Staphylococcus aureus viewed from the perspective of 40,000+ genomes

PeerJ
Robert A Petit, Timothy D Read

Abstract

Low-cost Illumina sequencing of clinically-important bacterial pathogens has generated thousands of publicly available genomic datasets. Analyzing these genomes and extracting relevant information for each pathogen and the associated clinical phenotypes requires not only resources and bioinformatic skills but organism-specific knowledge. In light of these issues, we created Staphopia, an analysis pipeline, database and application programming interface, focused on Staphylococcus aureus, a common colonizer of humans and a major antibiotic-resistant pathogen responsible for a wide spectrum of hospital and community-associated infections. Written in Python, Staphopia's analysis pipeline consists of submodules running open-source tools. It accepts raw FASTQ reads as an input, which undergo quality control filtration, error correction and reduction to a maximum of approximately 100× chromosome coverage. This reduction significantly reduces total runtime without detrimentally affecting the results. The pipeline performs de novo assembly-based and mapping-based analysis. Automated gene calling and annotation is performed on the assembled contigs. Read-mapping is used to call variants (single nucleotide polymorphisms and insertion/dele...Continue Reading

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Citations

Nov 2, 2018·Journal of Clinical Microbiology·Michelle SuTimothy D Read
Nov 30, 2018·The Journal of Infectious Diseases·Monique R BennettJames E Crowe
Mar 25, 2019·Applied and Environmental Microbiology·Abraham G MollerTimothy D Read
Jan 9, 2020·Microbial Genomics·Stefano G GiulieriDeborah A Williamson
Jan 29, 2019·Microbiology Resource Announcements·Eryn E BernardyJoanna B Goldberg
Dec 21, 2019·JAMA : the Journal of the American Medical Association·Lauren F CollinsMonica M Farley
Mar 7, 2020·Genome Biology·Ahmed M Moustafa, Paul J Planet
Aug 6, 2020·MSystems·Robert A Petit, Timothy D Read
Dec 18, 2019·Microbiology Spectrum·Jodi A Lindsay
Jul 6, 2021·Pediatric Pulmonology·Harry S PorterfieldAnthony J Fischer
Nov 20, 2021·Frontiers in Microbiology·Stéphanie NouwsSigrid C J De Keersmaecker

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Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

PATRIC
BLASTN
Staphopia analysis pipeline
Nextflow
MegaRes
CGC
Django
ENA
Ariba
MentaLiST

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