The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.

ABSTRACT: The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum [Formula: see text]-lactamase (ESBL)-producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodolog

SUBMITTER: Huisman JS 

PROVIDER: S-EPMC9393563 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature