Show simple item record

dc.contributor.authorMäklin, Tommi
dc.contributor.authorKallonen, Teemu
dc.contributor.authorAlanko, Jarno
dc.contributor.authorSamuelsen, Ørjan
dc.contributor.authorHegstad, Kristin
dc.contributor.authorMäkinen, Veli
dc.contributor.authorCorander, Jukka
dc.contributor.authorHeinz, Eva
dc.contributor.authorHonkela, Antti
dc.date.accessioned2022-01-25T13:41:54Z
dc.date.available2022-01-25T13:41:54Z
dc.date.issued2021-11-15
dc.description.abstractGenomic 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_US
dc.identifier.citationMäklin, Kallonen, Alanko, Samuelsen Ø, Hegstad K, Mäkinen, Corander, Heinz, Honkela. Bacterial genomic epidemiology with mixed samples. Microbial Genomics. 2021;7(11):1-18en_US
dc.identifier.cristinIDFRIDAID 1972918
dc.identifier.doi10.1099/MGEN.0.000691
dc.identifier.issn2057-5858
dc.identifier.urihttps://hdl.handle.net/10037/23803
dc.language.isoengen_US
dc.publisherMicrobiology Societyen_US
dc.relation.journalMicrobial Genomics
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020-EU.1.1./742158/Norway/Scalable inference algorithms for Bayesian evolutionary epidemiology/SCARABEE/en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/RCN/?/144501/Norway/?/?/en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2021 The Author(s)en_US
dc.titleBacterial genomic epidemiology with mixed samplesen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


File(s) in this item

Thumbnail

This item appears in the following collection(s)

Show simple item record