Author, as appears in the article.: Satta, G.; Atzeni, A.; McHugh, T. D.;
Department: Bioquímica i Biotecnologia
URV's Author/s: Atzeni, Alessandro
Keywords: Whole genome sequencing Rapid susceptibility testing Phylogenetic analysis Outbreak Online tools Mycobacterium tuberculosis Diagnosis Cultures Antibiotic-resistance rapid susceptibility testing phylogenetic analysis online tools mycobacterium tuberculosis
Abstract: Whole genome sequencing (WGS) has the potential to revolutionize the diagnosis of Mycobacterium tuberculosis infection but the lack of bioinformatic expertise among clinical microbiologists is a barrier for adoption. Software products for analysis should be simple, free of charge, able to accept data directly from the sequencer (FASTQ files) and to provide the basic functionalities all-in-one. The main aim of this narrative review is to provide a practical guide for the clinical microbiologist, with little or no practical experience of WGS analysis, with a specific focus on software products tailor-made for M. tuberculosis analysis. With sequencing performed by an external provider, it is now feasible to implement WGS analysis in the routine clinical practice of any microbiology laboratory, with the potential to detect resistance weeks before traditional phenotypic culture methods, but the clinical microbiologist should be aware of the limitations of this approach. (C) 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
Thematic Areas: Saúde coletiva Química Odontología Microbiology (medical) Microbiology Medicine (miscellaneous) Medicina veterinaria Medicina iii Medicina ii Medicina i Interdisciplinar Infectious diseases Farmacia Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Biotecnología Astronomia / física
licence for use: https://creativecommons.org/licenses/by/3.0/es/
Author's mail: alessandro.atzeni@urv.cat alessandro.atzeni@urv.cat
ISSN: 1198743X
Author identifier: 0000-0002-1804-8606 0000-0002-1804-8606
Record's date: 2023-05-14
Papper version: info:eu-repo/semantics/acceptedVersion
Link to the original source: https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(16)30392-5/fulltext
Papper original source: Clinical Microbiology And Infection. 23 (2): 69-72
APA: Satta, G.; Atzeni, A.; McHugh, T. D.; (2017). Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist. Clinical Microbiology And Infection, 23(2), 69-72. DOI: 10.1016/j.cmi.2016.09.005
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Article's DOI: 10.1016/j.cmi.2016.09.005
Entity: Universitat Rovira i Virgili
Journal publication year: 2017
Publication Type: Journal Publications
Repositori URV