Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

Abstract

BackgroundSpecies of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages.Methodology/Principal FindingsWe generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes.Conclusions/SignificanceGenome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.

Cronobacter spp. as emerging causes of healthcare-associated infection

“…A number of fimbriae clusters were identified in the genomes 15 of Cronobacter species. 1,[15][16][17] Many are common to all species, though there are some interesting 16 variations. C. sakazakii is the only Cronobacter species encoding for β-fimbriae, whereas the 17 genomes of the other species encode for curli fimbriae.…”

“…C. sakazakii is the only Cronobacter species encoding for β-fimbriae, whereas the 17 genomes of the other species encode for curli fimbriae. 1,16 This may reflect evolution to the host 18 ecosystem. 19…”

“…A number of iron assimilation mechanisms 21 have been found in Cronobacter species. 1,[15][16][17][18] Type VI secretion system (T6SS) is a newly described 22 system that may be involved in adherence, cytotoxicity, host-cell invasion, growth inside macrophages 23 and survival within the host. Five putative T6SS clusters have been identified Cronobacter spp.…”

“…24 genomes. 1,[17][18][19] It remains to be determined whether they encode functional type VI secretion systems. 25…”

Lack of continuity between Cronobacter biotypes and species as determined using multilocus sequence typing

“…However, some malonate utilizing strains (biotypes 8b & 8c) remained in the C. sakazakii species, hence causing some confusion in the use of phenotyping for speciation. This short communication reviews the limitations of the continued use of the biotyping scheme in the light of an improved understanding of the phylogeny of the Cronobacter genus as revealed by multilocus sequence typing (MLST), and supported by recent whole genome sequence analysis across the genus [8,9].…”