The phylogenomic landscape of the genus Serratia

Abstract

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We show that Serratia is a diverse genus which displays striking plasticity and ability to adapt to its environment, including a highly-varied portfolio of plasmids, and provide evidence of different patterns of gene flow across the genus. This work provides an essential platform for understanding the emergence of clinical and other lineages of Serratia.

Genomic epidemiology of the cholera outbreak in Yemen reveals the spread of a multi-drug resistance plasmid between diverse lineages of Vibrio cholerae

“…To predict the antigenic serogroup, we screened the assemblies against a custom reference database using Hamburger 63 . In brief, a database was constructed by selecting flanking and marker genes for the operon encoding the V. cholerae O-antigen, with representative genes for both O1 and non-O1 serogroups included (Table S15).…”