Bacterial Genomic Epidemiology with Mixed Samples

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

Research output: Contribution to journalArticleScientificpeer-review

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.
Original languageEnglish
Article number000691
JournalMicrobial Genomics
Volume7
Issue number11
Number of pages18
ISSN2057-5858
DOIs
Publication statusPublished - 15 Nov 2021
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 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

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