Bacterial genomic epidemiology with mixed samples

Mäklin, Tommi, Kallonen, Teemu, Alanko, Jarno, Samuelsen, Ørjan, Hegstad, Kristin, Mäkinen, Veli, Corander, Jukka, Heinz, Eva ORCID: https://orcid.org/0000-0003-4413-3756 and Honkela, Antti (2021) 'Bacterial genomic epidemiology with mixed samples'. Microbial Genomics, Vol 7, Issue 11.

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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.

Item Type:	Article
Subjects:	QU Biochemistry > Genetics > QU 460 Genomics. Proteomics QU Biochemistry > Genetics > QU 470 Genetic structures QW Microbiology and Immunology > QW 50 Bacteria (General). Bacteriology. Archaea
Faculty: Department:	Biological Sciences > Vector Biology Department
Digital Object Identifer (DOI):	https://doi.org/10.1099/mgen.0.000691
Depositing User:	Stacy Murtagh
Date Deposited:	16 Nov 2021 08:15
Last Modified:	16 Nov 2021 08:15
URI:	https://archive.lstmed.ac.uk/id/eprint/19441

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