Dataset Information

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

ABSTRACT: 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.

SUBMITTER: Afolayan AO

PROVIDER: S-EPMC8634317 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

Afolayan Ayorinde O AO Bernal Johan Fabian JF Gayeta June M JM Masim Melissa L ML Shamanna Varun V Abrudan Monica M Abudahab Khalil K Argimón Silvia S Carlos Celia C CC Sia Sonia S Ravikumar Kadahalli L KL Okeke Iruka N IN Donado-Godoy Pilar P Aanensen David M DM Underwood Anthony A

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20211201 Suppl_4

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, sequen ...[more]

PMID: 34850839

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Dataset Information

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

Publications

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

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