101
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Overton K, Mennon V, Mothobi N, Neild B, Martinez E, Masters J, Grant P, Akhunji Z, Su WY, Torda A, Whyte CM, Lloyd A, Weatherall C, Hofmeyr A, Foo H, Brookes K, Marriott D, Sintchenko V, Clezy K, Konecny P, Post JJ. Cluster of invasive Mycobacteria chimaera infections following cardiac surgery demonstrating novel clinical features and risks of aortic valve replacement. Intern Med J 2019; 48:1514-1520. [PMID: 30517986 DOI: 10.1111/imj.14093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/18/2018] [Accepted: 04/22/2018] [Indexed: 12/01/2022]
Abstract
There is a global outbreak of infections due to Mycobacterium chimaera associated with cardiac surgery. The most serious infections involve prosthetic material implantation, and all have followed surgical procedures involving cardiopulmonary bypass. We describe a cluster of four cases following cardiac surgery at a tertiary referral centre in Sydney, Australia. We report novel clinical findings, including haemolysis and kidney rupture possibly related to immune reconstitution inflammatory syndrome. The positive effect of corticosteroids on haemodynamic function in two cases and the failure of currently recommended antimicrobial therapy to sterilise prosthetic valve material in the absence of surgery despite months of treatment are also critically examined. Positron emission tomography was positive in two cases despite normal transoesophageal echocardiograms. The proportion of cases with M. chimaera infection after aortic valve replacement (4/890, 0.45%; 95% confidence interval 0.18-1.15%) was significantly higher than after all other cardiothoracic surgical procedures (0/2433, 0%; 95% confidence interval 0-0.16%).
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Affiliation(s)
- Kristen Overton
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Vidthyia Mennon
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Nomvuyo Mothobi
- Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, NSW, Australia
| | - Blake Neild
- Department of Infectious Diseases, Immunology and Sexual Health, St George Hospital, Kogarah, New South Wales, Australia.,St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology, Public Health, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Jeffrey Masters
- Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, NSW, Australia
| | - Peter Grant
- Department of Cardiothoracic Surgery, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Zakir Akhunji
- Department of Cardiothoracic Surgery, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Wei-Yuen Su
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Adrienne Torda
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Claudia M Whyte
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andrew Lloyd
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,The Kirby Institute, University of New South Wales, Kensington, New South Wales, Australia
| | - Chris Weatherall
- Department of Infectious Diseases, Immunology and Sexual Health, St George Hospital, Kogarah, New South Wales, Australia.,St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ann Hofmeyr
- Department of Microbiology and Infectious Diseases, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Hong Foo
- Department of Microbiology and Infectious Diseases, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Kim Brookes
- Clinical Governance Unit, South Eastern Sydney Local Health District, The Sutherland Hospital, Caringbah, New South Wales, Australia
| | - Debbie Marriott
- Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, Public Health, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Kate Clezy
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Pam Konecny
- Department of Infectious Diseases, Immunology and Sexual Health, St George Hospital, Kogarah, New South Wales, Australia.,St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jeffrey J Post
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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102
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Wattal C, Raveendran R. Newer Diagnostic Tests and their Application in Pediatric TB. Indian J Pediatr 2019; 86:441-447. [PMID: 30628039 DOI: 10.1007/s12098-018-2811-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/05/2018] [Indexed: 11/25/2022]
Abstract
The diagnosis of childhood tuberculosis is a challenge due to the pauci-bacillary nature of infection and the difficulty in obtaining appropriate sample. In the past 2-3 decades, many new tests were introduced for the diagnosis of tuberculosis (TB) and some of them have been evaluated for their application in pediatric tuberculosis as well. There is an attempt to improve smear microscopy by introducing light-emitting diode (LED) fluorescence microscopy and there are also some automated digital microscopy platforms under evaluation. Introduction of automated liquid culture platform along with rapid molecular based identification methods have considerably reduced the time delay in mycobacterial culture. Recent addition of many nucleic acid amplification platforms like Amplicor PCR, Genprobe, Xpert MTB/Rif, line probe assays, loop mediated isothermal amplification etc are also been found to be useful. Latest techniques like microarray and gene sequencing are also being used in clinical laboratories with variable results. Indirect methods of TB diagnosis like T cell based assays including tuberculin skin test and interferon-gamma release assays have their role primarily in the diagnosis of latent TB. Biomarkers are the latest addition in the battery of TB diagnostic tests facilitating diagnosis using easily accessible samples like urine, blood and breath of patients. Many biomarkers are still under evaluation and some of them are found to have a potential role as promising diagnostic tests of future.
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Affiliation(s)
- Chand Wattal
- Department of Clinical Microbiology & Immunology, Sir Ganga Ram Hospital, New Delhi, India.
| | - Reena Raveendran
- Department of Clinical Microbiology & Immunology, Sir Ganga Ram Hospital, New Delhi, India
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103
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Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019; 25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.
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Affiliation(s)
- V Mintzer
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; Leumit Health Services, Israel
| | - J Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - T Simon-Tuval
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel.
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104
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Aung HL, Nyunt WW, Fong Y, Cook GM, Aung ST. First 2 Extensively Drug-Resistant Tuberculosis Cases From Myanmar Treated With Bedaquiline. Clin Infect Dis 2019; 65:531-532. [PMID: 28444149 DOI: 10.1093/cid/cix365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Htin Lin Aung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Wint Wint Nyunt
- National Tuberculosis Reference Laboratory, National Tuberculosis Programme, Ministry of Health and Sports, Yangon, Myanmar
| | - Yang Fong
- Massey Genome Service, Institute of Fundamental Science, Massey University, Palmerston North
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Si Thu Aung
- National Tuberculosis Programme, Ministry of Health and Sports, Naypyitaw, Myanmar
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105
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Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Ködmön C, van der Werf MJ, Cirillo DM. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019; 25:1377-1382. [PMID: 30980928 DOI: 10.1016/j.cmi.2019.03.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.
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Affiliation(s)
- V Nikolayevskyy
- Public Health England, London, UK; Imperial College, London, UK.
| | - S Niemann
- Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany
| | - R Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - E Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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106
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Faksri K, Kaewprasert O, Ong RTH, Suriyaphol P, Prammananan T, Teo YY, Srilohasin P, Chaiprasert A. Comparisons of whole-genome sequencing and phenotypic drug susceptibility testing for Mycobacterium tuberculosis causing MDR-TB and XDR-TB in Thailand. Int J Antimicrob Agents 2019; 54:109-116. [PMID: 30981926 DOI: 10.1016/j.ijantimicag.2019.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/26/2019] [Accepted: 04/06/2019] [Indexed: 01/12/2023]
Abstract
Drug-resistant tuberculosis (TB) is a major public health problem. There is little information regarding the genotypic-phenotypic association of anti-TB drugs, especially for second-line drugs. This study compared phenotypic drug susceptibility testing (DST) with predictions based on whole-genome sequencing (WGS) data for 266 Mycobacterium tuberculosis isolates. Phenotypic DST used the standard proportional method. Clinical isolates of M. tuberculosis collected in Thailand between 1998 and 2013 comprised 51 drug-sensitive strains, six mono-resistant strains, two multiple-resistant strains, 88 multi-drug-resistant strains, 95 pre-extensively drug-resistant strains and 24 extensively drug-resistant strains. WGS analysis was performed using the computer programs PhyResSE and TB-Profiler. TB-Profiler had higher average concordance with phenotypic DST than PhyResSE for both first-line (91.96% vs. 91.4%) and second-line (79.67% vs. 78.20%) anti-TB drugs. The average sensitivity for all anti-TB drugs was also higher (83.13% vs. 72.08%) with slightly lower specificity (83.50% vs. 86.68%). Regardless of the program used, isoniazid, rifampicin and amikacin had the highest concordance with phenotypic DST (96.2%, 93.5% and 95.6%, respectively). Ethambutol, ethionamide and fluoroquinolones had the lowest concordance (87.34%, 81.44% and 73.85%, respectively). Concordance rates of ofloxacin (a second-generation fluoroquinolone), levofloxacin, moxifloxacin and gatifloxacin (third- and fourth-generation fluoroquinolones) were 91.79%, 76.62%, 72.64% and 57.35%, respectively. Discordance between phenotypic and WGS-based DSTs may be due, in part, to the choice of critical concentration and variable reproducibility of the phenotypic tests. It may also be due to limitations of the mutation databases (especially for the second-line drugs) and the analysis program used. Mutations related to fluoroquinolone resistance, especially the later generations, need to be identified.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand.
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Therdsak Prammananan
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Ministry of Science and Technology, Pathum Thani, Thailand
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Genome Institute of Singapore, Singapore; Department of Statistics and Applied Probability, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore
| | - Prapaporn Srilohasin
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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107
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Tembo J, Simulundu E, Changula K, Handley D, Gilbert M, Chilufya M, Asogun D, Ansumana R, Kapata N, Ntoumi F, Ippolito G, Zumla A, Bates M. Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease. Expert Rev Mol Diagn 2019; 19:325-340. [PMID: 30916590 DOI: 10.1080/14737159.2019.1595592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.
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Affiliation(s)
- John Tembo
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Edgar Simulundu
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Katendi Changula
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Dale Handley
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Matthew Gilbert
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Moses Chilufya
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Danny Asogun
- d Lassa fever research institute , Irrua University Teaching Hospital , Irrua , Nigeria
| | | | - Nathan Kapata
- f Zambia National Public Health Institute , Lusaka , Zambia
| | - Francine Ntoumi
- g Fondation Congolaise pour la Recherche Médicale , Brazzaville , Republic of Congo
| | - Giuseppe Ippolito
- h National Institute for Infectious Diseases , Lazzaro Spallanzani, IRCCS , Rome , Italy
| | - Alimuddin Zumla
- i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK.,j National Institute of Health and Research Biomedical Research Centre , UCL Hospitals National Health Service Foundation Trust , London , UK
| | - Matthew Bates
- a HerpeZ , University Teaching hospital , Lusaka , Zambia.,c School of Life Sciences , University of Lincoln , Lincoln , UK.,i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK
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108
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Yang P, Song Y, Xia X, Zhang AM. Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR. PeerJ 2019; 7:e6696. [PMID: 30972260 PMCID: PMC6448557 DOI: 10.7717/peerj.6696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
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Affiliation(s)
- Pengpeng Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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109
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Reid MJA, Arinaminpathy N, Bloom A, Bloom BR, Boehme C, Chaisson R, Chin DP, Churchyard G, Cox H, Ditiu L, Dybul M, Farrar J, Fauci AS, Fekadu E, Fujiwara PI, Hallett TB, Hanson CL, Harrington M, Herbert N, Hopewell PC, Ikeda C, Jamison DT, Khan AJ, Koek I, Krishnan N, Motsoaledi A, Pai M, Raviglione MC, Sharman A, Small PM, Swaminathan S, Temesgen Z, Vassall A, Venkatesan N, van Weezenbeek K, Yamey G, Agins BD, Alexandru S, Andrews JR, Beyeler N, Bivol S, Brigden G, Cattamanchi A, Cazabon D, Crudu V, Daftary A, Dewan P, Doepel LK, Eisinger RW, Fan V, Fewer S, Furin J, Goldhaber-Fiebert JD, Gomez GB, Graham SM, Gupta D, Kamene M, Khaparde S, Mailu EW, Masini EO, McHugh L, Mitchell E, Moon S, Osberg M, Pande T, Prince L, Rade K, Rao R, Remme M, Seddon JA, Selwyn C, Shete P, Sachdeva KS, Stallworthy G, Vesga JF, Vilc V, Goosby EP. Building a tuberculosis-free world: The Lancet Commission on tuberculosis. Lancet 2019; 393:1331-1384. [PMID: 30904263 DOI: 10.1016/s0140-6736(19)30024-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 12/20/2018] [Accepted: 12/25/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Michael J A Reid
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA.
| | - Nimalan Arinaminpathy
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | - Amy Bloom
- Tuberculosis Division, United States Agency for International Development, Washington, DC, USA
| | - Barry R Bloom
- Department of Global Health and Population, Harvard University, Cambridge, MA, USA
| | | | - Richard Chaisson
- Departments of Medicine, Epidemiology, and International Health, Johns Hopkins School of Medicine, Baltimore, MA, USA
| | | | | | - Helen Cox
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Mark Dybul
- Department of Medicine, Centre for Global Health and Quality, Georgetown University, Washington, DC, USA
| | | | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | | | - Paula I Fujiwara
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Timothy B Hallett
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Nick Herbert
- Global TB Caucus, Houses of Parliament, London, UK
| | - Philip C Hopewell
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chieko Ikeda
- Department of GLobal Health, Ministry of Heath, Labor and Welfare, Tokyo, Japan
| | - Dean T Jamison
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Aamir J Khan
- Interactive Research & Development, Karachi, Pakistan
| | - Irene Koek
- Global Health Bureau, United States Agency for International Development, Washington, DC, USA
| | - Nalini Krishnan
- Resource Group for Education and Advocacy for Community Health, Chennai, India
| | - Aaron Motsoaledi
- South African National Department of Health, Pretoria, South Africa
| | - Madhukar Pai
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada; McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Mario C Raviglione
- University of Milan, Milan, Italy; Global Studies Institute, University of Geneva, Geneva, Switzerland
| | - Almaz Sharman
- Academy of Preventive Medicine of Kazakhstan, Almaty, Kazakhstan
| | - Peter M Small
- Global Health Institute, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Zelalem Temesgen
- Department of Infectious Diseases, Mayo Clinic, Rochester, MI, USA
| | - Anna Vassall
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | | | | | - Gavin Yamey
- Center for Policy Impact in Global Health, Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Bruce D Agins
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sofia Alexandru
- Institutul de Ftiziopneumologie Chiril Draganiuc, Chisinau, Moldova
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Naomi Beyeler
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Stela Bivol
- Center for Health Policies and Studies, Chisinau, Moldova
| | - Grania Brigden
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Adithya Cattamanchi
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Danielle Cazabon
- McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Valeriu Crudu
- Center for Health Policies and Studies, Chisinau, Moldova
| | - Amrita Daftary
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada; McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Puneet Dewan
- Bill & Melinda Gates Foundation, New Delhi, India
| | - Laurie K Doepel
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | - Robert W Eisinger
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | - Victoria Fan
- T H Chan School of Public Health, Harvard University, Cambridge, MA, USA; Office of Public Health Studies, University of Hawaii, Mānoa, HI, USA
| | - Sara Fewer
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer Furin
- Division of Infectious Diseases & HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jeremy D Goldhaber-Fiebert
- Centers for Health Policy and Primary Care and Outcomes Research, Stanford University, Stanford, CA, USA
| | - Gabriela B Gomez
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - Stephen M Graham
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France; Department of Paediatrics, Center for International Child Health, University of Melbourne, Melbourne, VIC, Australia; Burnet Institute, Melbourne, VIC, Australia
| | - Devesh Gupta
- Revised National TB Control Program, New Delhi, India
| | - Maureen Kamene
- National Tuberculosis, Leprosy and Lung Disease Program, Ministry of Health, Nairobi, Kenya
| | | | - Eunice W Mailu
- National Tuberculosis, Leprosy and Lung Disease Program, Ministry of Health, Nairobi, Kenya
| | | | - Lorrie McHugh
- Office of the Secretary-General's Special Envoy on Tuberculosis, United Nations, Geneva, Switzerland
| | - Ellen Mitchell
- International Institute of Social Studies, Erasmus University Rotterdam, The Hague, Netherland
| | - Suerie Moon
- Department of Global Health and Population, Harvard University, Cambridge, MA, USA; Global Health Centre, The Graduate Institute Geneva, Geneva, Switzerland
| | | | - Tripti Pande
- McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Lea Prince
- Centers for Health Policy and Primary Care and Outcomes Research, Stanford University, Stanford, CA, USA
| | | | - Raghuram Rao
- Ministry of Health and Family Welfare, New Delhi, India
| | - Michelle Remme
- International Institute for Global Health, United Nations University, Kuala Lumpur, Malaysia
| | - James A Seddon
- Department of Medicine, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK; Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - Casey Selwyn
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Priya Shete
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Juan F Vesga
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | | | - Eric P Goosby
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
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Andrés M, van der Werf MJ, Ködmön C, Albrecht S, Haas W, Fiebig L. Molecular and genomic typing for tuberculosis surveillance: A survey study in 26 European countries. PLoS One 2019; 14:e0210080. [PMID: 30865640 PMCID: PMC6415850 DOI: 10.1371/journal.pone.0210080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/17/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Molecular typing and whole genome sequencing (WGS) information is used for (inter-) national outbreak investigations. To assist the implementation of these techniques for tuberculosis (TB) surveillance and outbreak investigations at European level there is a need for inter-country collaboration and standardization. This demands more information on molecular typing practices and capabilities of individual countries. We aimed to review the use of molecular/genomic typing for TB surveillance in European Union and European Economic Area countries in 2016; assess its public health value; and collect experiences on typing data use for cross-border cluster investigations. METHOD A web-based questionnaire was provided to all TB National Focal Points. The questionnaire consisted of three parts: i) Use and integration of molecular and genomic typing data into TB surveillance; ii) Cross-border cluster investigation and international collaboration, and iii) Perception and evaluation of public health benefits of molecular and genomic typing for TB surveillance. RESULTS Of 26 responding countries, 20 used molecular typing for TB surveillance, including nine applying WGS. The level of integration into the national surveillance was heterogeneous. Among six countries not using typing for TB surveillance, more than half planned its implementation soon. Overall, most countries perceived an added public health value of molecular typing for TB control. Concerning international cluster investigations, countries had little experience and did not have standard protocols to exchange typing data. CONCLUSION Our study shows a wide use of molecular and genomic typing data for TB surveillance in EU/EEA countries and reveals that transition to WGS-based typing is ongoing or is considered in most countries. However, our results also show a high heterogeneity in the use and integration of typing data for TB surveillance. Standardization of typing data use for TB surveillance is needed and formal procedures should be developed to facilitate international collaboration.
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Affiliation(s)
- Marta Andrés
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | | | - Csaba Ködmön
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Stefan Albrecht
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Walter Haas
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Lena Fiebig
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
- * E-mail: ,
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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: 178] [Impact Index Per Article: 35.6] [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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Khan PY, Yates TA, Osman M, Warren RM, van der Heijden Y, Padayatchi N, Nardell EA, Moore D, Mathema B, Gandhi N, Eldholm V, Dheda K, Hesseling AC, Mizrahi V, Rustomjee R, Pym A. Transmission of drug-resistant tuberculosis in HIV-endemic settings. THE LANCET. INFECTIOUS DISEASES 2019; 19:e77-e88. [PMID: 30554996 PMCID: PMC6474238 DOI: 10.1016/s1473-3099(18)30537-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
The emergence and expansion of the multidrug-resistant tuberculosis epidemic is a threat to the global control of tuberculosis. Multidrug-resistant tuberculosis is the result of the selection of resistance-conferring mutations during inadequate antituberculosis treatment. However, HIV has a profound effect on the natural history of tuberculosis, manifesting in an increased rate of disease progression, leading to increased transmission and amplification of multidrug-resistant tuberculosis. Interventions specific to HIV-endemic areas are urgently needed to block tuberculosis transmission. These interventions should include a combination of rapid molecular diagnostics and improved chemotherapy to shorten the duration of infectiousness, implementation of infection control measures, and active screening of multidrug-resistant tuberculosis contacts, with prophylactic regimens for individuals without evidence of disease. Development and improvement of the efficacy of interventions will require a greater understanding of the factors affecting the transmission of multidrug-resistant tuberculosis in HIV-endemic settings, including population-based molecular epidemiology studies. In this Series article, we review what we know about the transmission of multidrug-resistant tuberculosis in settings with high burdens of HIV and define the research priorities required to develop more effective interventions, to diminish ongoing transmission and the amplification of drug resistance.
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Affiliation(s)
- Palwasha Y Khan
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Interactive Research and Development, Karachi, Pakistan
| | - Tom A Yates
- Institute for Global Health, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | - Muhammad Osman
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- Department of Science and Technology/National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Yuri van der Heijden
- Vanderbilt Tuberculosis Center and Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nesri Padayatchi
- South African Medical Research Council HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Edward A Nardell
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
| | - David Moore
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Neel Gandhi
- Rollins School of Public Health and Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Vegard Eldholm
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Valerie Mizrahi
- Department of Science and Technology/National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roxana Rustomjee
- Division of AIDS, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Pym
- Department of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa.
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Macedo R, Pinto M, Borges V, Nunes A, Oliveira O, Portugal I, Duarte R, Gomes JP. Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 115:81-88. [PMID: 30948181 DOI: 10.1016/j.tube.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/15/2019] [Accepted: 02/22/2019] [Indexed: 11/27/2022]
Abstract
Whole-genome sequencing (WGS) offers unprecedented resolution for tracking Mycobacterium tuberculosis transmission and antibiotic-resistance spread. Still, the establishment of standardized WGS-based pipelines and the definition of epidemiological clusters based on genetic relatedness are under discussion. We aimed to implement a dynamic gene-by-gene approach, fully relying on freely available software, for prospective WGS-based tuberculosis surveillance, demonstrating its application for detecting transmission chains by retrospectively analysing all M/XDR strains isolated in 2013-2017 in Portugal. We observed a good correlation between genetic relatedness and epidemiological links, with strongly epilinked clusters displaying mean pairwise allele differences (AD) always below 0.3% (ratio of mean AD over the total number of shared loci between same-cluster strains). This data parallels the genetic distances acquired by the core-SNV analysis, while providing higher resolution and epidemiological concordance than MIRU-VNTR genotyping. The dynamic analysis of strain sub-sets (i.e., increasing the number of shared loci within each sub-set) also strengthens the confidence in detecting epilinked clusters. This gene-by-gene strategy also offers several practical benefits (e.g., reliance on freely-available software, scalability and low computational requirements) that further consolidated its suitability for a timely and robust prospective WGS-based laboratory surveillance of M/XDR-TB cases.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
| | - Olena Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B, PT Government Associate Laboratory, 4710-057, Braga/4805-017, Guimarães, Portugal; EPI Unit, Institute of Public Health, University of Porto, 4050-600 Porto, Portugal.
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, University of Lisbon, Lisbon, Portugal.
| | - Raquel Duarte
- EPI Unit, Institute of Public Health, University of Porto, 4050-600 Porto, Portugal; Clinical Epidemiology, Predictive Medicine and Public Health Department, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Pulmonology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho EPE, 4400-129 Vila Nova de Gaia, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
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Packer S, Green C, Brooks-Pollock E, Chaintarli K, Harrison S, Beck CR. Social network analysis and whole genome sequencing in a cohort study to investigate TB transmission in an educational setting. BMC Infect Dis 2019; 19:154. [PMID: 30760211 PMCID: PMC6375175 DOI: 10.1186/s12879-019-3734-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND TB outbreaks in educational institutions can result in significant transmission and pose a considerable threat to TB control. Investigation using traditional microbiological and epidemiological tools can lead to imprecise screening strategies due to difficulties characterising complex transmission networks. Application of whole genome sequencing (WGS) and social network analysis can provide additional information that may facilitate rapid directed public health action. We report the utility of these methods in combination with traditional approaches for the first time to investigate a TB outbreak in an educational setting. METHODS Latent tuberculosis infection (LTBI) cases were screenees with a positive T-SPOT®.TB test. Active TB cases were defined through laboratory confirmation of M. tuberculosis on culture or through clinical or radiological findings consistent with infection. Epidemiological data were collected from institutional records and screenees. Samples were cultured and analysed using traditional M. tuberculosis typing and WGS. We undertook multivariable multinomial regression and social network analysis to identify exposures associated with case status and risk communities. RESULTS We identified 189 LTBI cases (13.7% positivity rate) and nine active TB cases from 1377 persons screened. The LTBI positivity rate was 39.1% (99/253) among persons who shared a course with an infectious case (odds ratio 7.3, 95% confidence interval [CI] 5.2 to 10.3). The community structure analysis divided the students into five communities based on connectivity, as opposed to the 11 shared courses. Social network analysis identified that the community including the suspected index case was at significantly elevated risk of active disease (odds ratio 7.5, 95% CI 1.3 to 44.0) and contained eight persons who were lost to follow-up. Five sputum samples underwent WGS, four had zero single nucleotide polymorphism (SNP) differences and one had a single SNP difference. CONCLUSION This study demonstrates the public health impact an undiagnosed case of active TB disease can have in an educational setting within a low incidence area. Social network analysis and whole genome sequencing provided greater insight to evolution of the transmission network and identification of communities of risk. These tools provide further information over traditional epidemiological and microbiological approaches to direct public health action in this setting.
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Affiliation(s)
- Simon Packer
- Field Epidemiology Service, Public Health England, Bristol, UK
| | - Claire Green
- Heart and Lung Unit, Torbay and South Devon NHS Foundation Trust, Torbay, UK
| | - Ellen Brooks-Pollock
- NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK
| | | | | | - Charles R Beck
- Field Epidemiology Service, Public Health England, Bristol, UK. .,NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK. .,School of Social and Community Medicine, University of Bristol, Bristol, UK.
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115
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Tuberculosis risk factors and Mycobacterium tuberculosis transmission among HIV-infected patients in Vietnam. Tuberculosis (Edinb) 2019; 115:67-75. [PMID: 30948179 DOI: 10.1016/j.tube.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/18/2018] [Accepted: 02/03/2019] [Indexed: 01/28/2023]
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116
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Zaki M, Noorizhab Fakhruzzaman M, Abidin N, Aziz Z, Lim W, Richard J, Noorliza M, Hani M, Norhayati R, Zamzurina A, Farida Zuraina M, Hisyam M, Teh L, Norazmi M. Diversified lineages and drug-resistance profiles of clinical isolates of Mycobacterium tuberculosis complex in Malaysia. Int J Mycobacteriol 2019; 8:320-328. [DOI: 10.4103/ijmy.ijmy_144_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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117
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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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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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119
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Gurwitz D. Whole-genome sequencing for combatting antibiotic resistance. Drug Dev Res 2018; 80:3-5. [PMID: 30537253 DOI: 10.1002/ddr.21496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/11/2022]
Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol 2018; 26:1035-1048. [PMID: 30193960 PMCID: PMC6249990 DOI: 10.1016/j.tim.2018.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions.
| | - Ola Brønstad Brynildsrud
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway; These authors made equal contributions
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Hongbin Chen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Kathryn A Harris
- Great Ormond Street Hospital NHS Foundation Trust, Department of Microbiology, Virology & Infection Prevention & Control, London WC1N 3JH, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Vegard Eldholm
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
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Machado D, Couto I, Viveiros M. Advances in the molecular diagnosis of tuberculosis: From probes to genomes. INFECTION GENETICS AND EVOLUTION 2018; 72:93-112. [PMID: 30508687 DOI: 10.1016/j.meegid.2018.11.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/29/2022]
Abstract
Tuberculosis, disease caused by Mycobacterium tuberculosis, is currently the leading cause of death by a single infectious agent worldwide. Early, rapid and accurate identification of M. tuberculosis and the determination of drug susceptibility is essential for the treatment and management of this disease. Tuberculosis diagnosis is mainly based on chest radiography, smear microscopy and bacteriological culture. Smear microscopy has variable sensitivity, mainly in patients co-infected with the human immunodeficiency virus (HIV). Conventional culture for M. tuberculosis isolation, identification and drug susceptibility testing requires several weeks owning to the slow growth of M. tuberculosis. The delay in the time to results drives the prolongation of potentially inappropriate antituberculosis therapy contributing to the emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. For these reasons, novel diagnostic methods are need for timely identification of M. tuberculosis and determination of the antibiotic susceptibility profile of the infecting strain. Molecular methods offer enhanced sensitivity and specificity, early detection and the capacity to detect mixed infections. These technologies have improved turnaround time, cost effectiveness and are amenable for point-of-care testing. However, although these methods produce results within hours from sample collection, the phenotypic susceptibility testing is still needed for the determination of drug susceptibility and quantify the susceptibility levels of a given strain towards individual antibiotics. This review presents the history, advances and forthcoming promises in the molecular diagnosis of tuberculosis. An overview on the general principles, diagnostic value and the main advantages and disadvantages of the molecular methods used for the detection and identification of M. tuberculosis and its associated disease, is provided. It will be also discussed how the current phenotypic methods should be used in combination with the genotypic methods for rapid antituberculosis susceptibility testing.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal.
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Tagliani E, Nikolayevskyy V, Tortoli E, Cirillo DM. Laboratory diagnosis of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10021318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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123
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Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs. J Clin Microbiol 2018; 56:JCM.00923-18. [PMID: 30209183 PMCID: PMC6204665 DOI: 10.1128/jcm.00923-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022] Open
Abstract
The detection of laboratory cross-contamination and mixed tuberculosis infections is an important goal of clinical mycobacteriology laboratories. The objective of this study was to develop a method to detect mixtures of different Mycobacterium tuberculosis lineages in laboratories performing mycobacterial next-generation sequencing (NGS). The setting was the Public Health England National Mycobacteriology Laboratory Birmingham, which performs Illumina sequencing on DNA extracted from positive mycobacterial growth indicator tubes. We analyzed 4,156 samples yielding M. tuberculosis from 663 MiSeq runs, which were obtained during development and production use of a diagnostic process using NGS. The counts of the most common (major) variant and all other variants (nonmajor variants) were determined from reads mapping to positions defining M. tuberculosis lineages. Expected variation was estimated during process development. For each sample, we determined the nonmajor variant proportions at 55 sets of lineage-defining positions. The nonmajor variant proportion in the two most mixed lineage-defining sets (F2 metric) was compared with that of the 47 least-mixed lineage-defining sets (F47 metric). The following three patterns were observed: (i) not mixed by either metric; (ii) high F47 metric, suggesting mixtures of multiple lineages; and (iii) samples compatible with mixtures of two lineages, detected by differential F2 metric elevations relative to F47. Pattern ii was observed in batches, with similar patterns in the M. tuberculosis H37Rv control present in each run, and is likely to reflect cross-contamination. During production, the proportions of samples in the patterns were 97%, 2.8%, and 0.001%, respectively. The F2 and F47 metrics described could be used for laboratory process control in laboratories sequencing M. tuberculosis genomes.
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Fowler PW, Gibertoni Cruz AL, Hoosdally SJ, Jarrett L, Borroni E, Chiacchiaretta M, Rathod P, Lehmann S, Molodtsov N, Walker TM, Robinson E, Hoffmann H, Peto TEA, Cirillo DM, Smith GE, Crook DW. Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2018; 164:1522-1530. [PMID: 30351270 DOI: 10.1099/mic.0.000733] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
M. tuberculosis grows slowly and is challenging to work with experimentally compared with many other bacteria. Although microtitre plates have the potential to enable high-throughput phenotypic testing of M. tuberculosis, they can be difficult to read and interpret. Here we present a software package, the Automated Mycobacterial Growth Detection Algorithm (AMyGDA), that measures how much M. tuberculosis is growing in each well of a 96-well microtitre plate. The plate used here has serial dilutions of 14 anti-tuberculosis drugs, thereby permitting the MICs to be elucidated. The three participating laboratories each inoculated 38 96-well plates with 15 known M. tuberculosis strains (including the standard H37Rv reference strain) and, after 2 weeks' incubation, measured the MICs for all 14 drugs on each plate and took a photograph. By analysing the images, we demonstrate that AMyGDA is reproducible, and that the MICs measured are comparable to those measured by a laboratory scientist. The AMyGDA software will be used by the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) to measure the drug susceptibility profile of a large number (>30000) of samples of M. tuberculosis from patients over the next few years.
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Affiliation(s)
- Philip W Fowler
- 2National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.,1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK
| | - Ana Luíza Gibertoni Cruz
- 1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK
| | - Sarah J Hoosdally
- 1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK
| | - Lisa Jarrett
- 3National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Heartlands Hospital, Bordesley Green, Birmingham, B9 5SS, UK
| | - Emanuele Borroni
- 4Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Chiacchiaretta
- 4Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Priti Rathod
- 3National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Heartlands Hospital, Bordesley Green, Birmingham, B9 5SS, UK
| | - Sarah Lehmann
- 5SYNLAB Gauting and Institute of Microbiology and Laboratory Medicine, World Health OrganizationSupranational Reference Laboratory of Tuberculosis, Munich-Gauting, Germany
| | - Nikolay Molodtsov
- 5SYNLAB Gauting and Institute of Microbiology and Laboratory Medicine, World Health OrganizationSupranational Reference Laboratory of Tuberculosis, Munich-Gauting, Germany
| | - Timothy M Walker
- 1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK.,2National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Esther Robinson
- 3National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Heartlands Hospital, Bordesley Green, Birmingham, B9 5SS, UK
| | - Harald Hoffmann
- 5SYNLAB Gauting and Institute of Microbiology and Laboratory Medicine, World Health OrganizationSupranational Reference Laboratory of Tuberculosis, Munich-Gauting, Germany
| | - Timothy E A Peto
- 1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK.,6NIHR Health Protection Research Unit in Healthcare Associated Infection, Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Daniela Maria Cirillo
- 4Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Grace E Smith
- 3National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Heartlands Hospital, Bordesley Green, Birmingham, B9 5SS, UK
| | - Derrick W Crook
- 1Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU, UK.,6NIHR Health Protection Research Unit in Healthcare Associated Infection, Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
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125
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Gröschel MI, Walker TM, van der Werf TS, Lange C, Niemann S, Merker M. Pathogen-based precision medicine for drug-resistant tuberculosis. PLoS Pathog 2018; 14:e1007297. [PMID: 30335850 PMCID: PMC6193714 DOI: 10.1371/journal.ppat.1007297] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Matthias I. Gröschel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail:
| | - Timothy M. Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tjip S. van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christoph Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- International Health / Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
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126
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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127
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Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RTH, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med 2018; 379:1403-1415. [PMID: 30280646 PMCID: PMC6121966 DOI: 10.1056/nejmoa1800474] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).
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128
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Validation of Novel Mycobacterium tuberculosis Isoniazid Resistance Mutations Not Detectable by Common Molecular Tests. Antimicrob Agents Chemother 2018; 62:AAC.00974-18. [PMID: 30082293 DOI: 10.1128/aac.00974-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/03/2018] [Indexed: 01/20/2023] Open
Abstract
Resistance to the first-line antituberculosis (TB) drug isoniazid (INH) is widespread, and the mechanism of resistance is unknown in approximately 15% of INH-resistant (INH-R) strains. To improve molecular detection of INH-R TB, we used whole-genome sequencing (WGS) to analyze 52 phenotypically INH-R Mycobacterium tuberculosis complex (MTBC) clinical isolates that lacked the common katG S315T or inhA promoter mutations. Approximately 94% (49/52) of strains had mutations at known INH-associated loci that were likely to confer INH resistance. All such mutations would be detectable by sequencing more DNA adjacent to existing target regions. Use of WGS minimized the chances of missing infrequent INH resistance mutations outside commonly targeted hotspots. We used recombineering to generate 12 observed clinical katG mutations in the pansusceptible H37Rv reference strain and determined their impact on INH resistance. Our functional genetic experiments have confirmed the role of seven suspected INH resistance mutations and discovered five novel INH resistance mutations. All recombineered katG mutations conferred resistance to INH at a MIC of ≥0.25 μg/ml and should be added to the list of INH resistance determinants targeted by molecular diagnostic assays. We conclude that WGS is a useful tool for detecting uncommon INH resistance mutations that would otherwise be missed by current targeted molecular testing methods and suggest that its use (or use of expanded conventional or next-generation-based targeted sequencing) may provide earlier diagnosis of INH-R TB.
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129
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Cabibbe AM, Walker TM, Niemann S, Cirillo D. Whole genome sequencing of Mycobacterium tuberculosis. Eur Respir J 2018; 52:13993003.01163-2018. [DOI: 10.1183/13993003.01163-2018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/02/2018] [Indexed: 11/05/2022]
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130
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Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology 2018; 23:1098-1113. [PMID: 30189463 DOI: 10.1111/resp.13393] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/03/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is the deadliest infectious disease and the associated global threat has worsened with the emergence of drug resistance, in particular multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Although the World Health Organization (WHO) End-TB Strategy advocates for universal access to antimicrobial susceptibility testing, this is not widely available and/or it is still underused. The majority of drug resistance in clinical MTB strains is attributed to chromosomal mutations. Resistance-related mutations could also exert certain fitness cost to the drug-resistant MTB strains and growth fitness could be restored by the presence of compensatory mutations. Understanding these underlying mechanisms could provide an important insight into TB pathogenesis and predict the future trend of MDR-TB global pandemic. This review covers the mechanisms of resistance in MTB and provides a comprehensive overview of current phenotypic and molecular approaches for drug susceptibility testing, with particular attention to the methods endorsed and recommended by the WHO.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital Compound, The University of Hong Kong, Hong Kong, China
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131
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Kohl TA, Harmsen D, Rothgänger J, Walker T, Diel R, Niemann S. Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System. EBioMedicine 2018; 34:131-138. [PMID: 30115606 PMCID: PMC6116475 DOI: 10.1016/j.ebiom.2018.07.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
Background Global tuberculosis (TB) control is challenged by uncontrolled transmission of Mycobacterium tuberculosis complex (Mtbc) strains, esp. of multidrug (MDR) or extensively resistant (XDR) variants. Precise analysis of transmission networks is the basis to trace outbreak M/XDR clones and improve TB control. However, classical genotyping tools lack discriminatory power due to the high similarity of strains of particular successful lineages, e.g. Beijing or outbreak strains. This can be overcome by whole genome sequencing (WGS) approaches, but these are not yet standardized to facilitate larger investigations encompassing different laboratories or outbreak tracing across borders. Methods We established and improved a whole genome gene-by-gene multi locus sequence typing approach encompassing a stable set of core genome genes (cgMLST) and linked it to a web-based nomenclature server (cgMLST.org) facilitating assignment and storage of allele numbers. Findings We evaluated and refined a previously suggested cgMLST schema by using a reference strain set (n = 251) reflecting the global diversity of the Mtbc. A set of 2891 genes showed excellent performance with at least 97% of the genes reliably identified in strains of all Mtbc lineages and in discriminating outbreak strains. cgMLST allele numbers were automatically retrieved from and stored at cgMLST.org. Interpretation The refined cgMLST schema provides high resolution genome-based typing of clinical strains of all Mtbc lineages. Combined with a web-based nomenclature server, it facilitates rapid, high-resolution, and harmonized tracing of clinical Mtbc strains needed for prospective local and global surveillance.
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Affiliation(s)
- Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Dag Harmsen
- Department of Periodontology and Restorative Dentistry, University Hospital Münster, 48149 Münster, Germany
| | | | - Timothy Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, 24105 Kiel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany; German Center for Infection Research, Borstel Site, 23845 Borstel, Germany.
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132
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Wyllie DH, Sanderson N, Myers R, Peto T, Robinson E, Crook DW, Smith EG, Walker AS. Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline. J Clin Microbiol 2018; 56:e00104-18. [PMID: 29875188 PMCID: PMC6062814 DOI: 10.1128/jcm.00104-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Contact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artifactual variation between Mycobacterium tuberculosis isolates during routine next-generation sequencing of Mycobacterium spp., we investigated its basis in 2,018 consecutive M. tuberculosis isolates. In the routine process used, clinical samples were decontaminated and inoculated into broth cultures; from positive broth cultures DNA was extracted and sequenced, reads were mapped, and consensus sequences were determined. We investigated the process of consensus sequence determination, which selects the most common nucleotide at each position. Having determined the high-quality read depth and depth of minor variants across 8,006 M. tuberculosis genomic regions, we quantified the relationship between the minor variant depth and the amount of nonmycobacterial bacterial DNA, which originates from commensal microbes killed during sample decontamination. In the presence of nonmycobacterial bacterial DNA, we found significant increases in minor variant frequencies, of more than 1.5-fold, in 242 regions covering 5.1% of the M. tuberculosis genome. Included within these were four high-variation regions strongly influenced by the amount of nonmycobacterial bacterial DNA. Excluding these four regions from pairwise distance comparisons reduced biologically implausible variation from 5.2% to 0% in an independent validation set derived from 226 individuals. Thus, we demonstrated an approach identifying critical genomic regions contributing to clinically relevant artifactual variation in bacterial similarity searches. The approach described monitors the outputs of the complex multistep laboratory and bioinformatics process, allows periodic process adjustments, and will have application to quality control of routine bacterial genomics.
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Affiliation(s)
- David H Wyllie
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- Public Health England Academic Collaborating Centre, John Radcliffe Hospital, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, United Kingdom
| | - Nicholas Sanderson
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Myers
- Department of Bioinformatics, Public Health England, London, United Kingdom
| | - Tim Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, United Kingdom
| | - Esther Robinson
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, United Kingdom
| | - E Grace Smith
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, United Kingdom
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133
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Peacock SJ, Parkhill J, Brown NM. Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens. MICROBIOLOGY-SGM 2018; 164:1213-1219. [PMID: 30052172 PMCID: PMC7611365 DOI: 10.1099/mic.0.000700] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The current paradigm for hospital outbreak detection and investigation is based on methodology first developed over 150 years ago. Daily surveillance to detect patients positive for pathogens of particular importance for nosocomial infection is supported by epidemiological investigation to determine their relationship in time and place, and to identify any other factor that could link them. The antibiotic resistance pattern is commonly used as a surrogate for bacterial relatedness, although this lacks sensitivity and specificity. Typing may be used to define bacterial relatedness, although routine methods lack sufficient discriminatory power to distinguish relatedness beyond the level of bacterial clones. Ultimately, the identification of an outbreak remains a predominately subjective process reliant on the intuition of experienced infection control professionals. Here, we propose a redesign of hospital outbreak detection and investigation in which bacterial species associated with nosocomial transmission and infection undergo routine prospective whole-genome sequencing. Further investigation is based on the probability that isolates are associated with an outbreak, which is based on the degree of genetic relatedness between isolates. Evidence is provided that supports this model based on studies of MRSA (methicillin-resistant Staphylococcus aureus), together with the benefits of a 'Sequence First' approach. The feasibility of implementation is discussed, together with residual barriers that need to be overcome prior to implementation.
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Affiliation(s)
- Sharon J Peacock
- 3Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.,1London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,2Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Box 157 Hills Road, Cambridge CB2 0QQ, UK
| | - Julian Parkhill
- 3Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Nicholas M Brown
- 4Clinical Microbiology & Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Box 236 Hills Road, Cambridge CB2 0QW, UK
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134
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Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. J Clin Microbiol 2018; 56:JCM.00666-18. [PMID: 29848567 PMCID: PMC6062781 DOI: 10.1128/jcm.00666-18] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridization and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole-genome sequencing or phenotypic testing of resistance from cultures in a clinical setting. This improved turnaround time enables prompt appropriate treatment with associated patient and health service benefits. Improvements in sample preparation are necessary to ensure comparable sensitivities and complete resistance profile predictions in all cases.
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135
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Ruesen C, Riza AL, Florescu A, Chaidir L, Editoiu C, Aalders N, Nicolosu D, Grecu V, Ioana M, van Crevel R, van Ingen J. Linking minimum inhibitory concentrations to whole genome sequence-predicted drug resistance in Mycobacterium tuberculosis strains from Romania. Sci Rep 2018; 8:9676. [PMID: 29946139 PMCID: PMC6018741 DOI: 10.1038/s41598-018-27962-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/01/2018] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance poses a major threat to tuberculosis control. Current phenotypic tests for drug susceptibility are time-consuming, technically complex, and expensive. Whole genome sequencing is a promising alternative, though the impact of different drug resistance mutations on the minimum inhibitory concentration (MIC) remains to be investigated. We examined the genomes of 72 phenotypically drug-resistant Mycobacterium tuberculosis isolates from 72 Romanian patients for drug resistance mutations. MICs for first- and second-line drugs were determined using the MycoTB microdilution method. These MICs were compared to macrodilution critical concentration testing by the Mycobacterium Growth Indicator Tube (MGIT) platform and correlated to drug resistance mutations. Sixty-three (87.5%) isolates harboured drug resistance mutations; 48 (66.7%) were genotypically multidrug-resistant. Different drug resistance mutations were associated with different MIC ranges; katG S315T for isoniazid, and rpoB S450L for rifampicin were associated with high MICs. However, several mutations such as in rpoB, rrs and rpsL, or embB were associated with MIC ranges including the critical concentration for rifampicin, aminoglycosides or ethambutol, respectively. Different resistance mutations lead to distinct MICs, some of which may still be overcome by increased dosing. Whole genome sequencing can aid in the timely diagnosis of Mycobacterium tuberculosis drug resistance and guide clinical decision-making.
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Affiliation(s)
- Carolien Ruesen
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Anca Lelia Riza
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Adriana Florescu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Lidya Chaidir
- Health Research Unit, Faculty of Medicine, Padjadjaran University/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Cornelia Editoiu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Nicole Aalders
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Dragos Nicolosu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Victor Grecu
- "Victor Babes" Infectious Diseases and Pneumophtisiology Hospital Craiova, Dolj County, Romania
| | - Mihai Ioana
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Craiova, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud university medical center, Nijmegen, The Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
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136
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Lalor MK, Casali N, Walker TM, Anderson LF, Davidson JA, Ratna N, Mullarkey C, Gent M, Foster K, Brown T, Magee J, Barrett A, Crook DW, Drobniewski F, Thomas HL, Abubakar I. The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak. Eur Respir J 2018; 51:13993003.02313-2017. [PMID: 29748309 DOI: 10.1183/13993003.02313-2017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/26/2018] [Indexed: 11/05/2022]
Abstract
We used whole-genome sequencing (WGS) to delineate transmission networks and investigate the benefits of WGS during cluster investigation.We included clustered cases of multidrug-resistant (MDR) tuberculosis (TB)/extensively drug-resistant (XDR) TB linked by mycobacterial interspersed repetitive unit variable tandem repeat (MIRU-VNTR) strain typing or epidemiological information in the national cluster B1006, notified between 2007 and 2013 in the UK. We excluded from further investigation cases whose isolates differed by greater than 12 single nucleotide polymorphisms (SNPs). Data relating to patients' social networks were collected.27 cases were investigated and 22 had WGS, eight of which (36%) were excluded as their isolates differed by more than 12 SNPs to other cases. 18 cases were ruled into the transmission network based on genomic and epidemiological information. Evidence of transmission was inconclusive in seven out of 18 cases (39%) in the transmission network following WGS and epidemiological investigation.This investigation of a drug-resistant TB cluster illustrates the opportunities and limitations of WGS in understanding transmission in a setting with a high proportion of migrant cases. The use of WGS should be combined with classical epidemiological methods. However, not every cluster will be solvable, regardless of the quality of genomic data.
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Affiliation(s)
- Maeve K Lalor
- Tuberculosis Section, National Infection Service, Public Health England, London, UK.,Institute for Global Health, University College London, London, UK
| | - Nicola Casali
- PHE National Mycobacterium Reference Service South, Public Health England, London, UK.,Dept of Infectious Diseases, Imperial College London, London, UK
| | - Timothy M Walker
- Nuffield Dept of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Laura F Anderson
- Tuberculosis Section, National Infection Service, Public Health England, London, UK
| | - Jennifer A Davidson
- Tuberculosis Section, National Infection Service, Public Health England, London, UK
| | - Natasha Ratna
- Tuberculosis Section, National Infection Service, Public Health England, London, UK
| | - Cathy Mullarkey
- TB Health Visiting Service, Leeds Community Healthcare, Leeds, UK
| | - Mike Gent
- Yorkshire and the Humber Public Health England Centre, Public Health England, Leeds, UK
| | - Kirsty Foster
- North East Public Health England Centre, Public Health England, Newcastle, UK
| | - Tim Brown
- PHE National Mycobacterium Reference Service South, Public Health England, London, UK
| | - John Magee
- PHE North of England Mycobacterium Reference Centre, Freeman Hospital, Newcastle, UK.,School of Biology, Newcastle University, Newcastle, UK
| | - Anne Barrett
- PHE North of England Mycobacterium Reference Centre, Freeman Hospital, Newcastle, UK
| | - Derrick W Crook
- Nuffield Dept of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, London, UK
| | - Francis Drobniewski
- PHE National Mycobacterium Reference Service South, Public Health England, London, UK.,Dept of Infectious Diseases, Imperial College London, London, UK
| | - H Lucy Thomas
- Tuberculosis Section, National Infection Service, Public Health England, London, UK
| | - Ibrahim Abubakar
- Tuberculosis Section, National Infection Service, Public Health England, London, UK.,Institute for Global Health, University College London, London, UK
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137
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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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138
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Parvaresh L, Crighton T, Martinez E, Bustamante A, Chen S, Sintchenko V. Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing. BMC Infect Dis 2018; 18:265. [PMID: 29879906 PMCID: PMC5992641 DOI: 10.1186/s12879-018-3164-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/24/2018] [Indexed: 12/03/2022] Open
Abstract
Background The recurrence of tuberculosis (TB) disease in treated patients can serve as a marker of the efficacy of TB control programs. Recurrent disease represents either endogenous reactivation with the same strain of Mycobacterium tuberculosis due to non-compliance or inadequate therapy or exogenous reinfection with a new strain. Genotyping or whole genome sequencing (WGS) of M. tuberculosis isolates from initial and recurrent cases can differentiate between reinfection and reactivation. This study examined cases of recurrent TB in New South Wales, Australia, using genotyping and WGS. Methods Culture-confirmed TB cases diagnosed at least 12 months apart between January 2011 and December 2016 were included. Isolates of M. tuberculosis from patients were compared using 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-24) typing and WGS. Results Eighteen cases of recurrent disease were identified but isolates from only 15 (83%) were available for study. MIRU-24 findings classified 13 (13/15; 87%) as reactivation and two (13%), as reinfection. Sequencing 13 cultivable paired isolates demonstrated 11 reactivations and two reinfections. There was genomic similarity in 10 out of 13 pairs while one case (1/13; 8%) had 12 SNPS differences. Two other cases (2/13;15%) had > 200 SNPs differences and were classified as reinfection. No phenotypic or genomic evidence of drug resistance was observed. Conclusion TB control programs can achieve consistently low rates of recurrent disease in low incidence settings. WGS of implicated isolates augments the differentiation between reactivation and reinfection and indicates that the majority of recurrences are due to reactivation rather than reinfection. Predominance of reactivation over reinfection indicates high-quality public health practices and a low risk of local transmission. Trial registration This study was approved by the Western Sydney Local Health District (WSLHD) Human Research Ethics Committee (HREC Ref: AU RED LNR/17/WMEAD/190; SSA Ref: LNR SSA/17/WMEAD/191).
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Affiliation(s)
- Laila Parvaresh
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead, NSW, 2145, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead, NSW, 2145, Australia
| | - Andrea Bustamante
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead, NSW, 2145, Australia
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead, NSW, 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, and Sydney Medical School, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, cnr Hawkesbury and Darcy Roads, Westmead, NSW, 2145, Australia.,NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead, NSW, 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, and Sydney Medical School, The University of Sydney, Westmead, NSW, 2145, Australia
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139
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Hill-Cawthorne GA. Population monitoring for drug-resistant tuberculosis: is genomics the answer? THE LANCET. INFECTIOUS DISEASES 2018; 18:592-594. [PMID: 29574064 DOI: 10.1016/s1473-3099(18)30161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Grant A Hill-Cawthorne
- School of Public Health and Marie Bashir Institute, University of Sydney, Sydney, NSW 2006 Australia.
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140
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Validation of the FluoroType MTBDR Assay for Detection of Rifampin and Isoniazid Resistance in Mycobacterium tuberculosis Complex Isolates. J Clin Microbiol 2018; 56:JCM.00072-18. [PMID: 29593055 PMCID: PMC5971528 DOI: 10.1128/jcm.00072-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/15/2018] [Indexed: 11/20/2022] Open
Abstract
For Mycobacterium tuberculosis complex (MTBC), the rapid and accurate diagnosis of drug resistance is crucial to ensure early initiation of appropriate therapy. Recently, a new molecular diagnostic test, the FluoroType MTBDR, aimed at detecting rifampin and isoniazid resistance has become available. This study aimed to evaluate the FluoroType MTBDR in comparison to phenotypic drug susceptibility testing (DST) using M. tuberculosis complex isolates. MTBC isolates underwent phenotypic DST and were tested using the FluoroType MTBDR and Genotype MTBDRplus. Sanger sequencing of the key regions of rpoB, katG, inhA, and aphC was performed for isolates with discordant phenotypic and molecular results. Furthermore, isolates with specific wild-type bands missing in the Genotype MTBDRplus, indicating the presence of a mutation, were investigated by Sanger sequencing. Specificity and sensitivity, defined as the proportions of isolates correctly determined as susceptible and resistant by the FluoroType MTBDR compared to phenotypic DST, were calculated. A total of 180 culture isolates were included; phenotypic DST showed 85 isolates susceptible to isoniazid and rifampin, 7 with isoniazid monoresistance, 7 with rifampin monoresistance, and 81 with multidrug resistance. The specificity of the FluoroType MTBDR was 100% (95% confidence interval [CI], 96.0 to 100%) for both rifampin and isoniazid. The sensitivity was 91.7% (95% CI, 83.6 to 96.6%) for isoniazid and 98.9% (95% CI, 93.8 to 100.0%) for rifampin. The FluoroType MTBDR has a high sensitivity and specificity for the detection of rifampin and isoniazid resistance when using culture isolates.
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141
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Scriven JE, Scobie A, Verlander NQ, Houston A, Collyns T, Cajic V, Kon OM, Mitchell T, Rahama O, Robinson A, Withama S, Wilson P, Maxwell D, Agranoff D, Davies E, Llewelyn M, Soo SS, Sahota A, Cooper MA, Hunter M, Tomlins J, Tiberi S, Kendall S, Dedicoat M, Alexander E, Fenech T, Zambon M, Lamagni T, Smith EG, Chand M. Mycobacterium chimaera infection following cardiac surgery in the United Kingdom: clinical features and outcome of the first 30 cases. Clin Microbiol Infect 2018; 24:1164-1170. [PMID: 29803845 DOI: 10.1016/j.cmi.2018.04.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Mycobacterium chimaera infection following cardiac surgery, due to contaminated cardiopulmonary bypass heater-cooler units, has been reported worldwide. However, the spectrum of clinical disease remains poorly understood. To address this, we report the clinical and laboratory features, treatment and outcome of the first 30 UK cases. METHODS Case note review was performed for cases identified retrospectively through outbreak investigations and prospectively through ongoing surveillance. Case definition was Mycobacterium chimaera detected in any clinical specimen, history of cardiothoracic surgery with cardiopulmonary bypass, and compatible clinical presentation. RESULTS Thirty patients were identified (28 with prosthetic material) exhibiting a spectrum of disease including prosthetic valve endocarditis (14/30), sternal wound infection (2/30), aortic graft infection (4/30) and disseminated (non-cardiac) disease (10/30). Patients presented a median of 14 months post surgery (maximum 5 years) most commonly complaining of fever and weight loss. Investigations frequently revealed lymphopenia, thrombocytopenia, liver cholestasis and non-necrotizing granulomatous inflammation. Diagnostic sensitivity for a single mycobacterial blood culture was 68% but increased if multiple samples were sent. In all, 27 patients started macrolide-based combination treatment and 14 had further surgery. To date, 18 patients have died (60%) a median of 30 months (interquartile range 20-39 months) after initial surgery. Survival analysis identified younger age, mitral valve surgery, mechanical valve replacement, higher serum sodium concentration and lower C-reactive protein as factors associated with better survival. CONCLUSIONS Mycobacterium chimaera infection following cardiac surgery is associated with a wide spectrum of disease. The diagnosis should be considered in all patients who develop an unexplained illness following cardiac surgery.
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Affiliation(s)
- J E Scriven
- Department of Infection and Tropical Medicine, Birmingham Heartlands Hospital, Birmingham, UK; National Infection Service, Public Health England, Colindale, London, UK.
| | - A Scobie
- National Infection Service, Public Health England, Colindale, London, UK
| | - N Q Verlander
- Statistics Unit, National Infection Service, Public Health England, Colindale, London, UK
| | - A Houston
- Department of Infection, St Georges Universities NHS Foundation Trust, London, UK
| | - T Collyns
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - V Cajic
- Department of Infection, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - O M Kon
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust, London, UK
| | - T Mitchell
- Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - O Rahama
- Hull and East Yorkshire Hospitals NHS Trust, Hull, UK
| | - A Robinson
- Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - S Withama
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - P Wilson
- University College London Hospitals NHS Foundation Trust, London, UK
| | - D Maxwell
- Department of Respiratory Medicine, East Sussex Healthcare NHS Trust, Eastbourne, UK
| | - D Agranoff
- Department of Microbiology and Infection, Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - E Davies
- Public Health Wales Microbiology, Cardiff, UK
| | - M Llewelyn
- Department of Infectious Diseases, Royal Gwent Hospital, Newport, UK
| | - S-S Soo
- Department of Microbiology, Nottingham University Hospitals NHS Trust, QMC Campus, Nottingham, UK
| | - A Sahota
- Department of Infection and Tropical Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - M A Cooper
- Department of Microbiology, The Royal Wolverhampton Hospitals NHS Trust, Wolverhampton, UK
| | - M Hunter
- Department of Infectious Diseases, Royal Victoria Hospital, Belfast, UK
| | - J Tomlins
- Department of Infection, St Georges Universities NHS Foundation Trust, London, UK
| | - S Tiberi
- Division of Infection, Barts Health NHS Trust, Royal London Hospital, London, UK; Blizard Institute, Barts and the London School of Medicine and Dentistry, London, UK
| | - S Kendall
- Society for Cardiothoracic Surgery in Great Britain and Ireland, London, UK; South Tees Hospitals Foundation NHS Trust, Middlesbrough, UK
| | - M Dedicoat
- Department of Infection and Tropical Medicine, Birmingham Heartlands Hospital, Birmingham, UK
| | - E Alexander
- National Infection Service, Public Health England, Colindale, London, UK
| | | | - M Zambon
- National Infection Service, Public Health England, Colindale, London, UK
| | - T Lamagni
- National Infection Service, Public Health England, Colindale, London, UK
| | - E G Smith
- National Infection Service, Public Health England, Colindale, London, UK
| | - M Chand
- National Infection Service, Public Health England, Colindale, London, UK; National Institute for Health Research Health Protection Research Unit in Respiratory Infections, Imperial College London, London, UK; Guy's and St Thomas' NHS Foundation Trust, London, UK
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142
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Migliori GB, Sotgiu G, Rosales-Klintz S, Centis R, D'Ambrosio L, Abubakar I, Bothamley G, Caminero JA, Cirillo DM, Dara M, de Vries G, Aliberti S, Dinh-Xuan AT, Duarte R, Midulla F, Solovic I, Subotic DR, Amicosante M, Correia AM, Cirule A, Gualano G, Kunst H, Palmieri F, Riekstina V, Tiberi S, Verduin R, van der Werf MJ. ERS/ECDC Statement: European Union standards for tuberculosis care, 2017 update. Eur Respir J 2018; 51:13993003.02678-2017. [PMID: 29678945 DOI: 10.1183/13993003.02678-2017] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/11/2018] [Indexed: 12/31/2022]
Abstract
The International Standards for Tuberculosis Care define the essential level of care for managing patients who have or are presumed to have tuberculosis, or are at increased risk of developing the disease. The resources and capacity in the European Union (EU) and the European Economic Area permit higher standards of care to secure quality and timely TB diagnosis, prevention and treatment. On this basis, the European Union Standards for Tuberculosis Care (ESTC) were published in 2012 as standards specifically tailored to the EU setting. Since the publication of the ESTC, new scientific evidence has become available and, therefore, the standards were reviewed and updated.A panel of international experts, led by a writing group from the European Respiratory Society (ERS) and the European Centre for Disease Prevention and Control (ECDC), updated the ESTC on the basis of new published evidence. The underlying principles of these patient-centred standards remain unchanged. The second edition of the ESTC includes 21 standards in the areas of diagnosis, treatment, HIV and comorbidities, and public health and prevention.The ESTC target clinicians and public health workers, provide an easy-to-use resource and act as a guide through all the required activities to ensure optimal diagnosis, treatment and prevention of TB.
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Affiliation(s)
- Giovanni Battista Migliori
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Maugeri Care and Research Institute, Tradate, Italy.,Contributed equally
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy.,Contributed equally
| | - Senia Rosales-Klintz
- European Centre for Disease Prevention and Control, Stockholm, Sweden.,Contributed equally
| | - Rosella Centis
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Maugeri Care and Research Institute, Tradate, Italy.,Contributed equally
| | - Lia D'Ambrosio
- World Health Organization Collaborating Centre for Tuberculosis and Lung Diseases, Maugeri Care and Research Institute, Tradate, Italy.,Public Health Consulting Group, Lugano, Switzerland.,Contributed equally
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | | | - Jose Antonio Caminero
- Pneumology Dept, Hospital General de Gran Canaria "Dr. Negrin", Las Palmas de Gran Canaria, Spain.,MDR-TB Unit, Tuberculosis Division, International Union against Tuberculosis and Lung Disease (The Union), Paris, France
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Masoud Dara
- World Health Organization, Regional Office for Europe, UN City, Copenhagen, Denmark
| | | | - Stefano Aliberti
- School of Medicine and Surgery, University of Milan-Bicocca, UO Clinica Pneumologica, AO San Gerardo, Monza, Italy
| | - Anh Tuan Dinh-Xuan
- Dept of Respiratory Physiology, Cochin Hospital, Paris Descartes University, Paris, France
| | - Raquel Duarte
- National Reference Centre for MDR-TB, Hospital Centre Vila Nova de Gaia, Dept of Pneumology; Public Health Science and Medical Education Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Fabio Midulla
- Dept of Paediatrics, Paediatric Emergency Unit, "Sapienza" University of Rome, Rome, Italy
| | - Ivan Solovic
- National Institute for TB, Lung Diseases and Thoracic Surgery, Vysne Hagy, Catholic University Ruzomberok, Ruzomberok, Slovakia
| | | | - Massimo Amicosante
- Dept of Biomedicine and Prevention and Animal Technology Station, University of Rome "Tor Vergata", Rome, Italy
| | - Ana Maria Correia
- Regional Health Administration of the North, Dept of Public Health, Porto, Portugal
| | - Andra Cirule
- Centre of TB and Lung Diseases, Riga East University Hospital, Riga, Latvia
| | - Gina Gualano
- Respiratory Infectious Diseases Unit, National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Rome, Italy
| | - Heinke Kunst
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University, London UK
| | - Fabrizio Palmieri
- Respiratory Infectious Diseases Unit, National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Rome, Italy
| | - Vija Riekstina
- Dept of Methodology and Supervision, Riga East University Hospital, Riga, Latvia
| | - Simon Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University, London UK.,Division of Infection, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Remi Verduin
- Verduin Public Health Consult, Oegstgeest, The Netherlands
| | - Marieke J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden.,Contributed equally
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143
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McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther 2018; 16:433-442. [PMID: 29718745 DOI: 10.1080/14787210.2018.1472577] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The threat of resistance to anti-tuberculosis drugs is of global concern. Current efforts to monitor resistance rely on phenotypic testing where cultured bacteria are exposed to critical concentrations of the drugs. Capacity for such testing is low in TB endemic countries. Drug resistance is caused by mutations in the Mycobacterium tuberculosis genome and whole genome sequencing to detect these mutations offers an alternative means of assessing resistance. Areas covered: The challenges of assessing TB drug resistance are discussed. Progress in elucidating the M. tuberculosis resistome and evidence of the accuracy of next generation sequencing for detecting resistance is reviewed. Expert Commentary: There are considerable advantages to using next generation sequencing for TB drug resistance surveillance. Accuracy is high for detecting resistance to the major first-line drugs but is currently lower for the second-line drugs due to our incomplete knowledge regarding resistance causing mutations. With the advances in sequencing technology and the opportunity to replace phenotypic drug susceptibility testing with safer and more cost effective methods it would appear that the question is when to implement. Current bottlenecks are sample extraction to allow whole genome sequencing directly from sputum and the lack of bioinformatics expertise in some TB endemic countries.
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Affiliation(s)
- Ruth McNerney
- a Division of Pulmonary Medicine, Department of Medicine , University of Cape Town , Cape Town , South Africa
| | - Matteo Zignol
- b Global Tuberculosis Programme , World Health Organization , Geneva , Switzerland
| | - Taane G Clark
- c Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health , London School of Hygiene & Tropical Medicine , London , United Kingdom
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144
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Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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145
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Accuracy of whole genome sequencing versus phenotypic (MGIT) and commercial molecular tests for detection of drug-resistant Mycobacterium tuberculosis isolated from patients in Brazil and Mozambique. Tuberculosis (Edinb) 2018; 110:59-67. [DOI: 10.1016/j.tube.2018.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/26/2018] [Accepted: 04/03/2018] [Indexed: 02/05/2023]
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146
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Cabibbe AM, Trovato A, De Filippo MR, Ghodousi A, Rindi L, Garzelli C, Baretti S, Allodi G, Mannino R, Rossolini GM, Bartoloni A, Tortoli E, Cirillo DM. Countrywide implementation of whole genome sequencing: an opportunity to improve tuberculosis management, surveillance and contact tracing in low incidence countries. Eur Respir J 2018; 51:13993003.00387-2018. [DOI: 10.1183/13993003.00387-2018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/02/2018] [Indexed: 11/05/2022]
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147
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Lange C, Chesov D, Heyckendorf J, Leung CC, Udwadia Z, Dheda K. Drug-resistant tuberculosis: An update on disease burden, diagnosis and treatment. Respirology 2018; 23:656-673. [PMID: 29641838 DOI: 10.1111/resp.13304] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
Abstract
The emergence of antimicrobial resistance against Mycobacterium tuberculosis, the leading cause of mortality due to a single microbial pathogen worldwide, represents a growing threat to public health and economic growth. The global burden of multidrug-resistant tuberculosis (MDR-TB) has recently increased by an annual rate of more than 20%. According to the World Health Organization approximately only half of all patients treated for MDR-TB achieved a successful outcome. For many years, patients with drug-resistant tuberculosis (TB) have received standardized treatment regimens, thereby accelerating the development of MDR-TB through drug-specific resistance amplification. Comprehensive drug susceptibility testing (phenotypic and/or genotypic) is necessary to inform physicians about the best drugs to treat individual patients with tailor-made treatment regimens. Phenotypic drug resistance can now often, but with variable sensitivity, be predicted by molecular drug susceptibility testing based on whole genome sequencing, which in the future could become an affordable method for the guidance of treatment decisions, especially in high-burden/resource-limited settings. More recently, MDR-TB treatment outcomes have dramatically improved with the use of bedaquiline-based regimens. Ongoing clinical trials with novel and repurposed drugs will potentially further improve cure-rates, and may substantially decrease the duration of MDR-TB treatment necessary to achieve relapse-free cure.
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Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany.,Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Dumitru Chesov
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,Department of Pneumology and Allergology, State University of Medicine and Pharmacy "Nicolae Testemitanu", Chisinau, Republic of Moldova
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Chi C Leung
- Department of Health, Tuberculosis and Chest Service, Centre for Health Protection, Hong Kong, China
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital and Research Centre, Mumbai, India
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
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148
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Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis. Clin Microbiol Infect 2018; 25:82-86. [PMID: 29653190 DOI: 10.1016/j.cmi.2018.03.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 01/24/2023]
Abstract
OBJECTIVES Culture-based assays are currently the reference standard for drug susceptibility testing for Mycobacterium tuberculosis. They provide good sensitivity and specificity but are time consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture-based assays for drug susceptibility testing of M. tuberculosis. METHODS M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n = 211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first-line drug susceptibilities. WGS was performed for all isolates using the Illumina MiSeq system, and data were analysed using five software tools (PhyResSE, Mykrobe Predictor, TB Profiler, TGS-TB and KvarQ). Diagnostic time and reagent costs were estimated for both methods. RESULTS The sensitivity of the five software tools to predict any resistance among strains was almost identical, ranging from 74% to 80%, and specificity was more than 95% for all software tools except for TGS-TB. The sensitivity and specificity to predict resistance to individual drugs varied considerably among the software tools. Reagent costs for MGIT and WGS were €26 and €143 per isolate respectively. Turnaround time for MGIT was 19 days (range 10-50 days) for first-line drugs, and turnaround time for WGS was estimated to be 5 days (range 3-7 days). CONCLUSIONS WGS could be used as a prescreening assay for drug susceptibility testing with confirmation of resistant strains by MGIT. The functionality and ease of use of the software tools need to be improved.
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149
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Dallman T, Ashton P, Schafer U, Jironkin A, Painset A, Shaaban S, Hartman H, Myers R, Underwood A, Jenkins C, Grant K. SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. Bioinformatics 2018; 34:3028-3029. [DOI: 10.1093/bioinformatics/bty212] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/04/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Timothy Dallman
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
| | - Philip Ashton
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ulf Schafer
- Infectious Disease Informatics, National Infections Service, Public Health England, London, UK
| | - Aleksey Jironkin
- Infectious Disease Informatics, National Infections Service, Public Health England, London, UK
| | - Anais Painset
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
| | | | - Hassan Hartman
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
| | - Richard Myers
- Infectious Disease Informatics, National Infections Service, Public Health England, London, UK
| | - Anthony Underwood
- Infectious Disease Informatics, National Infections Service, Public Health England, London, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
| | - Kathie Grant
- Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK
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150
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Macedo R, Nunes A, Portugal I, Duarte S, Vieira L, Gomes JP. Dissecting whole-genome sequencing-based online tools for predicting resistance in Mycobacterium tuberculosis: can we use them for clinical decision guidance? Tuberculosis (Edinb) 2018; 110:44-51. [PMID: 29779772 DOI: 10.1016/j.tube.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/20/2018] [Accepted: 03/26/2018] [Indexed: 11/30/2022]
Abstract
Whole-genome sequencing (WGS)-based bioinformatics platforms for the rapid prediction of resistance will soon be implemented in the Tuberculosis (TB) laboratory, but their accuracy assessment still needs to be strengthened. Here, we fully-sequenced a total of 54 multidrug-resistant (MDR) and five susceptible TB strains and performed, for the first time, a simultaneous evaluation of the major four free online platforms (TB Profiler, PhyResSE, Mykrobe Predictor and TGS-TB). Overall, the sensitivity of resistance prediction ranged from 84.3% using Mykrobe predictor to 95.2% using TB profiler, while specificity was higher and homogeneous among platforms. TB profiler revealed the best performance robustness (sensitivity, specificity, PPV and NPV above 95%), followed by TGS-TB (all parameters above 90%). We also observed a few discrepancies between phenotype and genotype, where, in some cases, it was possible to pin-point some "candidate" mutations (e.g., in the rpsL promoter region) highlighting the need for their confirmation through mutagenesis assays and potential review of the anti-TB genetic databases. The rampant development of the bioinformatics algorithms and the tremendously reduced time-frame until the clinician may decide for a definitive and most effective treatment will certainly trigger the technological transition where WGS-based bioinformatics platforms could replace phenotypic drug susceptibility testing for TB.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, University of Lisbon, Lisbon, Portugal.
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health, Lisbon, Portugal.
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health, Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School, New University of Lisbon, Lisbon, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
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