Bacterial genomic epidemiology with mixed samples.
Microb Genom
; 7(11)2021 11.
Article
em En
| MEDLINE
| ID: mdl-34779765
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.
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Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Genoma Bacteriano
/
Genômica
Tipo de estudo:
Screening_studies
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article