1
|
Song Y, Zhao B, Wang S, Zheng Y, Zhou Y, Ou X, Xia H, Zhao Y. Proficiency of phenotypic drug susceptibility testing for Mycobacterium tuberculosis in China, 2008-2021. PLoS One 2024; 19:e0304265. [PMID: 38809914 PMCID: PMC11135779 DOI: 10.1371/journal.pone.0304265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
To analyze the results of proficiency testing for anti-tuberculosis drug susceptibility testing (DST) in China. Number of laboratory participating the proficiency testing performed DST, and the sensitivity, specificity, reproducibility, and accordance rate were calculated from data of 13 rounds proficiency testing results for DST from 2008 to 2021. A total of 30 and 20 strains of Mycobacterium tuberculosis with known susceptibility results were sent to each laboratory in 2008 to 2019, 2020 and 2021, respectively. The number of participating laboratories ranged from 30 in 2009 to 546 in 2021. L-J DST was the predominant method. The specificity presented relatively higher than sensitivity. Improvement of specificity were observed for all drugs through the years, while sensitivity did not show improvement for amikacin and capreomycin. Accordance rate of pyrazinamide and kanamycin and reproducibility of capreomycin and pyrazinamide were not significantly improved through the years. Most of the participating laboratories significantly improved the quality of their DST through the consecutive rounds of proficiency testing except for second-line injectable drugs and pyrazinamide. The results highlight the importance of developing novel and/or improving existing methods for phenotypic DST for certain drugs.
Collapse
Affiliation(s)
- Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, the People’s Republic of China
| |
Collapse
|
2
|
Hazra D, Lam C, Chawla K, Sintchenko V, Dhyani VS, Venkatesh BT. Impact of Whole-Genome Sequencing of Mycobacterium tuberculosis on Treatment Outcomes for MDR-TB/XDR-TB: A Systematic Review. Pharmaceutics 2023; 15:2782. [PMID: 38140122 PMCID: PMC10747601 DOI: 10.3390/pharmaceutics15122782] [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: 10/25/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence and persistence of drug-resistant tuberculosis is a major threat to global public health. Our objective was to assess the applicability of whole-genome sequencing (WGS) to detect genomic markers of drug resistance and explore their association with treatment outcomes for multidrug-resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB). METHODS Five electronic databases were searched for studies published in English from the year 2000 onward. Two reviewers independently conducted the article screening, relevant data extraction, and quality assessment. The data of the included studies were synthesized with a narrative method and are presented in a tabular format. RESULTS The database search identified 949 published articles and 8 studies were included. An unfavorable treatment outcome was reported for 26.6% (488/1834) of TB cases, which ranged from 9.7 to 51.3%. Death was reported in 10.5% (194/1834) of total cases. High-level fluoroquinolone resistance (due to gyrA 94AAC and 94GGC mutations) was correlated as the cause of unfavorable treatment outcomes and reported in three studies. Other drug resistance mutations, like kanamycin high-level resistance mutations (rrs 1401G), rpoB Ile491Phe, and ethA mutations, conferring prothionamide resistance were also reported. The secondary findings from this systematic review involved laboratory aspects of WGS, including correlations with phenotypic DST, cost, and turnaround time, or the impact of WGS results on public health actions, such as determining transmission events within outbreaks. CONCLUSIONS WGS has a significant capacity to provide accurate and comprehensive drug resistance data for MDR/XDR-TB, which can inform personalized drug therapy to optimize treatment outcomes.
Collapse
Affiliation(s)
- Druti Hazra
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Connie Lam
- Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia;
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Vijay Shree Dhyani
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | - Bhumika T. Venkatesh
- Public Health Evidence South Asia, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| |
Collapse
|
3
|
Rich ML, Khan U, Zeng C, LaHood A, Franke MF, Atwood S, Bastard M, Burhan E, Danielyan N, Dzhazibekova PM, Gadissa D, Ghafoor A, Hewison C, Islam MS, Kazmi E, Khan PY, Lecca L, Maama LB, Melikyan N, Naing YY, Philippe K, Saki NA, Seung KJ, Skrahina A, Tefera GB, Varaine F, Vilbrun SC, Võ L, Mitnick CD, Huerga H. Outcomes of WHO-conforming, longer, all-oral multidrug-resistant TB regimens and analysis implications. Int J Tuberc Lung Dis 2023; 27:451-457. [PMID: 37231598 PMCID: PMC10237267 DOI: 10.5588/ijtld.22.0613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND: Evidence of the effectiveness of the WHO-recommended design of longer individualized regimens for multidrug- or rifampicin-resistant TB (MDR/RR-TB) is limited.OBJECTIVES: To report end-of-treatment outcomes for MDR/RR-TB patients from a 2015-2018 multi-country cohort that received a regimen consistent with current 2022 WHO updated recommendations and describe the complexities of comparing regimens.METHODS: We analyzed a subset of participants from the endTB Observational Study who initiated a longer MDR/RR-TB regimen that was consistent with subsequent 2022 WHO guidance on regimen design for longer treatments. We excluded individuals who received an injectable agent or who received fewer than four likely effective drugs.RESULTS: Of the 759 participants analyzed, 607 (80.0%, 95% CI 77.0-82.7) experienced successful end-of-treatment outcomes. The frequency of success was high across groups, whether stratified on number of Group A drugs or fluoroquinolone resistance, and ranged from 72.1% to 90.0%. Regimens were highly variable regarding composition and the duration of individual drugs.CONCLUSIONS: Longer, all-oral, individualized regimens that were consistent with 2022 WHO guidance on regimen design had high frequencies of treatment success. Heterogeneous regimen compositions and drug durations precluded meaningful comparisons. Future research should examine which combinations of drugs maximize safety/tolerability and effectiveness.
Collapse
Affiliation(s)
- M L Rich
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA
| | - U Khan
- Interactive Research & Development Global, Singapore, Singapore
| | - C Zeng
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - A LaHood
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - M F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - S Atwood
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA
| | | | - E Burhan
- Persahabatan General Hospital, Jakarta, Indonesia
| | - N Danielyan
- Médecins Sans Frontières (MSF), Tbilisi, Georgia
| | | | - D Gadissa
- Partners In Health (PIH), Addis Ababa, Ethiopia
| | - A Ghafoor
- National Tuberculosis Programme (NTP), Ministry of National Health, Islamabad, Pakistan
| | | | - M S Islam
- Interactive Research & Development, Dhaka, Bangladesh
| | - E Kazmi
- Directorate General Health Services, Centers for Disease Control and Prevention, Sindh, Pakistan
| | - P Y Khan
- Partners In Health, Boston, MA, USA, Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - L Lecca
- Socios En Salud Sucursal, Lima, Peru
| | - L B Maama
- PIH, Maseru, Lesotho, NTP, Maseru, Lesotho
| | - N Melikyan
- Epicentre, Paris, France, MSF, Yerevan, Armenia
| | | | | | - N A Saki
- World Health Organization, Country Office, Dhaka, Bangladesh
| | - K J Seung
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA
| | | | - G B Tefera
- Partners In Health (PIH), Addis Ababa, Ethiopia
| | | | - S C Vilbrun
- GHESKIO Institute of Infectious Diseases and Reproductive Health, NTP, Port-au-Prince, Haiti
| | - L Võ
- Friends for International TB Relief, Ho Chi Minh City, Vietnam
| | - C D Mitnick
- Division of Global Health Equity, Brigham and Women´s Hospital, Boston, MA, Partners In Health, Boston, MA, USA, Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
4
|
Sinkov VV, Kondratov IG, Ogarkov OB, Zhdanova SN, Sokolnikova NA, Khromova PA, Orlova EA, Rychkova LV, Kolesnikova LI. Online Service with Automated Interpretation of Sequencing Data and Prediction of Pyrazinamide Resistance in Mycobacterium tuberculosis. Bull Exp Biol Med 2023; 174:623-627. [PMID: 37040038 DOI: 10.1007/s10517-023-05758-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 04/12/2023]
Abstract
Pyrazinamide plays an important role in the treatment of tuberculosis. However, the microbiological test for pyrazinamide resistance is more complex and less reliable than testing of susceptibility to other anti-tuberculosis drugs due to the need to grow the pathogen at pH 5.5. Identification of mutations that cause resistance to anti-tuberculosis drugs can replace microbiological methods. Mutations in the pncA gene are responsible for the main mechanism of the resistance to pyrazinamide and are found in more than 90% of resistant strains. However, the genetic method for determining drug susceptibility is very complex, because mutations leading to pyrazinamide resistance are diverse and scattered throughout the gene. We have developed a software package for automatic data interpretation and prediction of the resistance to pyrazinamide based on Sanger sequencing results. The effectiveness of detection of pyrazinamide resistance in 16 clinical samples was compared using the BACTEC MGIT 960 automated system and pncA gene Sanger sequencing with automated analysis of the results. A significant advantage of the developed method over a single microbiological study was shown, due to greater reliability of the results irrespective of the purity of isolates.
Collapse
Affiliation(s)
- V V Sinkov
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - I G Kondratov
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - O B Ogarkov
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia.
| | - S N Zhdanova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - N A Sokolnikova
- Irkutsk Regional Clinical Tuberculosis Hospital, Irkutsk, Russia
| | - P A Khromova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - E A Orlova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - L V Rychkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - L I Kolesnikova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| |
Collapse
|
5
|
Hasan Z, Razzak SA, Kanji A, Shakoor S, Hasan R. Whole-genome sequencing reveals genotypic resistance in phenotypically susceptible Mycobacterium tuberculosis clinical isolates. Int J Mycobacteriol 2023; 12:179-183. [PMID: 37338481 DOI: 10.4103/ijmy.ijmy_101_23] [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: 06/21/2023] Open
Abstract
Background Whole-genome sequencing (WGS) data of Mycobacterium tuberculosis (MTB) complex strains have revealed insights about genetic variants associated with drug resistance (DR). Rapid genome-based diagnostics are being sought for specific and sensitive identification of DR; however, correct prediction of resistance genotypes requires both informatics tools and understanding of available evidence. We analyzed WGS datasets from phenotypically susceptible MTB strains using MTB resistance identification software. Methods WGS data for 1526 MTB isolates classified as phenotypically drug susceptible were downloaded from the ReSeqTB database. The TB-Profiler software was used to call Single Nucleotide Variants (SNV) associated with resistance to rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide, fluoroquinolone (FLQ), streptomycin (STR), and aminoglycosides. The SNV were further matched against the 2021 World Health Organization (WHO) catalogue of resistance mutations. Results Genome analysis of 1526 MTB strains susceptible to first-line drugs revealed 39 SNV associated with DR to be present in across 14 genes in 5.9% (n = 90) isolates. Further interpretation of SNV based on the WHO catalog of mutations revealed resistance that 21 (1.4%) MTB isolates were resistant to first-line (4 to RIF, 14 to INH, 3 to EMB) drugs. While, 36 (2.6%) isolates were resistant to second-line (19 to STR, 14 to FLQ, and three to capreomycin) agents. The most frequent predictive SNV were; rpoB Ser450 Leu for RIF; katG Ser315Thr, inhA Ser94Ala, fabG1-15C >T (for INH); gyrA Asp94Gly for FLQ; embB Met306 Leu for EMB; rpsL Lys43Arg for STR; and tlyA Asn236 Lys for Capreomycin. Conclusions Our study highlights the value of WGS-based sequence data for identifying resistance in MTB. It also shows how MTB strains may be misclassified simply on phenotypic drug susceptibility testing, and that correct genome interpretation is key for correct interpretation of resistance genotypes that can be used to guide clinical treatment.
Collapse
Affiliation(s)
- Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| |
Collapse
|
6
|
Artificial Intelligence for Antimicrobial Resistance Prediction: Challenges and Opportunities towards Practical Implementation. Antibiotics (Basel) 2023; 12:antibiotics12030523. [PMID: 36978390 PMCID: PMC10044311 DOI: 10.3390/antibiotics12030523] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Antimicrobial resistance (AMR) is emerging as a potential threat to many lives worldwide. It is very important to understand and apply effective strategies to counter the impact of AMR and its mutation from a medical treatment point of view. The intersection of artificial intelligence (AI), especially deep learning/machine learning, has led to a new direction in antimicrobial identification. Furthermore, presently, the availability of huge amounts of data from multiple sources has made it more effective to use these artificial intelligence techniques to identify interesting insights into AMR genes such as new genes, mutations, drug identification, conditions favorable to spread, and so on. Therefore, this paper presents a review of state-of-the-art challenges and opportunities. These include interesting input features posing challenges in use, state-of-the-art deep-learning/machine-learning models for robustness and high accuracy, challenges, and prospects to apply these techniques for practical purposes. The paper concludes with the encouragement to apply AI to the AMR sector with the intention of practical diagnosis and treatment, since presently most studies are at early stages with minimal application in the practice of diagnosis and treatment of disease.
Collapse
|
7
|
Schaberg T, Brinkmann F, Feiterna-Sperling C, Geerdes-Fenge H, Hartmann P, Häcker B, Hauer B, Haas W, Heyckendorf J, Lange C, Maurer FP, Nienhaus A, Otto-Knapp R, Priwitzer M, Richter E, Salzer HJ, Schoch O, Schönfeld N, Stahlmann R, Bauer T. Tuberkulose im Erwachsenenalter. Pneumologie 2022; 76:727-819. [DOI: 10.1055/a-1934-8303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ZusammenfassungDie Tuberkulose ist in Deutschland eine seltene, überwiegend gut behandelbare Erkrankung. Weltweit ist sie eine der häufigsten Infektionserkrankungen mit ca. 10 Millionen Neuerkrankungen/Jahr. Auch bei einer niedrigen Inzidenz in Deutschland bleibt Tuberkulose insbesondere aufgrund der internationalen Entwicklungen und Migrationsbewegungen eine wichtige Differenzialdiagnose. In Deutschland besteht, aufgrund der niedrigen Prävalenz der Erkrankung und der damit verbundenen abnehmenden klinischen Erfahrung, ein Informationsbedarf zu allen Aspekten der Tuberkulose und ihrer Kontrolle. Diese Leitlinie umfasst die mikrobiologische Diagnostik, die Grundprinzipien der Standardtherapie, die Behandlung verschiedener Organmanifestationen, den Umgang mit typischen unerwünschten Arzneimittelwirkungen, die Besonderheiten in der Diagnostik und Therapie resistenter Tuberkulose sowie die Behandlung bei TB-HIV-Koinfektion. Sie geht darüber hinaus auf Versorgungsaspekte und gesetzliche Regelungen wie auch auf die Diagnosestellung und präventive Therapie einer latenten tuberkulösen Infektion ein. Es wird ausgeführt, wann es der Behandlung durch spezialisierte Zentren bedarf.Die Aktualisierung der S2k-Leitlinie „Tuberkulose im Erwachsenenalter“ soll allen in der Tuberkuloseversorgung Tätigen als Richtschnur für die Prävention, die Diagnose und die Therapie der Tuberkulose dienen und helfen, den heutigen Herausforderungen im Umgang mit Tuberkulose in Deutschland gewachsen zu sein.
Collapse
Affiliation(s)
- Tom Schaberg
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | - Folke Brinkmann
- Abteilung für pädiatrische Pneumologie/CF-Zentrum, Universitätskinderklinik der Ruhr-Universität Bochum, Bochum
| | - Cornelia Feiterna-Sperling
- Klinik für Pädiatrie mit Schwerpunkt Pneumologie, Immunologie und Intensivmedizin, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin und Humboldt-Universität zu Berlin, Berlin
| | | | - Pia Hartmann
- Labor Dr. Wisplinghoff Köln, Klinische Infektiologie, Köln
- Department für Klinische Infektiologie, St. Vinzenz-Hospital, Köln
| | - Brit Häcker
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | - Jan Heyckendorf
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Campus Kiel
| | - Christoph Lange
- Klinische Infektiologie, Forschungszentrum Borstel
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hamburg-Lübeck-Borstel-Riems
- Respiratory Medicine and International Health, Universität zu Lübeck, Lübeck
- Baylor College of Medicine and Texas Childrenʼs Hospital, Global TB Program, Houston, TX, USA
| | - Florian P. Maurer
- Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg
| | - Albert Nienhaus
- Institut für Versorgungsforschung in der Dermatologie und bei Pflegeberufen (IVDP), Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg
| | - Ralf Otto-Knapp
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
| | | | | | | | | | | | - Ralf Stahlmann
- Institut für klinische Pharmakologie und Toxikologie, Charité Universitätsmedizin, Berlin
| | - Torsten Bauer
- Deutsches Zentralkomitee zur Bekämpfung der Tuberkulose e. V. (DZK), Berlin
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin
| |
Collapse
|
8
|
Hong JM, Lee H, Menon NV, Lim CT, Lee LP, Ong CWM. Point-of-care diagnostic tests for tuberculosis disease. Sci Transl Med 2022; 14:eabj4124. [PMID: 35385338 DOI: 10.1126/scitranslmed.abj4124] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.
Collapse
Affiliation(s)
- Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Hyeyoung Lee
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Nishanth V Menon
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720-1764, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.,Harvard Medical School, Brigham and Women's Hospital, Harvard Institute of Medicine, Harvard University, Boston, MA 02115, USA.,Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
| |
Collapse
|
9
|
Rahman SMM, Ather MF, Nasrin R, Hoque MA, Khatun R, Rahman T, Uddin MKM, Ahmed S, Banu S. Performance of WHO-Endorsed Rapid Tests for Detection of Susceptibility to First-Line Drugs in Patients with Pulmonary Tuberculosis in Bangladesh. Diagnostics (Basel) 2022; 12:diagnostics12020410. [PMID: 35204501 PMCID: PMC8870910 DOI: 10.3390/diagnostics12020410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The fast and accurate detection of susceptibility in drugs is a major challenge for a successful tuberculosis (TB) control programme. This study evaluated the performance of WHO-endorsed rapid diagnostic tools, such as BACTEC MGIT 960 SIRE (MGIT SIRE), GenoType MTBDRplus (MTBDRplus) and Xpert MTB/RIF (Xpert), for detecting susceptibility to first-line anti-TB drugs among pulmonary TB patients in Bangladesh. A total of 825 sputum samples with results from drug susceptibility testing (DST) against first-line anti-TB drugs in the MGIT SIRE, MTBDRplus and Xpert assays were evaluated and compared with the gold standard proportion susceptibility method of the Lowenstein–Jensen (LJ) medium. The overall sensitivities of MGIT SIRE were 97.6%, 90.0%, 61.3% and 44.9%, while specificities were 89.9%, 94.5%, 91.3% and 92.2% for detection of susceptibility to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and ethambutol (EMB), respectively. For MTBDRplus, the sensitivities were 88.0% and 88.7%, and the specificities were 97.4% and 97.8% for the detection of susceptibility to INH and RIF, respectively. Xpert demonstrated a sensitivity and specificity of 94.8% and 99.5%, respectively, for the detection of RIF susceptibility. All tests performed significantly better in retreated TB patients compared with primary TB cases. For detection of RIF and INH susceptibility, all three assays showed almost perfect agreement with the LJ method, although MGIT SIRE exhibited low agreement for STR and EMB. Considering the high performance, shorter turnaround time and ease of use, molecular-based approaches Xpert and MTBDRplus can be widely implemented throughout the country for the rapid detection of drug-resistant TB.
Collapse
|
10
|
Realegeno S, Adeyiga O, Winston DJ, Beaird OE, Garner OB, Yang S. Utilization of whole genome sequencing for resolution of discrepant Mycobacterium tuberculosis drug susceptibility results: A case report. IDCases 2021; 26:e01308. [PMID: 34745885 PMCID: PMC8551521 DOI: 10.1016/j.idcr.2021.e01308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/26/2022] Open
Abstract
A 44-year-old woman undergoing therapy for acute promyelocytic leukemia (APL) developed disseminated tuberculosis. Mycobacterium tuberculosis (TB) was isolated from the blood and sputum. Initial drug susceptibility testing (DST) of the blood isolate revealed resistance to isoniazid and ethambutol but the sputum isolate showed no resistance. Due to drug resistance concerns, the patient was treated with multiple second and third-line drugs, and suffered from drug side effects. To further investigate the DST discrepancies, whole genome sequencing (WGS) was performed on both isolates. No known resistance mutations to first line or second line drugs were identified in either isolate, which was confirmed by additional susceptibility testing performed by a different reference laboratory and the California Department of Public Health (CDPH) laboratory. Treatment was reduced to a simpler and less toxic regimen due to these investigations. WGS is shown to be a valuable tool for resolving discordant phenotypic DST results of TB isolates and has the potential to provide accurate and timely results guiding appropriate therapy in the clinical setting.
Collapse
Affiliation(s)
- Susan Realegeno
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oladunni Adeyiga
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Drew J Winston
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Omer E Beaird
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Omai B Garner
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shangxin Yang
- UCLA Clinical Microbiology Laboratory, Department of Pathology & Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
11
|
Pérez-Herrán E, Mendoza A. Antimicrobial Susceptibility Testing for Mycobacterium sps in High-Throughput Format. Methods Mol Biol 2021; 2314:637-648. [PMID: 34235674 DOI: 10.1007/978-1-0716-1460-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The concept of antimicrobial susceptibility testing is an essential part of clinical microbiology. Antimicrobial testing has played a central role in the identification of new antibiotics and defining their clinical uses. Here we describe different approaches to determine the activity of compounds in medium or high-throughput format.
Collapse
Affiliation(s)
- Esther Pérez-Herrán
- Gobal Health Phama Research Unit, Tres Cantos Medicines Development Campus (TCMDC), GlaxoSmithKline, Madrid, Spain.
| | - Alfonso Mendoza
- Gobal Health Phama Research Unit, Tres Cantos Medicines Development Campus (TCMDC), GlaxoSmithKline, Madrid, Spain
| |
Collapse
|
12
|
Chiang SS, Brooks MB, Jenkins HE, Rubenstein D, Seddon JA, van de Water BJ, Lindeborg MM, Becerra MC, Yuen CM. Concordance of Drug-resistance Profiles Between Persons With Drug-resistant Tuberculosis and Their Household Contacts: A Systematic Review and Meta-analysis. Clin Infect Dis 2021; 73:250-263. [PMID: 32448887 DOI: 10.1093/cid/ciaa613] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Household contacts of patients with drug-resistant tuberculosis (TB) are at high risk for being infected with Mycobacterium tuberculosis and for developing TB disease. To guide regimen composition for the empirical treatment of TB infection and disease in these household contacts, we estimated drug-resistance profile concordance between index patients with drug-resistant TB and their household contacts. METHODS We performed a systematic review and meta-analysis of studies published through 24 July 2018 that reported resistance profiles of drug-resistant TB index cases and secondary cases within their households. Using a random-effects meta-analysis, we estimated resistance profile concordance, defined as the percentage of secondary cases whose M. tuberculosis strains were resistant to the same drugs as strains from their index cases. We also estimated isoniazid/rifampin concordance, defined as whether index and secondary cases had identical susceptibilities for isoniazid and rifampin only. RESULTS We identified 33 eligible studies that evaluated resistance profile concordance between 484 secondary cases and their household index cases. Pooled resistance profile concordance was 54.3% (95% confidence interval [CI], 40.7-67.6%; I2 = 85%). Pooled isoniazid/rifampin concordance was 82.6% (95% CI, 72.3-90.9%; I2 = 73%). Concordance estimates were similar in a subanalysis of 16 studies from high-TB-burden countries. There were insufficient data to perform a subanalysis among pediatric secondary cases. CONCLUSIONS Household contacts of patients with drug-resistant TB should receive treatment for TB infection and disease that assumes that they, too, are infected with a drug-resistant M. tuberculosis strain. Whenever possible, drug susceptibility testing should be performed for secondary cases to optimize regimen composition.
Collapse
Affiliation(s)
- Silvia S Chiang
- Department of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA.,Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Meredith B Brooks
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Helen E Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Dana Rubenstein
- Department of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - James A Seddon
- Department of Infectious Diseases, Imperial College London, London, United Kingdom.,Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Brittney J van de Water
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael M Lindeborg
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Mercedes C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Courtney M Yuen
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
13
|
Disputed rpoB Mutations in Mycobacterium tuberculosis and Tuberculosis Treatment Outcomes. Antimicrob Agents Chemother 2021; 65:e0157320. [PMID: 33846134 DOI: 10.1128/aac.01573-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discordant results between genotypic drug susceptibility testing (gDST) and phenotypic DST (pDST) for Mycobacterium tuberculosis isolates with disputed (discordance between gDST and pDST results) mutations affect rifampin (RIF)-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) treatments due to a lack of practical clinical guidelines. To investigate the role of disputed rpoB mutations in M. tuberculosis and TB treatment outcomes, initial isolates of 837 clinical RR- or MDR-TB cases confirmed during 2014 to 2018 were retested using agar-based RIF pDST and rpoB gene sequencing. MICs were determined for isolates with disputed rpoB mutations. Disputed rpoB mutations were identified in 77 (9.2%) M. tuberculosis isolates, including 50 (64.9%) and 14 (18.2%) phenotypically RIF- and rifabutin (RFB)-resistant isolates, respectively. The predominant single mutations were those encoding L533P (a change of L to P at position 533) (44.2%) and L511P (20.8%). Most of the isolates harboring mutations encoding L511P (87.5%), H526N (100%), D516Y (70.0%), and L533P (63.6%) had MICs of ≤1 mg/liter, whereas isolates harboring the mutation encoding H526L (75%) had a MIC of >1 mg/liter. Of the 63 cases with treatment outcomes available, 11 (17.5%) cases died, 1 (1.6%) case transferred out, and 51 (81%) cases had favorable outcomes, including 8 and 20 cases treated with standard-dose RIF- and RFB-containing regimens, respectively. Excluding cases that transferred out or received no or 1-day treatment, we observed statistically significant differences between the outcomes using active and inactive fluoroquinolones (FQs) (P = 0.008, odds ratio = 0.05 [95% confidence interval, 0.01 to 0.38]) in 57 cases (where active means a case susceptible to the drug and inactive means a case resistant to the drug or drug not used). We concluded that disputed rpoB mutations are not rare. Depending on the resources available, sequencing and/or MIC testing is recommended for better management of RR- and MDR-TB cases.
Collapse
|
14
|
Abstract
Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.
Collapse
|
15
|
Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics 2021; 36:100471. [PMID: 34256273 DOI: 10.1016/j.epidem.2021.100471] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 01/14/2020] [Accepted: 05/17/2021] [Indexed: 11/22/2022] Open
Abstract
As multi-drug resistant tuberculosis (MDR-TB) continues to spread, investigating the transmission potential of different drug-resistant strains becomes an ever more pressing topic in public health. While phylogenetic and transmission tree inferences provide valuable insight into possible transmission chains, phylodynamic inference combines evolutionary and epidemiological analyses to estimate the parameters of the underlying epidemiological processes, allowing us to describe the overall dynamics of disease spread in the population. In this study, we introduce an approach to Mycobacterium tuberculosis (M. tuberculosis) phylodynamic analysis employing an existing computationally efficient model to quantify the transmission fitness costs of drug resistance with respect to drug-sensitive strains. To determine the accuracy and precision of our approach, we first perform a simulation study, mimicking the simultaneous spread of drug-sensitive and drug-resistant tuberculosis (TB) strains. We analyse the simulated transmission trees using the phylodynamic multi-type birth-death model (MTBD, (Kühnert et al., 2016)) within the BEAST2 framework and show that this model can estimate the parameters of the epidemic well, despite the simplifying assumptions that MTBD makes compared to the complex TB transmission dynamics used for simulation. We then apply the MTBD model to an M. tuberculosis lineage 4 dataset that primarily consists of MDR sequences. Some of the MDR strains additionally exhibit resistance to pyrazinamide - an important first-line anti-tuberculosis drug. Our results support the previously proposed hypothesis that pyrazinamide resistance confers a transmission fitness cost to the bacterium, which we quantify for the given dataset. Importantly, our sensitivity analyses show that the estimates are robust to different prior distributions on the resistance acquisition rate, but are affected by the size of the dataset - i.e. we estimate a higher fitness cost when using fewer sequences for analysis. Overall, we propose that MTBD can be used to quantify the transmission fitness cost for a wide range of pathogens where the strains can be appropriately divided into two or more categories with distinct properties.
Collapse
|
16
|
Al-Mutairi NM, Ahmad S, Mokaddas E. Increasing prevalence of resistance to second-line drugs among multidrug-resistant Mycobacterium tuberculosis isolates in Kuwait. Sci Rep 2021; 11:7765. [PMID: 33833390 PMCID: PMC8032671 DOI: 10.1038/s41598-021-87516-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular methods detect genetic mutations associated with drug resistance. This study detected resistance-conferring mutations in gyrA/gyrB for fluoroquinolones and rrs/eis genes for second-line injectable drugs (SLIDs) among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates in Kuwait. Fifty pansusceptible M. tuberculosis and 102 MDR-TB strains were tested. Phenotypic susceptibility testing was performed by MGIT 960 system using SIRE drug kit. GenoType MTBDRsl version 1 (gMTBDRslv1) and GenoType MTBDRsl version 2 (gMTBDRslv2) tests were used for mutation detection. Results were validated by PCR-sequencing of respective genes. Fingerprinting was performed by spoligotyping. No mutations were detected in pansusceptible isolates. gMTBDRslv1 detected gyrA mutations in 12 and rrs mutations in 8 MDR-TB isolates. gMTBDRsl2 additionally detected gyrB mutations in 2 and eis mutation in 1 isolate. Mutations in both gyrA/gyrB and rrs/eis were not detected. gMTBDRslv1 also detected ethambutol resistance-conferring embB mutations in 59 isolates. Although XDR-TB was not detected, frequency of resistance-conferring mutations for fluoroquinolones or SLIDs was significantly higher among isolates collected during 2013–2019 versus 2006–2012. Application of both tests is warranted for proper management of MDR-TB patients in Kuwait as gMTBDRslv2 detected resistance to fluoroquinolones and/or SLIDs in 3 additional isolates while gMTBDRslv1 additionally detected resistance to ethambutol in 58% of MDR-TB isolates.
Collapse
Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| |
Collapse
|
17
|
Systematic Review of Mutations Associated with Isoniazid Resistance Points to Continuing Evolution and Subsequent Evasion of Molecular Detection, and Potential for Emergence of Multidrug Resistance in Clinical Strains of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:AAC.02091-20. [PMID: 33361298 DOI: 10.1128/aac.02091-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/13/2020] [Indexed: 01/24/2023] Open
Abstract
Molecular testing is rapidly becoming an integral component of global tuberculosis (TB) control. Uncommon mechanisms of resistance escape detection by these platforms and undermine our ability to contain outbreaks. This article is a systematic review of published articles that reported isoniazid (INH) resistance-conferring mutations between September 2013 and December 2019. The genes katG, inhA, and fabG1, and the intergenic region oxyR'-ahpC were considered in this review. Fifty-two articles were included that described 9,306 clinical isolates (5,804 INH resistant [INHr] and 3,502 INH susceptible [INHs]) from 31 countries. The three most frequently mutated loci continue to be locus 315 of katG (katG315; n = 4,271), locus -15 of inhA (inhA-15; n = 787), and locus -8 of inhA (inhA-8; 106). However, the diagnostic value of inhA-8 is far lower than previously thought, as it only appears in 25 (0.4%) of the INHr isolates lacking the first two mutations. I catalogued 45 new loci (29 katG, nine inhA, and seven ahpC) associated with INH resistance and identified 59 loci (common to this and previous reviews) as a reliable basis for molecular diagnostics. Including all observed mutations provides a cumulative sensitivity of 85.6%. In 14.4% of resistant isolates, no mechanism of resistance was detected, making them likely to escape molecular detection, and in the case of INH monoresistance, likely to convert to multidrug-resistant TB (MDR-TB). Integrating the information cataloged in this study into current diagnostic tools is essential for combating the emergence of MDR-TB, and its exclusion can lead to an unintended selection against common mechanisms and to diversifying evolution. Observation of many low-frequency resistance-conferring mutations points to an advantage of whole-genome sequencing (WGS) for diagnostics. Finally, I provide five recommendations for future diagnostic platforms.
Collapse
|
18
|
Lv J, Deng S, Zhang L. A review of artificial intelligence applications for antimicrobial resistance. BIOSAFETY AND HEALTH 2021. [DOI: 10.1016/j.bsheal.2020.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
19
|
Florentini EA, Angulo N, Gilman RH, Alcántara R, Roncal E, Antiparra R, Toscano E, Vallejos K, Kirwan D, Zimic M, Sheen P. Immunological detection of pyrazine-2-carboxylic acid for the detection of pyrazinamide resistance in Mycobacterium tuberculosis. PLoS One 2020; 15:e0241600. [PMID: 33151985 PMCID: PMC7643994 DOI: 10.1371/journal.pone.0241600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/17/2020] [Indexed: 11/18/2022] Open
Abstract
Pyrazinamide (PZA) susceptibility testing in Mycobacterium tuberculosis (Mtb) is a current area of development and PZA-resistant strains are increasingly prevalent. Previous studies have demonstrated that the detection of pyrazinoic acid (POA), the metabolite produced by the deamidation of PZA, is a good predictor for PZA resistance since a resistant strain would not convert PZA into POA at a critical required rate, whereas a susceptible strain will do, expelling POA to the extracellular environment at a certain rate, and allowing for quantification of this accumulated analyte. In order to quantify POA, an indirect competitive ELISA (icELISA) test using hyperimmune polyclonal rabbit serum against POA was developed: for this purpose, pure POA was first covalently linked to the highly immunogenic Keyhole Limpet Hemocyanine, and inoculated in rabbits. A construct made of bovine serum albumin (BSA) linked to pure POA and fixed at the bottom of wells was used as a competitor against spiked samples and liquid Mtb culture supernatants. When spiked samples (commercial POA alone) were analyzed, the half maximal inhibitory concentration (IC50) was 1.16 mg/mL, the limit of detection 200 μg/mL and the assay was specific (it did not detect PZA, IC50 > 20 mg/mL). However, culture supernatants (7H9-OADC-PANTA medium) disrupted the competition and a proper icELISA curve was not obtainable. We consider that, although we have shown that it is feasible to induce antibodies against POA, matrix effects could damage its analytical usefulness; multiple, upcoming ways to solve this obstacle are suggested.
Collapse
Affiliation(s)
- Edgar A. Florentini
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Noelia Angulo
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Roberto Alcántara
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Ricardo Antiparra
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Emily Toscano
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Katherine Vallejos
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Danni Kirwan
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
- * E-mail:
| |
Collapse
|
20
|
Jamal S, Khubaib M, Gangwar R, Grover S, Grover A, Hasnain SE. Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis. Sci Rep 2020; 10:5487. [PMID: 32218465 PMCID: PMC7099008 DOI: 10.1038/s41598-020-62368-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (M.tb), causes highest number of deaths globally for any bacterial disease necessitating novel diagnosis and treatment strategies. High-throughput sequencing methods generate a large amount of data which could be exploited in determining multi-drug resistant (MDR-TB) associated mutations. The present work is a computational framework that uses artificial intelligence (AI) based machine learning (ML) approaches for predicting resistance in the genes rpoB, inhA, katG, pncA, gyrA and gyrB for the drugs rifampicin, isoniazid, pyrazinamide and fluoroquinolones. The single nucleotide variations were represented by several sequence and structural features that indicate the influence of mutations on the target protein coded by each gene. We used ML algorithms - naïve bayes, k nearest neighbor, support vector machine, and artificial neural network, to build the prediction models. The classification models had an average accuracy of 85% across all examined genes and were evaluated on an external unseen dataset to demonstrate their application. Further, molecular docking and molecular dynamics simulations were performed for wild type and predicted resistance causing mutant protein and anti-TB drug complexes to study their impact on the conformation of proteins to confirm the observed phenotype.
Collapse
Affiliation(s)
- Salma Jamal
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Mohd Khubaib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Rishabh Gangwar
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Sonam Grover
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110 067, India
| | - Seyed E Hasnain
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India. .,Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Professor C.R. Rao Road, Hyderabad, 500046, India.
| |
Collapse
|
21
|
Nahid P, Mase SR, Migliori GB, Sotgiu G, Bothamley GH, Brozek JL, Cattamanchi A, Cegielski JP, Chen L, Daley CL, Dalton TL, Duarte R, Fregonese F, Horsburgh CR, Ahmad Khan F, Kheir F, Lan Z, Lardizabal A, Lauzardo M, Mangan JM, Marks SM, McKenna L, Menzies D, Mitnick CD, Nilsen DM, Parvez F, Peloquin CA, Raftery A, Schaaf HS, Shah NS, Starke JR, Wilson JW, Wortham JM, Chorba T, Seaworth B. Treatment of Drug-Resistant Tuberculosis. An Official ATS/CDC/ERS/IDSA Clinical Practice Guideline. Am J Respir Crit Care Med 2020; 200:e93-e142. [PMID: 31729908 PMCID: PMC6857485 DOI: 10.1164/rccm.201909-1874st] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: The American Thoracic Society, U.S. Centers for Disease Control and Prevention, European Respiratory Society, and Infectious Diseases Society of America jointly sponsored this new practice guideline on the treatment of drug-resistant tuberculosis (DR-TB). The document includes recommendations on the treatment of multidrug-resistant TB (MDR-TB) as well as isoniazid-resistant but rifampin-susceptible TB.Methods: Published systematic reviews, meta-analyses, and a new individual patient data meta-analysis from 12,030 patients, in 50 studies, across 25 countries with confirmed pulmonary rifampin-resistant TB were used for this guideline. Meta-analytic approaches included propensity score matching to reduce confounding. Each recommendation was discussed by an expert committee, screened for conflicts of interest, according to the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) methodology.Results: Twenty-one Population, Intervention, Comparator, and Outcomes questions were addressed, generating 25 GRADE-based recommendations. Certainty in the evidence was judged to be very low, because the data came from observational studies with significant loss to follow-up and imbalance in background regimens between comparator groups. Good practices in the management of MDR-TB are described. On the basis of the evidence review, a clinical strategy tool for building a treatment regimen for MDR-TB is also provided.Conclusions: New recommendations are made for the choice and number of drugs in a regimen, the duration of intensive and continuation phases, and the role of injectable drugs for MDR-TB. On the basis of these recommendations, an effective all-oral regimen for MDR-TB can be assembled. Recommendations are also provided on the role of surgery in treatment of MDR-TB and for treatment of contacts exposed to MDR-TB and treatment of isoniazid-resistant TB.
Collapse
|
22
|
Abidi S, Achar J, Assao Neino MM, Bang D, Benedetti A, Brode S, Campbell JR, Casas EC, Conradie F, Dravniece G, du Cros P, Falzon D, Jaramillo E, Kuaban C, Lan Z, Lange C, Li PZ, Makhmudova M, Maug AKJ, Menzies D, Migliori GB, Miller A, Myrzaliev B, Ndjeka N, Noeske J, Parpieva N, Piubello A, Schwoebel V, Sikhondze W, Singla R, Souleymane MB, Trébucq A, Van Deun A, Viney K, Weyer K, Zhang BJ, Ahmad Khan F. Standardised shorter regimens versus individualised longer regimens for rifampin- or multidrug-resistant tuberculosis. Eur Respir J 2020; 55:13993003.01467-2019. [PMID: 31862767 DOI: 10.1183/13993003.01467-2019] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/04/2019] [Indexed: 11/05/2022]
Abstract
We sought to compare the effectiveness of two World Health Organization (WHO)-recommended regimens for the treatment of rifampin- or multidrug-resistant (RR/MDR) tuberculosis (TB): a standardised regimen of 9-12 months (the "shorter regimen") and individualised regimens of ≥20 months ("longer regimens").We collected individual patient data from observational studies identified through systematic reviews and a public call for data. We included patients meeting WHO eligibility criteria for the shorter regimen: not previously treated with second-line drugs, and with fluoroquinolone- and second-line injectable agent-susceptible RR/MDR-TB. We used propensity score matched, mixed effects meta-regression to calculate adjusted odds ratios and adjusted risk differences (aRDs) for failure or relapse, death within 12 months of treatment initiation and loss to follow-up.We included 2625 out of 3378 (77.7%) individuals from nine studies of shorter regimens and 2717 out of 13 104 (20.7%) individuals from 53 studies of longer regimens. Treatment success was higher with the shorter regimen than with longer regimens (pooled proportions 80.0% versus 75.3%), due to less loss to follow-up with the former (aRD -0.15, 95% CI -0.17- -0.12). The risk difference for failure or relapse was slightly higher with the shorter regimen overall (aRD 0.02, 95% CI 0-0.05) and greater in magnitude with baseline resistance to pyrazinamide (aRD 0.12, 95% CI 0.07-0.16), prothionamide/ethionamide (aRD 0.07, 95% CI -0.01-0.16) or ethambutol (aRD 0.09, 95% CI 0.04-0.13).In patients meeting WHO criteria for its use, the standardised shorter regimen was associated with substantially less loss to follow-up during treatment compared with individualised longer regimens and with more failure or relapse in the presence of resistance to component medications. Our findings support the need to improve access to reliable drug susceptibility testing.
Collapse
Affiliation(s)
- Syed Abidi
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jay Achar
- Médecins Sans Frontières/Doctors without Borders, London, UK
| | | | - Didi Bang
- International Reference Laboratory of Mycobacteriology, National Centre for Antimicrobials and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Andrea Benedetti
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Dept of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sarah Brode
- West Park Healthcare Centre, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Jonathon R Campbell
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Esther C Casas
- Médecins Sans Frontières/Doctors without Borders, Amsterdam, The Netherlands
| | - Francesca Conradie
- Dept of Medicine, University of Witswatersrand, Johannesburg, South Africa
| | | | - Philipp du Cros
- Médecins Sans Frontières/Doctors without Borders, London, UK.,Burnet Institute, Melbourne, Australia
| | | | | | - Christopher Kuaban
- Faculty of Health Sciences, The University of Bamenda, Bambili, Cameroon
| | - Zhiyi Lan
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Christoph Lange
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research Clinical TB Unit, Borstel, Germany.,Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany.,Dept of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Pei Zhi Li
- Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | | | - Dick Menzies
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Giovanni Battista Migliori
- WHO Collaborating Centre for Tuberculosis and Lung Diseases, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | - Ann Miller
- Dept of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Bakyt Myrzaliev
- KNCV TB Foundation, Branch Office KNCV in Kyrgyzstan, Bishkek, Kyrgyzstan
| | - Norbert Ndjeka
- National TB Programme, Republic of South Africa, Pretoria, South Africa
| | | | | | - Alberto Piubello
- Damien Foundation, Brussels, Belgium.,International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Valérie Schwoebel
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Welile Sikhondze
- National TB Control Program, Eswatini Ministry of Health, Mbabane, Swaziland
| | - Rupak Singla
- National Institute of Tuberculosis and Respiratory Diseases, Delhi, India
| | | | - Arnaud Trébucq
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Armand Van Deun
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kerri Viney
- The University of Sydney, Sydney, Australia.,Karolinska Institutet, Stockholm, Sweden.,Australian National University, Canberra, Australia
| | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | - Betty Jingxuan Zhang
- McGill International TB Centre, Montreal, QC, Canada.,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Faiz Ahmad Khan
- McGill International TB Centre, Montreal, QC, Canada .,Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research and Evaluation, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| |
Collapse
|
23
|
Domotenko LV, Morozova TP, Shemyakin IG, Shepelin AP. [Experience of using TB test kit for the rapid drug susceptibility testing of M. tuberculosis.]. Klin Lab Diagn 2020; 65:122-130. [PMID: 32159311 DOI: 10.18821/0869-2084-2020-65-2-122-130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 01/04/2020] [Indexed: 11/17/2022]
Abstract
The results of the comparative testing of the susceptibility of M. tuberculosis clinical strains to isoniazid, streptomycin, rifampicin and ethambutol using the TB test kit, developed in SCRAMB, (Obolensk) and the absolute concentrations method; the TB test kit and the BACTEC MGIT 960 automated system are presented in the study. A total of 629 and 220 strains, respectively, were tested. A high degree of agreement of the results was shown: 89.1-98.6% for isoniazid, 96.2-98.0% for rifampicin, 91.5-98.2% for streptomycin and 89.1-95.9% for ethambutol. The smallest number of discrepancies in the results was obtained when comparing the TB test kit and BACTEC MGIT 960. The discrepant results analysis was performed by the proportion method, PCR sequencing, or re-testing on new lots of the TB test kit and Lowenstein-Jensen medium with anti-tuberculosis drugs, after which the sensitivity, the specificity and the efficiency of the TB test kit have exceeded 95 % for all anti-tuberculosis drugs. The turnaround time with the TB test kit (median 9.25-9.9 days, ranged from 8 to13 days) was significantly shorter than that with the absolute concentration method (median 21-23 days, ranged from 20 to 28 days) and is commensurate with the turnaround time with BACTEC MGIT 960 (average 7.2 days, ranged from 5 to 12 days). The TB test kit is easy to use, does not require expensive equipment and special staff training.
Collapse
Affiliation(s)
- L V Domotenko
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russia
| | - T P Morozova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russia
| | - I G Shemyakin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russia
| | - A P Shepelin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russia
| |
Collapse
|
24
|
Mehmood A, Khan MT, Kaushik AC, Khan AS, Irfan M, Wei DQ. Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance. Front Bioeng Biotechnol 2019; 7:404. [PMID: 31921809 PMCID: PMC6914729 DOI: 10.3389/fbioe.2019.00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/26/2019] [Indexed: 11/15/2022] Open
Abstract
Pyrazinamide (PZA) is one of the main FDA approved drugs to be used as the first line of defense against Mycobacterium Tuberculosis (MTB). It is activated into pyrazinoic acid (POA) via MTB's pncA gene-encoded pyrazinamidase (PZase). Mutations are most commonly responsible for PZA-resistance in nearly 70% of the resistant samples. In the present work, MTB positive samples were chosen for PZA drug susceptibility testing (DST) against critical concentration (100 ug/ml) of PZA. The resistant samples were subjected to pncA sequencing. As a result, 36 various mutations have been observed in the PZA resistant samples, uploaded to the NCBI (GeneBank accession no. MH461111). Here we report the mechanism of PZA resistance behind the three mutants (MTs), Asp12Ala, Pro54Leu, and His57Pro in comparison with the wild type (WT) through molecular dynamics simulation to unveil how these mutations affect the overall conformational stability. The post-simulation analyses revealed notable deviations as compared to the WT structure. Molecular docking studies of PZA with MTs and WT, pocket volume inspection and overall shape complementarity analysis confirmed the deleterious nature of these mutations and gave an insight into the mechanism behind PZA-resistance. These analyses provide vital information regarding MTB drug resistance and could be extremely useful in therapy management and overcoming its global burden.
Collapse
Affiliation(s)
- Aamir Mehmood
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | | | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Muhammad Irfan
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Dong-Qing Wei
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
Naidenov B, Lim A, Willyerd K, Torres NJ, Johnson WL, Hwang HJ, Hoyt P, Gustafson JE, Chen C. Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia. Front Microbiol 2019; 10:1446. [PMID: 31333599 PMCID: PMC6622151 DOI: 10.3389/fmicb.2019.01446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/07/2019] [Indexed: 01/21/2023] Open
Abstract
The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and E. meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations (MICs) for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies (ONT) and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning (ML) algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84, respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75, and 0.54, respectively. By producing two sets of quality biological predictors, pan-genome genes and core-genome SNPs, from long-read sequence data and applying an ensemble of ML techniques, our results demonstrated that accurate phenotypic inference, at multiple AMR resolutions, can be achieved.
Collapse
Affiliation(s)
- Bryan Naidenov
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Alexander Lim
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Karyn Willyerd
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Nathanial J. Torres
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - William L. Johnson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Hong Jin Hwang
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - Peter Hoyt
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - John E. Gustafson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| |
Collapse
|
27
|
Sergeev RS, Kavaliou IS, Sataneuski UV, Gabrielian A, Rosenthal A, Tartakovsky M, Tuzikov AV. Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-Learning Approach. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1398-1408. [PMID: 28678713 DOI: 10.1109/tcbb.2017.2720669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Emergence of drug-resistant microorganisms has been recognized as a serious threat to public health worldwide. This problem is extensively discussed in the context of tuberculosis treatment. Alterations in pathogen genomes are among the main mechanisms by which microorganisms exhibit drug resistance. Analysis of 144 M. tuberculosis strains of different phenotypes including drug susceptible, MDR, and XDR isolated in Belarus was fulfilled in this paper. A wide range of machine learning methods that can discover SNPs related to drug-resistance in the whole bacteria genomes was investigated. Besides single-SNP testing approaches, methods that allow detecting joint effects from interacting SNPs were considered. We proposed a framework for automated selection of the best performing statistical model in terms of recall, precision, and accuracy to identify drug resistance-associated mutations. Analysis of whole-genome sequences often leads to situations where the number of treated features exceeds the number of available observations. For this reason, special attention is paid to fair evaluation of the model prediction quality and minimizing the risk of overfitting while estimating the underlying parameters. Results of our experiments aimed at identifying top-scoring resistance mutations to the major first-line and second-line anti-TB drugs are presented.
Collapse
|
28
|
Factors affecting outcomes of individualised treatment for drug resistant tuberculosis in an endemic region. Indian J Tuberc 2019; 66:240-246. [PMID: 31151491 DOI: 10.1016/j.ijtb.2017.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/06/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Individualised treatment regimens for drug resistant tuberculosis have improved outcomes. This retrospective observational study examined potential factors that affect individualised treatment in an endemic region, and highlighted predictors of a successful outcome. METHODS We examined records of proven MDR, pre-XDR and XDR TB patients diagnosed and started on treatment between 2010 and 2014, and collected the following data for each patient: age, gender, comorbidities, past history of TB, diagnosis, site of disease, drug susceptibility testing (DST) results, treatment, adverse reactions to anti-tubercular drugs, treatment changes and outcomes, which were recorded as positive, negative or neutral. Tests of association were carried out between factors and outcomes, following which multiple logistic regression analysis was done to determine the predictors of a positive outcome such as patient cured after completion of treatment at 18 months or longer. RESULTS Fifty-nine patients completed treatment at our centre. The median age was 26 years (range 8-65 years). There were 31 (52.5%) female patients. Forty-four (74.6%) were successfully treated over a median treatment period of 23 months (range 18-30 months). Successful outcomes were associated with age less than 45 years (P=0.01, OR=6.67, 95% CI=1.73-23.47), resistance to fewer than five drugs (P=0.001, OR=9.51, 95% CI=2.50-38.18) and susceptibility to Group 4 drugs (P=0.04, OR=4.71, 95% CI=1.03-16.83). CONCLUSIONS Age and drug susceptibility were important predictors of treatment outcome.
Collapse
|
29
|
Collin SM, Wurie F, Muzyamba MC, de Vries G, Lönnroth K, Migliori GB, Abubakar I, Anderson SR, Zenner D. Effectiveness of interventions for reducing TB incidence in countries with low TB incidence: a systematic review of reviews. Eur Respir Rev 2019; 28:28/152/180107. [PMID: 31142548 DOI: 10.1183/16000617.0107-2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/22/2019] [Indexed: 12/18/2022] Open
Abstract
AIMS What is the evidence base for the effectiveness of interventions to reduce tuberculosis (TB) incidence in countries which have low TB incidence? METHODS We conducted a systematic review of interventions for TB control and prevention relevant to low TB incidence settings (<10 cases per 100 000 population). Our analysis was stratified according to "direct" or "indirect" effects on TB incidence. Review quality was assessed using AMSTAR2 criteria. We summarised the strength of review level evidence for interventions as "sufficient", "tentative", "insufficient" or "no" using a framework based on the consistency of evidence within and between reviews. RESULTS We found sufficient review level evidence for direct effects on TB incidence/case prevention of vaccination and treatment of latent TB infection. We also found sufficient evidence of beneficial indirect effects attributable to drug susceptibility testing and adverse indirect effects (measured as sub-optimal treatment outcomes) in relation to use of standardised first-line drug regimens for isoniazid-resistant TB and intermittent dosing regimens. We found insufficient review level evidence for direct or indirect effects of interventions in other areas, including screening, adherence, multidrug-resistant TB, and healthcare-associated infection. DISCUSSION Our review has shown a need for stronger evidence to support expert opinion and country experience when formulating TB control policy.
Collapse
Affiliation(s)
- Simon M Collin
- TB Unit, National Infection Service, Public Health England, London, UK
| | - Fatima Wurie
- TB Unit, National Infection Service, Public Health England, London, UK
| | - Morris C Muzyamba
- TB Unit, National Infection Service, Public Health England, London, UK
| | | | | | | | | | - Sarah R Anderson
- TB Unit, National Infection Service, Public Health England, London, UK
| | | |
Collapse
|
30
|
Faksri K, Kaewprasert O, Ong RTH, Suriyaphol P, Prammananan T, Teo YY, Srilohasin P, Chaiprasert A. Comparisons of whole-genome sequencing and phenotypic drug susceptibility testing for Mycobacterium tuberculosis causing MDR-TB and XDR-TB in Thailand. Int J Antimicrob Agents 2019; 54:109-116. [PMID: 30981926 DOI: 10.1016/j.ijantimicag.2019.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/26/2019] [Accepted: 04/06/2019] [Indexed: 01/12/2023]
Abstract
Drug-resistant tuberculosis (TB) is a major public health problem. There is little information regarding the genotypic-phenotypic association of anti-TB drugs, especially for second-line drugs. This study compared phenotypic drug susceptibility testing (DST) with predictions based on whole-genome sequencing (WGS) data for 266 Mycobacterium tuberculosis isolates. Phenotypic DST used the standard proportional method. Clinical isolates of M. tuberculosis collected in Thailand between 1998 and 2013 comprised 51 drug-sensitive strains, six mono-resistant strains, two multiple-resistant strains, 88 multi-drug-resistant strains, 95 pre-extensively drug-resistant strains and 24 extensively drug-resistant strains. WGS analysis was performed using the computer programs PhyResSE and TB-Profiler. TB-Profiler had higher average concordance with phenotypic DST than PhyResSE for both first-line (91.96% vs. 91.4%) and second-line (79.67% vs. 78.20%) anti-TB drugs. The average sensitivity for all anti-TB drugs was also higher (83.13% vs. 72.08%) with slightly lower specificity (83.50% vs. 86.68%). Regardless of the program used, isoniazid, rifampicin and amikacin had the highest concordance with phenotypic DST (96.2%, 93.5% and 95.6%, respectively). Ethambutol, ethionamide and fluoroquinolones had the lowest concordance (87.34%, 81.44% and 73.85%, respectively). Concordance rates of ofloxacin (a second-generation fluoroquinolone), levofloxacin, moxifloxacin and gatifloxacin (third- and fourth-generation fluoroquinolones) were 91.79%, 76.62%, 72.64% and 57.35%, respectively. Discordance between phenotypic and WGS-based DSTs may be due, in part, to the choice of critical concentration and variable reproducibility of the phenotypic tests. It may also be due to limitations of the mutation databases (especially for the second-line drugs) and the analysis program used. Mutations related to fluoroquinolone resistance, especially the later generations, need to be identified.
Collapse
Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand.
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Therdsak Prammananan
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Ministry of Science and Technology, Pathum Thani, Thailand
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Genome Institute of Singapore, Singapore; Department of Statistics and Applied Probability, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore
| | - Prapaporn Srilohasin
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
31
|
Su M, Satola SW, Read TD. Genome-Based Prediction of Bacterial Antibiotic Resistance. J Clin Microbiol 2019; 57:e01405-18. [PMID: 30381421 PMCID: PMC6425178 DOI: 10.1128/jcm.01405-18] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. We examine differences between calling antibiotic resistance profiles by the simple presence or absence of previously known genes and single-nucleotide polymorphisms (SNPs) against approaches that deploy machine learning and statistical models. Often, the limitations to genome-based prediction arise from limitations of accuracy of culture-based AST in addition to an incomplete knowledge of the genetic basis of resistance. However, we need to maintain phenotypic testing even as genome-based prediction becomes more widespread to ensure that the results do not diverge over time. We argue that standardization of WGS-AST by challenge with consistently phenotyped strain sets of defined genetic diversity is necessary to compare the efficacy of methods of prediction of antibiotic resistance based on genome sequences.
Collapse
Affiliation(s)
- Michelle Su
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antimicrobial Resistance and Therapeutic Discovery Training Program, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
| | - Sarah W Satola
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
- Emory Investigational Clinical Microbiology Laboratory, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Infectious Diseases, Emory University, Atlanta, Georgia, USA
- Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
- Emory Investigational Clinical Microbiology Laboratory, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
32
|
Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, van Crevel R, Alisjahbana B. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. J Glob Antimicrob Resist 2019; 16:170-177. [DOI: 10.1016/j.jgar.2018.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/06/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022] Open
|
33
|
Iwamoto T, Murase Y, Yoshida S, Aono A, Kuroda M, Sekizuka T, Yamashita A, Kato K, Takii T, Arikawa K, Kato S, Mitarai S. Overcoming the pitfalls of automatic interpretation of whole genome sequencing data by online tools for the prediction of pyrazinamide resistance in Mycobacterium tuberculosis. PLoS One 2019; 14:e0212798. [PMID: 30817803 PMCID: PMC6394917 DOI: 10.1371/journal.pone.0212798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/09/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Automated online software tools that analyse whole genome sequencing (WGS) data without the need for bioinformatics expertise can motivate the implementation of WGS-based molecular drug susceptibility testing (DST) in routine diagnostic settings for tuberculosis (TB). Pyrazinamide (PZA) is a key drug for current and future TB treatment regimens; however, it was reported that predictive power for PZA resistance by the available tools is low. Therefore, this low predictive power may make users hesitant to use the tools. This study aimed to elucidate why and to uncover the real performance of the tools when taking into account their variation calling lists (manual inspection), not just their automated reporting system (default setting) that was evaluated by previous studies. METHODS WGS data from 191 datasets comprising 108 PZA-resistant and 83 susceptible strains were used to evaluate the potential performance of the available online tools (TB Profiler, TGS-TB, PhyResSE, and CASTB) for predicting phenotypic PZA resistance. RESULTS When taking into consideration the variation calling lists, 73 variants in total (47 non-synonymous mutations and 26 indels) in pncA were detected by TGS-TB and PhyResSE, covering all mutations for the 108 PZA-resistant strains. The 73 variants were confirmed by Sanger sequencing. TB Profiler also detected all but three complete loss, two large deletion at the 3'-end, and one relatively large insertion of pncA. On the other hand, many of the 73 variants were lacking in the automated reporting systems except by TGS-TB; of these variants, CASTB detected only 20. By applying the 'non-wild type sequence' approach for predicting PZA resistance, accuracy of the results significantly improved compared with that of the automated results obtained by each tool. CONCLUSION Users can obtain more accurate predictions for PZA resistance than previously reported by manually checking the results and applying the 'non-wild type sequence' approach.
Collapse
Affiliation(s)
- Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe City, Japan
- * E-mail: (TI); (SM)
| | - Yoshiro Murase
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Akio Aono
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Takemasa Takii
- Molecular Epidemiology Division, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe City, Japan
| | - Seiya Kato
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
| | - Satoshi Mitarai
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose City, Tokyo, Japan
- Basic Mycobacteriosis, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, Nagasaki, Japan
- * E-mail: (TI); (SM)
| |
Collapse
|
34
|
Al-Mutairi NM, Ahmad S, Mokaddas E, Eldeen HS, Joseph S. Occurrence of disputed rpoB mutations among Mycobacterium tuberculosis isolates phenotypically susceptible to rifampicin in a country with a low incidence of multidrug-resistant tuberculosis. BMC Infect Dis 2019; 19:3. [PMID: 30606116 PMCID: PMC6318973 DOI: 10.1186/s12879-018-3638-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/19/2018] [Indexed: 11/17/2022] Open
Abstract
Background Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis in clinical specimens and culture isolates to first-line drugs is crucial for diagnosis and management of multidrug-resistant tuberculosis (MDR-TB). Resistance of M. tuberculosis to rifampicin is mainly due to mutations in hot-spot region of rpoB gene (HSR-rpoB). The prevalence of disputed (generally missed by rapid phenotypic DST methods) rpoB mutations, which mainly include L511P, D516Y, H526N, H526L, H526S, and L533P in HSR-rpoB and I572F in cluster II region of rpoB gene, is largely unknown. This study determined the occurrence of all disputed mutations in HSR-rpoB and at rpoB codon 572 in M. tuberculosis strains phenotypically susceptible to rifampicin in Kuwait. Methods A total of 242 M. tuberculosis isolates phenotypically susceptible to rifampicin were used. The DST against first-line drugs was performed by Mycobacteria growth indicator tube (MGIT) 960 system. Mutations in HSR-rpoB (and katG codon 315 and inhA-regulatory region for isoniazid resistance) were detected by GenoType MDBDRplus assay. The I572F mutation in cluster II region of rpoB was detected by developing a multiplex allele-specific (MAS)-PCR assay. Results were confirmed by PCR-sequencing of respective loci. Molecular detection of resistance for ethambutol and pyrazinamide and fingerprinting by spoligotyping were also performed for isolates with an rpoB mutation. Results Among 242 rifampicin-susceptible isolates, 0 of 130 pansusceptible/monodrug-resistant isolates but 4 of 112 polydrug-resistant isolates contained a disputed rpoB mutation. All 4 isolates were also resistant to isoniazid and molecular screening identified additional resistance to pyrazinamide and ethambutol in one isolate each. In final analysis, 2 of 4 isolates were resistant to all 4 first-line drugs. Spoligotyping showed that the isolates belonged to different M. tuberculosis lineages. Conclusions Four of 242 (1.7%) rifampicin-susceptible M. tuberculosis isolates contained a disputed rpoB mutation including 2 isolates resistant to all four first-line drugs. The occurrence of a disputed rpoB mutation in polydrug-resistant M. tuberculosis isolates resistant at least to isoniazid (MDR-TB) suggests that polydrug-resistant strains should be checked for genotypic rifampicin resistance for optimal patient management since the failure/relapse rates are nearly same in isolates with a canonical or disputed rpoB mutation.
Collapse
Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | | | - Susan Joseph
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| |
Collapse
|
35
|
Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology 2018; 23:1098-1113. [PMID: 30189463 DOI: 10.1111/resp.13393] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/03/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is the deadliest infectious disease and the associated global threat has worsened with the emergence of drug resistance, in particular multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Although the World Health Organization (WHO) End-TB Strategy advocates for universal access to antimicrobial susceptibility testing, this is not widely available and/or it is still underused. The majority of drug resistance in clinical MTB strains is attributed to chromosomal mutations. Resistance-related mutations could also exert certain fitness cost to the drug-resistant MTB strains and growth fitness could be restored by the presence of compensatory mutations. Understanding these underlying mechanisms could provide an important insight into TB pathogenesis and predict the future trend of MDR-TB global pandemic. This review covers the mechanisms of resistance in MTB and provides a comprehensive overview of current phenotypic and molecular approaches for drug susceptibility testing, with particular attention to the methods endorsed and recommended by the WHO.
Collapse
Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital Compound, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
36
|
Ssengooba W, Nakayita G, Namaganda CC, Joloba ML. Agreement of Middle brook 7H10 with Lowenstein Jensen and accuracy of the Sensititre MYCOTB plate using either method as a reference standard for Mycobacterium tuberculosis first line drug susceptibility testing. PLoS One 2018; 13:e0199638. [PMID: 29953491 PMCID: PMC6023171 DOI: 10.1371/journal.pone.0199638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/11/2018] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Although Sensititre Mycobacterium tuberculosis (MYCOTB) plate offers both drug susceptibility testing (DST) and minimum inhibitory concentration (MIC) results, it has not been evaluated against both Lowenstein Jensen (LJ) and Middlebrook 7H10 (MB7H10) DST methods at standard critical concentrations. MATERIALS AND METHODS We analyzed 76 M. tuberculosis isolates consisting of 54 isolates from the Uganda National TB drug resistance survey done December 2009-February 2011 and 22 isolates from the World Health Organization External Quality Assessment panel for the year 2011. All isolates were tested for LJ, MB7H10 and MYCOTB plate based DSTs for streptomycin, isoniazid, rifampicin and ethambutol anti-tuberculosis drugs. The agreement of MB7H10 with LJ and accuracy of MYCOTB plate using either LJ-DST or MB7H10 as a reference standard were determined. RESULTS The agreement (kappa) of MB7H10 with LJ was; 0.687 for rifampicin, 0.498 for isoniazid, 0.275 for streptomycin and 0.082 for ethambutol which as almost similar when compared with MYCOTB plate. The sensitivity (95% confidence interval; CI) of MYCOTB plate when LJ was used as a reference standard was higher for streptomycin 87.5% (81.6-98.4) followed by isoniazid 75.9% (65.1-95.6) and rifampicin 73.1% (52.2-88.4). When MB7H10 was used as reference standard, the sensitivity of MYCOTB plate improved significantly; isoniazid 96.2% (80.3-99.9), rifampicin 94.0 (83.4-98.7) and 93.8% (69.7-99.8). There was good agreement between MYCOTB plate and MB7H10; 1.00 for ethambutol, 0.959 for streptomycin, 0.915 for rifampicin and 0.778 for isoniazid. CONCLUSIONS The performance of the two culture-based reference standards for phenotypic first-line drug susceptibility testing methods, LJ and MB7H10, varied much even with acceptable MYCOTB plate MICs. There was acceptable agreement and accuracy of MYCOTB plate for drug susceptibility testing when MB7H10 was used as reference standard than with LJ-DST. Results from MIC information makes the MYCOTB plate more suitable for guiding clinicians on the choice of the most appropriate TB treatment regimen as well as limits of detection for TB drug resistance.
Collapse
Affiliation(s)
- Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Germine Nakayita
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Carolyn C. Namaganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Kampala, Uganda
| |
Collapse
|
37
|
Ruesen C, Riza AL, Florescu A, Chaidir L, Editoiu C, Aalders N, Nicolosu D, Grecu V, Ioana M, van Crevel R, van Ingen J. Linking minimum inhibitory concentrations to whole genome sequence-predicted drug resistance in Mycobacterium tuberculosis strains from Romania. Sci Rep 2018; 8:9676. [PMID: 29946139 PMCID: PMC6018741 DOI: 10.1038/s41598-018-27962-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/01/2018] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance poses a major threat to tuberculosis control. Current phenotypic tests for drug susceptibility are time-consuming, technically complex, and expensive. Whole genome sequencing is a promising alternative, though the impact of different drug resistance mutations on the minimum inhibitory concentration (MIC) remains to be investigated. We examined the genomes of 72 phenotypically drug-resistant Mycobacterium tuberculosis isolates from 72 Romanian patients for drug resistance mutations. MICs for first- and second-line drugs were determined using the MycoTB microdilution method. These MICs were compared to macrodilution critical concentration testing by the Mycobacterium Growth Indicator Tube (MGIT) platform and correlated to drug resistance mutations. Sixty-three (87.5%) isolates harboured drug resistance mutations; 48 (66.7%) were genotypically multidrug-resistant. Different drug resistance mutations were associated with different MIC ranges; katG S315T for isoniazid, and rpoB S450L for rifampicin were associated with high MICs. However, several mutations such as in rpoB, rrs and rpsL, or embB were associated with MIC ranges including the critical concentration for rifampicin, aminoglycosides or ethambutol, respectively. Different resistance mutations lead to distinct MICs, some of which may still be overcome by increased dosing. Whole genome sequencing can aid in the timely diagnosis of Mycobacterium tuberculosis drug resistance and guide clinical decision-making.
Collapse
Affiliation(s)
- Carolien Ruesen
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Anca Lelia Riza
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Adriana Florescu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Lidya Chaidir
- Health Research Unit, Faculty of Medicine, Padjadjaran University/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Cornelia Editoiu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Nicole Aalders
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Dragos Nicolosu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Victor Grecu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Mihai Ioana
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| |
Collapse
|
38
|
Rapid Microarray-Based Detection of Rifampin, Isoniazid, and Fluoroquinolone Resistance in Mycobacterium tuberculosis by Use of a Single Cartridge. J Clin Microbiol 2018; 56:JCM.01249-17. [PMID: 29212699 PMCID: PMC5786735 DOI: 10.1128/jcm.01249-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023] Open
Abstract
The rapid and robust identification of mutations in Mycobacterium tuberculosis complex (MTBC) strains mediating multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes is crucial to combating the MDR tuberculosis (TB) epidemic. Currently available molecular anti-TB drug susceptibility tests either are restricted to a single target or drug (i.e., the Xpert MTB/RIF test) or present a risk of cross-contamination due to the design limitations of the open platform (i.e., line probe assays). With a good understanding of the technical and commercial boundaries, we designed a test cartridge based on an oligonucleotide array into which dried reagents are introduced and which has the ability to identify MTBC strains resistant to isoniazid, rifampin, and the fluoroquinolones. The melting curve assay interrogates 43 different mutations in the rifampin resistance-determining region (RRDR) of rpoB, rpoB codon 572, katG codon 315, the inhA promoter region, and the quinolone resistance-determining region (QRDR) of gyrA in a closed cartridge system within 90 min. Assay performance was evaluated with 265 clinical MTBC isolates, including MDR/XDR, non-MDR, and fully susceptible isolates, from a drug resistance survey performed in Swaziland in 2009 and 2010. In 99.5% of the cases, the results were consistent with data previously acquired utilizing Sanger sequencing. The assay, which uses a closed cartridge system in combination with a battery-powered Alere q analyzer and which has the potential to extend the current gene target panel, could serve as a rapid and robust point-of-care test in settings lacking a comprehensive molecular laboratory infrastructure to differentiate TB patients infected with MDR and non-MDR strains and to assist clinicians with their early treatment decisions.
Collapse
|
39
|
Burke RM, Coronel J, Moore D. Minimum inhibitory concentration distributions for first- and second-line antimicrobials against Mycobacterium tuberculosis. J Med Microbiol 2017; 66:1023-1026. [PMID: 28759352 DOI: 10.1099/jmm.0.000534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the range of minimum inhibitory concentrations for six antimicrobial drugs in 228 clinical Mycobacterium tuberculosis (MTB) isolates from three distinct groups of patients (unselected patients, patients at high risk of drug-resistant TB and HIV-positive patients) in Lima, Peru. These data highlight the challenges of and discriminatory characteristics required for MTB drug susceptibility testing.
Collapse
Affiliation(s)
- Rachael M Burke
- Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, UK
| | - Jorge Coronel
- Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - David Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK.,Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru.,Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, UK
| |
Collapse
|
40
|
Kwak M, Lee WK, Lim YJ, Lee SH, Ryoo S. Systematic review and meta-analysis of the nitrate reductase assay for drug susceptibility testing of Mycobacterium tuberculosis and the detection limits in liquid medium. J Microbiol Methods 2017; 141:1-9. [PMID: 28694139 DOI: 10.1016/j.mimet.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 10/19/2022]
Abstract
Recently, the need for rapid, reliable, and low-cost drug susceptibility testing (DST) methods has increased due to the emergence of multidrug-resistant Mycobacterium tuberculosis. Colorimetric methods of DST provide results more quickly than standard culture methods and are inexpensive than molecular methods. Thus, colorimetric methods, such as the nitrate reductase assay (NRA), are being recommended. We searched Medline PubMed for reports on the NRA for DST of M. tuberculosis written in English and published within the last five years. We selected 20 reports on six major anti-TB drugs and conducted a meta-analysis using Meta-Disc software. The pooled sensitivities for isoniazid, rifampicin, streptomycin, ethambutol, ofloxacin, and kanamycin were 95.4%, 96.4%, 91.5%, 93.1%, 99.3%, and 88.4%, and the pooled specificities were 98.5%, 99.2%, 92.9%, 97.8%, 97.4%, and 99.4%, respectively. The area under the summary receiver operator curve for all drugs was 0.9723-0.9952. The time to results (TTR) for the direct and indirect NRAs was 7-28days and 6-15days, respectively. Quality assessments were conducted using the quality of diagnostic accuracy studies tool (QUADAS-2) items, and most reports showed good performance. However, ethambutol, streptomycin, and kanamycin showed relatively low sensitivity. We performed a quantitative NRA in liquid media at various inoculum concentrations. The TTR at 4.94×106, 1.67×104, and 2.27×102CFU/mL was 4, 14, and 14days, respectively. The minimum absorbance and nitrite concentration for positive samples were 0.8 and 168μM, respectively. We propose a quantitative standard to determine sample positivity to address the problems with the current standard NRA which is much less expensive than the conventional assay conducted on solid medium.
Collapse
Affiliation(s)
- Miri Kwak
- Hana Pharmaceutical Pangyo R&D Center, Innovally E-dong, 255, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13550, Republic of Korea
| | - Won-Kyu Lee
- Osong Medical Innovation Foundation, 123 Osongsaengmyeong-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Young Ju Lim
- CELLTRION, Academy-ro 51beon-gil, Yeonsu-gu, Incheon 22014, Republic of Korea
| | - Seung Heon Lee
- Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan 15355, Republic of Korea
| | - Sungweon Ryoo
- Korean National Tuberculosis Association, 57 Baumoe 6-gil, Seocho-gu 06763, Republic of Korea.
| |
Collapse
|
41
|
Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
Collapse
|
42
|
Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med 2016; 194:621-30. [PMID: 26910495 PMCID: PMC5027209 DOI: 10.1164/rccm.201510-2091oc] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/22/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The development of molecular diagnostics that detect both the presence of Mycobacterium tuberculosis in clinical samples and drug resistance-conferring mutations promises to revolutionize patient care and interrupt transmission by ensuring early diagnosis. However, these tools require the identification of genetic determinants of resistance to the full range of antituberculosis drugs. OBJECTIVES To determine the optimal molecular approach needed, we sought to create a comprehensive catalog of resistance mutations and assess their sensitivity and specificity in diagnosing drug resistance. METHODS We developed and validated molecular inversion probes for DNA capture and deep sequencing of 28 drug-resistance loci in M. tuberculosis. We used the probes for targeted sequencing of a geographically diverse set of 1,397 clinical M. tuberculosis isolates with known drug resistance phenotypes. We identified a minimal set of mutations to predict resistance to first- and second-line antituberculosis drugs and validated our predictions in an independent dataset. We constructed and piloted a web-based database that provides public access to the sequence data and prediction tool. MEASUREMENTS AND MAIN RESULTS The predicted resistance to rifampicin and isoniazid exceeded 90% sensitivity and specificity but was lower for other drugs. The number of mutations needed to diagnose resistance is large, and for the 13 drugs studied it was 238 across 18 genetic loci. CONCLUSIONS These data suggest that a comprehensive M. tuberculosis drug resistance diagnostic will need to allow for a high dimension of mutation detection. They also support the hypothesis that currently unknown genetic determinants, potentially discoverable by whole-genome sequencing, encode resistance to second-line tuberculosis drugs.
Collapse
MESH Headings
- Antitubercular Agents/pharmacology
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genes, Bacterial/drug effects
- Genes, Bacterial/genetics
- Humans
- Molecular Diagnostic Techniques
- Mutation/drug effects
- Mutation/genetics
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Multidrug-Resistant/microbiology
Collapse
Affiliation(s)
- Maha R. Farhat
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Razvan Sultana
- Genomics England, Queen Mary University, London, United Kingdom
| | - Oleg Iartchouk
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - James Galagan
- Department of Biomedical Engineering
- Department of Microbiology, and
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | | | | | - Hanna Nebenzahl-Guimaraes
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3Bs, PT Government Associate Laboratory, Braga/Guimaraes, Portugal
| | - Karen Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Devinder Kaur
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barry N. Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Leen Rigouts
- Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical Sciences, Antwerp University, Antwerp, Belgium; and
| | - Elizabeth M. Streicher
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tommie C. Victor
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M. Warren
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Dick van Soolingen
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| |
Collapse
|
43
|
Song KS, Nimse SB, Kim HJ, Yang J, Kim T. Accurate Detection of Rifampicin-Resistant Mycobacterium Tuberculosis Strains. SENSORS 2016; 16:s16030376. [PMID: 26999135 PMCID: PMC4813951 DOI: 10.3390/s16030376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 11/18/2022]
Abstract
In 2013 alone, the death rate among the 9.0 million people infected with Mycobacterium tuberculosis (TB) worldwide was around 14%, which is unacceptably high. An empiric treatment of patients infected with TB or drug-resistant Mycobacterium tuberculosis (MDR-TB) strain can also result in the spread of MDR-TB. The diagnostic tools which are rapid, reliable, and have simple experimental protocols can significantly help in decreasing the prevalence rate of MDR-TB strain. We report the evaluation of the 9G technology based 9G DNAChips that allow accurate detection and discrimination of TB and MDR-TB-RIF. One hundred and thirteen known cultured samples were used to evaluate the ability of 9G DNAChip in the detection and discrimination of TB and MDR-TB-RIF strains. Hybridization of immobilized probes with the PCR products of TB and MDR-TB-RIF strains allow their detection and discrimination. The accuracy of 9G DNAChip was determined by comparing its results with sequencing analysis and drug susceptibility testing. Sequencing analysis showed 100% agreement with the results of 9G DNAChip. The 9G DNAChip showed very high sensitivity (95.4%) and specificity (100%).
Collapse
Affiliation(s)
- Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Hee Jin Kim
- Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Cheongju-si 28158, Korea.
| | - Jeongseong Yang
- Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Cheongju-si 28158, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| |
Collapse
|
44
|
Coeck N, de Jong BC, Diels M, de Rijk P, Ardizzoni E, Van Deun A, Rigouts L. Correlation of different phenotypic drug susceptibility testing methods for four fluoroquinolones in Mycobacterium tuberculosis. J Antimicrob Chemother 2016; 71:1233-40. [PMID: 26851609 PMCID: PMC4830418 DOI: 10.1093/jac/dkv499] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Background Molecular resistance testing fails to explain all fluoroquinolone resistance, with a continued need for a suitable rapid phenotypic drug susceptibility testing method. Objective To evaluate the optimal method for phenotypic fluoroquinolone susceptibility testing. Methods Using Löwenstein–Jensen medium, Middlebrook 7H11 agar, BACTEC-MGIT 960 and the resazurin microtitre plate assay, we determined susceptibility to fluoroquinolones in Mycobacterium tuberculosis and investigated cross-resistance between ofloxacin, levofloxacin, moxifloxacin and gatifloxacin. We compared MICs of all four fluoroquinolones for 91 strains on Löwenstein–Jensen (as the gold standard) with their MICs in resazurin plates, and with ofloxacin susceptibility at a single concentration in MGIT and on 7H11 agar, in addition to sequencing of the gyrAB genes. Results and conclusions Applying a cut-off of 2 mg/L ofloxacin, 1 mg/L levofloxacin and 0.5 mg/L moxifloxacin and gatifloxacin in all methods, some discordance between solid medium and MGIT methods was observed, yet this tended to be explained by MICs around the cut-off. The high discordance between Löwenstein–Jensen (LJ) and resazurin plates suggests that the currently applied cut-offs for all fluoroquinolones in the resazurin method should decrease and minor changes in colour (from blue to purple) be considered as meaningful. High-level resistance in all assays to all drugs correlated well with the presence of gyrA mutations, in support of recent findings that fluoroquinolone resistance should be tested at different concentrations, as patients with lower levels of resistance may continue to benefit from high-dose fluoroquinolone-based therapy.
Collapse
Affiliation(s)
- Nele Coeck
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Medicine, Division of Infectious Diseases, New York University, New York, USA Vaccinology Department, Medical Research Council Unit, Fajara, The Gambia
| | - Maren Diels
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pim de Rijk
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elisa Ardizzoni
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Médecins Sans Frontières, Paris, France
| | - Armand Van Deun
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| |
Collapse
|
45
|
Lee RS, Behr MA. The implications of whole-genome sequencing in the control of tuberculosis. Ther Adv Infect Dis 2015; 3:47-62. [PMID: 27034776 DOI: 10.1177/2049936115624630] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The availability of whole-genome sequencing (WGS) as a tool for the diagnosis and clinical management of tuberculosis (TB) offers considerable promise in the fight against this stubborn epidemic. However, like other new technologies, the best application of WGS remains to be determined, for both conceptual and technical reasons. In this review, we consider the potential value of WGS in the clinical laboratory for the detection of Mycobacterium tuberculosis and the prediction of antibiotic resistance. We also discuss issues pertaining to data generation, interpretation and dissemination, given that WGS has to date been generally performed in research labs where results are not necessarily packaged in a clinician-friendly format. Although WGS is far more accessible now than it was in the past, the transition from a research tool to study TB into a clinical test to manage this disease may require further fine-tuning. Improvements will likely come through iterative efforts that involve both the laboratories ready to move TB into the genomic era and the front-line clinical/public health staff who will be interpreting the results to inform management decisions.
Collapse
Affiliation(s)
- Robyn S Lee
- McGill University, Department of Epidemiology, Biostatistics and Occupational Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Montreal, QC, Canada
| | | |
Collapse
|
46
|
Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. THE LANCET RESPIRATORY MEDICINE 2015; 4:49-58. [PMID: 26669893 PMCID: PMC4698465 DOI: 10.1016/s2213-2600(15)00466-x] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/17/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
Background Slow and cumbersome laboratory diagnostics for Mycobacterium tuberculosis complex (MTBC) risk delayed treatment and poor patient outcomes. Whole-genome sequencing (WGS) could potentially provide a rapid and comprehensive diagnostic solution. In this prospective study, we compare real-time WGS with routine MTBC diagnostic workflows. Methods We compared sequencing mycobacteria from all newly positive liquid cultures with routine laboratory diagnostic workflows across eight laboratories in Europe and North America for diagnostic accuracy, processing times, and cost between Sept 6, 2013, and April 14, 2014. We sequenced specimens once using local Illumina MiSeq platforms and processed data centrally using a semi-automated bioinformatics pipeline. We identified species or complex using gene presence or absence, predicted drug susceptibilities from resistance-conferring mutations identified from reference-mapped MTBC genomes, and calculated genetic distance to previously sequenced UK MTBC isolates to detect outbreaks. WGS data processing and analysis was done by staff masked to routine reference laboratory and clinical results. We also did a microcosting analysis to assess the financial viability of WGS-based diagnostics. Findings Compared with routine results, WGS predicted species with 93% (95% CI 90–96; 322 of 345 specimens; 356 mycobacteria specimens submitted) accuracy and drug susceptibility also with 93% (91–95; 628 of 672 specimens; 168 MTBC specimens identified) accuracy, with one sequencing attempt. WGS linked 15 (16% [95% CI 10–26]) of 91 UK patients to an outbreak. WGS diagnosed a case of multidrug-resistant tuberculosis before routine diagnosis was completed and discovered a new multidrug-resistant tuberculosis cluster. Full WGS diagnostics could be generated in a median of 9 days (IQR 6–10), a median of 21 days (IQR 14–32) faster than final reference laboratory reports were produced (median of 31 days [IQR 21–44]), at a cost of £481 per culture-positive specimen, whereas routine diagnosis costs £518, equating to a WGS-based diagnosis cost that is 7% cheaper annually than are present diagnostic workflows. Interpretation We have shown that WGS has a scalable, rapid turnaround, and is a financially feasible method for full MTBC diagnostics. Continued improvements to mycobacterial processing, bioinformatics, and analysis will improve the accuracy, speed, and scope of WGS-based diagnosis. Funding National Institute for Health Research, Department of Health, Wellcome Trust, British Colombia Centre for Disease Control Foundation for Population and Public Health, Department of Clinical Microbiology, Trinity College Dublin.
Collapse
|
47
|
Abstract
The concept of antimicrobial susceptibility testing is an essential part of clinical microbiology. Antimicrobial testing has played a central role in the identification of new antibiotics and defining their clinical uses. Here we describe different approaches to determine the activity of compounds in medium- or high-throughput format.
Collapse
|
48
|
Song KS, Nimse SB, Cho NH, Sung N, Kim HJ, Yang J, Kim T. MTB-DR-RIF 9G test: Detection and discrimination of tuberculosis and multi-drug resistant tuberculosis strains. Tuberculosis (Edinb) 2015; 95:780-785. [PMID: 26381057 DOI: 10.1016/j.tube.2015.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
Abstract
This report describes the evaluation of the novel MTB-DR-RIF 9G test for the accurate detection and discrimination of Mycobacterium tuberculosis (MTB) and rifampicin-resistant M. tuberculosis (MTB-DR-RIF) in the clinical samples. The procedure included the amplification of a nucleotide fragment of the rpoB gene of the MTB and MTB-DR-RIF strains and their hybridization with the immobilized probes. The MTB-DR-RIF 9G test was evaluated for its ability to detect and discriminate MTB and MTB-DR-RIF strains in 113 known clinical samples. The accuracy of the MTB-DR-RIF 9G test was determined by comparing its results with sequencing analysis and drug susceptibility testing. The sensitivity and specificity of the MTB-DR-RIF 9G test at 95% confidence interval were found to be 95.4% (89.5-98.5) and 100% (69.2-100), respectively. The positive predictive value and negative predictive value of the MTB-DR-RIF 9G test at 95% confidence interval were found to be 100% (85.0-95.9) and 66.7% (38.4-88.18), respectively. Sequencing analysis of all samples indicated that the mutations present in the regions identified with the MTB-DR-RIF 9G assay can be detected accurately.
Collapse
Affiliation(s)
- Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon, 200-161, Republic of Korea
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 200-702, Republic of Korea
| | - Nam Hoon Cho
- Department of Pathology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Nackmoon Sung
- National Masan Hospital, Clinical Research Center, Changwon, Republic of Korea
| | - Hee-Jin Kim
- Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Cheongju-si, Republic of Korea
| | - Jeongseong Yang
- Korea Mycobacterium Resource Center (KMRC), The Korean Institute of Tuberculosis, Cheongju-si, Republic of Korea
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 200-702, Republic of Korea.
| |
Collapse
|
49
|
Miotto P, Cirillo DM, Migliori GB. Drug resistance in Mycobacterium tuberculosis: molecular mechanisms challenging fluoroquinolones and pyrazinamide effectiveness. Chest 2015; 147:1135-1143. [PMID: 25846529 DOI: 10.1378/chest.14-1286] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Physicians are more and more often challenged by difficult-to-treat cases of TB. They include patients infected by strains of Mycobacterium tuberculosis that are resistant to at least isoniazid and rifampicin (multidrug-resistant TB) or to at least one fluoroquinolone (FQ) and one injectable, second-line anti-TB drug in addition to isoniazid and rifampicin (extensively drug-resistant TB). The drug treatment of these cases is very long, toxic, and expensive, and, unfortunately, the proportion of unsatisfactory outcomes is still considerably high. Although FQs and pyrazinamide (PZA) are backbone drugs in the available anti-TB regimens, several uncertainties remain about their mechanisms of action and even more remain about the mechanisms leading to drug resistance. From a clinical point of view, a better understanding of the genetic basis of drug resistance will aid (1) clinicians to provide quality clinical management to both drug-susceptible and drug-resistant TB cases (while preventing emergence of further resistance), and (2) developers of new molecular-based diagnostic assays to better direct their research efforts toward a new generation of sensitive, specific, cheap, and easy-to-use point-of-care diagnostics. In this review we provide an update on the molecular mechanisms leading to FQ- and PZA-resistance in M tuberculosis.
Collapse
Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Battista Migliori
- WHO Collaborating Centre for TB and Lung Diseases, Fondazione S. Maugeri, Care and Research Institute, Tradate, Italy.
| |
Collapse
|
50
|
Denkinger CM, Dolinger D, Schito M, Wells W, Cobelens F, Pai M, Zignol M, Cirillo DM, Alland D, Casenghi M, Gallarda J, Boehme CC, Perkins MD. Target product profile of a molecular drug-susceptibility test for use in microscopy centers. J Infect Dis 2015; 211 Suppl 2:S39-49. [PMID: 25765105 DOI: 10.1093/infdis/jiu682] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Current phenotypic testing for drug resistance in patients with tuberculosis is inadequate primarily with respect to turnaround time. Molecular tests hold the promise of an improved time to diagnosis. METHODS A target product profile for a molecular drug-susceptibility test (DST) was developed on the basis of a collaborative effort that included opinions gathered from researchers, clinicians, policy makers, and test developers on optimal clinical and operational characteristics in settings of intended use. In addition, the current diagnostic ecosystem and the diagnostic development landscape were mapped. RESULTS Molecular DSTs for detecting tuberculosis in microscopy centers should ideally evaluate for resistance to rifampin, fluoroquinolones, isoniazid, and pyrazinamide and enable the selection of the most appropriate treatment regimen. Performance characteristics of DSTs need to be optimized, but compromises can be made that depend on the trade-off between a false-positive result and a false-negative result. The operational requirements of a test will vary depending on the site of implementation. However, the most-important considerations pertain to quality control, maintenance and calibration, and the ability to export data. CONCLUSION This target product profile defines the needs as perceived by the tuberculosis stakeholder community and attempts to provide a means of communication with test developers to ensure that fit-for-purpose DSTs are being developed.
Collapse
Affiliation(s)
- Claudia M Denkinger
- FIND Division of Infectious Disease, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Marco Schito
- Division of AIDS, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | | | - Frank Cobelens
- KNCV Tuberculosis Foundation, the Hague Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - Madhukar Pai
- McGill International TB Centre Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | | | | | | | | | - Jim Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington
| | | | | |
Collapse
|