The genus Serratia revisited by genomics

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 highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.

Long-term dynamics of the “Serratia marcescenscomplex” in the hospital-built environment

“…The Serratia genus belongs to the order Enterobacterales 1 , comprising species widely distributed in water, soil, and the rhizosphere, which can become opportunistic pathogens for animals, humans, and plants [2][3][4] . In the health sector, Serratia accounts for only 1%-2% of hospital-acquired infections, which are often associated with unpredictable outbreaks of high morbidity and mortality in pediatric or intensive care unit (ICU) wards.…”

“…Phylogenetic analysis have lately categorized several emblematic Serratia species within a "Serratia marcescens complex" (SMC), thus highlighting the remarkable diversification of S. marcescens associated with its adaptation to various environments 2,9,10 .…”

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

“…To determine the placement of MosAIC isolates in their wider population structures, we selected three taxonomic groups for further analysis (Enterobacter, Serratia, and Elizabethkingia anophelis), owing to their high representation within the collection, biological interest amongst the mosquito-microbiome field (34), and good understanding of their genetic diversity and environmental / host-associated niches within a population (i.e., their population structure) (60)(61)(62). In total, 55 Enterobacter isolates, 16 Serratia isolates, and 7 El.…”

“…4G-H). 62), and (G, H) Elizabethkingia anophelis (60), with added mosquito-derived representation from MosAIC and a manually curated set of En. asburiae genomes.…”

“…anophelis. These have defined population structures (60)(61)(62); are well represented in the collection and are common mosquito symbionts (21,34).…”