title: Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.
abstract: Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed usingin silicoplasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novelin silicoplasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: Alex
authors.initials: A
authors.lastname: Orlek
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford Oxford, UK.
authors.forename: Nicole
authors.initials: N
authors.lastname: Stoesser
authors.affiliation: National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK; Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK.
authors.forename: Muna F
authors.initials: MF
authors.lastname: Anjum
authors.affiliation: Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK.
authors.forename: Michel
authors.initials: M
authors.lastname: Doumith
authors.affiliation: National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellington
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Peto
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: Derrick
authors.initials: D
authors.lastname: Crook
authors.affiliation: National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: Woodford
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: Hang
authors.initials: H
authors.lastname: Phan
authors.affiliation: Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Sheppard
keywords: antibiotic resistance; genomic epidemiology; network analysis; plasmid typing; whole-genome sequencing