Computational protocol: Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments

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[…] Cronobacter species are Gram-negative opportunistic pathogens associated with life-threatening infections, such as infantile meningitis, septicemia, and necrotizing enterocolitis (, ), and urinary tract infections, pneumonia, and wound infections in adults (, ). The Cronobacter genus consists of seven species, including C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, C. dublinensis, C. universalis, and C. condimenti (, ). The primary pathogen is C. sakazakii, and epidemiologically, infections have been linked to consumption of contaminated powdered infant formula. However, surveillance studies have shown that Cronobacter spp. are found in a variety of different foods, including dried foods (flour, spices, herbs, and cereal) and fresh ready-to-eat vegetables (). There is a growing body of evidence that plants may serve as a reservoir or ancestral host for Cronobacter spp. (, ). Although occurrences of Cronobacter spp. in foods of plant origin are increasingly being reported, relatively little genomic information on them is available. Here, we report the draft genome sequences of 29 C. sakazakii strains isolated from foods of plant origin and dried-food processing environments.Whole-genome sequencing (WGS) libraries of these C. sakazakii strains were constructed using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA). FASTQ data sets generated on the MiSeq platform (Illumina) were trimmed for de novo assembly using CLC Genomics Workbench version 9.0 (CLC bio, Aarhus, Denmark). The genomes were annotated using the Rapid Annotations using Subsystems Technology (RAST) annotation server (), and 16 sequence types were determined by using the Cronobacter multilocus sequence typing (MLST) website (http://pubmlst.org/cronobacter). The genome sizes and coding sequences (CDSs) of these assemblies ranged from 4.3 to 4.5 Mb and 3,977 to 4,256, respectively, with G+C contents of ∼57.0% ().All strains harbored a pESA3/pSP291-like virulence plasmid, which was found by comparing their genome assemblies with WGS of C. sakazakii BAA-894 (GenBank accession numbers NC_009778 and CP000783) and was confirmed by PCR analysis (). Four strains also possessed pESA2, and three possessed pCTU3.Other mobilome-like genes, such as integrase/transposase genes coding for COG0582, Tn7 (TnsA), and TnpA, and 19 to 40 phage-associated proteins, were present in some strains. Interestingly, all strains possessed a fosfomycin resistance (fosA) gene. Other genes identified in these strains included genes for multidrug resistance efflux pump-related proteins belonging to the acrAB operon, the resistance-nodulation-division, the major facilitator superfamily, ABC-type drug transport, and bicyclomycin resistance families. Heavy metal resistance genes and gene clusters involved in copper, hydroperoxide, fusaric acid, and tellurite resistance were also found. An albicidin (a phytotoxin that inhibits DNA gyrase in chloroplasts) resistance protein (, ) was observed in all the strains. Furthermore, all strains possessed an operon encoding a xylose utilization pathway, supporting the hypothesis that plants may be the ancestral econiche for Cronobacter spp., as posited by Chase et al. () and Schmid et al. (). However, the size of this gene cluster varied among the strains.These results add to the growing number of genomes of Cronobacter strains which have plant origins. The availability of genomic information from these strains will provide a better understanding of the genetic features linked to plant association and expands insights into the evolutionary history of this important foodborne pathogen. […]

Pipeline specifications

Software tools CLC Genomics Workbench, RAST
Application WGS analysis
Organisms Cronobacter sakazakii