$\textit{Mycobacterium tuberculosis}$ resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools

Autor: Schleusener, V, Köser, CU, Beckert, P, Niemann, S, Feuerriegel, S

Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analys

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71f9526e9ad8ce74bd04d6dd1d877927

A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for Mycobacterium tuberculosis complex.

Autor: Köser CU; Department of Genetics, University of Cambridge, Cambridge, UK cuk21@cam.ac.uk.; Both authors contributed equally., Miotto P; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.; Both authors contributed equally., Ismail N; South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa., Anthony RM; National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands., Utpatel C; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.; German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany., Merker M; Evolution of the Resistome, Research Center Borstel, Borstel, Germany., Niemann S; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.; German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany., Tahseen S; National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan., Rigouts L; Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium., Rodrigues C; Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mumbai, India., Omar SV; Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa., Farhat MR; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA., Antonenka U; Institute of Microbiology and Laboratory Medicine, Department IML red GmbH, WHO, Supranational Tuberculosis Reference Laboratory, Gauting, Germany., Hoffmann H; Institute of Microbiology and Laboratory Medicine, Department IML red GmbH, WHO, Supranational Tuberculosis Reference Laboratory, Gauting, Germany.; SYNLAB Gauting, SYNLAB MVZ Dachau GmbH, Munich, Germany., Cirillo DM; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy., Schön T; Department of Infectious Diseases, Region Östergötland, Linköping University Hospital, Linköping, Sweden.; Division of Infection and Inflammation, Institute of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.; Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden.

Publikováno v: The European respiratory journal [Eur Respir J] 2024 Jul 11; Vol. 64 (1). Date of Electronic Publication: 2024 Jul 11 (Print Publication: 2024).

The exceptions that prove the rule-a historical view of bedaquiline susceptibility.

Autor: Miotto P; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy., Cirillo DM; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy., Schön T; Department of Infectious Diseases, Region Östergötland, Linköping University Hospital, Linköping, Sweden.; Division of Infection and Inflammation, Institute of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.; Department of Infectious Diseases, Kalmar County Hospital, Linköping University, Kalmar, Sweden., Köser CU; Department of Genetics, University of Cambridge, Cambridge, UK. cuk21@cam.ac.uk.

Publikováno v: Genome medicine [Genome Med] 2024 Mar 13; Vol. 16 (1), pp. 39. Date of Electronic Publication: 2024 Mar 13.

Loss-of-function mutations in ndh do not confer delamanid, ethionamide, isoniazid, or pretomanid resistance in Mycobacterium tuberculosis .

Autor: Pandey S; Queensland Mycobacterium Reference Laboratory, Pathology Queensland , Brisbane, Queensland, Australia., Vilchèze C; Department of Microbiology and Immunology, Albert Einstein College of Medicine , Bronx, New York, USA., Werngren J; Public Health Agency of Sweden , Solna, Sweden., Bainomugisa A; Queensland Mycobacterium Reference Laboratory, Pathology Queensland , Brisbane, Queensland, Australia., Mansjö M; Public Health Agency of Sweden , Solna, Sweden., Groenheit R; Public Health Agency of Sweden , Solna, Sweden., Miotto P; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute , Milan, Italy., Cirillo DM; Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute , Milan, Italy., Coulter C; Queensland Mycobacterium Reference Laboratory, Pathology Queensland , Brisbane, Queensland, Australia., Baulard AR; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille , Lille, France., Schön T; Department of Infectious Diseases, Linköping University Hospital , Linköping, Sweden.; Division of Infection and Inflammation, Institute of Biomedical and Clinical Sciences, Linköping University , Linköping, Sweden.; Department of Infectious Diseases, Region Östergötland and Kalmar County Hospital, Linköping University , Linköping, Sweden., Jacobs WR Jr; Department of Microbiology and Immunology, Albert Einstein College of Medicine , Bronx, New York, USA., Djaout K; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille , Lille, France., Köser CU; Department of Genetics, University of Cambridge , Cambridge, United Kingdom.

Publikováno v: Antimicrobial agents and chemotherapy [Antimicrob Agents Chemother] 2024 Jan 10; Vol. 68 (1), pp. e0109623. Date of Electronic Publication: 2023 Dec 01.

Minimum inhibitory concentrations and sequencing data have to be analysed in more detail to set provisional epidemiological cut-off values for Mycobacterium tuberculosis complex.

Autor: Köser CU; Department of Genetics, University of Cambridge, Cambridge, UK cuk21@cam.ac.uk., Maurer FP; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.

Publikováno v: The European respiratory journal [Eur Respir J] 2023 May 05; Vol. 61 (5). Date of Electronic Publication: 2023 May 05 (Print Publication: 2023).