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

Title: Bacterial Genomic Epidemiology with Mixed Samples
Author: Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti
Contributor organization: Department of Mathematics and Statistics
Department of Computer Science
Date: 2021-11-15
Language: eng
Number of pages: 18
Belongs to series: Microbial Genomics
ISSN: 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000691
URI: http://hdl.handle.net/10138/336390
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.
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
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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