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Vasiliauskaitė L, Bakuła Z, Vasiliauskienė E, Bakonytė D, Decewicz P, Dziurzyński M, Proboszcz M, Davidavičienė EV, Nakčerienė B, Krenke R, Kačergius T, Stakėnas P, Jagielski T. Detection of multidrug-resistance in Mycobacterium tuberculosis by phenotype- and molecular-based assays. Ann Clin Microbiol Antimicrob 2024; 23:81. [PMID: 39198827 DOI: 10.1186/s12941-024-00741-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND The whole-genome sequencing (WGS) is becoming an increasingly effective tool for rapid and accurate detection of drug resistance in Mycobacterium tuberculosis complex (MTBC). This approach, however, has still been poorly evaluated on strains from Central and Eastern European countries. The purpose of this study was to assess the performance of WGS against conventional drug susceptibility testing (DST) for the detection of multi-drug resistant (MDR) phenotypes among MTBC clinical strains from Poland and Lithuania. METHODS The study included 208 MTBC strains (130 MDR; 78 drug susceptible), recovered from as many tuberculosis patients in Lithuania and Poland between 2018 and 2021. Resistance to rifampicin (RIF) and isoniazid (INH) was assessed by Critical Concentration (CC) and Minimum Inhibitory Concentration (MIC) DST as well as molecular-based techniques, including line-probe assay (LPA) and WGS. The analysis of WGS results was performed using bioinformatic pipeline- and software-based tools. RESULTS The results obtained with the CC DST were more congruent with those by LPA compared to pipeline-based WGS. Software-based tools showed excellent concordance with pipeline-based analysis in prediction of RIF/INH resistance. The RIF-resistant strains demonstrated a relatively homogenous MIC distribution with the mode at the highest tested MIC value. The most frequent RIF-resistance conferring mutation was rpoB S450L. The mode MIC for INH was two-fold higher among double katG and inhA mutants than among single katG mutants. The overall rate of discordant results between all methods was calculated at 5.3%. Three strains had discordant results by both genotypic methods (LPA and pipeline-based WGS), one strain by LPA only, three strains by MIC DST, two strains by both MIC DST and pipeline-based WGS, and the remaining two strains showed discordant results with all three methods, compared to CC DST. CONCLUSIONS Considering MIC DST results, current CCs of the first-line anti-TB drugs might be inappropriately high and may need to be revised. Both molecular methods demonstrated 100% specificity, while pipeline-based WGS had slightly lower sensitivity for RIF and INH than LPA, compared to CC DST.
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Affiliation(s)
- Laima Vasiliauskaitė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Centre of Laboratory Medicine, Laboratory of Infectious Diseases and Tuberculosis, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Zofia Bakuła
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Edita Vasiliauskienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Centre of Laboratory Medicine, Laboratory of Infectious Diseases and Tuberculosis, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Daiva Bakonytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Przemysław Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonology, and Allergology, Warsaw Medical University, Warsaw, Poland
| | - Edita Valerija Davidavičienė
- Department of Programs and State Tuberculosis Information System, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Birutė Nakčerienė
- Department of Programs and State Tuberculosis Information System, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonology, and Allergology, Warsaw Medical University, Warsaw, Poland
| | - Tomas Kačergius
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Petras Stakėnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Farhat M, Cox H, Ghanem M, Denkinger CM, Rodrigues C, Abd El Aziz MS, Enkh-Amgalan H, Vambe D, Ugarte-Gil C, Furin J, Pai M. Drug-resistant tuberculosis: a persistent global health concern. Nat Rev Microbiol 2024:10.1038/s41579-024-01025-1. [PMID: 38519618 DOI: 10.1038/s41579-024-01025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/25/2024]
Abstract
Drug-resistant tuberculosis (TB) is estimated to cause 13% of all antimicrobial resistance-attributable deaths worldwide and is driven by both ongoing resistance acquisition and person-to-person transmission. Poor outcomes are exacerbated by late diagnosis and inadequate access to effective treatment. Advances in rapid molecular testing have recently improved the diagnosis of TB and drug resistance. Next-generation sequencing of Mycobacterium tuberculosis has increased our understanding of genetic resistance mechanisms and can now detect mutations associated with resistance phenotypes. All-oral, shorter drug regimens that can achieve high cure rates of drug-resistant TB within 6-9 months are now available and recommended but have yet to be scaled to global clinical use. Promising regimens for the prevention of drug-resistant TB among high-risk contacts are supported by early clinical trial data but final results are pending. A person-centred approach is crucial in managing drug-resistant TB to reduce the risk of poor treatment outcomes, side effects, stigma and mental health burden associated with the diagnosis. In this Review, we describe current surveillance of drug-resistant TB and the causes, risk factors and determinants of drug resistance as well as the stigma and mental health considerations associated with it. We discuss recent advances in diagnostics and drug-susceptibility testing and outline the progress in developing better treatment and preventive therapies.
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Affiliation(s)
- Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Helen Cox
- Institute of Infectious Disease and Molecular Medicine, Wellcome Centre for Infectious Disease Research and Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Marwan Ghanem
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mirna S Abd El Aziz
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Debrah Vambe
- National TB Control Programme, Manzini, Eswatini
| | - Cesar Ugarte-Gil
- School of Public and Population Health, University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Madhukar Pai
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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Maitre T, Baulard A, Aubry A, Veziris N. Optimizing the use of current antituberculosis drugs to overcome drug resistance in Mycobacterium tuberculosis. Infect Dis Now 2024; 54:104807. [PMID: 37839674 DOI: 10.1016/j.idnow.2023.104807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Antibiotic-resistant tuberculosis continues to be one of the major threats to global tuberculosis control. After a hiatus of over 40 years in antituberculosis drug development, the last decade has seen a resurgence of research, yielding a number of promising compounds in the tuberculosis drug pipeline, with some that are now game changers in the treatment of MDRTB. Despite this progress, there are still obstacles restricting the use of these molecules as first-line drugs. The quick appearance of bacteria resistant to these new treatments highlights a continuing need to fuel the discovery and development of new molecules. With this in mind, alternative strategies aimed at optimizing the utilization of existing antituberculosis agents are currently under evaluation. They are focused on enhancing the efficacy of antibiotics against their bacterial targets, primarily by augmenting the quantity of antibiotic that engages with these targets. This objective can be achieved through two primary approaches: (1) Provided that toxicity concerns are not a limiting factor, increased dosing is a viable avenue, as demonstrated by rifampicin, isoniazid, and fluoroquinolones, for which escalated dosing has been effective; and (2) Employing enhancers such as drug activator boosters (ethionamide), efflux pump inhibitors, or hydrolytic enzyme inhibitors (kanamycin) can elevate the concentration of antibiotics in bacterial cells. These strategies offer the potential to mitigate antibiotic obsolescence and complement the discovery of new antibiotics.
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Affiliation(s)
- Thomas Maitre
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; Service de Pneumologie et d'Oncologie Thoracique, Centre constitutif maladies rares, Hôpital Tenon, AP-HP, Sorbonne-Université, Paris, France.
| | - Alain Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Universite, Hôpital Pitié Salpêtrière, Laboratoire de Bactériologie-Hygiene, Centre National de Référence des Mycobactéries, Paris France
| | - Nicolas Veziris
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Université, Hôpital Saint-Antoine, Département de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Hôpital Pitié-Salpêtrière, Paris, France
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García-Marín AM, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, González-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, González-Candelas F, Furió V, Comas I. Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis. THE LANCET. MICROBE 2024; 5:e43-e51. [PMID: 38061383 PMCID: PMC10790317 DOI: 10.1016/s2666-5247(23)00252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. METHODS In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. FINDINGS WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. INTERPRETATION We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. FUNDING European Research Council and the Spanish Ministerio de Ciencia.
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Affiliation(s)
- Ana María García-Marín
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain
| | - Irving Cancino-Muñoz
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain
| | | | | | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J Camarena
- Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Ester Colomer-Roig
- FISABIO Public Health, Valencia, Spain; Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lirios, Alcoy, Spain
| | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicante, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital Francesc de Borja, Gandía, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia, Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Hermelinda Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia, Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Victoria Furió
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain.
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
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Lale Ngema S, Dookie N, Perumal R, Nandlal L, Naicker N, Peter Letsoalo M, O'Donnell M, Khan A, Padayatchi N, Naidoo K. Isoniazid resistance-conferring mutations are associated with highly variable phenotypic resistance. J Clin Tuberc Other Mycobact Dis 2023; 33:100387. [PMID: 37554582 PMCID: PMC10405055 DOI: 10.1016/j.jctube.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
Background High-dose isoniazid is recommended in the 9-12 months short-course regimen for multidrug-resistant tuberculosis with inhA mutation. However, there is insufficient evidence to support the assumption of genotypic-phenotypic concordance. This study aimed to identify the genetic mutations associated with high-level phenotypic isoniazid resistance. Methods Clinical isolates from patients with drug-resistant tuberculosis were profiled by whole-genome sequencing and subjected to minimum inhibitory concentration (MIC) testing using MGIT based-method. MICs were performed in concentration ranges based on the mutation present: isolates with no isoniazid resistance-conferring mutations and H37Rv, 0.016-0.256 µg/ml; inhA, 0.256-4.0 µg/ml, katG 1.0-16.0 µg/ml; and inhA + katG, 4.0-64.0 µg/ml. Isolates demonstrating resistance at the upper limit of the concentration range were tested up to the maximum of 64.0 µg/ml. Bootstrap of the mean MICs was performed to increase the robustness of the estimates and an overlap index was used to compare the distributions of the MICs for each mutation profile. Results A total of 52 clinical isolates were included in this analysis. Bootstrap MIC means for inhA, katG and inhA + katG were 33.64 (95% CI, 9.47, 56.90), 6.79 (4.45, 9.70) and 52.34 (42.750, 61.66) µg/ml, respectively. There was high overlap between inhA and inhA + katG mutations (eta = 0.45) but not with inhA and katG (eta = 0.19). Furthermore, katG showed poor overlap with inhA + katG mutations (eta = 0.09). Unexpectedly, 4/8 (50.0%) of all InhA mutants demonstrated high-level resistance, while 20/24 (83.3%) of katG mutants demonstrated moderate-level resistance. Conclusions InhA mutations demonstrated unexpectedly high MICs and showed high overlap with inhA + katG. Contrary to the common belief that katG mutants are associated with high-level resistance, this mutation primarily showed moderate-level resistance.
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Affiliation(s)
- Senamile Lale Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nikita Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Marothi Peter Letsoalo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Max O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, & Department of Epidemiology, Columbia University Medical Center, New York City, NY, United States
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
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Mishra A, Das A, Banerjee T. Designing New Magic Bullets to Penetrate the Mycobacterial Shield: An Arduous Quest for Promising Therapeutic Candidates. Microb Drug Resist 2023; 29:213-227. [PMID: 37015080 DOI: 10.1089/mdr.2021.0441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Mycobacterium spp. intimidated mankind since time immemorial. The triumph over this organism was anticipated with the introduction of potent antimicrobials in the mid-20th century. However, the emergence of drug resistance in mycobacteria, Mycobacterium tuberculosis, in particular, caused great concern for the treatment. With the enemy growing stronger, there is an immediate need to equip the therapeutic arsenal with novel and potent chemotherapeutic agents. The task seems intricating as our understanding of the dynamic nature of the mycobacteria requires intense experimentation and research. Targeting the mycobacterial cell envelope appears promising, but its versatility allows it to escape the lethal effect of the molecules acting on it. The unique ability of hiding (inactivity during latency) also assists the bacterium to survive in a drug-rich environment. The drug delivery systems also require upgradation to allow better bioavailability and tolerance in patients. Although the resistance to the novel drugs is inevitable, our commitment to the research in this area will ensure the discovery of effective weapons against this formidable opponent.
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Affiliation(s)
- Anwita Mishra
- Department of Microbiology, Mahamana Pandit Madan Mohan Malviya Cancer Centre and Homi Bhabha Cancer Hospital, Varanasi, India
| | - Arghya Das
- Department of Microbiology, National Cancer Institute, All India Institute of Medical Sciences, New Delhi, India
| | - Tuhina Banerjee
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, India
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Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. Eur Respir J 2022; 60:2200239. [PMID: 35301246 PMCID: PMC9556810 DOI: 10.1183/13993003.00239-2022] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtained via the Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.
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Affiliation(s)
- The CRyPTIC Consortium
- For a list of all members of the CRyPTIC Consortium and their affiliations, please see the section at the end of this article
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Alffenaar JWC, Stocker SL, Forsman LD, Garcia-Prats A, Heysell SK, Aarnoutse RE, Akkerman OW, Aleksa A, van Altena R, de Oñata WA, Bhavani PK, Van't Boveneind-Vrubleuskaya N, Carvalho ACC, Centis R, Chakaya JM, Cirillo DM, Cho JG, D Ambrosio L, Dalcolmo MP, Denti P, Dheda K, Fox GJ, Hesseling AC, Kim HY, Köser CU, Marais BJ, Margineanu I, Märtson AG, Torrico MM, Nataprawira HM, Ong CWM, Otto-Knapp R, Peloquin CA, Silva DR, Ruslami R, Santoso P, Savic RM, Singla R, Svensson EM, Skrahina A, van Soolingen D, Srivastava S, Tadolini M, Tiberi S, Thomas TA, Udwadia ZF, Vu DH, Zhang W, Mpagama SG, Schön T, Migliori GB. Clinical standards for the dosing and management of TB drugs. Int J Tuberc Lung Dis 2022; 26:483-499. [PMID: 35650702 PMCID: PMC9165737 DOI: 10.5588/ijtld.22.0188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND: Optimal drug dosing is important to ensure adequate response to treatment, prevent development of drug resistance and reduce drug toxicity. The aim of these clinical standards is to provide guidance on 'best practice´ for dosing and management of TB drugs.METHODS: A panel of 57 global experts in the fields of microbiology, pharmacology and TB care were identified; 51 participated in a Delphi process. A 5-point Likert scale was used to score draft standards. The final document represents the broad consensus and was approved by all participants.RESULTS: Six clinical standards were defined: Standard 1, defining the most appropriate initial dose for TB treatment; Standard 2, identifying patients who may be at risk of sub-optimal drug exposure; Standard 3, identifying patients at risk of developing drug-related toxicity and how best to manage this risk; Standard 4, identifying patients who can benefit from therapeutic drug monitoring (TDM); Standard 5, highlighting education and counselling that should be provided to people initiating TB treatment; and Standard 6, providing essential education for healthcare professionals. In addition, consensus research priorities were identified.CONCLUSION: This is the first consensus-based Clinical Standards for the dosing and management of TB drugs to guide clinicians and programme managers in planning and implementation of locally appropriate measures for optimal person-centred treatment to improve patient care.
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Affiliation(s)
- J W C Alffenaar
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia
| | - S L Stocker
- School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Department of Clinical Pharmacology and Toxicology, St Vincent´s Hospital, Sydney, NSW, Australia, St Vincent´s Clinical Campus, University of NSW, Kensington, NSW, Australia
| | - L Davies Forsman
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Solna, Sweden, Department of Infectious Diseases Karolinska University Hospital, Solna, Sweden
| | - A Garcia-Prats
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa, Department of Pediatrics, University of Wisconsin, Madison, WI
| | - S K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - R E Aarnoutse
- Department of Pharmacy, Radboud Institute for Health Sciences & Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - O W Akkerman
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, The Netherlands, University of Groningen, University Medical Center Groningen, Tuberculosis Center Beatrixoord, Haren, The Netherlands
| | - A Aleksa
- Educational Institution "Grodno State Medical University", Grodno, Belarus
| | - R van Altena
- Asian Harm Reduction Network (AHRN) and Medical Action Myanmar (MAM) in Yangon, Myanmar
| | - W Arrazola de Oñata
- Belgian Scientific Institute for Public Health (Belgian Lung and Tuberculosis Association), Brussels, Belgium
| | - P K Bhavani
- Indian Council of Medical Research-National Institute for Research in Tuberculosis-International Center for Excellence in Research, Chennai, India
| | - N Van't Boveneind-Vrubleuskaya
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands, Department of Public Health TB Control, Metropolitan Public Health Services, The Hague, The Netherlands
| | - A C C Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos (LITEB), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - R Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
| | - J M Chakaya
- Department of Medicine, Therapeutics and Dermatology, Kenyatta University, Nairobi, Kenya, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - J G Cho
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia, Parramatta Chest Clinic, Parramatta, NSW, Australia
| | - L D Ambrosio
- Public Health Consulting Group, Lugano, Switzerland
| | - M P Dalcolmo
- Reference Center Hélio Fraga, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - P Denti
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - K Dheda
- Centre for Lung Infection and Immunity, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Cape Town, South Africa, University of Cape Town Lung Institute & South African MRC Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa, Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - G J Fox
- Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia, Woolcock Institute of Medical Research, Glebe, NSW, Australia
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - H Y Kim
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia
| | - C U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - B J Marais
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, Department of Infectious Diseases and Microbiology, The Children´s Hospital at Westmead, Westmead, NSW, Australia
| | - I Margineanu
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A G Märtson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - M Munoz Torrico
- Clínica de Tuberculosis, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico
| | - H M Nataprawira
- Division of Paediatric Respirology, Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Hasan Sadikin Hospital, Bandung, Indonesia
| | - C W M Ong
- Infectious Disease Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore, Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - R Otto-Knapp
- German Central Committee against Tuberculosis (DZK), Berlin, Germany
| | - C A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - D R Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - R Ruslami
- TB/HIV Research Centre, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia, Department of Biomedical Sciences, Division of Pharmacology and Therapy, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - P Santoso
- Division of Respirology and Critical Care, Department of Internal Medicine, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, Indonesia
| | - R M Savic
- Department of Bioengineering and Therapeutic Sciences, Division of Pulmonary and Critical Care Medicine, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA, USA
| | - R Singla
- Department of TB & Respiratory Diseases, National Institute of TB & Respiratory Diseases, New Delhi, India
| | - E M Svensson
- Department of Pharmacy, Radboud Institute for Health Sciences & Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands, Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - A Skrahina
- The Republican Research and Practical Centre for Pulmonology and TB, Minsk, Belarus
| | - D van Soolingen
- National Institute for Public Health and the Environment, TB Reference Laboratory (RIVM), Bilthoven, The Netherlands
| | - S Srivastava
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - M Tadolini
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy, Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - S Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - T A Thomas
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Z F Udwadia
- P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - D H Vu
- National Drug Information and Adverse Drug Reaction Monitoring Centre, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - W Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People´s Republic of China
| | - S G Mpagama
- Kilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania, Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, United Republic of Tanzania
| | - T Schön
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden, Institute of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden, Department of Infectious Diseases, Kalmar County Hospital, Kalmar, Linköping University, Linköping, Sweden
| | - G B Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
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9
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Identification of S315T mutation in katG gene using probe-free exclusive mismatch primers for a rapid diagnosis of isoniazid-resistant Mycobacterium tuberculosis by real-time loop-mediated isothermal amplification. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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10
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Li J, Ouyang J, Yuan J, Li T, Luo M, Wang J, Chen Y. Establishment and evaluation of an overlap extension polymerase chain reaction technique for rapid and efficient detection of drug-resistance in Mycobacterium tuberculosis. Infect Dis Poverty 2022; 11:31. [PMID: 35321759 PMCID: PMC8942611 DOI: 10.1186/s40249-022-00953-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rapid and accurate detection of drug resistance in Mycobacterium tuberculosis is critical for effective control of tuberculosis (TB). Herein, we established a novel, low cost strategy having high accuracy and speed for the detection of M. tuberculosis drug resistance, using gene splicing by overlap extension PCR (SOE PCR). METHODS The SOE PCR assay and Sanger sequencing are designed and constructed to detect mutations of rpoB, embB, katG, and inhA promoter, which have been considered as the major contributors to rifampicin (RFP), isoniazid (INH), and ethambutol (EMB) resistance in M. tuberculosis. One hundred and eight M. tuberculosis isolates came from mycobacterial cultures of TB cases at Chongqing Public Health Medical Center in China from December 2018 to April 2019, of which 56 isolates were tested with the GeneXpert MTB/RIF assay. Performance evaluation of the SOE PCR technique was compared with traditional mycobacterial culture and drug susceptibility testing (DST) or GeneXpert MTB/RIF among these isolates. Kappa identity test was used to analyze the consistency of the different diagnostic methods. RESULTS We found that the mutations of S531L, S315T and M306V were most prevalent for RFP, INH and EMB resistance, respectively, in the 108 M. tuberculosis isolates. Compared with phenotypic DST, the sensitivity and specificity of the SOE PCR assay for resistance detection were 100.00% and 88.00% for RFP, 94.64% and 94.23% for INH, and 68.97% and 79.75% for EMB, respectively. Compared with the GeneXpert MTB/RIF, the SOE PCR method was completely consistent with results of the GeneXpert MTB/RIF, with a concordance of 100% for resistance to RFP. CONCLUSIONS In present study, a novel SOE PCR diagnostic method was successfully developed for the accurate detection of M. tuberculosis drug resistance. Our results using this method have a high consistency with that of traditional phenotypic DST or GeneXpert MTB/RIF, and SOE PCR testing in clinical isolates can also be conducted rapidly and simultaneously for detection of drug resistance to RFP, EMB, and INH.
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Affiliation(s)
- Jungang Li
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Yuan
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Shapingba District, 109 Baoyu Road, Chongqing, 400036, China
| | - Tongxin Li
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Ming Luo
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wang
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China. .,Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China. .,Division of Infectious Diseases, Chongqing Public Health Medical Center, Shapingba District, 109 Baoyu Road, Chongqing, 400036, China.
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11
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Molecular Determinants of Ethionamide Resistance in Clinical Isolates of Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 11:antibiotics11020133. [PMID: 35203736 PMCID: PMC8868424 DOI: 10.3390/antibiotics11020133] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Ethionamide and prothionamide are now included in group C of the WHO recommended drugs for the treatment of tuberculosis resistant to rifampicin and multidrug-resistant tuberculosis. The clinical relevance of ethionamide and prothionamide has increased with the wide spread of resistant tuberculosis. Methods: We retrospectively analyzed 349 clinical isolates obtained between 2016 and 2020. The susceptibility to ethionamide was tested using both the BactecTM MGITTM 960 system and the SensititreTM MYCOTB plate. Results: The MIC of ethionamide increases with the total resistance of the isolates in a row from susceptible to XDR strains. A significant part of the isolates have a MIC below the breakpoint: 25%, 36%, and 50% for XDR, pre-XDR, and MDR strains. Sensitivity and specificity of detection of mutations were 96% and 86% using MGIT resistance as a reference. Conclusions: Phenotypic methods for testing ethionamide are imperfectly correlated, and the isolates with MIC of 5 mg/L have the intermediate resistance. A significant proportion of resistant TB cases are susceptible and eligible for ethionamide treatment. Resistance could be explained using only analysis of loci ethA, PfabG1, and inhA for most isolates in the Moscow region. The promoter mutation PfabG1 c(-15)t predicts resistance to ethionamide with high specificity but low sensitivity.
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12
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Correlating genetic mutations with isoniazid phenotypic levels of resistance in Mycobacterium tuberculosis isolates from patients with drug-resistant tuberculosis in a high burden setting. Eur J Clin Microbiol Infect Dis 2021; 40:2551-2561. [PMID: 34297229 DOI: 10.1007/s10096-021-04316-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
We analysed mutations in katG, inhA and rpoB genes, and isoniazid phenotypic resistance levels in Mycobacterium tuberculosis isolates from drug-resistant TB patients from São Paulo state, Brazil. Isolates resistant to the critical concentration of isoniazid in MGIT (0.1 µg/mL) were screened for mutations in katG 315 codon, inhA promoter region and rpoB RRDR by MTBDRplus assay and subjected to determination of isoniazid resistance levels by MGIT 960. Discordances were resolved by Sanger sequencing. Among the 203 isolates studied, 109 (54%) were isoniazid-monoresistant, 47 (23%) MDR, 29 (14%) polydrug-resistant, 12 (6%) pre-XDR and 6 (3%) XDR. MTBDRplus detected isoniazid mutations in 75% (153/203) of the isolates. Sequencing of the entire katG and inhA genes revealed mutations in 18/50 wild-type isolates by MTBDRplus (10 with novel mutations), resulting in a total of 32/203 (16%) isolates with no mutations detected. 81/83 (98%) isolates with katG 315 mutations alone had intermediate resistance. Of the 66 isolates with inhA C-15T mutation alone, 51 (77%) showed low-level, 14 (21%) intermediate and 1 (2%) high-level resistance. 5/6 (83%) isolates with mutations in both katG and inhA had high-level resistance. Inferred mutations corresponded to 22% (16/73) of all mutations found in rpoB. Mutations detected in katG regions other than codon 315 in this study might be potential new isoniazid resistance markers and could explain phenotypic resistance in some isolates without katG and inhA classic mutations. In our setting, 16% of isoniazid-resistant isolates, some with high-level resistance, presented no mutations either in katG or inhA.
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13
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Hegde P, Boshoff HIM, Rusman Y, Aragaw WW, Salomon CE, Dick T, Aldrich CC. Reinvestigation of the structure-activity relationships of isoniazid. Tuberculosis (Edinb) 2021; 129:102100. [PMID: 34116482 PMCID: PMC8324568 DOI: 10.1016/j.tube.2021.102100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/24/2021] [Accepted: 05/30/2021] [Indexed: 11/19/2022]
Abstract
Isoniazid (INH) remains a cornerstone for treatment of drug susceptible tuberculosis (TB), yet the quantitative structure-activity relationships for INH are not well documented in the literature. In this paper, we have evaluated a systematic series of INH analogs against contemporary Mycobacterium tuberculosis strains from different lineages and a few non-tuberculous mycobacteria (NTM). Deletion of the pyridyl nitrogen atom, isomerization of the pyridine nitrogen to other positions, replacement of the pyridine ring with isosteric heterocycles, and modification of the hydrazide moiety of INH abolishes antitubercular activity. Similarly, substitution of the pyridine ring at the 3-position is not tolerated while substitution at the 2-position is permitted with 2-methyl-INH 9 displaying antimycobacterial activity comparable to INH. To assess the specific activity of this series of INH analogs against mycobacteria, we assayed them against a panel of gram-positive and gram-negative bacteria, as well as a few fungi. As expected INH and its analogs display a narrow spectrum of activity and are inactive against all non-mycobacterial strains evaluated, except for 4, which has modest inhibitory activity against Cryptococcus neoformans. Our findings provide an updated analysis of the structure-activity relationship of INH that we hope will serve as useful resource for the community.
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Affiliation(s)
- Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Yudi Rusman
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Christine E Salomon
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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Zhou W, Yang B, Zou Y, Rahman K, Cao X, Lei Y, Lai R, Fu ZF, Chen X, Cao G. Screening of Compounds for Anti-tuberculosis Activity, and in vitro and in vivo Evaluation of Potential Candidates. Front Microbiol 2021; 12:658637. [PMID: 34276592 PMCID: PMC8278749 DOI: 10.3389/fmicb.2021.658637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is a debilitating infectious disease responsible for more than one million deaths per year. The emergence of drug-resistant TB poses an urgent need for the development of new anti-TB drugs. In this study, we screened a library of over 4,000 small molecules and found that orbifloxacin and the peptide AK15 possess significant bactericidal activity against Mycobacterium tuberculosis (Mtb) in vitro. Orbifloxacin also showed an effective ability on the clearance of intracellular Mtb and protect mice from a strong inflammatory response but not AK15. Moreover, we identified 17 nucleotide mutations responsible for orbifloxacin resistance by whole-genome sequencing. A critical point mutation (D94G) of the DNA gyrase (gyrA) gene was found to be the key role of resistance to orbifloxacin. The computational docking revealed that GyrA D94G point mutation can disrupt the orbifloxacin–protein gyrase interactions mediated by magnesium ion bridge. Overall, this study indicated the potential ability of orbifloxacin as an anti-tuberculosis drug, which can be used either alone or in combination with first-line antibiotics to achieve more effective therapy on TB.
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Affiliation(s)
- Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Khaista Rahman
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingying Lei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Bio-Medical Center, Huazhong Agricultural University, Wuhan, China.,Cooperative Innovation Center for Sustainable Pig Production (CICSPPS), Huazhong Agricultural University, Wuhan, China
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15
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De Maio F, Cingolani A, Bianco DM, Salustri A, Palucci I, Sanguinetti M, Delogu G, Sali M. First description of the katG gene deletion in a Mycobacterium tuberculosis clinical isolate and its impact on the mycobacterial fitness. Int J Med Microbiol 2021; 311:151506. [PMID: 33906074 DOI: 10.1016/j.ijmm.2021.151506] [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: 12/19/2020] [Revised: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
Isoniazid (INH) is the cornerstone of the anti-tuberculosis regimens and emergence of Mycobacterium tuberculosis (Mtb) resistant strains is a major threat to our ability to control tuberculosis (TB) at global level. Mutations in the gene coding the catalase KatG confer resistance to high level of INH. In this paper, we describe for the first time a complete deletion of the genomic region containing the katG gene in an Mtb clinical strain isolated in Italy in a patient with HIV infection that previously completed INH preventive therapy. We genotypically characterized the Mtb strain and showed that katG deletion confers high-level resistance to INH (MIC > 25.6 μg/mL). The katG deletion did not impact significantly on Mtb fitness as we did not detect enhanced susceptibility to H2O2 compared to the wild type Mtb strains nor impaired growth in in vitro infection models. These findings highlight the ability of Mtb to acquire resistance to INH while maintaining fitness and pathogenic potential.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonella Cingolani
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy; Dipartimento di Sicurezza e Bioetica, Sez. Malattie Infettive, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Delia Mercedes Bianco
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro Salustri
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ivana Palucci
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Delogu
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy; Mater Olbia Hospital, Olbia, Italy.
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
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16
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Detection of genomic mutations in katG and rpoB genes among multidrug-resistant Mycobacterium tuberculosis isolates from Tehran, Iran. New Microbes New Infect 2021; 41:100879. [PMID: 34012550 PMCID: PMC8113720 DOI: 10.1016/j.nmni.2021.100879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022] Open
Abstract
Multidrug-resistant (MDR) Mycobacterium tuberculosis strains, defined as resistant to at least isoniazid and rifampin, have emerged as a major worldwide health threat. Spontaneous point mutations in various genes of M. tuberculosis cause resistance to isoniazid, with the most frequent gene target being katG; and resistance to rifampin is usually due to mutation in the rpoB gene. The current study was aimed to detect the point mutations in the katG and rpoB regions related to isoniazid and rifampin resistance. A total of 203 respiratory specimens were collected from patients suspected of having tuberculosis respiratory infections referred to hospitals of Tehran, Iran, during 2018-2019. The isolation and identification of M. tuberculosis isolates were performed according to the WHO protocol. Drug susceptibility testing was carried out by proportional method. PCR analysis and sequencing were used to detect mutations in the selected katG and rpoB regions. Forty-four M. tuberculosis strains were isolated, of which 12 (27.3%) and 10 (22.7%) were resistant to isoniazid and rifampin, respectively. Ten isolates were resistant to both isoniazid and rifampin and were considered as MDR isolates. Of the ten MDR isolates, six (60%) carried mutations in both rpoB and katG. The most common mutations among isoniazid- and rifampin-resistant isolates were in codon 315 of the katG gene (70%) and codon 441 of the rpoB gene (50%), respectively. The results of this study indicated that MDR-TB continues to be a serious public health problem in Iran.
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17
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Cao Y, Parmar H, Gaur RL, Lieu D, Raghunath S, Via N, Battaglia S, Cirillo DM, Denkinger C, Georghiou S, Kwiatkowski R, Persing D, Alland D, Chakravorty S. Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum. J Clin Microbiol 2021; 59:e02314-20. [PMID: 33298611 PMCID: PMC8106700 DOI: 10.1128/jcm.02314-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
We describe the design, development, analytical performance, and a limited clinical evaluation of the 10-color Xpert MTB/XDR assay (CE-IVD only, not for sale in the United States). This assay is intended as a reflex test to detect resistance to isoniazid (INH), fluoroquinolones (FLQ), ethionamide (ETH), and second-line injectable drugs (SLIDs) in unprocessed sputum samples and concentrated sputum sediments which are positive for Mycobacterium tuberculosis The Xpert MTB/XDR assay simultaneously amplifies eight genes and promoter regions in M. tuberculosis and analyzes melting temperatures (Tm s) using sloppy molecular beacon (SMB) probes to identify mutations associated with INH, FLQ, ETH, and SLID resistance. Results can be obtained in under 90 min using 10-color GeneXpert modules. The assay can differentiate low- versus high-level resistance to INH and FLQ as well as cross-resistance versus individual resistance to SLIDs by identifying mutation-specific Tm s or Tm patterns generated by the SMB probes. The assay has a limit of detection comparable to that of the Xpert MTB/RIF assay and successfully detected 16 clinically significant mutations in a challenge set of clinical isolate DNA. In a clinical study performed at two sites with 100 sputum and 214 clinical isolates, the assay showed a sensitivity of 94% to 100% and a specificity of 100% for all drugs except for ETH compared to that of sequencing. The sensitivity and specificity were in the same ranges as those of phenotypic drug-susceptibility testing. Used in combination with a primary tuberculosis diagnostic test, this assay should expand the capacity for detection of drug-resistant tuberculosis near the point of care.
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Affiliation(s)
- Yuan Cao
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Heta Parmar
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | | | | | | | - Nova Via
- Cepheid Inc., Sunnyvale, California, USA
| | | | | | | | | | | | | | - David Alland
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Soumitesh Chakravorty
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- Cepheid Inc., Sunnyvale, California, USA
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18
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Alffenaar JWC, Gumbo T, Dooley KE, Peloquin CA, Mcilleron H, Zagorski A, Cirillo DM, Heysell SK, Silva DR, Migliori GB. Integrating Pharmacokinetics and Pharmacodynamics in Operational Research to End Tuberculosis. Clin Infect Dis 2021; 70:1774-1780. [PMID: 31560376 PMCID: PMC7146003 DOI: 10.1093/cid/ciz942] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) elimination requires innovative approaches. The new Global Tuberculosis Network (GTN) aims to conduct research on key unmet therapeutic and diagnostic needs in the field of TB elimination using multidisciplinary, multisectorial approaches. The TB Pharmacology section within the new GTN aims to detect and study the current knowledge gaps, test potential solutions using human pharmacokinetics informed through preclinical infection systems, and return those findings to the bedside. Moreover, this approach would allow prospective identification and validation of optimal shorter therapeutic durations with new regimens. Optimized treatment using available and repurposed drugs may have an increased impact when prioritizing a person-centered approach and acknowledge the importance of age, gender, comorbidities, and both social and programmatic environments. In this viewpoint article, we present an in-depth discussion on how TB pharmacology and the related strategies will contribute to TB elimination.
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Affiliation(s)
- Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead Hospital, Sydney, Australia
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, USA
| | - Kelly E Dooley
- Division of Clinical Pharmacology, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Helen Mcilleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Andre Zagorski
- Management Sciences for Health, Arlington, Virginia, USA
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Scott K Heysell
- University of Virginia, Division of Infectious Diseases and International Health, Charlottesville, Virginia, USA
| | - Denise Rossato Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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19
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Dookie N, Padayatchi N, Lessells RJ, Naicker CL, Chotoo S, Naidoo K. Individualized Treatment of Multidrug-resistant Tuberculosis Using Whole-Genome Sequencing and Expanded Drug-Susceptibility Testing. Clin Infect Dis 2020; 71:2981-2985. [PMID: 32384148 PMCID: PMC7778351 DOI: 10.1093/cid/ciaa526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/04/2020] [Indexed: 01/28/2023] Open
Abstract
A case of multidrug-resistant tuberculosis is presented. It highlights the role of whole-genome sequencing, expanded phenotypic drug susceptibility testing, and enhanced case management, offering a more complete understanding of drug susceptibility to Mycobacterium tuberculosis. This approach guides an effective individualized treatment strategy that results in rapid sustained culture conversion.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Cherise L Naicker
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal Durban, South Africa
| | - Sunitha Chotoo
- King Dinu-Zulu Hospital Complex, South African National Department of Health, eThekwini Health District, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal Durban, South Africa
- South African Medical Research Council-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal Durban, South Africa
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20
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Lempens P, Decroo T, Aung KJM, Hossain MA, Rigouts L, Meehan CJ, Van Deun A, de Jong BC. Initial resistance to companion drugs should not be considered an exclusion criterion for the shorter multidrug-resistant tuberculosis treatment regimen. Int J Infect Dis 2020; 100:357-365. [PMID: 32829049 PMCID: PMC7670168 DOI: 10.1016/j.ijid.2020.08.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES We investigated whether companion drug resistance was associated with adverse outcomes of the shorter multidrug-resistant tuberculosis (MDR-TB) treatment regimen in Bangladesh after adjustment for fluoroquinolone resistance. METHODS MDR-TB/rifampicin-resistant tuberculosis patients registered for treatment with a standardized gatifloxacin-based shorter MDR-TB treatment regimen were selected for the study. Drug resistance was determined by the proportion method, gatifloxacin and isoniazid minimum inhibitory concentration testing for selected isolates, and whole-genome sequencing. RESULTS Low-level fluoroquinolone resistance and high-level fluoroquinolone resistance were the most important predictors of adverse outcomes, with pyrazinamide resistance having a significant yet lower impact. In patients with fluoroquinolone-/second-line-injectable-susceptible tuberculosis, non-eligibility for the shorter MDR-TB treatment regimen (initial resistance to pyrazinamide, ethionamide, or ethambutol) was not associated with adverse outcome (adjusted odds ratio 1.01; 95% confidence interval 0.4-2.8). Kanamycin resistance was uncommon (1.3%). Increasing levels of resistance to isoniazid predicted treatment failure, also in a subgroup of patients with high-level fluoroquinolone-resistant tuberculosis. CONCLUSIONS Our results suggest that resistance to companion drugs in the shorter MDR-TB treatment regimen, except kanamycin resistance, is of no clinical importance as long as fluoroquinolone susceptibility is preserved. Hence, contrary to current WHO guidelines, exclusions to the standard regimen are justified only in the case of fluoroquinolone resistance. and possibly kanamycin resistance.
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Affiliation(s)
- Pauline Lempens
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Tom Decroo
- Unit of HIV/AIDS and Infectious Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Conor J Meehan
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Bouke C de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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21
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Tahseen S, Khanzada FM, Rizvi AH, Qadir M, Ghazal A, Baloch AQ, Mustafa T. Isoniazid resistance profile and associated levofloxacin and pyrazinamide resistance in rifampicin resistant and sensitive isolates/from pulmonary and extrapulmonary tuberculosis patients in Pakistan: A laboratory based surveillance study 2015-19. PLoS One 2020; 15:e0239328. [PMID: 32966321 PMCID: PMC7511002 DOI: 10.1371/journal.pone.0239328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background Pakistan is among top five high burden countries for tuberculosis and drug resistant TB. Among rifampicin sensitive new pulmonary TB (PTB), prevalence of isoniazid resistance is 8.3% (95%CI: 7.0–10.7) and resistance to fluoroquinolone is higher (11·1%, 95%CI: 7·8–14·3) than isoniazid resistance. Method Five year retrospective data (2015–2019) of drug susceptibility testing (DST) for Mycobacterium tuberculosis isolates, performed using recommended phenotypic (pDST) and/or genotypic (gDST) methods was analyzed stratified by rifampicin results for isoniazid resistance profiles and associated levofloxacin and pyrazinamide resistance. Findings DST data was analyzed from 11045 TB patients. Isolates were tested using pDST (87%), gDST (92%) and both methods (79.5%). For both rifampicin and isoniazid, a significant difference (P < .001) was noted between resistance detected by pDST and gDST. Among isolates, tested by both methods (8787), 49% were resistant to rifampicin and 51.7% to isoniazid with discordance in resistant results of 15.8% for each, with 13.2% (570) of rifampicin resistance reported sensitive by pDST and 14.2% (660) of isoniazid resistance missed by gDST. Estimated isoniazid resistance among rifampicin sensitive new PTB, extrapulmonary TB and previously treated PTB was 9.8% (95%CI: 8.7–11.1), 6.8% (95%CI: 5.4–8.5) and 14.6% (95%CI: 11.8–17.9) respectively. Significant differences were reported between the genotypic profile of isoniazid resistance associated with rifampicin-resistant and sensitive isolates including detectable mutations (87% vs 71.6%), frequency of inhA (7.6% and 30.2%) and katG mutations (76.1% vs 41.2%) respectively. Among rifampicin resistant and sensitive isolates, a significantly higher level of resistance to levofloxacin and pyrazinamide was seen associated with isoniazid resistance. Conclusion There are risks and many challenges in implementing WHO recommended treatment for isoniazid resistant tuberculosis. The laboratory based surveillance can complement random surveys in country specific planning for TB diagnostics and appropriate treatment regimens.
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Affiliation(s)
- Sabira Tahseen
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- * E-mail:
| | | | | | - Mahmood Qadir
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Aisha Ghazal
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Aurangzaib Quadir Baloch
- National TB Control Program, Ministry of National Health Services Regulation and Coordination, Islamabad, Pakistan
| | - Tehmina Mustafa
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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22
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Kayomo MK, Mbula VN, Aloni M, André E, Rigouts L, Boutachkourt F, de Jong BC, Nkiere NM, Dean AS. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep 2020; 10:10786. [PMID: 32612134 PMCID: PMC7329841 DOI: 10.1038/s41598-020-67479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The surveillance of drug resistance among tuberculosis (TB) patients is central to preventing the spread of antimicrobial resistance. The Democratic Republic of the Congo (DR Congo) is classified by the World Health Organization (WHO) as a country with a high burden of TB and multidrug-resistant TB (MDR-TB), but there are no nationally representative data on drug resistance. In 2016-2017, a national survey of TB patients was conducted in 108 microscopy centres across all 11 provinces of the country using innovative molecular approaches. Sputum samples were collected from 1,545 new and 163 previously treated patients. These were tested by the Xpert MTB/RIF assay, followed by targeted next-generation sequencing performed directly on sputum. The prevalence of rifampicin resistance was low, at 1.8% (95% CI: 1.0-3.2) among new and 17.3% (95% CI: 11.9-24.4) among previously treated patients. Resistance to pyrazinamide, fluoroquinolones and second-line injectables was also low. The prevalence of resistance to isoniazid among rifampicin-susceptible patients was higher, at 6.6% (95% CI: 4.4-9.8) among new and 8.7% (95% : 3.2-21.2) among previously treated patients. Diagnosing and treating isoniazid-resistant patients remains a challenge, given that many will be missed by the current national diagnostic algorithm that is driven by detecting rifampicin resistance by Xpert MTB/RIF. This is the first nationwide survey incorporating targeted sequencing directly on sputum. It serves as a proof-of-concept for other settings that do yet have rapid specimen transport networks or capacity to conduct culture.
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MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Child, Preschool
- Cross-Sectional Studies
- Democratic Republic of the Congo/epidemiology
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Middle Aged
- Mycobacterium tuberculosis/genetics
- Prevalence
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/genetics
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Affiliation(s)
- Michel Kaswa Kayomo
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Vital Nkake Mbula
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
| | - Muriel Aloni
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Emmanuel André
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Antwerp, Belgium
- Antwerp University, Antwerp, Belgium
| | - Fairouz Boutachkourt
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimental Et Clinique, UC Louvain, Brussels, Belgium
| | | | - Nicolas M Nkiere
- World Health Organization, Kinshasa, Democratic Republic of the Congo
| | - Anna S Dean
- Global TB Programme, World Health Organization, Geneva, Switzerland.
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23
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Dooley KE, Miyahara S, von Groote-Bidlingmaier F, Sun X, Hafner R, Rosenkranz SL, Ignatius EH, Nuermberger EL, Moran L, Donahue K, Swindells S, Vanker N. Early Bactericidal Activity of Different Isoniazid Doses for Drug-Resistant Tuberculosis (INHindsight): A Randomized, Open-Label Clinical Trial. Am J Respir Crit Care Med 2020; 201:1416-1424. [PMID: 31945300 PMCID: PMC7258626 DOI: 10.1164/rccm.201910-1960oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/15/2020] [Indexed: 11/16/2022] Open
Abstract
Rationale: High-dose isoniazid is recommended in short-course regimens for multidrug-resistant tuberculosis (TB). The optimal dose of isoniazid and its individual contribution to efficacy against TB strains with inhA or katG mutations are unknown.Objectives: To define the optimal dose of isoniazid for patients with isoniazid-resistant TB mediated by inhA mutations.Methods: AIDS Clinical Trials Group A5312 is a phase 2A, open-label trial in which individuals with smear-positive pulmonary TB with isoniazid resistance mediated by an inhA mutation were randomized to receive isoniazid 5, 10, or 15 mg/kg daily for 7 days (inhA group), and control subjects with drug-sensitive TB received the standard dose (5 mg/kg/d). Overnight sputum cultures were collected daily. The 7-day early bactericidal activity (EBA) of isoniazid was estimated as the average daily change in log10 cfu on solid media (EBAcfu0-7) or as time to positivity (TTP) in liquid media in hours (EBATTP0-7) using nonlinear mixed-effects models.Measurements and Main Results: Fifty-nine participants (88% with cavitary disease, 20% HIV-positive, 16 with isoniazid-sensitive TB, and 43 with isoniazid-monoresistant or multidrug-resistant TB) were enrolled at one site in South Africa. The mean EBAcfu0-7 at doses of 5, 10, and 15 mg/kg in the inhA group was 0.07, 0.17, and 0.22 log10 cfu/ml/d, respectively, and 0.16 log10 cfu/ml/d in control subjects. EBATTP0-7 patterns were similar. There were no drug-related grade ≥3 adverse events.Conclusions: Isoniazid 10-15 mg/kg daily had activity against TB strains with inhA mutations similar to that of 5 mg/kg against drug-sensitive strains. The activity of high-dose isoniazid against strains with katG mutations will be explored next.Clinical trial registered with www.clinicaltrials.gov (NCT01936831).
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Affiliation(s)
- Kelly E. Dooley
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sachiko Miyahara
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - Xin Sun
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Richard Hafner
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Susan L. Rosenkranz
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Frontier Science and Technology Research Foundation, Amherst, New York
| | - Elisa H. Ignatius
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eric L. Nuermberger
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura Moran
- Social & Scientific Systems, Inc., Silver Spring, Maryland; and
| | - Kathleen Donahue
- Frontier Science and Technology Research Foundation, Amherst, New York
| | - Susan Swindells
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Naadira Vanker
- TASK Applied Science and Stellenbosch University, Cape Town, South Africa
| | - on behalf of the A5312 Study Team
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- TASK Applied Science and Stellenbosch University, Cape Town, South Africa
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
- Frontier Science and Technology Research Foundation, Amherst, New York
- Social & Scientific Systems, Inc., Silver Spring, Maryland; and
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
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24
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Wasserman S, Furin J. Clarity with INHindsight: High-Dose Isoniazid for Drug-Resistant Tuberculosis with inhA Mutations. Am J Respir Crit Care Med 2020; 201:1331-1333. [PMID: 32078783 PMCID: PMC7258653 DOI: 10.1164/rccm.202002-0264ed] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Sean Wasserman
- Department of Medicine.,Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownCape Town, South Africaand
| | - Jennifer Furin
- Department of Global Health and Social MedicineHarvard Medical SchoolBoston, Massachusetts
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25
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Solo ES, Nakajima C, Kaile T, Bwalya P, Mbulo G, Fukushima Y, Chila S, Kapata N, Shah Y, Suzuki Y. Mutations in rpoB and katG genes and the inhA operon in multidrug-resistant Mycobacterium tuberculosis isolates from Zambia. J Glob Antimicrob Resist 2020; 22:302-307. [PMID: 32169686 DOI: 10.1016/j.jgar.2020.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES It is established that resistance to rifampicin (RIF) in 90% of RIF-resistant Mycobacterium tuberculosis isolates is attributable to point mutations in the rpoB gene, whilst 50-95% of M. tuberculosis resistance to isoniazid (INH) is caused by mutations in the katG gene. However, the patterns and frequencies of mutations vary by geographical region. In Zambia, the genetic mechanisms of resistance of M. tuberculosis to RIF and INH were unreported before this study. METHODS Using gene sequencing, the rpoB, katG and inhA genes of 99 multidrug-resistant M. tuberculosis (MDR-TB) and 49 pan-susceptible M. tuberculosis isolates stored at a tuberculosis reference laboratory from 2013 to 2016 were analysed and were compared with published profiles from other African countries. RESULTS Of the 99 MDR-TB isolates, 95 (96.0%) carried mutations in both rpoB and katG. No mutations were detected among the pan-susceptible isolates. The most common mutations among RIF- and INH-resistant isolates were in codon 531 of the rpoB gene (55.6%; 55/99) and codon 315 of the katG gene (94.9%; 94/99), respectively. Distinctly, katG mutations were predominantly high among Zambian isolates (96.0%) compared with other countries in the region. CONCLUSION Resistance-associated mutations to RIF and INH circulating in Zambia are similar to those reported globally, therefore these data validate the applicability of molecular diagnostic tools in Zambia. However, katG mutations were predominantly high among M. tuberculosis isolates in this study compared with other regional countries and might distinguish cross-boundary transmission of MDR-TB from other African nations.
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Affiliation(s)
- Eddie S Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Trevor Kaile
- University of Zambia, School of Medicine, Lusaka, Zambia
| | - Precious Bwalya
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Grace Mbulo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | | | | | - Yogendra Shah
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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26
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Charoenpak R, Santimaleeworagun W, Suwanpimolkul G, Manosuthi W, Kongsanan P, Petsong S, Puttilerpong C. Association Between the Phenotype and Genotype of Isoniazid Resistance Among Mycobacterium tuberculosis Isolates in Thailand. Infect Drug Resist 2020; 13:627-634. [PMID: 32158238 PMCID: PMC7047971 DOI: 10.2147/idr.s242261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/31/2020] [Indexed: 01/21/2023] Open
Abstract
Purpose The emergence of isoniazid-resistant tuberculosis (HR-TB) is a global public health problem, causing treatment failure and high mortality rates. This study aimed to determine the minimal inhibitory concentration (MIC) of isoniazid and detect the gene mutation in HR-TB and any association between the level of isoniazid resistance and gene mutation. Methods We collected 74 clinical HR-TB isolates from two tertiary-care centers in Thailand. MICs were established using broth macrodilution. A line probe assay (LPA) was used to detect gene mutations that confer resistance to isoniazid, rifampicin, aminoglycosides, and fluoroquinolones. Results Sixty-one (82.4%) isolates were monoresistant to isoniazid and 44 (72.1%) were highly resistant to isoniazid. From the clinical isolates, the range of isoniazid MICs was 0.4–16 μg/mL. The katG S315T gene mutation was the prominent mutation in both isoniazid-monoresistant TB (70.5%) and multidrug-resistant TB (72.7%) isolates. The positive predictive value (PPV) of katG was 100% in detecting high levels of isoniazid resistance. The PPV of the inhA mutation was 93.8% in detecting low levels of isoniazid resistance. Five isolates (6.8%) exhibited low-level phenotypic resistance, whereas an LPA failed to detect an isoniazid gene mutation. Our study found one HR-TB isolate with a gyrA fluoroquinolone-resistant gene mutation. Conclusion Most HR-TB isolates had high isoniazid-resistance levels associated with the katG gene mutation. High-dose isoniazid should be used with caution in patients with HR-TB. Early detection of drug resistance by genotypic assay can help determine an appropriate regimen.
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Affiliation(s)
| | | | - Gompol Suwanpimolkul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Tuberculosis Research Unit, Chulalongkorn University, Bangkok, Thailand.,Emerging Infectious Diseases Clinical Center, Thai Red Cross, Bangkok, Thailand
| | - Weerawat Manosuthi
- Bamrasnaradura Infectious Diseases Institute, Ministry of Public Health, Nonthaburi, Thailand
| | - Paweena Kongsanan
- Bamrasnaradura Infectious Diseases Institute, Ministry of Public Health, Nonthaburi, Thailand
| | - Suthidee Petsong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chankit Puttilerpong
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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Kardan-Yamchi J, Kazemian H, Battaglia S, Abtahi H, Rahimi Foroushani A, Hamzelou G, Cirillo DM, Ghodousi A, Feizabadi MM. Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran. J Clin Med 2020; 9:jcm9020465. [PMID: 32046149 PMCID: PMC7073636 DOI: 10.3390/jcm9020465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.
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Affiliation(s)
- Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Hamidreza Abtahi
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Gholamreza Hamzelou
- Tehran Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
- Correspondence: (A.G.); (M.M.F.)
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Correspondence: (A.G.); (M.M.F.)
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Prevalence and genetic profiles of isoniazid resistance in tuberculosis patients: A multicountry analysis of cross-sectional data. PLoS Med 2020; 17:e1003008. [PMID: 31961877 PMCID: PMC6974034 DOI: 10.1371/journal.pmed.1003008] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The surveillance of drug resistance among tuberculosis (TB) patients is central to combatting the global TB epidemic and preventing the spread of antimicrobial resistance. Isoniazid and rifampicin are two of the most powerful first-line anti-TB medicines, and resistance to either of them increases the risk of treatment failure, relapse, or acquisition of resistance to other drugs. The global prevalence of rifampicin resistance is well documented, occurring in 3.4% (95% CI 2.5%-4.4%) of new TB patients and 18% (95% CI 7.6%-31%) of previously treated TB patients in 2018, whereas the prevalence of isoniazid resistance at global and regional levels is less understood. In 2018, the World Health Organization (WHO) recommended a modified 6-month treatment regimen for people with isoniazid-resistant, rifampicin-susceptible TB (Hr-TB), which includes rifampicin, pyrazinamide, ethambutol, and levofloxacin. We estimated the global prevalence of Hr-TB among TB patients and investigated associated phenotypic and genotypic drug resistance patterns. METHODS AND FINDINGS Aggregated drug resistance data reported to WHO from either routine continuous surveillance or nationally representative periodic surveys of TB patients for the period 2003-2017 were reviewed. Isoniazid data were available from 156 countries or territories for 211,753 patients. Among these, the global prevalence of Hr-TB was 7.4% (95% CI 6.5%-8.4%) among new TB patients and 11.4% (95% CI 9.4%-13.4%) among previously treated TB patients. Additional data on pyrazinamide and levofloxacin resistance were available from 6 countries (Azerbaijan, Bangladesh, Belarus, Pakistan, the Philippines, and South Africa). There were no cases of resistance to both pyrazinamide and levofloxacin among Hr-TB patients, except for the Philippines (1.8%, 95% CI 0.2-6.4) and Belarus (5.3%, 95% CI 0.1-26.0). Sequencing data for all genomic regions involved in isoniazid resistance were available for 4,563 patients. Among the 1,174 isolates that were resistant by either phenotypic testing or sequencing, 78.6% (95% CI 76.1%-80.9%) had resistance-conferring mutations in the katG gene and 14.6% (95% CI 12.7%-16.8%) in both katG and the inhA promoter region. For 6.8% (95% CI 5.4%-8.4%) of patients, mutations occurred in the inhA promoter alone, for whom an increased dose of isoniazid may be considered. The main limitations of this study are that most analyses were performed at the national rather than individual patient level and that the quality of laboratory testing may vary between countries. CONCLUSIONS In this study, the prevalence of Hr-TB among TB patients was higher than the prevalence of rifampicin resistance globally. Many patients with Hr-TB would be missed by current diagnostic algorithms driven by rifampicin testing, highlighting the need for new rapid molecular technologies to ensure access to appropriate treatment and care. The low prevalence of resistance to pyrazinamide and fluoroquinolones among patients with Hr-TB provides further justification for the recommended modified treatment regimen.
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Spitaleri A, Ghodousi A, Miotto P, Cirillo DM. Whole genome sequencing in Mycobacterium tuberculosis. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S197. [PMID: 31656776 DOI: 10.21037/atm.2019.07.28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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30
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Mokrousov I. Current topics of molecular mycobacteriology. INFECTION GENETICS AND EVOLUTION 2019; 73:132-138. [PMID: 31048076 DOI: 10.1016/j.meegid.2019.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/20/2022]
Abstract
The 2nd St. Petersburg Symposium on Tuberculosis and Mycobacteria: Molecular Approach, was held in St. Petersburg, Russia on 5-6 December 2018. A special issue of Infection, Genetics and Evolution will publish articles based on the selected presentations. In this paper, I will discuss some of the hot topics of molecular mycobacteriology highlighted at this meeting that I had the pleasure to organize and honor to chair. The symposium addressed interrelated fundamental and applied issues of modern mycobacteriology such as molecular evolution and phylogenomics, host-microbe interactions and pathogenesis, coevolution of M. tuberculosis with humans, new genomic and postgenomic technologies. Molecular methods for TB diagnostics and drug resistance detection are supported by WHO and whole genome/next generation sequencing presents a comprehensive approach. At the same time, cost and implementation of new methods for direct analysis of clinical samples and/or in low-resource settings remain a great challenge. A due attention was also given to the medically important nontuberculous mycobacteria. Assessment of spectrum of the circulating mycobacterial species in the Russian Federation and the countries of the European Union was presented and the underlying reasons of the observed diversity were discussed. To conclude, the symposium became a multidisciplinary event that was useful to promote networking and exchange of knowledge and experience. The next (third) symposium was planned to be organized in 2021.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia.
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