, London

  • Consultants

    Dr. Sheela Rangan, Independent Research Consultant
    Dr. Yatin Dholakia, Clinical Consultant
    Dr. Ramnath Subbaraman, Tufts University School of Medicine, USA

  • Project Team

    A team of consultants comprising of clinical consultants Dr. Yatin Dholakia, Dr. Sheela Rangan and Dr. David Osrin (SNEHA) closely worked with the qualitative researchers. The field qualitative team comprised of 12 (six male & six female) researchers, six each for Mumbai and Patna respectively. The team in Mumbai included three researchers from PUKAR as well. FMR staff Ms. Eunice Lobo, Ms. Shimoni Shah, Ms. Swaran Kamble, Ms. Sanchi Shah were involved in data analysis.

  • Funded by

    Sambodhi Research & Communications Pvt. Ltd.

  • Duration

    December 2013– May 2018

  • Budget

    INR 198.7 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

A private sector engagement model for control of TB, the public private interface agency (PPIA) was attempted in response to the National Strategic Plan in Mumbai and Patna for drug sensitive (DS) and drug resistant (DR) TB patients. The former was evaluated over 2 years after maturity to examine effect on reduction of patient pathways and retention. The model engaged private providers, diagnostic facilities and pharmacies into an effective network providing free diagnostic tests and treatment.

KEY FINDINGS/ACHIEVEMENTS

    Drug Sensitive TB Patients

  • Patients first accessing engaged facilities at first point of care had shorter pathways from symptoms to initiation of treatment.
  • The NTEP in Mumbai provided early diagnosis compared to private providers engaged with PPIA.
  • Good retention of patients post diagnosis was experienced in Mumbai and Patna, but a hub-spoke model in Mumbai hampered retention emphasizing effects of local design. Multiple diagnosis in patients were a common feature. On average DS-TB patients accessed 2-3 providers during the pathway.
  • Drug Resistant – TB patients

  • Total pathway from symptom to treatment initiation in new/primary DR cases was twice that of treatment patients (190 vs. 69 days)
  • Qualitative research highlighted the role of awareness action gap in patients, the extensive distance that DR patients had to travel to avail diagnosis treatment (89-650 kms). The case histories were vastly heterogenous implying that a wide breadth of case features (comprehensive care would need to be implemented)
  • Uncertainties and bewilderment plague the pathway when on an average 7-9 providers are seen comprising both public and private providers

The Project undertaken on initiation by the BMGF spanning 5 years constituted the longest national field study undertaken by the Foundation. The FMR was considerably strengthened in field work measures through this experience and was able to contribute meaningfully with recommendations for improving patient care.

PUBLICATIONS

  • Shah, S., Shah, S., Rangan, S., Rai, S., Lobo, E., Kamble, S., Dholakia, Y. & Mistry, N.F. (2020). Effect of public-private interface agency in Patna and Mumbai, India: Does it alter durations and delays in care seeking for drug-sensitive pulmonary tuberculosis? Gates Open Research, 4: 1-15.
  • Bhattacharya Chakravarty, A., Rangan, S., Rai, S., Kamble, S.,Raste, T., Shah, S., Dholakia, Y. Shah, S.& Mistry, N.(2019). Such a long journey: What health seeking pathways of patients with drug resistant tuberculosis in Mumbai tell us?PLOS One, 14: e0209924.
  • Lobo, E.,Shah, S., Rangan, S., Dholakia, Y. & Mistry, N.(2018). Pathway to care for drug resistant tuberculosis cases during a retrospective study conducted in high TB burden wards in Mumbai. Gates Open Research, 2: 1-6.
  • Mistry, N., Lobo, E., Rangan, S. & Dholakia, Y. (2017). Pulmonary tuberculosis in Patna India: duration delays and health care seeking behavior among patients identified through household survey. J. Epidemiology & Global Health, 7: 241-248.
  • Dholakia, Y., Mistry, N., Lobo, E. &Rangan, S. (2016). Use of standardized patients to assess quality of tuberculosis care. Lancet Infect Dis, 16: 23.
  • Mistry, N., Rangan, S., Dholakia, Y., Lobo, E., Shah, S. & Patil, A. (2016). Duration and delay in care seeking, diagnosis and treatment initiation in uncomplicated pulmonary tuberculosis patients in Mumbai. PLOS One, 11: e0152287.

CONFERENCE PRESENTATIONS

  • Mistry, N. Methods and results from patient pathway analysis. Oral Presentation. Brainstorm/planning workshop to plan “Possible studies that can evaluate the impact of the private sector engagement in India”, organized by Bill and Melinda Gates Foundation, Hyderabad, 3rd November 2019.
  • Dholakia, Y. Lessons from Public Private Interface Agency (PPIA) intervention in TB care: Mumbai, Patna, India”. Poster Presentation. 50th Union World Conference on Lung Health on “Ending the emergency: Science leadership action”, organized by The Union, Hyderabad, 2nd November 2019.
  • Dev, P. Footfalls and days: Journey of pulmonary drug resistant TB patients in Mumbai. Poster Presentation. 50th Union World Conference on Lung Health on “Ending the emergency: Science leadership action”, organized by The Union, Hyderabad, 31st October 2019.
  • Mistry, N. Optimizing private engagement to streamline patient pathways. Panel Discussion. Global Coalition Against TB Expert Group Meeting on “Patient pathways and challenges that TB care seekers face in navigating a complex ecosystem and adapting existing interventions to improving access to care while ensuring affordable care which is agnostic to sector in which it is sought” organized by Global Health Strategies, New Delhi, 28th March 2019.
  • Dholakia, Y. TB care seeking in Mumbai: Duration, movements and retention in care. Oral Presentation. 73rd NATCON conference on “Tuberculosis and chest diseases” organized by Indira Gandhi Govt. Medical college and TB association of Maharashtra, Nagpur, from 4th - 6th January 2019.
  • Mistry, N. DS-PTB patient Retention / Movement in Mumbai. Panel Discussion on “ Patient Retention and Tuberculosis” organized by Harvard T.H. Chan School of Public Health and Foundation for Medical Research, Mumbai, 29th August 2018.
  • Mistry, N. Patient pathways to care in TB. Invited speaker. Winter Symposium on “Advances in Tuberculosis Research”, organized by Christian Medical College Vellore, RePORT and Indo US consortium, Vellore, 11th to 13th February 2016.
  • Principal Investigator

    Dr. Prajakta Dandekar, Institute of Chemical Technology, Mumbai

  • Co-Investigator

    Dr. Nerges Mistry

  • Project Team

    Dr. Kayzad Nilgiriwala, Dr. Kalpana Sriraman, Ms. Urvashi Panghal, Dr. Rahul Upadhyay, Dr. Purva Bhatter

  • Funded by

    Department of Biotechnology

  • Duration

    June 2013 – May 2015

  • Budget

    INR 7.92 Lakhs

  • Status

    Completed

ABOUT THE PROJECT

This project aimed at exploitation of RNA interference (RNAi) approach for reducing the intramacrophage load of Mycobacterium tuberculosis. This was proposed to be accomplished through siRNA-loaded nanoplexes targeting intramacrophage proteins required for the survival of the bacteria. The role of FMR was to test the specificity of siRNA through checking for the expression of host bfl-1 posttreatment with the generated siRNA’s using quantitative real-time PCR and determine the bactericidal potential of the siRNA particles through use of routinely practiced in-vitro macrophage model.

KEY FINDINGS/ACHIEVEMENTS

  • The study showed the chitosan nanoplexes developed by ICT, Mumbai, were found to be significantly (99.1%) inhibitory to TB bacteria at a modest concentration of 500 μg/ mL and non-toxic to host cells (macrophages)
  • The study was one of the first reports demonstrating the inhibitory effect of water-soluble chitosan oligosaccharides nanoplexes against TB bacteria and that it could be potentially employed for the development of effective drug delivery vehicles or systems against TB bacteria
  • Further, the study demonstrated that chitosan nanoplexes could efficiently deliver siRNAs directed against host proteins required for TB survival into host cells and therefore can be potentially used as a treatment option for TB.

PUBLICATIONS

  • Koli, U., Nilgiriwala, K., Sriraman, K., Jain R, Dandekar P. Targeting tuberculosis infection in macrophages using chitosan oligosaccharide nanoplexes. 2019. J Nanopart Res 21, 200.