Bacterial Genomic Epidemiology with Mixed Samples

Tommi Mäklin, Teemu Kallonen, Jarno Alanko, Ørjan Samuelsen, Kristin Hegstad, Veli Mäkinen, Jukka Corander, Eva Heinz, Antti Honkela

Forskningsoutput: TidskriftsbidragArtikelPeer review

Sammanfattning

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.
Originalspråkengelska
Artikelnummer000691
TidskriftMicrobial Genomics
Volym7
Utgåva11
Antal sidor18
ISSN2057-5858
DOI
StatusPublicerad - 15 nov 2021
MoE-publikationstypA1 Tidskriftsartikel-refererad

Vetenskapsgrenar

  • 11832 Mikrobiologi och virologi
  • 1184 Genetik, utvecklingsbiologi, fysiologi

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