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Sanchini A, Lanni A, Giannoni F, Mustazzolu A. Exploring diagnostic methods for drug-resistant tuberculosis: A comprehensive overview. Tuberculosis (Edinb) 2024; 148:102522. [PMID: 38850839 DOI: 10.1016/j.tube.2024.102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Despite available global efforts and funding, Tuberculosis (TB) continues to affect a considerable number of patients worldwide. Policy makers and stakeholders set clear goals to reduce TB incidence and mortality, but the emergence of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) complicate the reach of these goals. Drug-resistance TB needs to be diagnosed rapidly and accurately to effectively treat patients, prevent the transmission of MDR-TB, minimise mortality, reduce treatment costs and avoid unnecessary hospitalisations. In this narrative review, we provide a comprehensive overview of laboratory methods for detecting drug resistance in MTB, focusing on phenotypic, molecular and other drug susceptibility testing (DST) techniques. We found a large variety of methods used, with the BACTEC MGIT 960 being the most common phenotypic DST and the Xpert MTB/RIF being the most common molecular DST. We emphasise the importance of integrating phenotypic and molecular DST to address issues like resistance to new drugs, heteroresistance, mixed infections and low-level resistance mutations. Notably, most of the analysed studies adhered to the outdated definition of XDR-TB and did not consider the pre-XDR definition, thus posing challenges in aligning diagnostic methods with the current landscape of TB resistance.
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Affiliation(s)
| | - Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
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2
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Surie D, Sathyanarayanan MK, Lavanya J, Smith JP, Shanmugam SK, Tamilzhalagan S, Selvaraj A, Ramesh G, Tripathy S, Khaparde SD, Ho CS, Hall-Eidson PJ, Ranganathan UDK, Selvaraju S, Moonan PK. Long-term follow-up of persons diagnosed with multidrug-resistant TB in Chennai, India, 2013-2020. Int J Tuberc Lung Dis 2024; 28:54-56. [PMID: 38178300 PMCID: PMC10859871 DOI: 10.5588/ijtld.23.0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Affiliation(s)
- D Surie
- Centers for Disease Control and Prevention, Division of Global HIV and Tuberculosis, Atlanta, GA, United States of America
| | - M K Sathyanarayanan
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - J Lavanya
- Chennai Municipal Corporation, Chennai
| | - J P Smith
- Centers for Disease Control and Prevention, Division of Global HIV and Tuberculosis, Atlanta, GA, United States of America
| | - S K Shanmugam
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - S Tamilzhalagan
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - A Selvaraj
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - G Ramesh
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - S Tripathy
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
- Dr. D Y Patil Medical College, Hospital and Research Centre, Pune
| | - S D Khaparde
- Government of India, Ministry of Health and Family Welfare, Directorate of Health Services - Central TB Division, New Delhi, India
| | - C S Ho
- Centers for Disease Control and Prevention, Division of Global HIV and Tuberculosis, Atlanta, GA, United States of America
| | - P J Hall-Eidson
- Centers for Disease Control and Prevention, Division of Global HIV and Tuberculosis, Atlanta, GA, United States of America
| | - U D K Ranganathan
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - S Selvaraju
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai
| | - P K Moonan
- Centers for Disease Control and Prevention, Division of Global HIV and Tuberculosis, Atlanta, GA, United States of America
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Rao M, Wollenberg K, Harris M, Kulavalli S, Thomas L, Chawla K, Shenoy VP, Varma M, Saravu K, Hande HM, Shanthigrama Vasudeva CS, Jeffrey B, Gabrielian A, Rosenthal A. Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India. Microbiol Spectr 2023; 11:e0453122. [PMID: 37671895 PMCID: PMC10580826 DOI: 10.1128/spectrum.04531-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 07/03/2023] [Indexed: 09/07/2023] Open
Abstract
Whole-genome sequencing has created a revolution in tuberculosis management by providing a comprehensive picture of the various genetic polymorphisms with unprecedented accuracy. Studies mapping genomic heterogeneity in clinical isolates of Mycobacterium tuberculosis using a whole-genome sequencing approach from high tuberculosis burden countries are underrepresented. We report whole-genome sequencing results of 242 clinical isolates of culture-confirmed M. tuberculosis isolates from tuberculosis patients referred to a tertiary care hospital in Southern India. Phylogenetic analysis revealed that the isolates in our study belonged to five different lineages, with Indo-Oceanic (lineage 1, n = 122) and East-African Indian (lineage 3, n = 80) being the most prevalent. We report several mutations in genes conferring resistance to first and second line antitubercular drugs including the genes rpoB, katG, ahpC, inhA, fabG1, embB, pncA, rpsL, rrs, and gyrA. The majority of these mutations were identified in relatively high proportions in lineage 1. Our study highlights the utility of whole-genome sequencing as a potential supplemental tool to the existing genotypic and phenotypic methods, in providing expedited comprehensive surveillance of mutations that may be associated with antitubercular drug resistance as well as lineage characterization of M. tuberculosis isolates. Further larger-scale whole-genome datasets with linked minimum inhibition concentration testing are imperative for resolving the discrepancies between whole-genome sequencing and phenotypic drug sensitivity testing results and quantifying the level of the resistance associated with the mutations for optimization of antitubercular drug and precise dose selection in clinics. IMPORTANCE Studies mapping genetic heterogeneity of clinical isolates of M. tuberculosis for determining their strain lineage and drug resistance by whole-genome sequencing are limited in high tuberculosis burden settings. We carried out whole-genome sequencing of 242 M. tuberculosis isolates from drug-sensitive and drug-resistant tuberculosis patients, identified and collected as part of the TB Portals Program, to have a comprehensive insight into the genetic diversity of M. tuberculosis in Southern India. We report several genetic variations in M. tuberculosis that may confer resistance to antitubercular drugs. Further wide-scale efforts are required to fully characterize M. tuberculosis genetic diversity at a population level in high tuberculosis burden settings for providing precise tuberculosis treatment.
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Affiliation(s)
- Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kurt Wollenberg
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Harris
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shrivathsa Kulavalli
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavitha Saravu
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - H. Manjunatha Hande
- Department of Medicine, Kasturba Medical College, Manipal, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Brendan Jeffrey
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrei Gabrielian
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Department of Health and Human Services, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Zhang M, Lu Y, Zhu Y, Wu K, Chen S, Zhou L, Wang F, Peng Y, Li X, Pan J, Chen B, Liu Z, Wang X. Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Drug Resistance: A Retrospective Observational Study in Eastern China. Antibiotics (Basel) 2023; 12:1257. [PMID: 37627677 PMCID: PMC10451829 DOI: 10.3390/antibiotics12081257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Pulmonary tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB). Whole-genome sequencing (WGS) holds great promise as an advanced technology for accurately predicting anti-TB drug resistance. The development of a reliable method for detecting drug resistance is crucial in order to standardize anti-TB treatments, enhance patient prognosis, and effectively reduce the risk of transmission. In this study, our primary objective was to explore and determine the potential of WGS for assessing drug resistance based on genetic variants recommended by the World Health Organization (WHO). A total of 1105 MTB strains were selected from samples collected from 2014-2018 in Zhejiang Province, China. Phenotypic drug sensitivity tests (DST) of the anti-TB drugs were conducted for isoniazid (INH), rifampicin (RFP), streptomycin, ethambutol, fluoroquinolones (levofloxacin and moxifloxacin), amikacin, kanamycin, and capreomycin, and the drug-resistance rates were calculated. The clean WGS data of the 1105 strains were acquired and analyzed. The predictive performance of WGS was evaluated by the comparison between genotypic and phenotypic DST results. For all anti-TB drugs, WGS achieved good specificity values (>90%). The sensitivity values for INH and RFP were 91.78% and 82.26%, respectively; however, they were ≤60% for other drugs. The positive predictive values for anti-TB drugs were >80%, except for ethambutol and moxifloxacin, and the negative predictive values were >90% for all drugs. In light of the findings from our study, we draw the conclusion that WGS is a valuable tool for identifying genome-wide variants. Leveraging the genetic variants recommended by the WHO, WGS proves to be effective in detecting resistance to RFP and INH, enabling the identification of multi-drug resistant TB patients. However, it is evident that the genetic variants recommended for predicting resistance to other anti-TB drugs require further optimization and improvement.
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Affiliation(s)
- Mingwu Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310020, China; (Y.L.); (X.L.)
| | - Yelei Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Kunyang Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Songhua Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Lin Zhou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Fei Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Ying Peng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310020, China; (Y.L.); (X.L.)
| | - Junhang Pan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Bin Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Zhengwei Liu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Xiaomeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
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Yusoof KA, García JI, Schami A, Garcia-Vilanova A, Kelley HV, Wang SH, Rendon A, Restrepo BI, Yotebieng M, Torrelles JB. Tuberculosis Phenotypic and Genotypic Drug Susceptibility Testing and Immunodiagnostics: A Review. Front Immunol 2022; 13:870768. [PMID: 35874762 PMCID: PMC9301132 DOI: 10.3389/fimmu.2022.870768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
Tuberculosis (TB), considered an ancient disease, is still killing one person every 21 seconds. Diagnosis of Mycobacterium tuberculosis (M.tb) still has many challenges, especially in low and middle-income countries with high burden disease rates. Over the last two decades, the amount of drug-resistant (DR)-TB cases has been increasing, from mono-resistant (mainly for isoniazid or rifampicin resistance) to extremely drug resistant TB. DR-TB is problematic to diagnose and treat, and thus, needs more resources to manage it. Together with+ TB clinical symptoms, phenotypic and genotypic diagnosis of TB includes a series of tests that can be used on different specimens to determine if a person has TB, as well as if the M.tb strain+ causing the disease is drug susceptible or resistant. Here, we review and discuss advantages and disadvantages of phenotypic vs. genotypic drug susceptibility testing for DR-TB, advances in TB immunodiagnostics, and propose a call to improve deployable and low-cost TB diagnostic tests to control the DR-TB burden, especially in light of the increase of the global burden of bacterial antimicrobial resistance, and the potentially long term impact of the coronavirus disease 2019 (COVID-19) disruption on TB programs.
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Affiliation(s)
- Kizil A. Yusoof
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Juan Ignacio García
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Alyssa Schami
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andreu Garcia-Vilanova
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Holden V. Kelley
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Shu-Hua Wang
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine and Global One Health Initiative, The Ohio State University, Columbus, OH, United States
| | - Adrian Rendon
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias (CIPTIR), Hospital Universitario de Monterrey Universidad Autónoma de Nuevo León (UANL), Monterrey, Mexico
| | - Blanca I. Restrepo
- School of Public Health, University of Texas Health Science Center at Houston, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Marcel Yotebieng
- Division of General Internal Medicine, Department of Medicine, Albert Einstein College of Medicine, New York City, NY, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
| | - Jordi B. Torrelles
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX, United States
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
- *Correspondence: Juan Ignacio García, ; Blanca I. Restrepo, ; Marcel Yotebieng, ; Jordi B. Torrelles,
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