Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

Autor:	Afolayan AO; Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria., Bernal JF; Colombian Integrated Program for Antimicrobial Resistance Surveillance, Centro de Investigatión Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, Tibaitatá, Mosquera, Cundinamarca, Colombia., Gayeta JM; Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines., Masim ML; Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines., Shamanna V; Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India., Abrudan M; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Abudahab K; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Argimón S; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Carlos CC; Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines., Sia S; Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines., Ravikumar KL; Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India., Okeke IN; The NIHR Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance., Donado-Godoy P; Colombian Integrated Program for Antimicrobial Resistance Surveillance, Centro de Investigatión Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, Tibaitatá, Mosquera, Cundinamarca, Colombia., Aanensen DM; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Underwood A; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
Jazyk:	angličtina
Zdroj:	Clinical infectious diseases : an official publication of the Infectious Diseases Society of America [Clin Infect Dis] 2021 Dec 01; Vol. 73 (Suppl_4), pp. S267-S274.
DOI:	10.1093/cid/ciab785
Abstrakt:	Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, national, and global scales. To derive WGS-based outputs, a series of processes are required, beginning with sample and metadata collection, followed by nucleic acid extraction, library preparation, sequencing, and analysis. Throughout this pathway there are many data-related operations required (informatics) combined with more biologically focused procedures (bioinformatics). For a laboratory aiming to implement pathogen genomics, the informatics and bioinformatics activities can be a barrier to starting on the journey; for a laboratory that has already started, these activities may become overwhelming. Here we describe these data bottlenecks and how they have been addressed in laboratories in India, Colombia, Nigeria, and the Philippines, as part of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance. The approaches taken include the use of reproducible data parsing pipelines and genome sequence analysis workflows, using technologies such as Data-flo, the Nextflow workflow manager, and containerization of software dependencies. By overcoming barriers to WGS implementation in countries where genome sampling for some species may be underrepresented, a body of evidence can be built to determine the concordance of antimicrobial sensitivity testing and genome-derived resistance, and novel high-risk clones and unknown mechanisms of resistance can be discovered. (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.)
Databáze:	MEDLINE
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