101
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Abstract
We present a case of a 59-year-old man, who on being evaluated for abdominal pain and headache, was found to have a pancreatic head mass and inflammatory hypophysitis. Xpert MTB/Rif of the pancreatic mass biopsy showed the presence of tuberculosis (TB) with a very low load, and rifampicin resistance was detected with absence of probes A and B. Pyrosequencing (a novel genotypic test for TB) of the Xpert MTB/Rif isolate detected a single, rare, high-confidence mutation (S512T) in the rpoB region (rifampicin resistance determining region in the MTB genome). The TB mycobacteria growth indicator tube (TBMGIT) phenotypic drug susceptibility test (DST), however, showed rifampicin susceptibility. Incidentally, he was unable to tolerate rifampicin and responded well to a non-rifampicin-based regimen. We discuss a possible hypothesis of the Xpert-DST discordance in accordance with a recent literature review on phenotypic DST methods. We also discuss the utility of pyrosequencing in clinical practice for the diagnosis of TB and its resistance patterns.
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Affiliation(s)
- Umang Agrawal
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Krutarth Kanjiya
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Camilla Rodrigues
- Department of Microbiology, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - Ayesha Sunavala
- Department of Infectious Diseases, PD Hinduja National Hospital and Medical Research Centre, Mumbai, Maharashtra, India
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102
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de Vos M, Scott L, David A, Trollip A, Hoffmann H, Georghiou S, Carmona S, Ruhwald M, Stevens W, Denkinger CM, Schumacher SG. Comparative Analytical Evaluation of Four Centralized Platforms for the Detection of Mycobacterium tuberculosis Complex and Resistance to Rifampicin and Isoniazid. J Clin Microbiol 2021; 59:e02168-20. [PMID: 33268535 PMCID: PMC8106716 DOI: 10.1128/jcm.02168-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/21/2020] [Indexed: 01/25/2023] Open
Abstract
Failure to rapidly identify drug-resistant tuberculosis (TB) increases the risk of patient mismanagement, the amplification of drug resistance, and ongoing transmission. We generated comparative analytical data for four automated assays for the detection of TB and multidrug-resistant TB (MDR-TB): Abbott RealTime MTB and MTB RIF/INH (Abbott), Hain Lifescience FluoroType MTBDR (Hain), BD Max MDR-TB (BD), and Roche cobas MTB and MTB-RIF/INH (Roche). We included Xpert MTB/RIF (Xpert) and GenoType MTBDRplus as comparators for TB and drug resistance detection, respectively. We assessed analytical sensitivity for the detection of the Mycobacterium tuberculosis complex using inactivated strains (M. tuberculosis H37Rv and M. bovis) spiked into TB-negative sputa and computed the 95% limits of detection (LOD95). We assessed the accuracy of rifampicin and isoniazid resistance detection using well-characterized M. tuberculosis strains with high-confidence mutations accounting for >85% of first-line resistance mechanisms globally. For H37Rv and M. bovis, we measured LOD95 values of 3,781 and 2,926 (Xpert), 322 and 2,182 (Abbott), 826 and 4,301 (BD), 10,398 and 23,139 (Hain), and 2,416 and 2,136 (Roche) genomes/ml, respectively. Assays targeting multicopy genes or targets (Abbott, BD, and Roche) showed increased analytical sensitivity compared to Xpert. Quantification of the panel by quantitative real-time PCR prevents the determination of absolute values, and results reported here can be interpreted for comparison purposes only. All assays showed accuracy comparable to that of Genotype MTBDRplus for the detection of rifampicin and isoniazid resistance. The data from this analytical study suggest that the assays may have clinical performances similar to those of WHO-recommended molecular TB and MDR-TB assays.
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Affiliation(s)
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anura David
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andre Trollip
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO-Supranational Reference Laboratory of Tuberculosis, Munich-Gauting, Germany
- SYNLAB Gauting, SYNLAB Human Genetics Munich, Munich-Gauting, Germany
| | | | - Sergio Carmona
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Morten Ruhwald
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Claudia M Denkinger
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
- Division of Tropical Medicine, Center of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
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103
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Cao Y, Parmar H, Gaur RL, Lieu D, Raghunath S, Via N, Battaglia S, Cirillo DM, Denkinger C, Georghiou S, Kwiatkowski R, Persing D, Alland D, Chakravorty S. Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum. J Clin Microbiol 2021; 59:e02314-20. [PMID: 33298611 PMCID: PMC8106700 DOI: 10.1128/jcm.02314-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
We describe the design, development, analytical performance, and a limited clinical evaluation of the 10-color Xpert MTB/XDR assay (CE-IVD only, not for sale in the United States). This assay is intended as a reflex test to detect resistance to isoniazid (INH), fluoroquinolones (FLQ), ethionamide (ETH), and second-line injectable drugs (SLIDs) in unprocessed sputum samples and concentrated sputum sediments which are positive for Mycobacterium tuberculosis The Xpert MTB/XDR assay simultaneously amplifies eight genes and promoter regions in M. tuberculosis and analyzes melting temperatures (Tm s) using sloppy molecular beacon (SMB) probes to identify mutations associated with INH, FLQ, ETH, and SLID resistance. Results can be obtained in under 90 min using 10-color GeneXpert modules. The assay can differentiate low- versus high-level resistance to INH and FLQ as well as cross-resistance versus individual resistance to SLIDs by identifying mutation-specific Tm s or Tm patterns generated by the SMB probes. The assay has a limit of detection comparable to that of the Xpert MTB/RIF assay and successfully detected 16 clinically significant mutations in a challenge set of clinical isolate DNA. In a clinical study performed at two sites with 100 sputum and 214 clinical isolates, the assay showed a sensitivity of 94% to 100% and a specificity of 100% for all drugs except for ETH compared to that of sequencing. The sensitivity and specificity were in the same ranges as those of phenotypic drug-susceptibility testing. Used in combination with a primary tuberculosis diagnostic test, this assay should expand the capacity for detection of drug-resistant tuberculosis near the point of care.
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Affiliation(s)
- Yuan Cao
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Heta Parmar
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | | | | | | | - Nova Via
- Cepheid Inc., Sunnyvale, California, USA
| | | | | | | | | | | | | | - David Alland
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Soumitesh Chakravorty
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- Cepheid Inc., Sunnyvale, California, USA
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104
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Vázquez-Chacón CA, Rodríguez-Gaxiola FDJ, López-Carrera CF, Cruz-Rivera M, Martínez-Guarneros A, Parra-Unda R, Arámbula-Meraz E, Fonseca-Coronado S, Vaughan G, López-Durán PA. Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas. PLoS Negl Trop Dis 2021; 15:e0009145. [PMID: 33591982 PMCID: PMC7886168 DOI: 10.1371/journal.pntd.0009145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023] Open
Abstract
Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals.
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Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, México
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | | | | | - Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | - Ricardo Parra-Unda
- Unidad de Investigaciones en Salud Pública, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
| | - Gilberto Vaughan
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
| | - Paúl Alexis López-Durán
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
- * E-mail:
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105
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Caminero Luna JA, Pérez Mendoza G, Rodríguez de Castro F. Multi-drug resistant tuberculosis, ten years later. Med Clin (Barc) 2021; 156:393-401. [PMID: 33531151 DOI: 10.1016/j.medcli.2020.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 10/22/2022]
Abstract
Drug-resistant tuberculosis, especially those with resistance to rifampicin (RR-TB), has become one of the main obstacles to achieving the dream of eradicating tuberculosis. Furthermore, it is necessary to combine three or four different drugs in the attempt to cure TB, however, unfortunately, there are few available that can be considered genuinely effective. Fortunately, the notable worldwide increase in RR-TB in recent years has led to the investment of resources in the development of new drugs for TB, and other drugs investigated for other diseases have been successfully tested on TB. This has resulted in a clear change in the clinical management of these patients over the last 3-4 years, and it is now easier to design therapeutic regimens and achieve higher success rates. All these changes are updated in this review.
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Affiliation(s)
- José Antonio Caminero Luna
- Unidad de Tuberculosis y Micobacteriosis, Servicio de Neumología, Hospital General de Gran Canaria «Dr. Negrin», Las Palmas de Gran CanariaEspaña.
| | - Guillermo Pérez Mendoza
- Unidad de Tuberculosis y Micobacteriosis, Servicio de Neumología, Hospital General de Gran Canaria «Dr. Negrin», Las Palmas de Gran CanariaEspaña
| | - Felipe Rodríguez de Castro
- Unidad de Tuberculosis y Micobacteriosis, Servicio de Neumología, Hospital General de Gran Canaria «Dr. Negrin», Las Palmas de Gran CanariaEspaña
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106
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Gopie F, Commiesie E, Baldi S, Kamst M, Kaur D, de Lange W, Pinas P, Stijnberg D, Wongsokarijo M, Zijlmans C, de Zwaan R, van Soolingen D, Vreden S, de Vries G. Should treatment of low-level rifampicin mono-resistant tuberculosis be different? J Clin Tuberc Other Mycobact Dis 2021; 23:100222. [PMID: 33598570 PMCID: PMC7869001 DOI: 10.1016/j.jctube.2021.100222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Rifampicin resistant tuberculosis (RR-TB) was frequently detected in Suriname after the introduction of Xpert MTB/RIF in 2012. Subsequent phenotypic drug-susceptibility testing (DST) was not conclusive at that moment, while RR-TB patients treated with first-line tuberculostatics had good treatment outcome. In our study, we analysed this interesting observation. Methods We collected demographic and clinical characteristics and treatment outcome of TB patients from May 2012-December 2018 and performed a univariate and multivariate analysis to assess possible associations with resistance to rifampicin. Secondly, we conducted whole genome sequencing on all available Mycobacterium tuberculosis isolates that had a rifampicin resistance in the Xpert MTB/RIF test and performed phenotypic DST on selected isolates. Findings RR-TB was detected in 59 (9.6%) patients confirmed by Xpert. These patients were treated with rifampicin-containing regimens in most (88%) of the cases. In all 32 samples examined, a D435Y mutation in the rpoB gene was identified; only one isolate revealed an additional isoniazid mutation. Phenotypic DST indicated low-level rifampicin resistance. In multivariate analysis, the Creole ethnicity was a factor associated with rifampicin resistance (aOR 3.5; 95%CI 1.9–6.4). The treatment success rate for patients with RR-TB (78.0%) was comparable to the treatment outcome in non-RR-TB patients 77.8%. Interpretation This study confirms a low-level rifampicin mono-resistance in TB patients of Suriname. These patients could benefit from a first-line regimen with high dose rifampicin (or rifabutin), rather than from the lengthy treatment regimens for rifampicin-resistant and multi-drug resistant TB, a concept of stratified medicine also advocated for the treatment of TB. Funding None.
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Affiliation(s)
- F.A. Gopie
- Academic Hospital Paramaribo, Paramaribo, Suriname
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
- Corresponding author at: Academic Hospital Paramaribo, Paramaribo, Suriname.
| | - E. Commiesie
- National Tuberculosis Program, Paramaribo, Suriname
| | - S. Baldi
- Central Laboratory, Paramaribo, Suriname
| | - M. Kamst
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. Kaur
- Massachusetts Supranational TB Reference Laboratory, University of Massachusetts Medical School, Jamaica Plane, MA, USA
| | - W.C.M. de Lange
- Department Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, the Netherlands
| | - P.S. Pinas
- Central Laboratory, Paramaribo, Suriname
| | - D. Stijnberg
- National Tuberculosis Program, Paramaribo, Suriname
| | | | - C.W.R. Zijlmans
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - R. de Zwaan
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D. van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - G. de Vries
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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107
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Laniado-Laborín R. Clinical Interpretation of Drug Susceptibility Tests in Tuberculosis. CURRENT RESPIRATORY MEDICINE REVIEWS 2021. [DOI: 10.2174/1573398x16999201007164411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Prompt and accurate diagnosis of drug resistance is essential for optimal treatment of
drug-resistant tuberculosis. However, only 20% of the more than half a million patients eligible for
the treatment of MDR-TB/RR-TB receive an appropriate drug regimen. Drug-resistant TB regimens
must include a sufficient number of effective medications, a significant challenge for clinicians
worldwide, as most are forced to make therapeutic decisions without any, or very little information
on drug susceptibility testing. Although phenotypic DST is still commonly regarded as the
gold standard for determining M. tuberculosis susceptibility to antituberculosis drugs, it has several
limitations, mainly its prolonged turnaround time. Molecular methods based on M. tuberculosis genomic
DNA sequencing have been developed during the past two decades, to identify the most
common mutations involved in drug resistance. The Xpert
®
MTB/RIF is a real-time polymerase
chain reaction that offers results in less than two hours and has an overall sensitivity for rifampin resistance
of 96% and 98% specificity. Line probe assays (LPAs) are commercial DNA strip-based
tests for detecting the most frequent mutations responsible for resistance to rifampin, isoniazid, fluoroquinolones,
and second-line injectable drugs.
:
Discrepancies between phenotypic and genotyping methods are a problem that the clinician will
face in everyday practice. However, any resistance result (with any type of test) in a person with
risk factors for harboring resistant microorganisms should be considered appropriate while the results
of complementary tests are available.
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Affiliation(s)
- Rafael Laniado-Laborín
- Clinica y Laboratorio de Tuberculosis, Hospital General Tijuana, ISESALUD, Mexicali, Mexico
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108
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Khan T, Khan A, Ali SS, Ali S, Wei DQ. A computational perspective on the dynamic behaviour of recurrent drug resistance mutations in the pncA gene from Mycobacterium tuberculosis. RSC Adv 2021; 11:2476-2486. [PMID: 35424144 PMCID: PMC8693711 DOI: 10.1039/d0ra09326b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis is still one of the top 10 causes of death worldwide, particularly with the emergence of multidrug-resistant tuberculosis. As the most effective first-line anti-tuberculosis drug, pyrazinamide also develops resistance due to the mutation in the pncA gene. Among these mutations, seven mutations at positions F94L, F94S, K96N, K96R, G97C, G97D, and G97S are classified as high-level resistance mutations. However, the resistance mechanism of Mtb to PZA (pyrazinamide) caused by these mutations is still unclear. In this work, we combined molecular dynamics simulation, molecular mechanics/generalized-Born surface area calculation, principal component analysis, and free energy landscape analysis to explore the resistance mechanism of Mtb to PZA due to F94L, F94S, K96N, K96R, G97C, G97D, and G97S mutations, as well as compare interaction changes in wild-type and mutant PZA-bound complexes. The results of molecular mechanics/generalized-Born surface area calculations indicated that the binding free energy of PZA with seven mutants decreased. In mutant systems, the most significant interactions with His137 and Cys138 were lost. Besides, PCA and FEL confirmed significant variations in the protein dynamics during the simulation specifically by altering the Fe2+ binding and its destabilization. Furthermore, mutants also flipped the β-sheet 2, which also affects the binding of Fe2+ and PZA. In the G97D mutant, reported as most lethal, mutation causes the binding pocket to change considerably, so that the position of PZA has a large movement in the binding pocket. In this study, the resistance mechanism of PZA at the atomic level is proposed. The proposed drug-resistance mechanism will provide valuable guidance for the design of anti-tuberculosis drugs.
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Affiliation(s)
- Taimoor Khan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Abbas Khan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat Swat KP Pakistan
| | - Shahid Ali
- Center for Biotechnology and Microbiology, University of Swat Swat KP Pakistan
| | - Dong-Qing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200030 P.R. China
- Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nashan District Shenzhen Guangdong 518055 P.R. China
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109
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Alffenaar JWC, Gumbo T, Dooley KE, Peloquin CA, Mcilleron H, Zagorski A, Cirillo DM, Heysell SK, Silva DR, Migliori GB. Integrating Pharmacokinetics and Pharmacodynamics in Operational Research to End Tuberculosis. Clin Infect Dis 2021; 70:1774-1780. [PMID: 31560376 PMCID: PMC7146003 DOI: 10.1093/cid/ciz942] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) elimination requires innovative approaches. The new Global Tuberculosis Network (GTN) aims to conduct research on key unmet therapeutic and diagnostic needs in the field of TB elimination using multidisciplinary, multisectorial approaches. The TB Pharmacology section within the new GTN aims to detect and study the current knowledge gaps, test potential solutions using human pharmacokinetics informed through preclinical infection systems, and return those findings to the bedside. Moreover, this approach would allow prospective identification and validation of optimal shorter therapeutic durations with new regimens. Optimized treatment using available and repurposed drugs may have an increased impact when prioritizing a person-centered approach and acknowledge the importance of age, gender, comorbidities, and both social and programmatic environments. In this viewpoint article, we present an in-depth discussion on how TB pharmacology and the related strategies will contribute to TB elimination.
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Affiliation(s)
- Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead Hospital, Sydney, Australia
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas, USA
| | - Kelly E Dooley
- Division of Clinical Pharmacology, Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Helen Mcilleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Andre Zagorski
- Management Sciences for Health, Arlington, Virginia, USA
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Scott K Heysell
- University of Virginia, Division of Infectious Diseases and International Health, Charlottesville, Virginia, USA
| | - Denise Rossato Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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110
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Tagliani E, Anthony R, Kohl TA, de Neeling A, Nikolayevskyy V, Ködmön C, Maurer FP, Niemann S, van Soolingen D, van der Werf MJ, Cirillo DM. Use of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study. Eur Respir J 2021; 57:13993003.02272-2020. [PMID: 32732329 PMCID: PMC7784142 DOI: 10.1183/13993003.02272-2020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/17/2020] [Indexed: 01/31/2023]
Abstract
Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system. WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability. A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 cross-border clusters with increased likelihood of recent transmission (≤5 SNPs distance) comprising 316 RR/MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries. This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGS-based surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters. The implementation of a WGS-based surveillance system for monitoring the emergence of MDR-TB outbreaks in Europe is feasible and has the potential to provide supporting evidence to better elucidate cross-border transmission patternshttps://bit.ly/2ZTnPjk
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Affiliation(s)
- Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Richard Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance (IDS), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Both authors contributed equally
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center, Borstel, Germany.,German Center for Infection Research, partner site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany.,Both authors contributed equally
| | - Albert de Neeling
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance (IDS), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Csaba Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Florian P Maurer
- Diagnostic Mycobacteriology, National Reference Center for Mycobacteria, Borstel, Germany.,Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center, Borstel, Germany.,German Center for Infection Research, partner site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance (IDS), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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111
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Nonghanphithak D, Kaewprasert O, Chaiyachat P, Reechaipichitkul W, Chaiprasert A, Faksri K. Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB. PLoS One 2020; 15:e0244829. [PMID: 33382836 PMCID: PMC7775048 DOI: 10.1371/journal.pone.0244829] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 11/18/2022] Open
Abstract
Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.
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Affiliation(s)
- Ditthawat Nonghanphithak
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Pratchakan Chaiyachat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Wipa Reechaipichitkul
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Chaiprasert
- Drug Resistant Tuberculosis Research Fund Laboratory, Research and Development Affairs, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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112
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Banaei N, Musser KA, Salfinger M, Somoskovi A, Zelazny AM. Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases. Clin Lab Med 2020; 40:535-552. [DOI: 10.1016/j.cll.2020.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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113
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LncRNA MEG3 control Mycobacterium Tuberculosis infection via controlled MiR-145-5p expression and modulation of macrophages proliferation. Microb Pathog 2020; 149:104550. [DOI: 10.1016/j.micpath.2020.104550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
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114
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Bainomugisa A, Gilpin C, Coulter C, Marais BJ. New Xpert MTB/XDR: added value and future in the field. Eur Respir J 2020; 56:56/5/2003616. [PMID: 33214169 DOI: 10.1183/13993003.03616-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/26/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Arnold Bainomugisa
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | | | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | - Ben J Marais
- The Marie Bashir Institute for Infectious Diseases and Biosecurity (MBI), University of Sydney, Sydney, Australia
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115
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Li G, Guo Q, Liu H, Wan L, Jiang Y, Li M, Zhao LL, Zhao X, Liu Z, Wan K. Detection of Resistance to Fluoroquinolones and Second-Line Injectable Drugs Among Mycobacterium tuberculosis by a Reverse Dot Blot Hybridization Assay. Infect Drug Resist 2020; 13:4091-4104. [PMID: 33204126 PMCID: PMC7666996 DOI: 10.2147/idr.s270209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/07/2020] [Indexed: 01/23/2023] Open
Abstract
Background Reliable and timely determination of second-line drug resistance is essential for early initiation effective anti-tubercular treatment among multi-drug resistant (MDR) patients and blocking the spread of MDR and extensively drug-resistant tuberculosis. Molecular methods have the potency to provide accurate and rapid drug susceptibility results. We aimed to establish and evaluate the accuracy of a reverse dot blot hybridization (RDBH) assay to simultaneously detect the resistance of fluoroquinolones (FQs), kanamycin (KN), amikacin (AMK), capreomycin (CPM) and second-line injectable drugs (SLIDs) in Mycobacterium tuberculosis. Methods We established and evaluated the accuracy of the RDBH assay by comparing to the phenotypic drug susceptibility testing (DST) and sequencing in 170 M. tuberculosis, of which 94 and 27 were respectively resistant to ofloxacin (OFX) and SLIDs. Results The results show that, compared to phenotypic DST, the sensitivity and specificity of the RDBH assay for resistance detection were 63.8% and 100.0% for OFX, 60.0% and 100.0% for KN, 61.5% and 98.1% for AMK, 50.0% and 99.3% for CPM, and 55.6% and 100% for SLIDs, respectively; compared to sequencing, the sensitivity and specificity of the RDBH assay were 95.2% and 100.0% for OFX, 93.8% and 100.0% for SLIDs or KN (both based on mutations in rrs 1400 region and eis promoter), and 91.6% and 100.0% for AMK or CPM (both based on mutations in rrs 1400 region), respectively. The turnaround time of the RDBH assay was 7 h for testing 42 samples. Conclusion Our data suggested that compared to sequencing, the RDBH assay could serve as a rapid and reliable method for testing the resistance of M. tuberculosis against OFX and SLIDs, enabling early administration of appropriate treatment regimens among MDR tuberculosis patients.
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Affiliation(s)
- Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Qian Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Molecular Biology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
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Portelli S, Myung Y, Furnham N, Vedithi SC, Pires DEV, Ascher DB. Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Sci Rep 2020; 10:18120. [PMID: 33093532 PMCID: PMC7581776 DOI: 10.1038/s41598-020-74648-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/21/2020] [Indexed: 01/23/2023] Open
Abstract
Rifampicin resistance is a major therapeutic challenge, particularly in tuberculosis, leprosy, P. aeruginosa and S. aureus infections, where it develops via missense mutations in gene rpoB. Previously we have highlighted that these mutations reduce protein affinities within the RNA polymerase complex, subsequently reducing nucleic acid affinity. Here, we have used these insights to develop a computational rifampicin resistance predictor capable of identifying resistant mutations even outside the well-defined rifampicin resistance determining region (RRDR), using clinical M. tuberculosis sequencing information. Our tool successfully identified up to 90.9% of M. tuberculosis rpoB variants correctly, with sensitivity of 92.2%, specificity of 83.6% and MCC of 0.69, outperforming the current gold-standard GeneXpert-MTB/RIF. We show our model can be translated to other clinically relevant organisms: M. leprae, P. aeruginosa and S. aureus, despite weak sequence identity. Our method was implemented as an interactive tool, SUSPECT-RIF (StrUctural Susceptibility PrEdiCTion for RIFampicin), freely available at https://biosig.unimelb.edu.au/suspect_rif/ .
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Affiliation(s)
- Stephanie Portelli
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, 3004, VIC, Australia
| | - Yoochan Myung
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, 3004, VIC, Australia
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, 3004, VIC, Australia
- School of Computing and Information Systems, University of Melbourne, Victoria, 3010, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria, 3010, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, 3004, VIC, Australia.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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117
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Catanzaro DG, Colman RE, Linger Y, Georghiou SB, Kukhtin AV, Seifert M, Holmberg RC, Mshaiel H, Chiles P, Hillery N, Cooney CG, Rodwell TC. Laboratory Evaluation of a Lateral-Flow Cell for Molecular Detection of First-Line and Second-Line Antituberculosis Drug Resistance. J Clin Microbiol 2020; 58:e01417-20. [PMID: 32817085 PMCID: PMC7587100 DOI: 10.1128/jcm.01417-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/12/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the WHO's call for universal drug susceptibility testing for all patients being evaluated for tuberculosis (TB), a lack of rapid diagnostic tests which can fully describe TB resistance patterns is a major challenge in ensuring that all persons diagnosed with drug-resistant TB are started on an appropriate treatment regime. We evaluated the accuracy of the Akonni Biosystems XDR-TB TruArray and lateral-flow cell (XDR-LFC), a novel multiplex assay to simultaneously detect mutations across seven genes that confer resistance to both first- and second-line anti-TB drugs. The XDR-LFC includes 271 discrete three-dimensional gel elements with target-specific probes for identifying mutations in katG, inhA promoter, and ahpC promoter (isoniazid), rpoB (rifampin), gyrA (fluoroquinolones), rrs and eis promoter (kanamycin), and rrs (capreomycin and amikacin). We evaluated XDR-LFC performance with 87 phenotypically and genotypically characterized clinical Mycobacterium tuberculosis isolates. The overall assay levels of accuracy for mutation detection in specific genes were 98.6% for eis promoter and 100.0% for the genes katG, inhA promoter, ahpC promoter, rpoB, gyrA, and rrs The sensitivity and specificity against phenotypic reference were 100% and 100% for isoniazid, 98.4% and 50% for rifampin (specificity increased to 100% once the strains with documented low-level resistance mutations in rpoB were excluded), 96.2% and 100% for fluoroquinolones, 92.6% and 100% for kanamycin, 93.9% and 97.4% for capreomycin, and 80% and 100% for amikacin. The XDR-LFC solution appears to be a promising new tool for accurate detection of resistance to both first- and second-line anti-TB drugs.
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Affiliation(s)
- Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rebecca E Colman
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | | | | | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | - Haifa Mshaiel
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Peter Chiles
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Naomi Hillery
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA
| | | | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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118
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Jaillard M, Palmieri M, van Belkum A, Mahé P. Interpreting k-mer-based signatures for antibiotic resistance prediction. Gigascience 2020; 9:giaa110. [PMID: 33068113 PMCID: PMC7568433 DOI: 10.1093/gigascience/giaa110] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/23/2020] [Accepted: 09/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Recent years have witnessed the development of several k-mer-based approaches aiming to predict phenotypic traits of bacteria on the basis of their whole-genome sequences. While often convincing in terms of predictive performance, the underlying models are in general not straightforward to interpret, the interplay between the actual genetic determinant and its translation as k-mers being generally hard to decipher. RESULTS We propose a simple and computationally efficient strategy allowing one to cope with the high correlation inherent to k-mer-based representations in supervised machine learning models, leading to concise and easily interpretable signatures. We demonstrate the benefit of this approach on the task of predicting the antibiotic resistance profile of a Klebsiella pneumoniae strain from its genome, where our method leads to signatures defined as weighted linear combinations of genetic elements that can easily be identified as genuine antibiotic resistance determinants, with state-of-the-art predictive performance. CONCLUSIONS By enhancing the interpretability of genomic k-mer-based antibiotic resistance prediction models, our approach improves their clinical utility and hence will facilitate their adoption in routine diagnostics by clinicians and microbiologists. While antibiotic resistance was the motivating application, the method is generic and can be transposed to any other bacterial trait. An R package implementing our method is available at https://gitlab.com/biomerieux-data-science/clustlasso.
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Affiliation(s)
| | | | | | - Pierre Mahé
- bioMérieux, Chemin de l'Orme, 69280 Marcy l'Etoile, France
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119
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Kuhlin J, Davies Forsman L, Mansjö M, Jonsson Nordvall M, Wijkander M, Wagrell C, Jonsson J, Groenheit R, Werngren J, Schön T, Bruchfeld J. Genotypic resistance of pyrazinamide but not MIC is associated with longer time to sputum culture conversion in patients with multidrug-resistant tuberculosis. Clin Infect Dis 2020; 73:e3511-e3517. [PMID: 33011791 DOI: 10.1093/cid/ciaa1509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND PZA resistance in multidrug-resistant tuberculosis (MDR-TB) is common and it is not clear how it affects interim and treatment outcomes. Although rarely performed, phenotypic drug susceptibility testing (pDST) is used to define PZA resistance but genotypic DST (gDST) and minimum inhibitory concentration (MIC) could be beneficial. We aimed to assess the impact of PZA gDST and MIC on time to sputum culture conversion (SCC) and treatment outcome in patients with MDR-TB. METHODS Clinical, microbiological and treatment data was collected in this cohort study for all patients diagnosed with MDR-TB in Sweden 1992-2014. MIC, pDST and whole genome sequencing of the pncA, rpsA and panD genes were used to define PZA resistance. A Cox regression model was used for statistical analyses. RESULTS Of 157 patients with MDR-TB, 56.1% (n=88) had PZA resistant strains and 49.7% (n=78) were treated with PZA. In crude and adjusted analyses, PZA gDST resistance was associated with a 29-day longer time to SCC (hazard ratio [HR] 0.57, 95% confidence interval [CI] 0.36-0.89, p=0.013 and HR 0.49, 95% CI 0.29-0.82, p=0.007, respectively). A two-fold decrease in dilutions of PZA MIC for PZA susceptible strains showed no association with SCC in crude or adjusted analyses (HR 0.98, 95% CI 0.73-1.31, p=0.89). Genotypic DST and MIC for PZA were not associated with treatment outcome. CONCLUSION In patients with MDR-TB, gDST PZA resistance was associated with a longer time to SCC. Rapid PZA gDST is important to identify patients who may benefit from PZA treatment.
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Affiliation(s)
- Johanna Kuhlin
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Lina Davies Forsman
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Mansjö
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | | | - Maria Wijkander
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Charlotta Wagrell
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Jerker Jonsson
- Department of Public Health Analysis and Data Management, Public Health Agency of Sweden, Stockholm, Sweden
| | - Ramona Groenheit
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Jim Werngren
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Thomas Schön
- Department of Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden.,Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University
| | - Judith Bruchfeld
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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120
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Advances in the diagnosis of tuberculosis- Journey from smear microscopy to whole genome sequencing. Indian J Tuberc 2020; 67:S61-S68. [PMID: 33308673 DOI: 10.1016/j.ijtb.2020.09.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
The laboratory plays an important role in diagnosing tuberculosis (TB) and the identification and drug sensitivity testing (DST) of Mycobacterium tuberculosis. With a timely diagnosis and treatment with appropriate anti-TB drugs, most people who develop TB can be cured and onward transmission of infection curtailed. For a long time, laboratories used only microscopy and conventional culture-based diagnosis, however these procedures are slow and may require 3-4 weeks to yield results. Given the increasing rate of drug resistance, it has been necessary to look for new and rapid diagnostic methods. Various molecular based diagnostic technologies became available in the beginning of early 90s, providing rapid detection, identification and DST of M. tuberculosis. Molecular technologies offer the greatest potential for laboratories because they have the highest sensitivity and specificity. The present article will review some of the new methodology that has been introduced in the clinical laboratory.
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121
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Dousa KM, Kurz SG, Bark CM, Bonomo RA, Furin JJ. Drug-Resistant Tuberculosis: A Glance at Progress and Global Challenges. Infect Dis Clin North Am 2020; 34:863-886. [PMID: 33011048 DOI: 10.1016/j.idc.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Multidrug-resistant Mycobacterium tuberculosis remains a major public health threat; its management poses a significant economic burden. Treatment requires a programmatic approach with access to laboratory services, second-line medications, and adequate clinical resources. In recent years, we have seen rapid developments in diagnostic techniques with whole genome sequencing-based drug susceptibility prediction now in reach, an array of new drugs that transform treatment regimens to purely oral formulations, and a steady stream of multinational trials that inform us about most efficient combinations. Our hope is that the current momentum keeps the ambitious goal to end tuberculosis in 2030 in reach.
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Affiliation(s)
- Khalid M Dousa
- Division of Infectious Diseases & HIV Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Sebastian G Kurz
- Mount Sinai National Jewish Health Respiratory Institute, 10 East 102nd Street, New York City, NY 10029, USA
| | - Charles M Bark
- Division of Infectious Diseases, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
| | - Jennifer J Furin
- Division of Infectious Diseases & HIV Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA.
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Singh PK, Singh U, Jain A. Emergence of Specific gyrA Mutations Associated High-Level Fluoroquinolone-Resistant Mycobacterium tuberculosis among Multidrug-Resistant Tuberculosis Cases in North India. Microb Drug Resist 2020; 27:647-651. [PMID: 32991238 DOI: 10.1089/mdr.2020.0240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aim: This study aims to determine the frequency and pattern of gyrA/B mutations in multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains and also to assess the association between different gyrA/B mutations with phenotypic resistance to moxifloxacin (MOX) at clinical breakpoint (CB) drug concentration. Method: A total of 106 clinical MTB isolates carrying gyrA/B mutations were included consecutively. Culture-based MOX susceptibility was tested at CB (1.0 μg/mL) followed by its correlation with gyrA/B mutations using Genotype MTBDRsl assay. The mutations associated with phenotypic resistance were further analyzed on a large dataset of 1,825 MDR tuberculosis (TB) patients. Result: D94G and A90V mutations within gyrA were significantly associated with resistance and susceptible phenotype (p < 0.001), respectively. Of 1,825 MDR patients, gyrA/B mutations were found in 58.8% cases, of which fluoroquinolone (FQ) resistance was concluded among 97.9%, 0.8%, and 1.3% patients due to mutation in gyrA, gyrB, and in both the genes, respectively. D94G alone (45.9%) followed by A90V (21.2%) mutations in gyrA gene was most frequent. Conclusion: Our study showed that MDR-TB has emerged in northern India with additional FQ resistance. Different selection pressure and transmission may result in prevailing accumulation of specific gyrA mutations causing high-level FQ resistance, therefore, current control measures need to be strengthened.
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Affiliation(s)
- Pravin Kumar Singh
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Urmila Singh
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, India
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Brandao AP, Pinhata JMW, Simonsen V, Oliveira RS, Ghisi KT, Rabello MCS, Fukasava S, Ferrazoli L. Transmission of Mycobacterium tuberculosis presenting unusually high discordance between genotypic and phenotypic resistance to rifampicin in an endemic tuberculosis setting. Tuberculosis (Edinb) 2020; 125:102004. [PMID: 33017720 DOI: 10.1016/j.tube.2020.102004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND Since the implementation of the Xpert MTB/RIF in Sao Paulo, Brazil, numerous Mycobacterium tuberculosis isolates presenting "rifampicin-resistant genotype with rifampicin-susceptible phenotype" were observed. OBJECTIVE To evaluate the prevalence, rpoB mutations and transmission of M. tuberculosis resistant to rifampicin on Xpert MTB/RIF but susceptible on BACTEC MGIT system, in Sao Paulo state. METHODS Patients' isolates with this pattern of rifampicin discordance, collected from 2014 to 2017, had their rpoB predominant rifampicin-resistance-determining region sequenced and were genotyped by IS6110 restriction fragment-length polymorphism. FINDINGS The prevalence of rifampicin-discordant M. tuberculosis with genotypic resistance was 55.1% (156/283). Among the sequenced and genotyped isolates, 75.5% (111/147) were in clusters, largely associated with the type of rpoB mutation. Most isolates (98.6%; 72/73) harbouring the predominant mutation, His445Asn, were pooled into the two largest clusters, SP2ga (42/72; 58.3%) and SP5o (12/72; 16.7%). Ranking second, isolates carrying the silent mutation Phe433Phe were mostly (92.3%; 24/26) gathered into four groups of the family SP25. CONCLUSION These findings suggest that this unusual high rifampicin discrepancy proportion was greatly influenced by few actively circulating clusters. Further studies on many of the rpoB mutations identified in our setting are needed to elucidate their association with phenotypic rifampicin resistance.
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Affiliation(s)
- Angela Pires Brandao
- Instituto Adolfo Lutz, São Paulo, SP, Brazil; IOC/FIOCRUZ, Rio de Janeiro, RJ, Brazil.
| | | | | | | | | | | | - Suely Fukasava
- Centro de Vigilância Epidemiológica do Estado de São Paulo, São Paulo, SP, Brazil
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124
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David A, Singh L, Da Silva P, Scott L, Stevens W. The Performance of the Abbott Real Time MTB RIF/INH Compared to the MTBDR plus V2 for the Identification of MDR-TB Among Isolates. Infect Drug Resist 2020; 13:3301-3308. [PMID: 33061477 PMCID: PMC7532077 DOI: 10.2147/idr.s247524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/08/2020] [Indexed: 11/23/2022] Open
Abstract
Background The GenoType MTBDRplus V2 line-probe assay (LPA) is routinely used in clinical patient management to characterise the susceptibility of Mycobacterium tuberculosis complex to rifampicin (Rif) and isoniazid (INH) directly from sputum and cultured isolates. The laboratory workflow requires skill and three separate areas to minimize contamination and banding pattern interpretation requires experienced laboratory personnel. We explored the use of the RT MTB RIF/INH assay performed on the Abbott m2000 platform as an alternative laboratory platform. Methods Isolates (n=93) consisting of fully susceptible, Rif- or INH-mono-resistant and multi-drug resistant (MDR) strains were tested on both MTBDRplus v2 and RT MTB RIF/INH assays. Both assays target the rpoB, katG and inhA genes for resistance-detection mutations. Concordance was assessed using percent agreement and the kappa statistic. Those specimens with discordant results were further assessed using Sanger sequencing. Results A total of 89% (83/93) of cultured isolates generated successful results on the RT MTB/RIF-INH assay and MTBDRplus assays. Of the 10 discordant results, where sequencing was used as the reference method, the RT MTB RIF/INH assays misclassified six resistance isolates, while the LPA misclassified seven. Discussion Overall, the RT MTB RIF/INH demonstrated good agreement with the LPA, and a better correlation with sequencing on discrepant isolates specifically with mutations occurring in codon 511 of the rpoB gene. The RT MTB RIF/INH therefore can be used to complement existing laboratory algorithms determining Rif and INH resistance profiles, with less emphasis on manual laboratory processing.
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Affiliation(s)
- Anura David
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lyndel Singh
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Da Silva
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
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125
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Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00632-20. [PMID: 32727827 PMCID: PMC7512157 DOI: 10.1128/jcm.00632-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were resequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics, and variant calling were computed using an in-house pipeline and compared to the reference MiniSeq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depths of coverage were 4,151× and 4,177× on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug-resistant markers, including full gene deletions. In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases.
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126
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Salimiyan Rizi K, Aryan E, Meshkat Z, Ranjbar G, Sankian M, Ghazvini K, Farsiani H, Pourianfar HR, Rezayi M. The overview and perspectives of biosensors and Mycobacterium tuberculosis: A systematic review. J Cell Physiol 2020; 236:1730-1750. [PMID: 32930412 DOI: 10.1002/jcp.30007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) is referred to as a "consumption" or phthisis, which has been a fatal human disease for thousands of years. Mycobacterium tuberculosis (M. tb) might have been responsible for the death of more humans than any other bacterial pathogens. Therefore, the rapid diagnosis of this bacterial infection plays a pivotal role in the timely and appropriate treatment of the patients, as well as the prevention of disease spread. More than 98% of TB cases are reported in developing countries, and due to the lack of well-equipped and specialized diagnostic laboratories, development of effective diagnostic methods based on biosensors is essential for this bacterium. In this review, original articles published in English were retrieved from multiple databases, such as PubMed, Scopus, Google Scholar, Science Direct, and Cochrane Library during January 2010-October 2019. In addition, the reference lists of the articles were also searched. Among 109 electronically searched citations, 42 articles met the inclusion criteria. The highest potential and wide usage of biosensors for the diagnosis of M. tb and its drug resistance belonged to DNA electrochemical biosensors (isoniazid and rifampin strains). Use of biosensors is expanding for the detection of resistant strains of anti-TB antibiotics with high sensitivity and accuracy, while the speed of these sensory methods is considered essential as well. Furthermore, the lowest limit of detection (0.9 fg/ml) from an electrochemical DNA biosensor was based on graphene-modified iron-oxide chitosan hybrid deposited on fluorine tin oxide for the MPT64 antigen target. According to the results, the most common methods used for M. tb detection include acid-fast staining, cultivation, and polymerase chain reaction (PCR). Although molecular techniques (e.g., PCR and real-time PCR) are rapid and sensitive, they require sophisticated laboratory and apparatuses, as well as skilled personnel and expertise in the commentary of the results. Biosensors are fast, valid, and cost-efficient diagnostic method, and the improvement of their quality is of paramount importance in resource-constrained settings.
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Affiliation(s)
- Kobra Salimiyan Rizi
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Aryan
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Golnaz Ranjbar
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Division of Immunobiochemistry, Immunology Research Centre, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Farsiani
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid R Pourianfar
- Research Department of Industrial Fungi Biotechnology, Research Institute for Industrial Biotechnology, Academic Centre for Education, Culture and Research [ACECR]-Khorasan Razavi Province Branch, Mashhad, Iran
| | - Majid Rezayi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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127
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Tornheim JA, Starks AM, Rodwell TC, Gardy JL, Walker TM, Cirillo DM, Jayashankar L, Miotto P, Zignol M, Schito M. Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex. Clin Infect Dis 2020; 69:1631-1633. [PMID: 30883637 PMCID: PMC6792097 DOI: 10.1093/cid/ciz219] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis is the primary infectious disease killer worldwide, with a growing threat from multidrug-resistant cases. Unfortunately, classic growth-based phenotypic drug susceptibility testing (DST) remains difficult, costly, and time consuming, while current rapid molecular testing options are limited by the diversity of antimicrobial-resistant genotypes that can be detected at once. Next-generation sequencing (NGS) offers the opportunity for rapid, comprehensive DST without the time or cost burden of phenotypic tests and can provide useful information for global surveillance. As access to NGS expands, it will be important to ensure that results are communicated clearly, consistent, comparable between laboratories, and associated with clear guidance on clinical interpretation of results. In this viewpoint article, we summarize 2 expert workshops regarding a standardized report format, focusing on relevant variables, terminology, and required minimal elements for clinical and laboratory reports with a proposed standardized template for clinical reporting NGS results for Mycobacterium tuberculosis.
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Affiliation(s)
- Jeffrey A Tornheim
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Timothy C Rodwell
- Foundation for Innovative New Diagnostics, Geneva, Switzerland.,Division of Pulmonary, Critical Care, and Sleep Medicine, University of San Diego, California
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Canada.,Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | | | - Lakshmi Jayashankar
- Columbus Technologies, Inc. Contractor to the National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland
| | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Matteo Zignol
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | - Marco Schito
- Critical Path to Tuberculosis Drug Regimens, Critical Path Institute, Tucson, Arizona
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128
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Köser CU, Cirillo DM, Miotto P. How To Optimally Combine Genotypic and Phenotypic Drug Susceptibility Testing Methods for Pyrazinamide. Antimicrob Agents Chemother 2020; 64:e01003-20. [PMID: 32571824 PMCID: PMC7449218 DOI: 10.1128/aac.01003-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/17/2020] [Indexed: 11/20/2022] Open
Abstract
False-susceptible phenotypic drug-susceptibility testing (DST) results for pyrazinamide due to mutations with MICs close to the critical concentration (CC) confound the classification of pncA resistance mutations, leading to an underestimate of the specificity of genotypic DST. This could be minimized by basing treatment decisions on well-understood mutations and by adopting an area of technical uncertainty for phenotypic DST rather than only testing the CC, as is current practice for the Mycobacterium tuberculosis complex.
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Affiliation(s)
- Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS Ospedale San Raffaele, Milan, Italy
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129
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Feuerriegel S, Kohl TA, Utpatel C, Andres S, Maurer FP, Heyckendorf J, Jouet A, Badalato N, Foray L, Fouad Kamara R, Conteh OS, Supply P, Niemann S. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB. Eur Respir J 2020; 57:13993003.01796-2020. [DOI: 10.1183/13993003.01796-2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 11/05/2022]
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130
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Outcomes and adverse events of pre- and extensively drug-resistant tuberculosis patients in Kinshasa, Democratique Republic of the Congo: A retrospective cohort study. PLoS One 2020; 15:e0236264. [PMID: 32750060 PMCID: PMC7402497 DOI: 10.1371/journal.pone.0236264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/01/2020] [Indexed: 11/30/2022] Open
Abstract
Background Extensively drug-resistant tuberculosis (XDR TB) is a very serious form of tuberculosis that is burdened with a heavy mortality toll, especially before the advent of new TB drugs. The Democratic Republic of the Congo (DRC) is among the countries most affected by this new epidemic. Methods A retrospective analysis was performed of the records of all patients with pre- and extensively drug-resistant tuberculosis hospitalized from January 1, 2015 to December 31, 2017 and monitored for at least 6 months to one year after the end of their treatment in Kinshasa; an individualized therapeutic regimen with bedaquiline for 20 months was built for each patient. The adverse effects were systematically monitored. Results Of the 40 laboratory-confirmed patients, 32 (80%) patients started treatment, including 29 preXRB and 3 XDR TB patients. In the eligible group, 3 patients (9.4%) had HIV-TB coinfections. The therapeutic success rate was 53.2%, and the mortality rate was 46.8% (15/32); there were no relapses, failures or losses to follow-up. All coinfected HIV–TB patients died during treatment. The cumulative patient survival rate was 62.5% at 3 months, 53.1% at 6 months and 53.1% at 20 months. The most common adverse events were vomiting, Skin rash, anemia and peripheral neuropathy. Conclusion The new anti-tuberculosis drugs are a real hope for the management of Drug Resistant tuberculosis patient and other new therapeutic combinations may improve favorable outcomes.
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131
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Goig GA, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Navarro D, Borrás R, Comas I. Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study. THE LANCET MICROBE 2020; 1:e175-e183. [DOI: 10.1016/s2666-5247(20)30060-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
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132
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Caminero JA, García-García JM, Caylà JA, García-Pérez FJ, Palacios JJ, Ruiz-Manzano J. Update of SEPAR guideline «Diagnosis and Treatment of Drug-Resistant Tuberculosis». Arch Bronconeumol 2020; 56:514-521. [PMID: 32446667 DOI: 10.1016/j.arbres.2020.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 01/30/2023]
Abstract
New evidence and knowledge about the clinical management of drug-resistant tuberculosis (TB) in the last 3 years, makes it necessary to update the recent guideline published by SEPAR in 2017, mainly in relation to new diagnostic methods, drug classification, and regimens of treatment recommended to treat patients with isoniazid-resistance TB, rifampicin resistance TB and multidrug-resistant TB. With respect to tuberculosis diagnosis, we recommend the use of rapid molecular assays that also help to detect mutations associated with resistance. In relation to the treatment of multidrug-resistant TB we prioritize effective all-oral shorter treatment regimens including bedaquiline, a fluoroquinolone (levofloxacin or moxifloxacin), bedaquiline and linezolid, instead of the previously recommended short-course treatment with aminoglycosides and other less effective and more toxic drugs. The design of these regimens (initial schedule and changes in the regimen if necessary) should be made in accordance with drug-resistant TB experts; the treatment should be the responsibility of personnel with experience in the treatment of TB and in TB units guaranteeing the follow-up of the treatment and the management of drugs adverse effects.
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Affiliation(s)
- José A Caminero
- Servicio de Neumología, Hospital General de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, España; Unión Internacional contra la Tuberculosis y Enfermedades Respiratorias (La Unión), París, Francia; Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España
| | - José-María García-García
- Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España; Unidad de Gestión Clínica de Neumología, Hospital Universitario San Agustín, Avilés, Asturias, España.
| | - Joan A Caylà
- Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España; Fundación de la Unidad de Investigación en Tuberculosis (fuiTB) de Barcelona, España
| | - Francisco J García-Pérez
- Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España; Servicio de Neumología, Hospital Universitario de La Princesa, Madrid, España
| | - Juan J Palacios
- Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España; Unidad de Referencia Regional de Micobacterias, Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, España
| | - Juan Ruiz-Manzano
- Programa Integrado de Investigación en Tuberculosis (PII TB) de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR), Barcelona, España; Centro Médico Teknon, Barcelona, España
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133
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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil. Sci Rep 2020; 10:12891. [PMID: 32732910 PMCID: PMC7393130 DOI: 10.1038/s41598-020-69755-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.
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134
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Wan L, Liu H, Li M, Jiang Y, Zhao X, Liu Z, Wan K, Li G, Guan CX. Genomic Analysis Identifies Mutations Concerning Drug-Resistance and Beijing Genotype in Multidrug-Resistant Mycobacterium tuberculosis Isolated From China. Front Microbiol 2020; 11:1444. [PMID: 32760357 PMCID: PMC7373740 DOI: 10.3389/fmicb.2020.01444] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/04/2020] [Indexed: 12/02/2022] Open
Abstract
Development of modern genomics provides us an effective method to understand the molecular mechanism of drug resistance and diagnose drug-resistant Mycobacterium tuberculosis. In this study, mutations in 18 genes or intergenic regions acquired by whole-genome sequencing (WGS) of 183 clinical M. tuberculosis strains, including 137 multidrug-resistant and 46 pan-susceptible isolates from China, were identified and used to analyze their associations with resistance of isoniazid, rifampin, ethambutol, and streptomycin. Using the proportional method as the gold standard method, the accuracy values of WGS to predict resistance were calculated. The association between synonymous or lineage definition mutations with different genotypes were also analyzed. The results show that, compared to the phenotypic proportional method, the sensitivity and specificity of WGS for resistance detection were 94.2 and 100.0% for rifampicin (based on mutations in rpoB), 90.5 and 97.8% for isoniazid (katG), 83.0 and 97.8% for streptomycin (rpsL combined with rrs 530 loop and 912 loop), and 90.9 and 65.1% for ethambutol (embB), respectively. WGS data also showed that mutations in the inhA promoter increased only 2.2% sensitivity for INH based on mutations in katG. Synonymous mutation rpoB A1075A was confirmed to be associated with the Beijing genotype. This study confirmed that mutations in rpoB, katG, rrs 530 loop and 912 loop, and rpsL were excellent biomarkers for predicting rifampicin, isoniazid, and streptomycin resistance, respectively, and provided clues in clarifying the drug-resistance mechanism of M. tuberculosis isolates from China.
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Affiliation(s)
- Li Wan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiguang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Cha-Xiang Guan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, China
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Dheda K, Gumbo T, Maartens G, Dooley KE, Murray M, Furin J, Nardell EA, Warren RM. The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis. THE LANCET RESPIRATORY MEDICINE 2020; 7:820-826. [PMID: 31486393 DOI: 10.1016/s2213-2600(19)30263-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 01/23/2023]
Abstract
The Lancet Respiratory Medicine Commission on drug-resistant tuberculosis was published in 2017, which comprehensively reviewed and provided recommendations on various aspects of the disease. Several key new developments regarding drug-resistant tuberculosis are outlined in this Commission Update. The WHO guidelines on treating drug-resistant tuberculosis were updated in 2019 with a reclassification of second line anti-tuberculosis drugs. An injection-free MDR tuberculosis treatment regimen is now recommended. Over the past 3 years, advances in treatment include the recognition of the safety and mortality benefit of bedaquiline, the finding that the 9-11 month injectable-based 'Bangladesh' regimen was non-inferior to longer regimens, and promising interim results of a novel 6 month 3-drug regimen (bedaquiline, pretomanid, and linezolid). Studies of explanted lungs from patients with drug-resistant tuberculosis have shown substantial drug-specific gradients across pulmonary cavities, suggesting that alternative dosing and drug delivery strategies are needed to reduce functional monotherapy at the site of disease. Several controversies are discussed including the optimal route of drug administration, optimal number of drugs constituting a regimen, selection of individual drugs for a regimen, duration of the regimen, and minimal desirable standards of antibiotic stewardship. Newer rapid nucleic acid amplification test platforms, including point-of-care systems that facilitate active case-finding, are discussed. The rapid diagnosis of resistance to other drugs, (notably fluoroquinolones), and detection of resistance by targeted or whole genome sequencing will probably change the diagnostic landscape in the near future.
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Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kelly E Dooley
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA; T H Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Edward A Nardell
- T H Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Robin M Warren
- South African Medical Research Council Centre for Tuberculosis Research/Department of Science and Technology/ National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
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136
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Kayomo MK, Mbula VN, Aloni M, André E, Rigouts L, Boutachkourt F, de Jong BC, Nkiere NM, Dean AS. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep 2020; 10:10786. [PMID: 32612134 PMCID: PMC7329841 DOI: 10.1038/s41598-020-67479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The surveillance of drug resistance among tuberculosis (TB) patients is central to preventing the spread of antimicrobial resistance. The Democratic Republic of the Congo (DR Congo) is classified by the World Health Organization (WHO) as a country with a high burden of TB and multidrug-resistant TB (MDR-TB), but there are no nationally representative data on drug resistance. In 2016-2017, a national survey of TB patients was conducted in 108 microscopy centres across all 11 provinces of the country using innovative molecular approaches. Sputum samples were collected from 1,545 new and 163 previously treated patients. These were tested by the Xpert MTB/RIF assay, followed by targeted next-generation sequencing performed directly on sputum. The prevalence of rifampicin resistance was low, at 1.8% (95% CI: 1.0-3.2) among new and 17.3% (95% CI: 11.9-24.4) among previously treated patients. Resistance to pyrazinamide, fluoroquinolones and second-line injectables was also low. The prevalence of resistance to isoniazid among rifampicin-susceptible patients was higher, at 6.6% (95% CI: 4.4-9.8) among new and 8.7% (95% : 3.2-21.2) among previously treated patients. Diagnosing and treating isoniazid-resistant patients remains a challenge, given that many will be missed by the current national diagnostic algorithm that is driven by detecting rifampicin resistance by Xpert MTB/RIF. This is the first nationwide survey incorporating targeted sequencing directly on sputum. It serves as a proof-of-concept for other settings that do yet have rapid specimen transport networks or capacity to conduct culture.
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MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Child, Preschool
- Cross-Sectional Studies
- Democratic Republic of the Congo/epidemiology
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Middle Aged
- Mycobacterium tuberculosis/genetics
- Prevalence
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/genetics
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Affiliation(s)
- Michel Kaswa Kayomo
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Vital Nkake Mbula
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
| | - Muriel Aloni
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Emmanuel André
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Antwerp, Belgium
- Antwerp University, Antwerp, Belgium
| | - Fairouz Boutachkourt
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimental Et Clinique, UC Louvain, Brussels, Belgium
| | | | - Nicolas M Nkiere
- World Health Organization, Kinshasa, Democratic Republic of the Congo
| | - Anna S Dean
- Global TB Programme, World Health Organization, Geneva, Switzerland.
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137
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Genome sequencing of Mycobacterium tuberculosis clinical isolates revealed isoniazid resistance mechanisms undetected by conventional molecular methods. Int J Antimicrob Agents 2020; 56:106068. [PMID: 32603684 DOI: 10.1016/j.ijantimicag.2020.106068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/14/2020] [Accepted: 06/21/2020] [Indexed: 11/22/2022]
Abstract
A combination of targeted molecular methods and phenotypic drug-susceptibility testing is the most widely used approach to detect drug resistance in Mycobacterium tuberculosis isolates. We report the delay in the introduction of an efficient anti-tuberculous drug regimen because of a M. tuberculosis strain displaying a high level of resistance to isoniazid, in the absence of the common mutations associated with isoniazid-resistance, including katG mutations and inhA promoter mutations. Whole-genome sequencing (WGS) identified a large loss-of-function insertion (>1000 pb) at the end of katG in the isolate together with a -57C>T ahpC mutation, a resistance mechanism that would have remained undetected by a conventional molecular targeted approach. A retrospective search using publicly available WGS data of more than 1200 isoniazid-resistant isolates and a similar sized control dataset of isoniazid-susceptible isolates revealed that most (22/31) isoniazid-resistant, KatG loss-of-function mutants had an associated rare ahpC promoter mutation. In contrast, only 7 of 1411 isoniazid-susceptible strains carried a rare ahpC promoter mutation, including shared mutations with the 31 isoniazid-resistant KatG loss-of-function mutants. These results indicate that rare ahpC promoter mutations could be used as a proxy for investigating simultaneous KatG loss-of-function or missense mutations. In addition, WGS in routine diagnosis would improve drug susceptibility testing in M. tuberculosis clinical isolates and is an efficient tool for detecting resistance mechanisms undetected by conventional molecular methods.
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138
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Lv C, Wu J, Pierre-Audigier C, Lu L, Alame-Emane AK, Takiff H, Xu Y, Wang J, Gicquel B, Liu S. Combination of Xpert MTB/RIF and MTBDRplus for Diagnosing Tuberculosis in a Chinese District. Med Sci Monit 2020; 26:e923508. [PMID: 32504464 PMCID: PMC7297034 DOI: 10.12659/msm.923508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background The incidence of tuberculosis (TB) remains high in many countries, including some middle- and high-income countries without financial constraints for diagnosis and treatment. The implementation of an improved algorithm for diagnosis using 2 rapid molecular tests should help reduce the TB burden. Material/Methods Between April 2018 and March 2019, sputum samples from 711 patients suspected of TB in Nanshan, Shenzhen, China, were included in this prospective study. All sputum samples were examined by smear microscopy, Mycobacterium Growth Indicator Tube (MGIT) 960 culture, and Xpert MTB/RIF. The sputum remnants of Xpert MTB/RIF were used for MTBDRplus to confirm the Xpert results both for the presence of TB bacilli and for resistance to rifampicin (RIF), and also to diagnose multidrug-resistant tuberculosis (MDR-TB). Results In total, 200 (28.1%) of the 711 sputa were positive for TB by Xpert MTB/RIF, and the sputum remnants were used for MTBDRplus. The simultaneous use of Xpert MTB/RIF and MTBDRplus directly on sputum samples permitted accurate bacteriologic confirmation of TB in 64% (119/187) of cases and detection of 70% (7/10) of strains that were MDR. Conclusions The implementation of 2 rapid nucleic acid-based tests on sputum samples could facilitate the prompt and appropriate treatment of most TB cases.
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Affiliation(s)
- Chunfang Lv
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Jianhong Wu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | | | - Liuzhu Lu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Amel Kévin Alame-Emane
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Howard Takiff
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Yangfeng Xu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Jian Wang
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Brigitte Gicquel
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Shengyuan Liu
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
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139
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Dohál M, Porvazník I, Pršo K, Rasmussen EM, Solovič I, Mokrý J. Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis. Tuberculosis (Edinb) 2020; 123:101946. [PMID: 32741530 DOI: 10.1016/j.tube.2020.101946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
Abstract
The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia.
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia; Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
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140
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Georghiou SB, Schumacher SG, Rodwell TC, Colman RE, Miotto P, Gilpin C, Ismail N, Rodrigues C, Warren R, Weyer K, Zignol M, Arafah S, Cirillo DM, Denkinger CM. Guidance for Studies Evaluating the Accuracy of Rapid Tuberculosis Drug-Susceptibility Tests. J Infect Dis 2020; 220:S126-S135. [PMID: 31593599 DOI: 10.1093/infdis/jiz106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development and implementation of rapid molecular diagnostics for tuberculosis (TB) drug-susceptibility testing is critical to inform treatment of patients and to prevent the emergence and spread of resistance. Optimal trial planning for existing tests and those in development will be critical to rapidly gather the evidence necessary to inform World Health Organization review and to support potential policy recommendations. The evidence necessary includes an assessment of the performance for TB and resistance detection as well as an assessment of the operational characteristics of these platforms. The performance assessment should include analytical studies to confirm the limit of detection and assay ability to detect mutations conferring resistance across globally representative strains. The analytical evaluation is typically followed by multisite clinical evaluation studies to confirm diagnostic performance in sites and populations of intended use. This paper summarizes the considerations for the design of these analytical and clinical studies.
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Affiliation(s)
| | | | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Nazir Ismail
- University of Pretoria, South Africa.,National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,University Hospital Heidelberg, Division of Tropical Medicine, Centre of Infectious Diseases, Germany
| | | | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
| | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | | | | | | | - Claudia M Denkinger
- FIND, Geneva, Switzerland.,University of Heidelberg, Centre of Infectious Diseases, Germany
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141
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Shi W, Davies Forsman L, Hu Y, Zheng X, Gao Y, Li X, Jiang W, Bruchfeld J, Diwan VK, Hoffner S, Xu B. Improved treatment outcome of multidrug-resistant tuberculosis with the use of a rapid molecular test to detect drug resistance in China. Int J Infect Dis 2020; 96:390-397. [PMID: 32353546 DOI: 10.1016/j.ijid.2020.04.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/08/2020] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES Numerous studies investigate the advantages of rapid molecular drug susceptibility testing (DST) in comparison to phenotypic DST, but the clinical impact on treating multi/extensively drug resistant TB(M/XDR-TB) is less studied. Therefore, we examined how molecular DST testing may improve MDR-TB treatment management and outcome in Chinese settings. METHODS We performed a comparative study of patient cohorts before and after the implementation of molecular DST diagnosis with Genotype MTBDRsl/MTBDRplus assay in two Chinese hospitals. We collected clinical information including time to sputum culture conversion and final treatment outcome. RESULTS In total, 242 MDR-TB patients were studied including 114 before (pre-implementation group) and 128 after the implementation (post-implementation group) of molecular DST. Time to MDR-TB diagnosis was significantly reduced for patients in the post-implementation group, as compared to the pre-implementation group (median,16 vs 62 days; P < 0.001). Patients with early available molecular DST results had a more rapid culture conversion (aHR1.94 95% CI: 1.37-2.73; median,12 vs 24 months, respectively; P < 0.001) and higher rate of treatment success (68% vs 47%, P < 0.01). CONCLUSIONS The use of molecular DST in routine care for MDR-TB diagnosis as compared to phenotypic DST was associated with a decreased time to culture conversion and improved treatment outcome, highlighting its important clinical value.
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Affiliation(s)
- Wenpei Shi
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Lina Davies Forsman
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Yi Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China.
| | - Xubin Zheng
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yazhou Gao
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Xuliang Li
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Weili Jiang
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Judith Bruchfeld
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Vinod K Diwan
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Biao Xu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China; Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
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Engelthaler DM, Streicher EM, Kelley EJ, Allender CJ, Wiggins K, Jimenez D, Lemmer D, Vittinghoff E, Theron G, Sirgel FA, Warren RM, Metcalfe JZ. Minority Mycobacterium tuberculosis Genotypic Populations as an Indicator of Subsequent Phenotypic Resistance. Am J Respir Cell Mol Biol 2020; 61:789-791. [PMID: 31774334 DOI: 10.1165/rcmb.2019-0178le] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | | | - Erin J Kelley
- Translational Genomics Research InstituteFlagstaff, Arizona
| | | | | | - Dulce Jimenez
- Translational Genomics Research InstituteFlagstaff, Arizona
| | - Darrin Lemmer
- Translational Genomics Research InstituteFlagstaff, Arizona
| | - Eric Vittinghoff
- University of California-San FranciscoSan Francisco, Californiaand
| | | | | | | | - John Z Metcalfe
- University of California, San FranciscoSan Francisco, California
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143
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Wan L, Guo Q, Wei JH, Liu HC, Li MC, Jiang Y, Zhao LL, Zhao XQ, Liu ZG, Wan KL, Li GL, Guan CX. Accuracy of a reverse dot blot hybridization assay for simultaneous detection of the resistance of four anti-tuberculosis drugs in Mycobacterium tuberculosis isolated from China. Infect Dis Poverty 2020; 9:38. [PMID: 32299480 PMCID: PMC7164301 DOI: 10.1186/s40249-020-00652-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/24/2020] [Indexed: 01/02/2023] Open
Abstract
Background Drug resistant tuberculosis poses a great challenge for tuberculosis control worldwide. Timely determination of drug resistance and effective individual treatment are essential for blocking the transmission of drug resistant Mycobacterium tuberculosis. We aimed to establish and evaluate the accuracy of a reverse dot blot hybridization (RDBH) assay to simultaneously detect the resistance of four anti-tuberculosis drugs in M. tuberculosis isolated in China. Methods In this study, we applied a RDBH assay to simultaneously detect the resistance of rifampicin (RIF), isoniazid (INH), streptomycin (SM) and ethambutol (EMB) in 320 clinical M. tuberculosis isolates and compared the results to that from phenotypic drug susceptibility testing (DST) and sequencing. The RDBH assay was designed to test up to 42 samples at a time. Pearson’s chi-square test was used to compute the statistical measures of the RDBH assay using the phenotypic DST or sequencing as the gold standard method, and Kappa identity test was used to determine the consistency between the RDBH assay and the phenotypic DST or sequencing. Results The results showed that the concordances between phenotypic DST and RDBH assay were 95% for RIF, 92.8% for INH, 84.7% for SM, 77.2% for EMB and the concordances between sequencing and RDBH assay were 97.8% for RIF, 98.8% for INH, 99.1% for SM, 93.4% for EMB. Compared to the phenotypic DST results, the sensitivity and specificity of the RDBH assay for resistance detection were 92.4 and 98.5% for RIF, 90.3 and 97.3% for INH, 77.4 and 91.5% for SM, 61.4 and 85.7% for EMB, respectively; compared to sequencing, the sensitivity and specificity of the RDBH assay were 97.7 and 97.9% for RIF, 97.9 and 100.0% for INH, 97.8 and 100.0% for SM, 82.6 and 99.1% for EMB, respectively. The turnaround time of the RDBH assay was 7 h for testing 42 samples. Conclusions Our data suggested that the RDBH assay could serve as a rapid and efficient method for testing the resistance of M. tuberculosis against RIF, INH, SM and EMB, enabling early administration of appropriate treatment regimens to the affected drug resistant tuberculosis patients.
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Affiliation(s)
- Li Wan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Qian Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Molecular Biology, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Jian-Hao Wei
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.,Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Hai-Can Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Ma-Chao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiu-Qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhi-Guang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kang-Lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Gui-Lian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.
| | - Cha-Xiang Guan
- Department of Physiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, China.
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An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data. INFECTION GENETICS AND EVOLUTION 2020; 79:104152. [DOI: 10.1016/j.meegid.2019.104152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022]
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145
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Abstract
The control of tuberculosis (TB) is hampered by the emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis (Mtb) strains, defined as resistant to at least isoniazid and rifampin, the two bactericidal drugs essential for the treatment of the disease. Due to the worldwide estimate of almost half a million incident cases of MDR/rifampin-resistant TB, it is important to continuously update the knowledge on the mechanisms involved in the development of this phenomenon. Clinical, biological and microbiological reasons account for the generation of resistance, including: (i) nonadherence of patients to their therapy, and/or errors of physicians in therapy management, (ii) complexity and poor vascularization of granulomatous lesions, which obstruct drug distribution to some sites, resulting in resistance development, (iii) intrinsic drug resistance of tubercle bacilli, (iv) formation of non-replicating, drug-tolerant bacilli inside the granulomas, (v) development of mutations in Mtb genes, which are the most important molecular mechanisms of resistance. This review provides a comprehensive overview of these issues, and releases up-dated information on the therapeutic strategies recently endorsed and recommended by the World Health Organization to facilitate the clinical and microbiological management of drug-resistant TB at the global level, with attention also to the most recent diagnostic methods.
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Whitfield MG, Marras SAE, Warren RM, Van Rie A, Rice J, Wangh LJ, Kreiswirth BN. Rapid Pyrazinamide Drug Susceptibility Testing using a Closed-Tube PCR Assay of the Entire pncA gene. Sci Rep 2020; 10:4234. [PMID: 32144379 PMCID: PMC7060184 DOI: 10.1038/s41598-020-61286-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 12/18/2019] [Indexed: 11/23/2022] Open
Abstract
The continued use of pyrazinamide in the treatment of tuberculosis in the absence of a rapid, accurate and standardized pyrazinamide drug susceptibility assays is of great concern. While whole genome sequencing holds promise, it is not yet feasible option in low resource settings as it requires expensive instruments and bioinformatic analysis. We investigated the diagnostic performance of a closed-tube Linear-After-The-Exponential (LATE)-PCR assay for pyrazinamide susceptibility in Mycobacterium tuberculosis. Based on a set of 654 clinical Mycobacterium tuberculosis culture isolates with known mutations throughout the pncA gene as determined by Sanger sequencing, the assay displays excellent sensitivity of 96.9% (95% CI: 95.2-98.6) and specificity of 97.9% (95% CI: 96.1-99.7). In a subset of 384 isolates with phenotypic drug susceptibility testing, we also observed high sensitivity of 98.9% (95% CI: 97.5-100) but lower specificity of 91.8% (95% CI: 87.9-95.8) when compared to phenotypic drug susceptibility testing. We conclude that the LATE PCR assay offers both a rapid and accurate prediction of pyrazinamide susceptibility.
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Affiliation(s)
- Michael G Whitfield
- South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa.
| | - Salvatore A E Marras
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Rob M Warren
- South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Annelies Van Rie
- Department of Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - John Rice
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Lawrence J Wangh
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Nutley, New Jersey, United States of America
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147
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Merker M, Kohl TA, Barilar I, Andres S, Fowler PW, Chryssanthou E, Ängeby K, Jureen P, Moradigaravand D, Parkhill J, Peacock SJ, Schön T, Maurer FP, Walker T, Köser C, Niemann S. Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex. Genome Med 2020; 12:27. [PMID: 32143680 PMCID: PMC7060619 DOI: 10.1186/s13073-020-00726-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS We investigated mutations in 92 genes implicated in resistance to 21 anti-tuberculosis drugs using the genomes of 405 phylogenetically diverse MTBC strains. The role of phylogenetically informative mutations was assessed by routine phenotypic DST data for the first-line drugs isoniazid, rifampicin, ethambutol, and pyrazinamide from a separate collection of over 7000 clinical strains. Selected mutations/strains were further investigated by minimum inhibitory concentration (MIC) testing. RESULTS Out of 547 phylogenetically informative mutations identified, 138 were classified as not correlating with resistance to first-line drugs. MIC testing did not reveal a discernible impact of a Rv1979c deletion shared by M. africanum lineage 5 strains on resistance to clofazimine. Finally, we found molecular evidence that some MTBC subgroups may be hyper-susceptible to bedaquiline and clofazimine by different loss-of-function mutations affecting a drug efflux pump subunit (MmpL5). CONCLUSIONS Our findings underline that the genetic diversity in MTBC has to be studied more systematically to inform the design of clinical trials and to define sound epidemiologic cut-off values (ECOFFs) for new and repurposed anti-tuberculosis drugs. In that regard, our comprehensive variant catalogue provides a solid basis for the interpretation of mutations in genotypic as well as in phenotypic DST assays.
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Affiliation(s)
- Matthias Merker
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany.
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Ivan Barilar
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kristian Ängeby
- Department of Clinical Science and Education, Emergency Medicine, Stockholm South General Hospital, Karolinska Institute, Stockholm, Sweden
| | | | - Danesh Moradigaravand
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Claudio Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
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148
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Islam MM, Tan Y, Hameed HMA, Liu Y, Chhotaray C, Cai X, Liu Z, Lu Z, Wang S, Cai X, Su B, Li X, Tan S, Liu J, Zhang T. Prevalence and molecular characterization of amikacin resistance among Mycobacterium tuberculosis clinical isolates from southern China. J Glob Antimicrob Resist 2020; 22:290-295. [PMID: 32142951 DOI: 10.1016/j.jgar.2020.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 01/22/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES Amikacin is the only second-line injectable antituberculosis (anti-TB) drug still recommended for multidrug-resistant tuberculosis (MDR-TB) treatment when a short MDR-TB regimen is designed. Mutations in rrs and eis are reported to be associated with resistance to amikacin. In this study, we investigated the incidence of rrs, eis, tap and whiB7 mutations in amikacin-resistant Mycobacterium tuberculosis clinical isolates to find the proportion of different mutations related to amikacin resistance. METHODS A total of 395 clinical isolates of M. tuberculosis were used for phenotypic drug susceptibility testing (DST) to 10 drugs with the Löwenstein-Jensen (L-J) method. We sequenced rrs, eis, tap and whiB7 genes in 178 M. tuberculosis clinical isolates (89 amikacin-resistant isolates and 89 of 306 amikacin-susceptible isolates). RESULTS Our data showed that 22.53% (89/395) M. tuberculosis clinical isolates were resistant to amikacin. Of the 89 amikacin-resistant isolates, 89.89% (80/89) were MDR-TB, of which 12.36% (11/89) were pre-extensively drug-resistant TB (pre-XDR-TB) and 77.53% (69/89) were XDR-TB. The rrs mutations were found in 82% (73/89) in amikacin-resistant M. tuberculosis clinical isolates. The A1401G alteration in the rrs gene was the most dominant mutation (80.90%; 72/89). Five mutations were detected as new in rrs, tap and whiB7. Notably, 13.48% (12/89) amikacin-resistant isolates had no known mutation in these genes. CONCLUSIONS Our data reveal that the rrs mutation is a predominant molecular marker of amikacin resistance in southern China. Analysis of the rrs gene mutations will significantly reduce the time and cost to diagnose amikacin resistance in TB patients. Other unknown amikacin resistance mechanism(s) exist.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Xiaoyin Cai
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Xingshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Biyi Su
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, 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 (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.
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149
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Saber MM, Shapiro BJ. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes. Microb Genom 2020; 6:e000337. [PMID: 32100713 PMCID: PMC7200059 DOI: 10.1099/mgen.0.000337] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWASs) have the potential to reveal the genetics of microbial phenotypes such as antibiotic resistance and virulence. Capitalizing on the growing wealth of bacterial sequence data, microbial GWAS methods aim to identify causal genetic variants while ignoring spurious associations. Bacteria reproduce clonally, leading to strong population structure and genome-wide linkage, making it challenging to separate true 'hits' (i.e. mutations that cause a phenotype) from non-causal linked mutations. GWAS methods attempt to correct for population structure in different ways, but their performance has not yet been systematically and comprehensively evaluated under a range of evolutionary scenarios. Here, we developed a bacterial GWAS simulator (BacGWASim) to generate bacterial genomes with varying rates of mutation, recombination and other evolutionary parameters, along with a subset of causal mutations underlying a phenotype of interest. We assessed the performance (recall and precision) of three widely used single-locus GWAS approaches (cluster-based, dimensionality-reduction and linear mixed models, implemented in plink, pyseer and gemma) and one relatively new multi-locus model implemented in pyseer, across a range of simulated sample sizes, recombination rates and causal mutation effect sizes. As expected, all methods performed better with larger sample sizes and effect sizes. The performance of clustering and dimensionality reduction approaches to correct for population structure were considerably variable according to the choice of parameters. Notably, the multi-locus elastic net (lasso) approach was consistently amongst the highest-performing methods, and had the highest power in detecting causal variants with both low and high effect sizes. Most methods reached the level of good performance (recall >0.75) for identifying causal mutations of strong effect size [log odds ratio (OR) ≥2] with a sample size of 2000 genomes. However, only elastic nets reached the level of reasonable performance (recall=0.35) for detecting markers with weaker effects (log OR ~1) in smaller samples. Elastic nets also showed superior precision and recall in controlling for genome-wide linkage, relative to single-locus models. However, all methods performed relatively poorly on highly clonal (low-recombining) genomes, suggesting room for improvement in method development. These findings show the potential for multi-locus models to improve bacterial GWAS performance. BacGWASim code and simulated data are publicly available to enable further comparisons and benchmarking of new methods.
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Affiliation(s)
- Morteza M. Saber
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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150
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Salvato RS, Costa ERD, Reis AJ, Schiefelbein SH, Halon ML, Barcellos RB, Unis G, Dias CF, Viveiros M, Portugal I, da Silva PEA, Kritski AL, Perdigão J, Rossetti MLR. First insights into circulating XDR and pre-XDR Mycobacterium tuberculosis in Southern Brazil. INFECTION GENETICS AND EVOLUTION 2020; 78:104127. [DOI: 10.1016/j.meegid.2019.104127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/20/2019] [Accepted: 11/24/2019] [Indexed: 11/30/2022]
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