151
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Cancino-Muñoz I, Moreno-Molina M, Furió V, Goig GA, Torres-Puente M, Chiner-Oms Á, Villamayor LM, Sanz F, Guna-Serrano MR, Comas I. Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis. J Infect Dis 2020; 220:316-320. [PMID: 30875421 PMCID: PMC6581888 DOI: 10.1093/infdis/jiz104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
Understanding why some multidrug-resistant tuberculosis cases are not detected by rapid phenotypic and genotypic routine clinical tests is essential to improve diagnostic assays and advance toward personalized tuberculosis treatment. Here, we combine whole-genome sequencing with single-colony phenotyping to identify a multidrug-resistant strain that had infected a patient for 9 years. Our investigation revealed the failure of rapid testing and genome-based prediction tools to identify the multidrug-resistant strain. The false-negative findings were caused by uncommon rifampicin and isoniazid resistance mutations. Although whole-genome sequencing data helped to personalize treatment, the patient developed extensively drug-resistant tuberculosis, highlighting the importance of coupling new diagnostic methods with appropriate treatment regimens.
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Affiliation(s)
- Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas.,Genomics and Health Unit, FISABIO Public Health, Consorci Hospital General Universitari de València, Valencia, Spain
| | - Miguel Moreno-Molina
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Victoria Furió
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Galo A Goig
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Manuela Torres-Puente
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Álvaro Chiner-Oms
- Unidad Mixta "Infección y Salud Pública," Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Conselleria de Sanitat Universal i Salut Pública
| | - Luis M Villamayor
- Genomics and Health Unit, FISABIO Public Health, Consorci Hospital General Universitari de València, Valencia, Spain
| | - Francisco Sanz
- Departamento de Neumología, Consorci Hospital General Universitari de València, Valencia, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
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152
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Katale BZ, Mbelele PM, Lema NA, Campino S, Mshana SE, Rweyemamu MM, Phelan JE, Keyyu JD, Majigo M, Mbugi EV, Dockrell HM, Clark TG, Matee MI, Mpagama S. Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. BMC Genomics 2020; 21:174. [PMID: 32085703 PMCID: PMC7035673 DOI: 10.1186/s12864-020-6577-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/12/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB. RESULTS This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant's clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29-44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI < 18 kg/m2 respectively. MDR-TB participants had MTBC with multiple mutant genes, compared to those with mono or polyresistant TB, and the majority belonged to lineage 3 Central Asian Strain (CAS). Also, MDR-TB was associated with delayed culture-conversion (median: IQR (83: 60-180 vs. 51:30-66) days). WGS had high concordance with both culture-based DST and Xpert® MTB/RIF assay in detecting drug resistance (kappa = 1.00). CONCLUSION This study offers comparison of mutations detected by Xpert and WGS with phenotypic DST of M. tuberculosis isolates in Tanzania. The high concordance between the different methods and further insights provided by WGS such as PZA-DST, which is not routinely performed in most resource-limited-settings, provides an avenue for inclusion of WGS into diagnostic matrix of TB including drug-resistant TB.
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Affiliation(s)
- Bugwesa Z Katale
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Peter M Mbelele
- Kibong'oto Infectious Disease Hospital (KIDH), Sanya Juu, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Nsiande A Lema
- Field Epidemiology and Laboratory Training Programme, Dar es Salaam, Tanzania
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Stephen E Mshana
- Department of Medical Microbiology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Mark M Rweyemamu
- Southern African Centre for Infectious Diseases Surveillance (SACIDS), Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Mtebe Majigo
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Erasto V Mbugi
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania
| | - Hazel M Dockrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene &Tropical Medicine (LSHTM), Keppel Street, London, WC1E 7HT, UK
| | - Mecky I Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences (MUHAS), Dar es Salaam, Tanzania.
| | - Stellah Mpagama
- Kibong'oto Infectious Disease Hospital (KIDH), Sanya Juu, Tanzania
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153
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Kardan-Yamchi J, Kazemian H, Battaglia S, Abtahi H, Rahimi Foroushani A, Hamzelou G, Cirillo DM, Ghodousi A, Feizabadi MM. Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran. J Clin Med 2020; 9:jcm9020465. [PMID: 32046149 PMCID: PMC7073636 DOI: 10.3390/jcm9020465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.
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Affiliation(s)
- Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Hamidreza Abtahi
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Gholamreza Hamzelou
- Tehran Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
- Correspondence: (A.G.); (M.M.F.)
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Correspondence: (A.G.); (M.M.F.)
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154
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Campelo TA, Lima LNC, Lima KVB, Silva CS, da Conceição ML, Barreto JAP, Mota APP, Sancho SDO, Frota CC. Molecular characterization of pre-extensive drug resistant Mycobacterium tuberculosis in Northeast Brazil. Rev Inst Med Trop Sao Paulo 2020; 62:e4. [PMID: 32049255 PMCID: PMC7014566 DOI: 10.1590/s1678-9946202062004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
In Fortaleza, the capital of Ceara State, Brazil, the detection rate of tuberculosis (TB) in 2018 was 65.5/100,000 inhabitants with a cure rate of 59.1%, which is higher than the country average. This study investigated the risk factors associated with drug-resistant tuberculosis (DR-TB) and identified the drug-resistance phenotype and resistance-conferring mutations. The geographic distribution of DR-TB in Fortaleza, Brazil, was also determined. From March 2017 to February 2018, 41 DR-TB isolates and 69 drug-susceptible pulmonary TB isolates were obtained from patients seen at a referral hospital in Fortaleza, Brazil. Samples were subjected to phenotypic and genetic analysis of resistance; the spatial distribution of the participants was also analyzed. Primary resistance was high (50.9%) among participants. The following risk factors for DR were identified: being female ( p = 0.03), having diabetes ( p < 0.01), history of previous TB disease ( p < 0.01), and the number of intra-domiciliary contacts ( p < 0.01). Analysis by multiplex allele-specific polymerase chain reaction detected mutations in the genes katG (65.8%) , rpoB (43.9%), inhA promoter (14.6%), and gyrA (9.8%). Sequencing identified mutations in the the genes katG (75.6%), inhA promoter (19.5%), rpoB (85.4%), and gyrA (100%). There was no mutation in the rrs gene. Spatial analysis showed DR-TB isolates distributed in areas of low socioeconomic status in the city of Fortaleza. Our results emphasized the importance of detecting resistance to TB drugs. The resistance found in the gene gyrA is of concern due to the high number of pre-extensive DR-TB cases in Fortaleza.
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Affiliation(s)
- Thales Alves Campelo
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Luana Nepomuceno Costa Lima
- Instituto Evandro Chagas , Seção de Bacteriologia e Micologia, Ananindeua , Pará , Brazil
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | - Karla Valéria Batista Lima
- Instituto Evandro Chagas , Seção de Bacteriologia e Micologia, Ananindeua , Pará , Brazil
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | - Caroliny Soares Silva
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Marília Lima da Conceição
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | | | - Aquiles Paulino Peres Mota
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Soraya de Oliveira Sancho
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Cristiane Cunha Frota
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
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155
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Karmakar M, Rodrigues CHM, Horan K, Denholm JT, Ascher DB. Structure guided prediction of Pyrazinamide resistance mutations in pncA. Sci Rep 2020; 10:1875. [PMID: 32024884 PMCID: PMC7002382 DOI: 10.1038/s41598-020-58635-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
Pyrazinamide plays an important role in tuberculosis treatment; however, its use is complicated by side-effects and challenges with reliable drug susceptibility testing. Resistance to pyrazinamide is largely driven by mutations in pyrazinamidase (pncA), responsible for drug activation, but genetic heterogeneity has hindered development of a molecular diagnostic test. We proposed to use information on how variants were likely to affect the 3D structure of pncA to identify variants likely to lead to pyrazinamide resistance. We curated 610 pncA mutations with high confidence experimental and clinical information on pyrazinamide susceptibility. The molecular consequences of each mutation on protein stability, conformation, and interactions were computationally assessed using our comprehensive suite of graph-based signature methods, mCSM. The molecular consequences of the variants were used to train a classifier with an accuracy of 80%. Our model was tested against internationally curated clinical datasets, achieving up to 85% accuracy. Screening of 600 Victorian clinical isolates identified a set of previously unreported variants, which our model had a 71% agreement with drug susceptibility testing. Here, we have shown the 3D structure of pncA can be used to accurately identify pyrazinamide resistance mutations. SUSPECT-PZA is freely available at: http://biosig.unimelb.edu.au/suspect_pza/.
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Affiliation(s)
- Malancha Karmakar
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at The Peter Doherty Institute for Infection &Immunity, Melbourne, Victoria, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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156
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Migliori GB, Tiberi S, Zumla A, Petersen E, Chakaya JM, Wejse C, Muñoz Torrico M, Duarte R, Alffenaar JW, Schaaf HS, Marais BJ, Cirillo DM, Alagna R, Rendon A, Pontali E, Piubello A, Figueroa J, Ferlazzo G, García-Basteiro A, Centis R, Visca D, D'Ambrosio L, Sotgiu G. MDR/XDR-TB management of patients and contacts: Challenges facing the new decade. The 2020 clinical update by the Global Tuberculosis Network. Int J Infect Dis 2020; 92S:S15-S25. [PMID: 32032752 DOI: 10.1016/j.ijid.2020.01.042] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/20/2022] Open
Abstract
The continuous flow of new research articles on MDR-TB diagnosis, treatment, prevention and rehabilitation requires frequent update of existing guidelines. This review is aimed at providing clinicians and public health staff with an updated and easy-to-consult document arising from consensus of Global Tuberculosis Network (GTN) experts. The core published documents and guidelines have been reviewed, including the recently published MDR-TB WHO rapid advice and ATS/CDC/ERS/IDSA guidelines. After a rapid review of epidemiology and risk factors, the clinical priorities on MDR-TB diagnosis (including whole genome sequencing and drug-susceptibility testing interpretations) and treatment (treatment design and management, TB in children) are discussed. Furthermore, the review comprehensively describes the latest information on contact tracing and LTBI management in MDR-TB contacts, while providing guidance on post-treatment functional evaluation and rehabilitation of TB sequelae, infection control and other public health priorities.
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Affiliation(s)
- Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Via Roncaccio 16, Tradate, Varese, 21049, Italy.
| | - Simon Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Division of Infection, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom.
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, United Kingdom.
| | - Eskild Petersen
- Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman; Institute for Clinical Medicine, Faculty of Health Science, University of Aarhus, Denmark; ESCMID Emerging Infections Task Force, Basel, Switzerland.
| | - Jeremiah Muhwa Chakaya
- The International Union Against Tuberculosis and Lung Disease, Paris, France; Department of Medicine, Therapeutics, Dermatology and Psychiatry, Kenyatta University, Nairobi, Kenya.
| | - Christian Wejse
- Department of Infectious Disease, Aarhus University Hospital and School of Public Health, Faculty of Health Sciences, University of Aarhus, Denmark.
| | - Marcela Muñoz Torrico
- Clínica de Tuberculosis, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico.
| | - Raquel Duarte
- National Reference Centre for MDR-TB, Hospital Centre Vila Nova de Gaia, Department of Pneumology, Public Health Science and Medical Education Department, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - Jan Willem Alffenaar
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia; Westmead Hospital, Sydney, Australia; Dept. Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, The Netherlands.
| | - H Simon Schaaf
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Ben J Marais
- The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia; The University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, New South Wales, Australia.
| | - Daniela Maria Cirillo
- Emerging Pathogens Unit, TB Supranational Reference Laboratory, San Raffaele Scientific Institute, Milan, Italy.
| | - Riccardo Alagna
- Emerging Pathogens Unit, TB Supranational Reference Laboratory, San Raffaele Scientific Institute, Milan, Italy.
| | - Adrian Rendon
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias CIPTIR, University Hospital of Monterrey UANL (Universidad Autonoma de Nuevo Leon), Monterrey, Mexico.
| | - Emanuele Pontali
- Department of Infectious Diseases, Galliera Hospital, Genova, Italy.
| | - Alberto Piubello
- The International Union Against Tuberculosis and Lung Disease, Paris, France; Tuberculosis Division, Damien Foundation, Niamey, Niger.
| | - José Figueroa
- National Health Service (NHS) England, London, United Kingdom.
| | - Gabriella Ferlazzo
- Southern Africa Medical Unit, Médecins Sans Frontières, Cape Town, South Africa.
| | - Alberto García-Basteiro
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
| | - Rosella Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Via Roncaccio 16, Tradate, Varese, 21049, Italy.
| | - Dina Visca
- Division of Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS, Tradate, Italy; Department of Medicine and Surgery, Respiratory Diseases, University of Insubria, Varese, Italy.
| | | | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy.
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157
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Doyle RM, O'Sullivan DM, Aller SD, Bruchmann S, Clark T, Coello Pelegrin A, Cormican M, Diez Benavente E, Ellington MJ, McGrath E, Motro Y, Phuong Thuy Nguyen T, Phelan J, Shaw LP, Stabler RA, van Belkum A, van Dorp L, Woodford N, Moran-Gilad J, Huggett JF, Harris KA. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom 2020; 6:e000335. [PMID: 32048983 PMCID: PMC7067211 DOI: 10.1099/mgen.0.000335] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/17/2020] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories.
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Affiliation(s)
- Ronan M. Doyle
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Denise M. O'Sullivan
- Molecular and Cell Biology Team, National Measurement Laboratory, Queens Road, Teddington, Middlesex, UK
| | - Sean D. Aller
- Institute for Infection and Immunity, St George’s, University of London, Cranmer Terrace, London, UK
| | - Sebastian Bruchmann
- Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Taane Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Andreu Coello Pelegrin
- Clinical Unit, bioMérieux, La Balme Les Grottes, France
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Ernest Diez Benavente
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Elaine McGrath
- Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Yair Motro
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Thi Phuong Thuy Nguyen
- Department of BiNano Technology, College of BiNano Technology, Gachon University, Seoul, Republic of Korea
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Liam P. Shaw
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | | | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Neil Woodford
- NIS Laboratories, National Infection Service, Public Health England, London, UK
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jim F. Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, Queens Road, Teddington, Middlesex, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | - Kathryn A. Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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158
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Alffenaar JWC, Akkerman OW, Kim HY, Tiberi S, Migliori GB. Precision and personalized medicine and anti-TB treatment: Is TDM feasible for programmatic use? Int J Infect Dis 2020; 92S:S5-S9. [PMID: 31996324 DOI: 10.1016/j.ijid.2020.01.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 10/25/2022] Open
Abstract
Therapeutic Drug Monitoring (TDM) is increasingly recommended to ensure the correct drug dose thereby minimizing adverse events and maximizing regimen efficacy. To facilitate implementation in TB programs, a framework for TDM is urgently needed. TDM is only useful for dose optimization if a patient is on an appropriate regimen guided by drug susceptibility testing. TDM using a targeted approach selecting patients with risk factors for suboptimal drug exposure (e.g. diabetes) or not responding to treatment for drugs with a clear concentration-response relationship may provide the best value for money. Semiquantitative point-of-care tests for detection of low or high drug concentration should be implemented at community level while quantitative assays can be performed at regional or central level. Expanding PK/PD research followed by clinical trials including both clinical outcome as well as cost-effectiveness will increase the level of evidence supporting TDM.
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Affiliation(s)
- Jan-Willem C Alffenaar
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia; Westmead Hospital, Westmead, NSW 2145, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Onno W Akkerman
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, TB Center Beatrixoord, Haren, The Netherlands
| | - Hannah Yejin Kim
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia; Westmead Hospital, Westmead, NSW 2145, Australia
| | - Simon Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Department of Infection, Royal London and Newham Hospitals, Barts Health NHS Trust, London, United Kingdom
| | - Giovanni Battista Migliori
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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159
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Genotypic characterization of 'inferred' rifampin mutations in GenoType MTBDRplus assay and its association with phenotypic susceptibility testing of Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2020; 96:114995. [PMID: 32037037 DOI: 10.1016/j.diagmicrobio.2020.114995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 12/23/2022]
Abstract
In GenoType MTBDRplus assay [line probe assay (LPA)], when Mycobacterium tuberculosis (M. tuberculosis) sample DNA fails to hybridize to at least 1 rpoB wild-type probe and any mutation probe, it is inferred as rifampin (RIF)-resistant. In this study, we sought to identify such 'inferred' mutations in M. tuberculosis isolates (n = 203) by rpoB gene sequencing and determined their association with phenotypic resistance. D516Y, H526N, L511P mutations were associated with both phenotypically sensitive (59%, n = 38/64) and resistant (23.7%, n = 33/139) antimicrobial susceptibility testing (AST) results, whereas S531W mutation was associated with only RIF-resistant isolates (33%, n = 46/139). These results demonstrated that, at standard drug concentrations, some 'inferred' mutations may be missed by RIF-AST (phenotypically sensitive). The use of LPA permits identification of these RIF-resistant isolates, and incorporation of additional mutation probes (e.g., S531W) could further increase LPA specificity. Further studies are needed to establish the significance of the type of 'inferred' mutation with clinical/treatment outcomes.
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160
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Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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161
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Xia H, van den Hof S, Cobelens F, Zhou Y, Zhao B, Wang S, Zhao Y. Value of pyrazinamide for composition of new treatment regimens for multidrug-resistant Mycobacterium tuberculosis in China. BMC Infect Dis 2020; 20:19. [PMID: 31910878 PMCID: PMC6947908 DOI: 10.1186/s12879-020-4758-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/31/2019] [Indexed: 11/29/2022] Open
Abstract
Background Pyrazinamide still may be a useful drug for treatment of rifampin-resistant (RR-TB) or multidrug-resistant tuberculosis (MDR-TB) in China while awaiting scale up of new drugs and regimens including bedaquiline and linezolid. The level of pyrazinamide resistance among MDR-TB patients in China is not well established. Therefore, we assessed pyrazinamide resistance in a representative sample and explored determinants and patterns of pncA mutations. Methods MDR-TB isolates from the 2007 national drug resistance survey of China were sub-cultured and examined for pyrazinamide susceptibility by BACTEC MGIT 960 method. pncA mutations were identified by sequencing. Characteristics associated with pyrazinamide resistance were analyzed using univariable and multivariable log-binominal regression. Results Of 401 MDR-TB isolates, 324 were successfully sub-cultured and underwent drug susceptibility testing. Pyrazinamide resistance was prevalent in 40.7% of samples, similarly among new and previously treated MDR-TB patients. Pyrazinamide resistance in MDR-TB patients was associated with lower age (adjusted OR 0.54; 95% CI, 0.34–0.87 for those aged ≧60 years compared to < 40 years). Pyrazinamide resistance was not associated with gender, residential area, previous treatment history and Beijing genotype. Of 132 patients with pyrazinamide resistant MDR-TB, 97 (73.5%) had a mutation in the pncA gene; with 61 different point mutations causing amino acid change, and 11 frameshifts in the pncA gene. The mutations were scattered throughout the whole pncA gene and no hot spot region was identified. Conclusions Pyrazinamide resistance among MDR-TB patients in China is common, although less so in elderly patients. Therefore, pyrazinamide should only be used for treatment of RR/MDR-TB in China if susceptibility is confirmed. Molecular testing for detection of pyrazinamide resistance only based on pncA mutations has certain value for the rapid detection of pyrazinamide resistance in MDR-TB strains but other gene mutations conferring to pyrazinamide resistance still need to be explored to increase its predictive ability .
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Affiliation(s)
- Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Susan van den Hof
- KNCV Tuberculosis Foundation, The Hague, The Netherlands.,National Institute of Public Health and the Environment, Centre for Infectious Disease Epidemiology and Surveillance, Bilthoven, The Netherlands
| | - Frank Cobelens
- Department of Global Health and Amsterdam Institute for Global Health and Development, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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162
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A pre-clinical validation plan to evaluate analytical sensitivities of molecular diagnostics such as BD MAX MDR-TB, Xpert MTB/Rif Ultra and FluoroType MTB. PLoS One 2020; 15:e0227215. [PMID: 31910223 PMCID: PMC6946130 DOI: 10.1371/journal.pone.0227215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/13/2019] [Indexed: 01/09/2023] Open
Abstract
Rapid diagnosis of tuberculosis (TB) and antibiotic resistances are imperative to initiate effective treatment and to stop transmission of the disease. A new generation of more sensitive, automated molecular TB diagnostic tests has been recently launched giving microbiologists more choice between several assays with the potential to detect resistance markers for rifampicin and isoniazid. In this study, we determined analytical sensitivities as 95% limits of detection (LoD95) for Xpert MTB/Rif Ultra (XP-Ultra) and BD-MAX MDR-TB (BD-MAX) as two representatives of the new test generation, in comparison to the conventional FluoroType MTB (FT-MTB). Test matrices used were physiological saline solution, human and a mucin-based artificial sputum (MUCAS) each spiked with Mycobacterium tuberculosis in declining culture- and qPCR-controlled concentrations. With BD-MAX, XP-Ultra, and FT-MTB, we measured LoD95TB values of 2.1 cfu/ml (CI95%: 0.9–23.3), 3.1 cfu/ml (CI95%: 1.2–88.9), and 52.1 cfu/ml (CI95%: 16.7–664.4) in human sputum; of 6.3 cfu/ml (CI95%: 2.9–31.8), 1.5 cfu/ml (CI95%: 0.7–5.0), and 30.4 cfu/ml (CI95%: 17.4–60.7) in MUCAS; and of 2.3 cfu/ml (CI95%: 1.1–12.0), 11.5 cfu/ml (CI95%: 5.6–47.3), and 129.1 cfu/ml (CI95%: 82.8–273.8) in saline solution, respectively. LoD95 of resistance markers were 9 to 48 times higher compared to LoD95TB. BD-MAX and XP-Ultra have an equal and significantly increased analytical sensitivity compared to conventional tests. MUCAS resembled human sputum, while both yielded significantly different results than normal saline. MUCAS proved to be suitable for quality control of PCR assays for TB diagnostics.
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163
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Prevalence and genetic profiles of isoniazid resistance in tuberculosis patients: A multicountry analysis of cross-sectional data. PLoS Med 2020; 17:e1003008. [PMID: 31961877 PMCID: PMC6974034 DOI: 10.1371/journal.pmed.1003008] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The surveillance of drug resistance among tuberculosis (TB) patients is central to combatting the global TB epidemic and preventing the spread of antimicrobial resistance. Isoniazid and rifampicin are two of the most powerful first-line anti-TB medicines, and resistance to either of them increases the risk of treatment failure, relapse, or acquisition of resistance to other drugs. The global prevalence of rifampicin resistance is well documented, occurring in 3.4% (95% CI 2.5%-4.4%) of new TB patients and 18% (95% CI 7.6%-31%) of previously treated TB patients in 2018, whereas the prevalence of isoniazid resistance at global and regional levels is less understood. In 2018, the World Health Organization (WHO) recommended a modified 6-month treatment regimen for people with isoniazid-resistant, rifampicin-susceptible TB (Hr-TB), which includes rifampicin, pyrazinamide, ethambutol, and levofloxacin. We estimated the global prevalence of Hr-TB among TB patients and investigated associated phenotypic and genotypic drug resistance patterns. METHODS AND FINDINGS Aggregated drug resistance data reported to WHO from either routine continuous surveillance or nationally representative periodic surveys of TB patients for the period 2003-2017 were reviewed. Isoniazid data were available from 156 countries or territories for 211,753 patients. Among these, the global prevalence of Hr-TB was 7.4% (95% CI 6.5%-8.4%) among new TB patients and 11.4% (95% CI 9.4%-13.4%) among previously treated TB patients. Additional data on pyrazinamide and levofloxacin resistance were available from 6 countries (Azerbaijan, Bangladesh, Belarus, Pakistan, the Philippines, and South Africa). There were no cases of resistance to both pyrazinamide and levofloxacin among Hr-TB patients, except for the Philippines (1.8%, 95% CI 0.2-6.4) and Belarus (5.3%, 95% CI 0.1-26.0). Sequencing data for all genomic regions involved in isoniazid resistance were available for 4,563 patients. Among the 1,174 isolates that were resistant by either phenotypic testing or sequencing, 78.6% (95% CI 76.1%-80.9%) had resistance-conferring mutations in the katG gene and 14.6% (95% CI 12.7%-16.8%) in both katG and the inhA promoter region. For 6.8% (95% CI 5.4%-8.4%) of patients, mutations occurred in the inhA promoter alone, for whom an increased dose of isoniazid may be considered. The main limitations of this study are that most analyses were performed at the national rather than individual patient level and that the quality of laboratory testing may vary between countries. CONCLUSIONS In this study, the prevalence of Hr-TB among TB patients was higher than the prevalence of rifampicin resistance globally. Many patients with Hr-TB would be missed by current diagnostic algorithms driven by rifampicin testing, highlighting the need for new rapid molecular technologies to ensure access to appropriate treatment and care. The low prevalence of resistance to pyrazinamide and fluoroquinolones among patients with Hr-TB provides further justification for the recommended modified treatment regimen.
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164
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Rowneki M, Aronson N, Du P, Sachs P, Blakemore R, Chakravorty S, Levy S, Jones AL, Trivedi G, Chebore S, Addo D, Byarugaba DK, Njobvu PD, Wabwire-Mangen F, Erima B, Ramos ES, Evans CA, Hale B, Mancuso JD, Alland D. Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears. PLoS One 2020; 15:e0232343. [PMID: 32384098 PMCID: PMC7209238 DOI: 10.1371/journal.pone.0232343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Drug susceptibility testing for Mycobacterium tuberculosis (MTB) is difficult to perform in resource-limited settings where Acid Fast Bacilli (AFB) smears are commonly used for disease diagnosis and monitoring. We developed a simple method for extraction of MTB DNA from AFB smears for sequencing-based detection of mutations associated with resistance to all first and several second-line anti-tuberculosis drugs. METHODS We isolated MTB DNA by boiling smear content in a Chelex solution, followed by column purification. We sequenced PCR-amplified segments of the rpoB, katG, embB, gyrA, gyrB, rpsL, and rrs genes, the inhA, eis, and pncA promoters and the entire pncA gene. RESULTS We tested our assay on 1,208 clinically obtained AFB smears from Ghana (n = 379), Kenya (n = 517), Uganda (n = 262), and Zambia (n = 50). Coverage depth varied by target and slide smear grade, ranging from 300X to 12000X on average. Coverage of ≥20X was obtained for all targets in 870 (72%) slides overall. Mono-resistance (5.9%), multi-drug resistance (1.8%), and poly-resistance (2.4%) mutation profiles were detected in 10% of slides overall, and in over 32% of retreatment and follow-up cases. CONCLUSION This rapid AFB smear DNA-based method for determining drug resistance may be useful for the diagnosis and surveillance of drug-resistant tuberculosis.
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Affiliation(s)
- Mazhgan Rowneki
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- * E-mail: (DA); (MR)
| | - Naomi Aronson
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Peicheng Du
- Office of Advanced Research Computing, Rutgers University, Newark, New Jersey, United States of America
| | - Paige Sachs
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Robert Blakemore
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Soumitesh Chakravorty
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Shawn Levy
- Genomics Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Angela L. Jones
- Genomics Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Geetika Trivedi
- Genomics Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Sheilla Chebore
- Kenya Medical Research Institute, U.S. Army Medical Research Directorate-Africa, Kericho, Kenya
| | - Dennis Addo
- Ghana Armed Forces Tuberculosis Control Program, 37 Military Hospital, Accra, Ghana
| | | | | | | | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Eric S. Ramos
- Innovation For Health And Development, Laboratory for Research and Development (IFHAD), Universidad Peruana Cayetano Heredia, Lima, Peru
- Innovacion Por la Salud Y el Desarollo (IPSYD), Asociación Benéfica Prisma, Lima, Peru
| | - Carlton A Evans
- Innovation For Health And Development, Laboratory for Research and Development (IFHAD), Universidad Peruana Cayetano Heredia, Lima, Peru
- Infectious Diseases & Immunity, Wellcome Trust Imperial College Centre for Global Health Research, London, United Kingdom
| | - Braden Hale
- Naval Health Research Center, Defense Health Agency, San Diego, California, United States of America
- University of California San Diego, La Jolla, California, United States of America
| | - James D. Mancuso
- Armed Forces Health Surveillance Branch, Silver Spring, Maryland, United States of America
| | - David Alland
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- * E-mail: (DA); (MR)
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165
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Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Wellcome Open Res 2019; 4:191. [PMID: 32055708 PMCID: PMC7004237 DOI: 10.12688/wellcomeopenres.15603.1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations. Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data. We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.
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Affiliation(s)
- Martin Hunt
- European Bioinformatics Institute, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Simon Grandjean Lapierre
- Centre de Recherche du Centre Hospitalier de l'Universite de Montreal, Montreal, Canada
- Infectiology & immunology department, Universite de Montreal Microbiology, Montreal, Canada
| | - Simon Heys
- European Bioinformatics Institute, Cambridge, UK
| | - Mark Thomsit
- European Bioinformatics Institute, Cambridge, UK
| | | | | | | | - Timothy M. Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Daniela M. Cirillo
- Emerging Bacterial Pathogens Unit, WHO collaborating Centre and TB Supranational Reference laboratory, IRCCS San Raffaele Scientific institute, Milan, Italy
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- FISABIO Public Health, Valencia, Spain
- CIBER in Epidemiology and Public Health, Madrid, Spain
| | | | - Phillip Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Vancouver, Canada
- Bill and Melinda Gates Foundation, Seattle, USA
| | - Nazir Ismail
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Thomas A. Kohl
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Matthias Merker
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Stefan Niemann
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
- German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Shaheed Vally Omar
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, University of Sydney, Sydney, Australia
| | - Grace Smith
- National Mycobacterial Reference Service, Public Health England Public Health Laboratory, Birmingham, UK
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunite de Lille, Lille, France
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB control Program, Islamabad, Pakistan
| | - Mark Wilcox
- Leeds Teaching Hospital NHS Trust, Leeds, UK
- University of Leeds, Leeds, UK
| | - Irena Arandjelovic
- Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Tim E. A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Cambridge, UK
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166
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Dara M, Ehsani S, Mozalevskis A, Vovc E, Simões D, Avellon Calvo A, Casabona I Barbarà J, Chokoshvili O, Felker I, Hoffner S, Kalmambetova G, Noroc E, Shubladze N, Skrahina A, Tahirli R, Tsertsvadze T, Drobniewski F. Tuberculosis, HIV, and viral hepatitis diagnostics in eastern Europe and central Asia: high time for integrated and people-centred services. THE LANCET. INFECTIOUS DISEASES 2019; 20:e47-e53. [PMID: 31740252 DOI: 10.1016/s1473-3099(19)30524-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022]
Abstract
Globally, high rates (and in the WHO European region an increasing prevalence) of co-infection with tuberculosis and HIV and HIV and hepatitis C virus exist. In eastern European and central Asian countries, the tuberculosis, HIV, and viral hepatitis programmes, including diagnostic services, are separate vertical structures. In this Personal View, we consider underlying reasons for the poor integration for these diseases, particularly in the WHO European region, and how to address this with an initial focus on diagnostic services. In part, this low integration has reflected different diagnostic development histories, global funding sources, and sample types used for diagnosis (eg, typically sputum for tuberculosis and blood for HIV and hepatitis C). Cooperation between services improved as patients with tuberculosis needed routine testing for HIV and vice versa, but financial, infection control, and logistical barriers remain. Multidisease diagnostic platforms exist, but to be used optimally, appropriate staff training and sensible understanding of different laboratory and infection control risks needs rapid implementation. Technically these ideas are all feasible. Poor coordination between these vertical systems remains unhelpful. There is a need to increase political and operational integration of diagnostic and treatment services and bring them closer to patients.
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Affiliation(s)
- Masoud Dara
- Communicable Diseases Department, Division of Health Emergencies and Communicable Diseases, Regional Office for Europe, World Health Organization, Copenhagen, Denmark.
| | - Soudeh Ehsani
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Antons Mozalevskis
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Elena Vovc
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Daniel Simões
- EPI Unit, Institute of Public Health, University of Porto, Porto, Portugal
| | - Ana Avellon Calvo
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | - Jordi Casabona I Barbarà
- Center for Epidemiological Studies on STI and AIDS in Catalonia and Research Network on Biomedical Research, Epidemiology and Public Health, Catalan Agency of Public Health, Badalona, Spain
| | - Otar Chokoshvili
- Infectious diseases and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Irina Felker
- Scientific department, Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | | | - Ecatarina Noroc
- National AIDS Programme, Dermatology and Communicable Diseases Hospital, Chisinau, Moldova
| | - Natalia Shubladze
- National Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Alena Skrahina
- Clinical department, Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Rasim Tahirli
- Laboratory for Medical Service, Specialized Treatment Institution, Main Medical Department, Ministry of Justice, Baku, Azerbaijan
| | - Tengiz Tsertsvadze
- Infectious Diseases and Clinical Immunology Research Center, Tbilisi State University, Tbilisi, Georgia
| | - Francis Drobniewski
- Global Health and Tuberculosis, Imperial College London, London, UK; WHO European Laboratory Initiative on Tuberculosis, HIV and Viral hepatitis, WHO Regional Office of Europe, Copenhagen, Denmark
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167
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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 2019; 200:e93-e142. [PMID: 31729908 PMCID: PMC6857485 DOI: 10.1164/rccm.201909-1874st] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [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.
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168
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Kontsevaya I, Werngren J, Holicka Y, Klaos K, Tran A, Nikolayevskyy V. Non-commercial phenotypic assays for the detection of Mycobacterium tuberculosis drug resistance: a systematic review. Eur J Clin Microbiol Infect Dis 2019; 39:415-426. [PMID: 31667670 DOI: 10.1007/s10096-019-03723-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
Several rapid non-commercial culture-based methods and assays for drug susceptibility testing (DST) of Mycobacterium tuberculosis have emerged over the last decades. The aim of the current review was to summarise evidence on the performance of microscopic observation of drug susceptibility (MODS), thin-layer agar (TLA) and colorimetric redox-indicator (CRI) assays for detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. Forty-three publications satisfying selection criteria were selected for data extraction. MODS and CRI assays demonstrated pooled sensitivity and specificity of > 93% for the detection of resistance to rifampicin and isoniazid and confirmed their utility for an accurate detection of multidrug-resistant TB (MDR-TB) in various settings. Sensitivity and specificity values for indirect DST for ethambutol (EMB) using CRI assays were 94.0% and 82.0%, respectively, suggesting that CRIs could be used to rule out resistance to EMB. Performance for other drugs varied more substantially across the reports. There was no sufficient evidence on the performance of the TLA assay for making any conclusion on its utility for DST. Our data suggests that non-commercial assays could be used for a rapid and accurate DST in settings where the use of commercial World Health Organization-endorsed assays could be limited due to a variety of reasons including limited resources, laboratory facilities or trained personnel. While inexpensive and easy-to-perform MODS and TLA assays can be used in low-income settings, using CRI assays for determination of minimal inhibitory concentrations may be implemented in middle- and high-income countries with high MDR-TB burden to guide clinical management of TB patients.
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Affiliation(s)
- Irina Kontsevaya
- Imperial College London, Du Cane Road, London, W12 0NN, UK.,Research Center Borstel, Parkallee 1-40, D-23845, Borstel, Germany
| | - Jim Werngren
- Public Health Agency of Sweden, Nobels väg 18, 17165, Solna, Sweden
| | - Yen Holicka
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Kadri Klaos
- Department of Pulmonary Medicine, University of Tartu, Puusepa 8, 50406, Tartu, Estonia.,Department of Mycobacteriology, United Laboratories, Tartu University Hospital, Puusepa 1A, 50406, Tartu, Estonia
| | - Anh Tran
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Vladyslav Nikolayevskyy
- Imperial College London, Du Cane Road, London, W12 0NN, UK. .,Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.
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169
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170
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A Rare D94F Change in gyrA Gene of Multidrug-Resistant Mycobacterium tuberculosis Possibly Contributing to an Unfavorable Treatment Outcome. Antimicrob Agents Chemother 2019; 63:AAC.01312-19. [PMID: 31501146 DOI: 10.1128/aac.01312-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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171
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Xu Y, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, González-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, Colijn C, Comas I. High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS Med 2019; 16:e1002961. [PMID: 31671150 PMCID: PMC6822721 DOI: 10.1371/journal.pmed.1002961] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened. METHODS AND FINDINGS We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 [95% CI 0.02-1.10], p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region. CONCLUSIONS In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.
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Affiliation(s)
- Yuanwei Xu
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J. Camarena
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Ester Colomer-Roig
- Genomics and Health Unit, FISABIO Public Health, Valencia, Spain
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lírios, Alcoy, Spain
| | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicante, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital San Francesc de Borja, Gandía, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Herme Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Caroline Colijn
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (CC); (IC)
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
- * E-mail: (CC); (IC)
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Ng KCS, Ngabonziza JCS, Lempens P, de Jong BC, van Leth F, Meehan CJ. Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data. PeerJ 2019; 7:e7564. [PMID: 31523514 PMCID: PMC6714962 DOI: 10.7717/peerj.7564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 02/01/2023] Open
Abstract
Background Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance. Methods We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs-Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data. Results The MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda. Conclusion Overall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the national information system for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation are available at https://github.com/KamelaNg/MTBGT.
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Affiliation(s)
- Kamela C S Ng
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Jean Claude S Ngabonziza
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Services, Rwanda Biomedical Center, Kigali, Rwanda
| | - Pauline Lempens
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Frank van Leth
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, The Netherlands.,Department of Global Health, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Conor J Meehan
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,School of Chemistry and Biosciences, University of Bradford, Bradford, UK
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173
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Lange C, Dheda K, Chesov D, Mandalakas AM, Udwadia Z, Horsburgh CR. Management of drug-resistant tuberculosis. Lancet 2019; 394:953-966. [PMID: 31526739 DOI: 10.1016/s0140-6736(19)31882-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/08/2019] [Accepted: 07/18/2019] [Indexed: 12/11/2022]
Abstract
Drug-resistant tuberculosis is a major public health concern in many countries. Over the past decade, the number of patients infected with Mycobacterium tuberculosis resistant to the most effective drugs against tuberculosis (ie, rifampicin and isoniazid), which is called multidrug-resistant tuberculosis, has continued to increase. Globally, 4·6% of patients with tuberculosis have multidrug-resistant tuberculosis, but in some areas, like Kazakhstan, Kyrgyzstan, Moldova, and Ukraine, this proportion exceeds 25%. Treatment for patients with multidrug-resistant tuberculosis is prolonged (ie, 9-24 months) and patients with multidrug-resistant tuberculosis have less favourable outcomes than those treated for drug-susceptible tuberculosis. Individualised multidrug-resistant tuberculosis treatment with novel (eg, bedaquiline) and repurposed (eg, linezolid, clofazimine, or meropenem) drugs and guided by genotypic and phenotypic drug susceptibility testing can improve treatment outcomes. Some clinical trials are evaluating 6-month regimens to simplify management and improve outcomes of patients with multidrug-resistant tuberculosis. Here we review optimal diagnostic and treatment strategies for patients with drug-resistant tuberculosis and their contacts.
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Affiliation(s)
- Christoph Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany; Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany; German Center for Infection Research Clinical Tuberculosis Unit, Borstel, Germany; Department of Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Keertan Dheda
- Department of Medicine, Division of Pulmonology, Centre for Lung Infection and Immunity, Lung Institute, and Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; South African Medical Research Council, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Dumitru Chesov
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany; Department of Pneumology and Alergollogy, Nicoale Testemitanu State University of Medicine and Pharmacy, Chisinau, Moldova
| | - Anna Maria Mandalakas
- The Global Tuberculosis Programme, Texas Children's Hospital, and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Zarir Udwadia
- Hinduja Hospital and Research Center, Veer Savarkar Marg, Mumbai, India
| | - C Robert Horsburgh
- Department of Medicine, School of Medicine, and Department of Epidemiology, Department of Biostatistics, and Department of Global Health, School of Public Health, Boston University, Boston, MA, USA
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174
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El Achkar S, Demanche C, Osman M, Rafei R, Ismail MB, Yaacoub H, Pinçon C, Duthoy S, De Matos F, Gaudin C, Trovato A, Cirillo DM, Hamze M, Supply P. Drug-Resistant Tuberculosis, Lebanon, 2016 - 2017. Emerg Infect Dis 2019; 25:564-568. [PMID: 30789124 PMCID: PMC6390733 DOI: 10.3201/eid2503.181375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.
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175
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Chen X, He G, Wang S, Lin S, Chen J, Zhang W. Evaluation of Whole-Genome Sequence Method to Diagnose Resistance of 13 Anti-tuberculosis Drugs and Characterize Resistance Genes in Clinical Multi-Drug Resistance Mycobacterium tuberculosis Isolates From China. Front Microbiol 2019; 10:1741. [PMID: 31417530 PMCID: PMC6685394 DOI: 10.3389/fmicb.2019.01741] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022] Open
Abstract
Background: Whole-genome sequencing (WGS) is a viable and financially feasible tool for timely and comprehensive diagnosis of drug resistance in developed countries. With the increase in the incidence of multidrug-resistant tuberculosis (MDR-TB), second-line anti-TB drugs are gaining importance. However, genetic resistance to second-line anti-TB drugs based on WGS has not been fully studied. Methods: We randomly selected 100 MDR-TB and 10 non-MDR-TB isolates from a hospital in Zhejiang Province, China. Drug susceptibility tests against 13 anti-TB drugs were performed, and 34 drug resistance-related genes were analyzed using WGS in all isolates. For each drug, the accuracy, sensitivity, specificity, and positive and negative predictive values of WGS were compared with those of the conventional drug susceptibility test. Results: The overall sensitivity and specificity for WGS were respectively, 99.0 and 100.0% for isoniazid (INH), 99.0 and 100.0% for rifampicin (RIF), 94.8 and 65.3% for ethambutol (EMB), 86.2 and 84.4% for pyrazinamide (PZA), 95.6 and 95.6% for levofloxacin (LFX), 89.5 and 65.3% for moxifloxacin (MFX), 91.3 and 95.1% for streptomycin (SM), 90.9 and 99.0% for kanamycin, 90.9 and 100.0% for amikacin, 88.9 and 98.0% for capreomycin, 87.0 and 85.1% for prothionamide (PTO), 85.7 and 99.0% for para-aminosalicylic acid (PAS), and 66.7 and 95.9% for clofazimine (CLO). Conclusions: WGS is a promising approach to predict resistance to INH, RIF, PZA, LFX, SM, second-line injectable drugs (SLIDs), and PTO with satisfactory accuracy, sensitivity, and specificity of over 85.0%. The specificity of WGS in diagnosing resistance to EMB, and high-level resistance to MFX (2.0 mg/L) needs to be improved.
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Affiliation(s)
- Xinchang Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Guiqing He
- Sixth People's Hospital of Wenzhou City, Shenzhen, China
| | - Shiyong Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Siran Lin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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176
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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Personalized Approach as a Basis for the Future Diagnosis of Tuberculosis (Literature Review). ACTA BIOMEDICA SCIENTIFICA 2019. [DOI: 10.29413/abs.2019-4.3.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The global spread of tuberculosis remains one of actual problems of public health despite of introduction of public health safety programs. Early, rapid and accurate identification of M. tuberculosis and determination of drug susceptibility are essential for treatment and management of this disease. Delay in delivering results prolongs potentially inappropriate antituberculosis therapy, contributing to emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen, thus improving patient outcomes and reducing overall healthcare costs. The treatment of infection based on the using of massive antimicrobial therapy with analysis of bacterial strains resistance to first line drugs (FLD) isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), ethambutol (EMB) and streptomycin (SM). However, the public health practitioners pay no attention to functional activity of human immune system genes. The interaction of bacterial genomes and immune system genes plays the major role in infection progress. There is growing evidence that, together with human and environmental factors, Mycobacterium tuberculosis complex strain diversity contributes to the variable outcome of infection and disease in human TB. We suppose that the future of diagnosis and treatment of tuberculosis lies in the field of personal medicine with comprehensive analysis of host and pathogen genes.
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178
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Munir A, Kumar N, Ramalingam SB, Tamilzhalagan S, Shanmugam SK, Palaniappan AN, Nair D, Priyadarshini P, Natarajan M, Tripathy S, Ranganathan UD, Peacock SJ, Parkhill J, Blundell TL, Malhotra S. Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India. Sci Rep 2019; 9:10283. [PMID: 31311987 PMCID: PMC6635374 DOI: 10.1038/s41598-019-46756-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/28/2019] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis. There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.
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Affiliation(s)
- Asma Munir
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK
| | - Narender Kumar
- 0000000121885934grid.5335.0Department of Medicine, University of Cambridge, Hills Rd., Cambridge, CB2 0QQ UK
| | - Suresh Babu Ramalingam
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Sembulingam Tamilzhalagan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Siva Kumar Shanmugam
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | | | - Dina Nair
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Padma Priyadarshini
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Mohan Natarajan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Srikanth Tripathy
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Uma Devi Ranganathan
- 0000 0004 1767 6138grid.417330.2ICMR-National Institute for Research in Tuberculosis, Chennai, 600031 India
| | - Sharon J. Peacock
- 0000000121885934grid.5335.0Department of Medicine, University of Cambridge, Hills Rd., Cambridge, CB2 0QQ UK ,0000 0004 0425 469Xgrid.8991.9London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Julian Parkhill
- 0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA UK
| | - Tom L. Blundell
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK
| | - Sony Malhotra
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Tennis Court. Rd., Cambridge, CB2 1GA UK ,0000 0001 2161 2573grid.4464.2Present Address: Birkbeck College, University of London, Malet Street, WC1E7HX London, UK
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179
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Kateete DP, Kamulegeya R, Kigozi E, Katabazi FA, Lukoye D, Sebit SI, Abdi H, Arube P, Kasule GW, Musisi K, Dlamini MG, Khumalo D, Joloba ML. Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014-2016). BMC Pulm Med 2019; 19:124. [PMID: 31291943 PMCID: PMC6617586 DOI: 10.1186/s12890-019-0891-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pulmonary tuberculosis is a leading cause of morbidity and mortality in developing countries. Drug resistance, a huge problem in this contagious disease, is driven by point mutations in the Mycobacterium tuberculosis genome however, their frequencies vary geographically and this affects applicability of molecular diagnostics for rapid detection of resistance. Here, we report the frequency and patterns of mutations associated with resistance to second-line anti-TB drugs in multidrug-resistant (MDR) M. tuberculosis isolates from eSwatini, Somalia and Uganda that were resistant to a second-line anti-TB drug. METHODS The quinolone resistance determining region (QRDR) of gyrA/gyrB genes and the drug resistance associated fragment of rrs gene from 80 isolates were sequenced and investigated for presence of drug resistance mutations. Of the 80 isolates, 40 were MDR, of which 28 (70%) were resistant to a second-line anti-TB injectable drug, 18 (45%) were levofloxacin resistant while 12 (30%) were extensively drug resistant (XDR). The remaining 40 isolates were susceptible to anti-TB drugs. MIRU-VNTR analysis was performed for M/XDR isolates. RESULTS We successfully sub-cultured 38 of the 40 M/XDR isolates. The gyrA resistance mutations (Gly88Ala/Cys/Ala, Ala90Val, Ser91Pro, Asp94Gly/Asn) and gyrB resistance mutations (Asp500His, Asn538Asp) were detected in 72.2% (13/18) and 22.2% (4/18) of the MDR and levofloxacin resistant isolates, respectively. Overall, drug resistance mutations in gyrA/gyrB QRDRs occurred in 77.8% (14/18) of the MDR and levofloxacin resistant isolates. Furthermore, drug resistance mutations a1401g and g1484 t in rrs occurred in 64.3% (18/28) of the MDR isolates resistant to a second-line anti-TB injectable drug. Drug resistance mutations were not detected in drug susceptible isolates. CONCLUSIONS The frequency of resistance mutations to second-line anti-TB drugs in MDR-TB isolates resistant to second line anti-TB drugs from eSwatini, Somalia and Uganda is high, implying that rapid molecular tests are useful in detecting second-line anti-TB drug resistance in those countries. Relatedly, the frequency of fluoroquinolone resistance mutations in gyrB/QRDR is high relative to global estimates, and they occurred independently of gyrA/QRDR mutations implying that their absence in panels of molecular tests for detecting fluoroquinolone resistance may yield false negative results in our setting.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Kamulegeya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Deus Lukoye
- National Tuberculosis/Leprosy Program, Ministry of Health Uganda, Kampala, Uganda
| | | | - Hergeye Abdi
- Ministry of Health, Hargeisa, Somaliland Somalia
| | | | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Kampala, Uganda
| | - Myalo Glen Dlamini
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Derrick Khumalo
- National TB Reference Laboratory / eSwatini Health Laboratory Services, Ministry of Health, Hospital Hill Mbabane, Mbabane, eSwatini
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
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180
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Seifert M, Capparelli E, Catanzaro DG, Rodwell TC. Using Mycobacterium tuberculosis Single-Nucleotide Polymorphisms To Predict Fluoroquinolone Treatment Response. Antimicrob Agents Chemother 2019; 63:e00076-19. [PMID: 31085512 PMCID: PMC6591594 DOI: 10.1128/aac.00076-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Clinical phenotypic fluoroquinolone susceptibility testing of Mycobacterium tuberculosis is currently based on M. tuberculosis growth at a single critical concentration, which provides limited information for a nuanced clinical response. We propose using specific resistance-conferring M. tuberculosis mutations in gyrA together with population pharmacokinetic and pharmacodynamic modeling as a novel tool to better inform fluoroquinolone treatment decisions. We sequenced the gyrA resistance-determining region of 138 clinical M. tuberculosis isolates collected from India, Moldova, Philippines, and South Africa and then determined each strain's MIC against ofloxacin, moxifloxacin, levofloxacin, and gatifloxacin. Strains with specific gyrA single-nucleotide polymorphisms (SNPs) were grouped into high or low drug-specific resistance categories based on their empirically measured MICs. Published population pharmacokinetic models were then used to explore the pharmacokinetics and pharmacodynamics of each fluoroquinolone relative to the empirical MIC distribution for each resistance category to make predictions about the likelihood of patients achieving defined therapeutic targets. In patients infected with M. tuberculosis isolates containing SNPs associated with a fluoroquinolone-specific low-level increase in MIC, models suggest increased fluoroquinolone dosing improved the probability of achieving therapeutic targets for gatifloxacin and moxifloxacin but not for levofloxacin and ofloxacin. In contrast, among patients with isolates harboring SNPs associated with a high-level increase in MIC, increased dosing of levofloxacin, moxifloxacin, gatifloxacin, or ofloxacin did not meaningfully improve the probability of therapeutic target attainment. We demonstrated that quantifiable fluoroquinolone drug resistance phenotypes could be predicted from rapidly detectable gyrA SNPs and used to support dosing decisions based on the likelihood of patients reaching therapeutic targets. Our findings provide further supporting evidence for the moxifloxacin clinical breakpoint recently established by the World Health Organization.
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Affiliation(s)
- Marva Seifert
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Edmund Capparelli
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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181
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Isoniazid Resistance in Mycobacterium tuberculosis Is a Heterogeneous Phenotype Composed of Overlapping MIC Distributions with Different Underlying Resistance Mechanisms. Antimicrob Agents Chemother 2019; 63:AAC.00092-19. [PMID: 31010866 PMCID: PMC6591585 DOI: 10.1128/aac.00092-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 12/22/2022] Open
Abstract
MIC testing using the Bactec mycobacteria growth indicator tube system 960 of 70 phylogenetically diverse, isoniazid-resistant clinical strains of Mycobacterium tuberculosis revealed a complex pattern of overlapping MIC distributions. Whole-genome sequencing explained most of the levels of resistance observed. MIC testing using the Bactec mycobacteria growth indicator tube system 960 of 70 phylogenetically diverse, isoniazid-resistant clinical strains of Mycobacterium tuberculosis revealed a complex pattern of overlapping MIC distributions. Whole-genome sequencing explained most of the levels of resistance observed. The MIC distribution of strains with only inhA promoter mutations was split by the current concentration endorsed by the Clinical and Laboratory Standards Institute to detect low-level resistance to isoniazid and is, consequently, likely not optimally set.
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182
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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183
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Migliori GB, Nardell E, Yedilbayev A, D'Ambrosio L, Centis R, Tadolini M, van den Boom M, Ehsani S, Sotgiu G, Dara M. Reducing tuberculosis transmission: a consensus document from the World Health Organization Regional Office for Europe. Eur Respir J 2019; 53:13993003.00391-2019. [PMID: 31023852 DOI: 10.1183/13993003.00391-2019] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/18/2019] [Indexed: 12/11/2022]
Abstract
Evidence-based guidance is needed on 1) how tuberculosis (TB) infectiousness evolves in response to effective treatment and 2) how the TB infection risk can be minimised to help countries to implement community-based, outpatient-based care.This document aims to 1) review the available evidence on how quickly TB infectiousness responds to effective treatment (and which factors can lower or boost infectiousness), 2) review policy options on the infectiousness of TB patients relevant to the World Health Organization European Region, 3) define limitations of the available evidence and 4) provide recommendations for further research.The consensus document aims to target all professionals dealing with TB (e.g TB specialists, pulmonologists, infectious disease specialists, primary healthcare professionals, and other clinical and public health professionals), as well as health staff working in settings where TB infection is prevalent.
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Affiliation(s)
- Giovanni Battista Migliori
- Respiratory Diseases Clinical Epidemiology Unit, Clinical Scientific Institutes Maugeri, IRCCS, Tradate, Italy.,These authors contributed equally to this work
| | - Edward Nardell
- Division of Global Health Equity, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.,These authors contributed equally to this work
| | | | | | - Rosella Centis
- Respiratory Diseases Clinical Epidemiology Unit, Clinical Scientific Institutes Maugeri, IRCCS, Tradate, Italy
| | - Marina Tadolini
- Dept of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Martin van den Boom
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, WHO Regional Office for Europe, Copenhagen, Denmark.,These authors contributed equally to this work
| | - Soudeh Ehsani
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, WHO Regional Office for Europe, Copenhagen, Denmark
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy.,These authors contributed equally to this work
| | - Masoud Dara
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, WHO Regional Office for Europe, Copenhagen, Denmark
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184
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Gabrielian A, Engle E, Harris M, Wollenberg K, Juarez-Espinosa O, Glogowski A, Long A, Patti L, Hurt DE, Rosenthal A, Tartakovsky M. TB DEPOT (Data Exploration Portal): A multi-domain tuberculosis data analysis resource. PLoS One 2019; 14:e0217410. [PMID: 31120982 PMCID: PMC6532897 DOI: 10.1371/journal.pone.0217410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/10/2019] [Indexed: 02/06/2023] Open
Abstract
The NIAID TB Portals Program (TBPP) established a unique and growing database repository of socioeconomic, geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis (DR-TB). Currently, there are 2,428 total cases from nine country sites (Azerbaijan, Belarus, Moldova, Georgia, Romania, China, India, Kazakhstan, and South Africa), 1,611 (66%) of which are multidrug- or extensively-drug resistant and 1,185 (49%), 863 (36%), and 952 (39%) of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. We introduce the Data Exploration Portal (TB DEPOT, https://depot.tbportals.niaid.nih.gov) to visualize and analyze these multi-domain data. The TB DEPOT leverages the TBPP integration of clinical, socioeconomic, genomic, and imaging data into standardized formats and enables user-driven, repeatable, and reproducible analyses. It furthers the TBPP goals to provide a web-enabled analytics platform to countries with a high burden of multidrug-resistant TB (MDR-TB) but limited IT resources and inaccessible data, and enables the reusability of data, in conformity with the NIH's Findable, Accessible, Interoperable, and Reusable (FAIR) principles. TB DEPOT provides access to "analysis-ready" data and the ability to generate and test complex clinically-oriented hypotheses instantaneously with minimal statistical background and data processing skills. TB DEPOT is also promising for enhancing medical training and furnishing well annotated, hard to find, MDR-TB patient cases. TB DEPOT, as part of TBPP, further fosters collaborative research efforts to better understand drug-resistant tuberculosis and aid in the development of novel diagnostics and personalized treatment regimens.
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Affiliation(s)
- Andrei Gabrielian
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Eric Engle
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael Harris
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Octavio Juarez-Espinosa
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alexander Glogowski
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alyssa Long
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Lisa Patti
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Darrell E. Hurt
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Alex Rosenthal
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
| | - Mike Tartakovsky
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, United States of America
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185
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GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun 2019; 10:2128. [PMID: 31086182 PMCID: PMC6513847 DOI: 10.1038/s41467-019-10110-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/18/2019] [Indexed: 01/28/2023] Open
Abstract
Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.
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186
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Whole-Genome Sequencing in Relation to Resistance of Mycobacterium Tuberculosis. ACTA MEDICA MARTINIANA 2019. [DOI: 10.2478/acm-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract
Tuberculosis, a disease caused by Mycobacterium tuberculosis, represents one of the deadliest infections worldwide. The incidence of resistant forms is increasing year by year; therefore, it is necessary to involve new methods for rapid diagnostics and treatment. One of the possible solutions is the use of whole-genome sequencing (WGS).
The WGS provides an identification of complete genome of the microorganism, including all genes responsible for resistance, in comparison with other genotypic methods (eg. Xpert MTB / RIF or Hain line-probes) that are capable to detect only basic genes. WGS data are available in 1-9 days and several online software tools (TBProfiler, CASTB, Mykrobe PredictorTB) are used for their interpretation and analysis, compared to 3-8 weeks in the case of classic phenotypic evaluation.
Furthermore, WGS predicts resistance to the first-line antituberculotics with a sensitivity of 85-100% and a specificity of 85-100%.
This review elucidates the importance and summarizes the current knowledge about the possible use of WGS in diagnosis and treatment of resistant forms of tuberculosis elucidates.
WGS of M. tuberculosis brings new possibilities for rapid and accurate diagnostics of resistant forms of tuberculosis. Introducing WGS into routine practice can help to reduce the spread of resistant forms of tuberculosis as well as to increase the success rate of the treatment, especially through an appropriate combination of antituberculotics ATs. Introduction of WGS into routine diagnostics can, in spite of the financial difficulty, significantly improve patient care.
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187
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Mahé P, El Azami M, Barlas P, Tournoud M. A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis. PeerJ 2019; 7:e6857. [PMID: 31106066 PMCID: PMC6500375 DOI: 10.7717/peerj.6857] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/25/2019] [Indexed: 02/02/2023] Open
Abstract
Recent years saw a growing interest in predicting antibiotic resistance from whole-genome sequencing data, with promising results obtained for Staphylococcus aureus and Mycobacterium tuberculosis. In this work, we gathered 6,574 sequencing read datasets of M. tuberculosis public genomes with associated antibiotic resistance profiles for both first and second-line antibiotics. We performed a systematic evaluation of TBProfiler and Mykrobe, two widely recognized softwares allowing to predict resistance in M. tuberculosis. The size of the dataset allowed us to obtain confident estimations of their overall predictive performance, to assess precisely the individual predictive power of the markers they rely on, and to study in addition how these softwares behave across the major M. tuberculosis lineages. While this study confirmed the overall good performance of these tools, it revealed that an important fraction of the catalog of mutations they embed is of limited predictive power. It also revealed that these tools offer different sensitivity/specificity trade-offs, which is mainly due to the different sets of mutation they embed but also to their underlying genotyping pipelines. More importantly, it showed that their level of predictive performance varies greatly across lineages for some antibiotics, therefore suggesting that the predictions made by these softwares should be deemed more or less confident depending on the lineage inferred and the predictive performance of the marker(s) actually detected. Finally, we evaluated the relevance of machine learning approaches operating from the set of markers detected by these softwares and show that they present an attractive alternative strategy, allowing to reach better performance for several drugs while significantly reducing the number of candidate mutations to consider.
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Affiliation(s)
- Pierre Mahé
- Data Analytics Department, bioMérieux, Marcy l'Etoile, France
| | - Meriem El Azami
- Data Analytics Department, bioMérieux, Marcy l'Etoile, France
| | | | - Maud Tournoud
- Data Analytics Department, bioMérieux, Marcy l'Etoile, France
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188
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Brandao AP, Pinhata JMW, Oliveira RS, Galesi VMN, Caiaffa-Filho HH, Ferrazoli L. Speeding up the diagnosis of multidrug-resistant tuberculosis in a high-burden region with the use of a commercial line probe assay. J Bras Pneumol 2019; 45:e20180128. [PMID: 31017225 PMCID: PMC6733744 DOI: 10.1590/1806-3713/e20180128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/12/2018] [Indexed: 12/02/2022] Open
Abstract
Objective: To evaluate the rapid diagnosis of multidrug-resistant tuberculosis, by using a commercial line probe assay for rifampicin and isoniazid detection (LPA-plus), in the routine workflow of a tuberculosis reference laboratory. Methods: The LPA-plus was prospectively evaluated on 341 isolates concurrently submitted to the automated liquid drug susceptibility testing system. Results: Among 303 phenotypically valid results, none was genotypically rifampicin false-susceptible (13/13; 100% sensitivity). Two rifampicin-susceptible isolates harboured rpoB mutations (288/290; 99.3% specificity) which, however, were non-resistance-conferring mutations. LPA-plus missed three isoniazid-resistant isolates (23/26; 88.5% sensitivity) and detected all isoniazid-susceptible isolates (277/277; 100% specificity). Among the 38 (11%) invalid phenotypic results, LPA-plus identified 31 rifampicin- and isoniazid-susceptible isolates, one isoniazid-resistant and six as non-Mycobacterium tuberculosis complex. Conclusions: LPA-plus showed excellent agreement (≥91%) and accuracy (≥99%). Implementing LPA-plus in our setting can speed up the diagnosis of multidrug-resistant tuberculosis, yield a significantly higher number of valid results than phenotypic drug susceptibility testing and provide further information on the drug-resistance level.
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Affiliation(s)
- Angela Pires Brandao
- . Instituto Adolfo Lutz - São Paulo (SP), Brazil.,. Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro (RJ) Brazil
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189
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Colman RE, Mace A, Seifert M, Hetzel J, Mshaiel H, Suresh A, Lemmer D, Engelthaler DM, Catanzaro DG, Young AG, Denkinger CM, Rodwell TC. Whole-genome and targeted sequencing of drug-resistant Mycobacterium tuberculosis on the iSeq100 and MiSeq: A performance, ease-of-use, and cost evaluation. PLoS Med 2019; 16:e1002794. [PMID: 31039166 PMCID: PMC6490892 DOI: 10.1371/journal.pmed.1002794] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Accurate, comprehensive, and timely detection of drug-resistant tuberculosis (TB) is essential to inform patient treatment and enable public health surveillance. This is crucial for effective control of TB globally. Whole-genome sequencing (WGS) and targeted next-generation sequencing (NGS) approaches have potential as rapid in vitro diagnostics (IVDs), but the complexity of workflows, interpretation of results, high costs, and vulnerability of instrumentation have been barriers to broad uptake outside of reference laboratories, especially in low- and middle-income countries. A new, solid-state, tabletop sequencing instrument, Illumina iSeq100, has the potential to decentralize NGS for individual patient care. METHODS AND FINDINGS In this study, we evaluated WGS and targeted NGS for TB on both the new iSeq100 and the widely used MiSeq (both manufactured by Illumina) and compared sequencing performance, costs, and usability. We utilized DNA libraries produced from Mycobacterium tuberculosis clinical isolates for the evaluation. We conducted WGS on three strains and observed equivalent uniform genome coverage with both platforms and found the depth of coverage obtained was consistent with the expected data output. Utilizing the standardized, cloud-based ReSeqTB bioinformatics pipeline for variant analysis, we found the two platforms to have 94.0% (CI 93.1%-94.8%) agreement, in comparison to 97.6% (CI 97%-98.1%) agreement for the same libraries on two MiSeq instruments. For the targeted NGS approach, 46 M. tuberculosis-specific amplicon libraries had 99.6% (CI 98.0%-99.9%) agreement between the iSeq100 and MiSeq data sets in drug resistance-associated SNPs. The upfront capital costs are almost 5-fold lower for the iSeq100 ($19,900 USD) platform in comparison to the MiSeq ($99,000 USD); however, because of difference in the batching capabilities, the price per sample for WGS was higher on the iSeq100. For WGS of M. tuberculosis at the minimum depth of coverage of 30x, the cost per sample on the iSeq100 was $69.44 USD versus $28.21 USD on the MiSeq, assuming a 2 × 150 bp run on a v3 kit. In terms of ease of use, the sequencing workflow of iSeq100 has been optimized to only require 27 minutes total of hands-on time pre- and post-run, and the maintenance is simplified by a single-use cartridge-based fluidic system. As these are the first sequencing attempts on the iSeq100 for M. tuberculosis, the sequencing pool loading concentration still needs optimization, which will affect sequencing error and depth of coverage. Additionally, the costs are based on current equipment and reagent costs, which are subject to change. CONCLUSIONS The iSeq100 instrument is capable of running existing TB WGS and targeted NGS library preparations with comparable accuracy to the MiSeq. The iSeq100 has reduced sequencing workflow hands-on time and is able to deliver sequencing results in <24 hours. Reduced capital and maintenance costs and lower-throughput capabilities also give the iSeq100 an advantage over MiSeq in settings of individualized care but not in high-throughput settings such as reference laboratories, where sample batching can be optimized to minimize cost at the expense of workflow complexity and time.
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Affiliation(s)
- Rebecca E. Colman
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
- * E-mail:
| | - Aurélien Mace
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
| | - Marva Seifert
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - Jonathan Hetzel
- Illumina Inc., San Diego, California, United States of America
| | - Haifa Mshaiel
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - Anita Suresh
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Donald G. Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Amanda G. Young
- Illumina Inc., San Diego, California, United States of America
| | | | - Timothy C. Rodwell
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
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190
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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191
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Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.02175-18. [PMID: 30718257 PMCID: PMC6496161 DOI: 10.1128/aac.02175-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/25/2019] [Indexed: 01/10/2023] Open
Abstract
Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.
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192
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Sun F, Li Y, Chen Y, Guan W, Jiang X, Wang X, Ren P, Li J, Shi J, He G, Wu M, Tang P, Wang F, Sheng Y, Huang F, Zhou Z, Huang H, Hong L, Liu Q, Zhang Y, Zhang W. Introducing molecular testing of pyrazinamide susceptibility improves multidrug-resistant tuberculosis treatment outcomes: a prospective cohort study. Eur Respir J 2019; 53:13993003.01770-2018. [PMID: 30578402 DOI: 10.1183/13993003.01770-2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/14/2018] [Indexed: 11/05/2022]
Abstract
The current treatment for multidrug-resistant tuberculosis (MDR-TB) takes a lengthy period of 18-24 months and has a poor cure rate of 50-60%. A multicenter, prospective cohort study was conducted to assess the role of testing for molecular susceptibility to pyrazinamide (PZA) in optimising treatment for MDR-TB.We assigned 76 patients to an optimised molecular susceptibility group and 159 patients to a regular treatment group where PZA susceptibility was not determined. Of these patients, 152 were matched after propensity score matching (76 in the optimised group and 76 in the regular group). Treatment success rate was measured in the propensity-matched cohort as the primary outcome.Patients in the optimised group achieved a higher treatment success rate than those in the regular group (76.3% versus 55.3%, p=0.006). Of 51 patients with isolates that were susceptible to PZA and who were receiving a 12-month regimen, 42 (82.4%) were treated successfully. The optimised group showed faster culture conversion than the regular group (p=0.024). After exclusion of pre-extensively drug-resistant TB (pre-XDR-TB), the treatment outcome in the optimised group was still better than the regular group (83.1% versus 62.1%, p=0.009).Introducing molecular susceptibility testing for PZA improved the treatment outcomes for MDR-TB without the use of new drugs. Introducing PZA for patients with PZA-susceptible (PZA-S) MDR-TB allows the current regimen to be shortened to 12 months with comparable success rates to the World Health Organization (WHO) recommended shorter regimen.
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Affiliation(s)
- Feng Sun
- Dept of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,These authors contributed equally to this work
| | - Yang Li
- Dept of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,These authors contributed equally to this work
| | - Yu Chen
- Dept of Tuberculosis, Henan Province Infectious Diseases Hospital, Zhengzhou, China.,These authors contributed equally to this work
| | - Wenlong Guan
- The Chest Hospital of Xinjiang Uyghur Autonomous Region, Ürümqi, China.,These authors contributed equally to this work
| | - Xiangao Jiang
- Dept of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China.,These authors contributed equally to this work
| | - Xiaomeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.,These authors contributed equally to this work
| | - Pengfei Ren
- Dept of Tuberculosis, Henan Province Infectious Diseases Hospital, Zhengzhou, China
| | - Junlian Li
- The Chest Hospital of Xinjiang Uyghur Autonomous Region, Ürümqi, China
| | - Jichan Shi
- Dept of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
| | - Guiqing He
- Dept of Infectious Diseases, Wenzhou Central Hospital, Wenzhou, China
| | - Meiying Wu
- Suzhou Fifth People's Hospital, Suzhou, China
| | - Peijun Tang
- Suzhou Fifth People's Hospital, Suzhou, China
| | - Fei Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yunfeng Sheng
- Tuberculosis Treatment Center, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Fuli Huang
- Dept of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zumo Zhou
- People's Hospital of Zhuji, Zhuji, China
| | | | - Liang Hong
- Dept of Infectious Diseases, The Third Affiliated Hospital to Wenzhou Medical College, Rui'an, China
| | - Qihui Liu
- Dept of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Dept of Molecular Microbiology and Immunology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Wenhong Zhang
- Dept of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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193
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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: 180] [Impact Index Per Article: 36.0] [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.
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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
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194
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Bouzouita I, Cabibbe AM, Trovato A, Daroui H, Ghariani A, Midouni B, Essalah L, Mehiri E, Cirillo DM, Saidi LS. Whole-Genome Sequencing of Drug-Resistant Mycobacterium tuberculosis Strains, Tunisia, 2012-2016. Emerg Infect Dis 2019; 25:538-546. [PMID: 30789128 PMCID: PMC6390741 DOI: 10.3201/eid2503.181370] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To investigate transmission of drug-resistant strains of Mycobacterium tuberculosis in Tunisia, we performed whole-genome sequencing on 46 multidrug-resistant strains isolated during 2012-2016. Core-genome multilocus sequence typing grouped 30 strains (65.2%) into 3 clusters, indicating extensive recent transmission and Haarlem clone predominance. Whole-genome sequencing might help public health services undertake appropriate control actions.
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195
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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.
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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)
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196
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Zürcher K, Ballif M, Fenner L, Borrell S, Keller PM, Gnokoro J, Marcy O, Yotebieng M, Diero L, Carter EJ, Rockwood N, Wilkinson RJ, Cox H, Ezati N, Abimiku AG, Collantes J, Avihingsanon A, Kawkitinarong K, Reinhard M, Hömke R, Huebner R, Gagneux S, Böttger EC, Egger M. Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study. THE LANCET. INFECTIOUS DISEASES 2019; 19:298-307. [PMID: 30744962 DOI: 10.1016/s1473-3099(18)30673-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/07/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Drug resistance is a challenge for the global control of tuberculosis. We examined mortality in patients with tuberculosis from high-burden countries, according to concordance or discordance of results from drug susceptibility testing done locally and in a reference laboratory. METHODS This multicentre cohort study was done in Côte d'Ivoire, Democratic Republic of the Congo, Kenya, Nigeria, South Africa, Peru, and Thailand. We collected Mycobacterium tuberculosis isolates and clinical data from adult patients aged 16 years or older. Patients were stratified by HIV status and tuberculosis drug resistance. Molecular or phenotypic drug susceptibility testing was done locally and at the Swiss National Center for Mycobacteria, Zurich, Switzerland. We examined mortality during treatment according to drug susceptibility test results and treatment adequacy in multivariable logistic regression models adjusting for sex, age, sputum microscopy, and HIV status. FINDINGS We obtained M tuberculosis isolates from 871 patients diagnosed between 2013 and 2016. After exclusion of 237 patients, 634 patients with tuberculosis were included in this analysis; the median age was 33·2 years (IQR 26·9-42·5), 239 (38%) were women, 272 (43%) were HIV-positive, and 69 (11%) patients died. Based on the reference laboratory drug susceptibility test, 394 (62%) strains were pan-susceptible, 45 (7%) monoresistant, 163 (26%) multidrug-resistant (MDR), and 30 (5%) had pre-extensively or extensively drug resistant (pre-XDR or XDR) tuberculosis. Results of reference and local laboratories were concordant for 513 (81%) of 634 patients and discordant for 121 (19%) of 634. Overall, sensitivity to detect any resistance was 90·8% (95% CI 86·5-94·2) and specificity 84·3% (80·3-87·7). Mortality ranged from 6% (20 of 336) in patients with pan-susceptible tuberculosis treated according to WHO guidelines to 57% (eight of 14) in patients with resistant strains who were under-treated. In logistic regression models, compared with concordant drug susceptibility test results, the adjusted odds ratio of death was 7·33 (95% CI 2·70-19·95) for patients with discordant results potentially leading to under-treatment. INTERPRETATION Inaccurate drug susceptibility testing by comparison with a reference standard leads to under-treatment of drug-resistant tuberculosis and increased mortality. Rapid molecular drug susceptibility test of first-line and second-line drugs at diagnosis is required to improve outcomes in patients with MDR tuberculosis and pre-XDR or XDR tuberculosis. FUNDING National Institutes of Allergy and Infectious Diseases, Swiss National Science Foundation, Swiss National Center for Mycobacteria.
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Affiliation(s)
- Kathrin Zürcher
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Marie Ballif
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Joachim Gnokoro
- Centre de Prise en Charge de Recherche et de Formation, Yopougon, Abidjan, Côte d'Ivoire
| | - Olivier Marcy
- Bordeaux Population Health Research Center, Inserm U1219, University of Bordeaux, Bordeaux, France
| | - Marcel Yotebieng
- Ohio State University, College of Public Health, Columbus, OH, USA
| | - Lameck Diero
- Department of Medicine, Moi University School of Medicine, and Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - E Jane Carter
- Department of Medicine, Moi University School of Medicine, and Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Neesha Rockwood
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa; Department of Medicine, Imperial College London, London, UK
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa; Department of Medicine, Imperial College London, London, UK; Francis Crick Institute, London, UK
| | - Helen Cox
- Division of Medical Microbiology and the Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicholas Ezati
- Institute of Human Virology, Abuja, Nigeria; National Tuberculosis and Leprosy Training Center, Saye, Zaria, Kaduna State, Nigeria
| | | | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Kamon Kawkitinarong
- HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand; Tuberculosis Research Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Rico Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Robin Huebner
- National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa.
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197
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Jhun BW, Huh HJ, Koh WJ. Diagnosis of pulmonary tuberculosis. JOURNAL OF THE KOREAN MEDICAL ASSOCIATION 2019. [DOI: 10.5124/jkma.2019.62.1.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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198
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Havlicek J, Dachsel B, Slickers P, Andres S, Beckert P, Feuerriegel S, Niemann S, Merker M, Labugger I. Rapid microarray-based assay for detection of pyrazinamide resistant Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2018; 94:147-154. [PMID: 30733004 PMCID: PMC6531379 DOI: 10.1016/j.diagmicrobio.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/17/2018] [Accepted: 12/24/2018] [Indexed: 01/25/2023]
Abstract
Pyrazinamide (PZA) is a key antibiotic for the treatment of drug susceptible tuberculosis. PZA-resistance is mainly mediated by mutations in the pncA gene; however the current gold standard is a phenotypic drug susceptibility test requiring a well-adjusted pH-value for reliable results. Our melting curve assay detects a non-wild type genotype in selected pncA regions in at least 3750 gene copies/mL within 2.5 hours. The prototype assay was further evaluated by analyzing 271 Mycobacterium tuberculosis complex isolates from Swaziland originating from a previously published drug resistance survey and including 118 isolates with pncA mutations. Sensitivity was 83% (95% CI 75-89%) and specificity was 100% (95% CI 98-100%). Under consideration of further improvements with regard to the target range our melting curve assay has the potential as a rapid rule-in test for PZA susceptibility (wild type pncA), however false resistant results (mutant pncA, but PZA susceptible) cannot be ruled out completely.
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Affiliation(s)
| | | | | | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany.
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199
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Panossian B, Salloum T, Araj GF, Khazen G, Tokajian S. First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon. BMC Infect Dis 2018; 18:710. [PMID: 30594126 PMCID: PMC6311033 DOI: 10.1186/s12879-018-3626-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022] Open
Abstract
Background Lebanon hosts a heterogeneous population coming from underdeveloped and developing countries, resulting in increasing incidences of tuberculosis over the past years. The genetic heterogeneity and lineages associated with tuberculosis, along with their resistance determinants have not been studied at the genomic level previously in the region. Methods Isolates were recovered from the American University of Beirut Medical Center (AUBMC). Antimicrobial susceptibility profiles were determined using the MGIT automated system for the first-line drugs at AUBMC, while second-line drug susceptibility was tested at Mayo Clinic Laboratories. Whole Genome Sequencing (WGS) was performed to classify mycobacterial lineages and highlight single nucleotide mutations causing resistance to both 1st line and 2nd line antimicrobials. wgSNP analysis provided insights on the phylogeny of the isolates along with spoligotyping and core genomic SNVs, IS6110 insertion sites, and variable number tandem repeats (VNTR). Results The analyzed isolates carry distinct resistance determinants to isoniazid, rifampicin, ethambutol, quinolones, and streptomycin. The isolates belonged to different lineages including the Euro/American lineage (Lineage 4) (53.8%), M. bovis (15.4%) and Delhi/Central Asia (Lineage 1) (15.4%), Beijing/East Asia (Lineage 2) (7.7%), and East Africa/Indian Ocean lineage (Lineage 3) (7.7%) showing great phylogenetic differences at the genomic level. Conclusions The population diversity in Lebanon holds an equally diverse and uncharacterized population of drug resistant mycobacteria. To achieve the WHO “END-TB” milestones of 2025 and 2035, Lebanon must decrease TB incidences by 95% in the next decade. This can only be done through WGS-based patient centered diagnosis with higher throughput and genomic resolution to improve treatment outcomes and to monitor transmission patterns. Electronic supplementary material The online version of this article (10.1186/s12879-018-3626-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Balig Panossian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon
| | - George F Araj
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Georges Khazen
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, P.O. Box 36, Byblos, Lebanon.
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200
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Hazbón MH, Rigouts L, Schito M, Ezewudo M, Kudo T, Itoh T, Ohkuma M, Kiss K, Wu L, Ma J, Hamada M, Strong M, Salfinger M, Daley CL, Nick JA, Lee JS, Rastogi N, Couvin D, Hurtado-Ortiz R, Bizet C, Suresh A, Rodwell T, Albertini A, Lacourciere KA, Deheer-Graham A, Alexander S, Russell JE, Bradford R, Riojas MA. Mycobacterial biomaterials and resources for researchers. Pathog Dis 2018; 76:4978419. [PMID: 29846561 DOI: 10.1093/femspd/fty042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/18/2018] [Indexed: 11/12/2022] Open
Abstract
There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.
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Affiliation(s)
- Manzour Hernando Hazbón
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Leen Rigouts
- BCCM/ITM Mycobacteria Collection, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd, suite 200, Tucson, AZ 85718, USA
| | - Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd, suite 200, Tucson, AZ 85718, USA
| | - Takuji Kudo
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Takashi Itoh
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Moriya Ohkuma
- RIKEN BioResource Center (RIKEN BRC) - Japan Collection of Microorganisms (JCM), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, JAPAN
| | - Katalin Kiss
- ATCC®, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Linhuan Wu
- WFCC-MIRCEN World Data Center for Microorganisms (WDCM), Institute of Microbiology, Chinese Academy of Sciences, NO.1-3 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Juncai Ma
- WFCC-MIRCEN World Data Center for Microorganisms (WDCM), Institute of Microbiology, Chinese Academy of Sciences, NO.1-3 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson St., Denver, CO 80206, USA
| | - Max Salfinger
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Charles L Daley
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Jerry A Nick
- National Jewish Health, Department of Medicine, 1400 Jackson St., Denver, CO 80206, USA
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil. Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Nalin Rastogi
- Institut Pasteur de la Guadeloupe, BP 484, Morne Jolivière, 97183 ABYMES Cedex, Guadeloupe, France
| | - David Couvin
- Institut Pasteur de la Guadeloupe, BP 484, Morne Jolivière, 97183 ABYMES Cedex, Guadeloupe, France
| | - Raquel Hurtado-Ortiz
- CRBIP-Biological Resource Centre, Institut Pasteur, 25 rue du Dr Roux 75015, Paris, France
| | - Chantal Bizet
- CIP-Collection of Institut Pasteur, Institut Pasteur, 25 rue du Dr Roux 75015, Paris, France
| | - Anita Suresh
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Timothy Rodwell
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Audrey Albertini
- Foundation for Innovative New Diagnostics, Campus Biotech, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Karen A Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Ana Deheer-Graham
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Sarah Alexander
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Julie E Russell
- Culture Collections, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Rebecca Bradford
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
| | - Marco A Riojas
- ATCC ®, 10801 University Boulevard, Manassas, VA 20110, USA.,BEI Resources, 10801 University Boulevard, Manassas, VA 20110, USA
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