Bacterial Genomic Epidemiology with Mixed Samples

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http://hdl.handle.net/10138/336390

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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

Titel: Bacterial Genomic Epidemiology with Mixed Samples
Författare: Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti
Upphovmannens organisation: Department of Mathematics and Statistics
Department of Computer Science
Datum: 2021-11-15
Språk: eng
Sidantal: 18
Tillhör serie: Microbial Genomics
ISSN: 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000691
Permanenta länken (URI): http://hdl.handle.net/10138/336390
Abstrakt: 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.
Subject: ALGORITHM
CULTURE
DIVERSITY
EMERGENCE
ESCHERICHIA-COLI
METAGENOMICS
POPULATION-STRUCTURE
R PACKAGE
SINGLE-CELL
STRATEGIES
genomic epidemiology
pathogen surveillance
plate sweeps
probabilistic modelling
pseudoalignment
11832 Microbiology and virology
1184 Genetics, developmental biology, physiology
Referentgranskad: Ja
Licens: cc_by
Användningsbegränsning: openAccess
Parallelpublicerad version: publishedVersion


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