AUTHOR=Aly Mohamed A. , Domig Konrad J. , Kneifel Wolfgang , Reimhult Erik 

TITLE=Whole Genome Sequencing-Based Comparison of Food Isolates of Cronobacter sakazakii

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01464

DOI=10.3389/fmicb.2019.01464

ISSN=1664-302X

ABSTRACT=<p><italic>Cronobacter sakazakii</italic> is an emerging foodborne pathogen, which is linked to life-threatening infections causing septicemia, meningitis, and necrotizing enterocolitis. These infections have been epidemiologically connected to ingestion of contaminated reconstituted powder infant formula. Even at low water activity <italic>C. sakazakii</italic> can survive for a long time; it is capable of protective biofilm formation and occasionally shows high virulence and pathogenicity even following stressful environmental conditions. Hence it is a challenging task for the food industry to control contamination of food ingredients and products through the entire production chain, since an increasing number of severe food-related outbreaks of <italic>C. sakazakii</italic> infections has been observed. The seemingly great capability of <italic>C. sakazakii</italic> to survive even strict countermeasures combined with its prevalence in many food ingredients requires a greater in depth understanding of its virulence factors to master the food safety issues related to this organism. In this context, we present the whole genome sequence (WGS) of two different <italic>C. sakazakii</italic> isolated from skimmed milk powder (C7) and ready-to-eat salad mix (C8), respectively. These are compared to other, already sequenced, <italic>C. sakazakii</italic> genomes. Sequencing of the <italic>fusA</italic> allele revealed that both isolates were <italic>C. sakazakii</italic>. We investigated the molecular characteristics of both isolates relevant for genes associated with pathogenesis and virulence factors, resistance to stressful environmental conditions (e.g., osmotic and heat), survival in desiccation as well as conducted a comparative genomic analysis. By using multi-locus sequence typing (MLST), the genetic type of both isolates is assessed and the number of unique genes is determined. DNA of <italic>C. sakazakii</italic> C8 is shown to hold a novel and unique sequence type; the number of unique genes identified in the genomic sequence of <italic>C. sakazakii</italic> C7 and C8 were 109 and 188, respectively. Some of the determined unique genes such as the <italic>rhs</italic> and <italic>VgrG</italic> genes are linked to the Type VI Secretion System cluster, which is associated with pathogenicity and virulence factors. Moreover, seven genes encoding for multi-drug resistance were found in both isolates. The finding of a number of genes linked to producing capsules and biofilm are likely related to the observed resistance to desiccation.</p>