PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.

ABSTRACT:

Background

Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.

Results

Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, r

SUBMITTER: de Nies L 

PROVIDER: S-EPMC7890817 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature