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; Web browser; Tuberculosis; Software; Sequence analysis, dna; Rapid susceptibility testing; Phylogeny; Phylogenetic analysis; Outbreak; Online tools; Mycobacterium tuberculosis; Microbial sensitivity tests; Humans; Genome, bacterial; Diagnosis; Cultures; Computational biology; Bacterial typing techniques; Antitubercular agents; 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/
ISSN: 1198743X
Author's mail: alessandro.atzeni@urv.cat; alessandro.atzeni@urv.cat
Record's date: 2025-02-08
Paper version: info:eu-repo/semantics/acceptedVersion
Link to the original source: https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(16)30392-5/fulltext
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Paper 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
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