Bacterial Genomic Epidemiology with Mixed Samples

Show simple item record

dc.contributor.author Mäklin, Tommi
dc.contributor.author Kallonen, Teemu
dc.contributor.author Alanko, Jarno
dc.contributor.author Samuelsen, Ørjan
dc.contributor.author Hegstad, Kristin
dc.contributor.author Mäkinen, Veli
dc.contributor.author Corander, Jukka
dc.contributor.author Heinz, Eva
dc.contributor.author Honkela, Antti
dc.date.accessioned 2021-11-16T14:16:02Z
dc.date.available 2021-11-16T14:16:02Z
dc.date.issued 2021-11-15
dc.identifier.citation Mäklin , T , Kallonen , T , Alanko , J , Samuelsen , Ø , Hegstad , K , Mäkinen , V , Corander , J , Heinz , E & Honkela , A 2021 , ' Bacterial Genomic Epidemiology with Mixed Samples ' , Microbial Genomics , vol. 7 , no. 11 , 000691 . https://doi.org/10.1099/mgen.0.000691
dc.identifier.other PURE: 169792850
dc.identifier.other PURE UUID: 4700ba5c-17c8-4a1d-93ef-70ad60a30fbd
dc.identifier.other ORCID: /0000-0003-4454-1493/work/103297477
dc.identifier.other ORCID: /0000-0001-9193-8093/work/103299806
dc.identifier.other ORCID: /0000-0003-0970-3514/work/103301345
dc.identifier.other ORCID: /0000-0002-8003-9225/work/103301850
dc.identifier.other WOS: 000729240200013
dc.identifier.uri http://hdl.handle.net/10138/336390
dc.description.abstract Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples. en
dc.format.extent 18
dc.language.iso eng
dc.relation.ispartof Microbial Genomics
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject ALGORITHM
dc.subject CULTURE
dc.subject DIVERSITY
dc.subject EMERGENCE
dc.subject ESCHERICHIA-COLI
dc.subject METAGENOMICS
dc.subject POPULATION-STRUCTURE
dc.subject R PACKAGE
dc.subject SINGLE-CELL
dc.subject STRATEGIES
dc.subject genomic epidemiology
dc.subject pathogen surveillance
dc.subject plate sweeps
dc.subject probabilistic modelling
dc.subject pseudoalignment
dc.subject 11832 Microbiology and virology
dc.subject 1184 Genetics, developmental biology, physiology
dc.title Bacterial Genomic Epidemiology with Mixed Samples en
dc.type Article
dc.contributor.organization Department of Mathematics and Statistics
dc.contributor.organization Department of Computer Science
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1099/mgen.0.000691
dc.relation.issn 2057-5858
dc.rights.accesslevel openAccess
dc.type.version publishedVersion
dc.identifier.url https://www.biorxiv.org/content/10.1101/2020.04.03.021501

Files in this item

Total number of downloads: Loading...

Files Size Format View
bacterial.pdf 7.061Mb PDF View/Open

This item appears in the following Collection(s)

Show simple item record