RT Journal Article SR Electronic(1) A1 Mäklin, Tommi A1 Kallonen, Teemu A1 Alanko, Jarno A1 Samuelsen, Ørjan A1 Hegstad, Kristin A1 Mäkinen, Veli A1 Corander, Jukka A1 Heinz, Eva A1 Honkela, AnttiYR 2021 T1 Bacterial genomic epidemiology with mixed samples JF Microbial Genomics, VO 7 IS 11 OP SP 000691 DO https://doi.org/10.1099/mgen.0.000691 PB Microbiology Society, SN 2057-5858, AB 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., UL https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000691