P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics.

ABSTRACT:

Summary

Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods and user-friendly software, accessible to users without a strong bioinformatics proficiency. To overcome these issues we developed P-DOR, a novel tool for rapid bacterial outbreak characterization. P-DOR accepts genome assemblies as input, it automatically selects a background of publicly available genomes using k-mer distances and adds it to the analysis dataset before inferring a Single-Nucleotide Polymorphism (SNP)-based phylogeny. Epidemiological clusters are identified

SUBMITTER: Batisti Biffignandi G 

PROVIDER: S-EPMC10533420 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature