Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them

Eduardo Abreo,Nora Altier

doi:10.1038/s41598-018-37118-0

Abstract

Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.

Highlights

Serratia marcescens is a Gram-negative rod-shaped bacterium of the Enterobacteriaceae family that has been isolated from different environmental and nosocomial sources
The average nucleotide identity (ANI) of whole genome sequences of 49 selected isolates, representing diverse environments and countries and including ATCC 13880 type strain, confirmed that 45 strains could be assigned to S. marcescens as they showed ANI values > 95.0% with S. marcescens type strain ATCC 13880 (Table 1)
Among the four strains with ANI values below 95.0, that were not considered as S. marcescens and were no further analyzed, MSU97 -reported as a plant growth promoting rhizobacteria (PGPR) strain- had the lowest ANI value (93.77)

Summary

Introduction

Serratia marcescens is a Gram-negative rod-shaped bacterium of the Enterobacteriaceae family that has been isolated from different environmental and nosocomial sources. Virulence factors of indirect action but whose presence increase virulence are related to bacteria motility and antibiotic resistance Some of these virulence factors, most notably those of secondary importance, may confer competence for any strain to strive in different hosts like insects and plants surfaces, and soil and water. In this work we have used the PGAdb-builder[19], a recently available web-based tool, to create a pangenome allele database for this species and to apply wgMLST schemes to genomes of nosocomial, environmental and PGPR strains of S. marcescens available at GenBank to address questions regarding the link between origin, PGPR status and genotype. The ultimate goal is to use the growing resource of genomic information to draw preliminary conclusions on the diversity and genetic make-up of S. marcescens populations and their suitability to be used as PGPR

Methods

Results

Conclusion