Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species

Abstract

BackgroundThe genus Cronobacter (formerly called Enterobacter sakazakii) is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified.Methodology/Principal FindingsWe report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content) and two plasmids; 31 kb (51% GC) and 131 kb (56% GC). The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH) was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10–17% absence of genes.Conclusions/SignificanceCGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from outbreaks in neonatal intensive care units.

Cronobacter spp. – opportunistic food-borne pathogens. A review of their virulence and environmental-adaptive traits

“…The reclassification scheme described by Iversen et al (2007Iversen et al ( , 2008a was supported subsequently by both optical mapping and genome sequencing data, which confirmed the revision of the taxonomic positions of the seven species (Yan et al, 2012;Kotewicz & Tall, 2009;Kucerova et al, 2010;Stephan et al, 2011;Joseph et al, 2012;Grim et al, 2013). Although C. sakazakii and C. malonaticus were found to be closely related and difficult to distinguish by 16S rDNA gene sequence analysis, a MLST scheme reported by Baldwin et al (2009) was shown to support the separation of these two species (Yan et al, 2012).…”

“…They reported that neither mannose-sensitive type 1 fimbriae nor type 3 fimbriae were involved in the adhesion of Cronobacter to the cells. Comparatively, one striking difference among Cronobacter as reported by Kucerova et al (2010), Jospeh & Forsythe (2011) and Stephan et al (2011) is the finding that C. sakazakii does not possess the genes encoding curli, whereas C. turicensis does. However, the implications of these findings in virulence have not been fully studied.…”

“…Kothary et al (2007) reported the presence of a zinc metalloprotease that deforms CHO cells, eventually causing their rounding and leading to cell damage. The genes for a haemolysin (hly) have been identified, but no activity has been found (Kucerova et al, 2010;Cruz et al, 2011;Grim et al, 2013). Townsend et al (2007a) provided evidence that the presence of endotoxin along with C. sakazakii in infant formula enhanced the translocation of C. sakazakii from rat guts through the BBB.…”

“…Many meningitis-causing bacteria, such as Neisseria meningitidis, Haemophilus influenzae and P. aeruginosa utilize type IV pili to colonize intestinal tissues and to later overcome the shear forces of the capillary blood flow before crossing the BBB (Kucerova et al, 2010;Grim et al, 2013). Cronobacter have been mostly implicated in meningitis in infants following the consumption of reconstituted and temperature-abused PIF (Hunter & Bean, 2013).…”

“…Among the annotated genes inspected, Kucerova et al (2010) also showed that the complete cation efflux system (cusA, cusB, cusC and cusF) and its regulatory gene cusR were present in strains associated with neonatal infections, but missing in the other strains, which may explain the fact that not all Cronobacter spp. are equally pathogenic and cause meningitis.…”