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

Abstract

Cronobacter sakazakii 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 C. sakazakii 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 C. sakazakii infections has been observed. The seemingly great capability of C. sakazakii 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 C. sakazakii isolated from skimmed milk powder (C7) and ready-to-eat salad mix (C8), respectively. These are compared to other, already sequenced, C. sakazakii genomes. Sequencing of the fusA allele revealed that both isolates were C. sakazakii . 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 C. sakazakii C8 is shown to hold a novel and unique sequence type; the number of unique genes identified in the genomic sequence of C. sakazakii C7 and C8 were 109 and 188, respectively. Some of the determined unique genes such as the rhs and VgrG 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.

Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk

“…The antibiotic target protection gene (vgaC) was present in only three of the six isolates and the marA gene, whose function is as a transcription factor that upregulates multidrug efflux and downregulates membrane permeability, was found in all the isolates. As in our study, Aly et al [69] found msbA, emrR, H-NS, emrB, marA, CRP, and PBP3 to be associated with resistance to several antibiotics such as beta-lactams, tetracycline, macrolide, fluoroquinolone, penams, cephalosporin, and cephamycin. Active flow pumps provide a mechanism to increase resistance by improving the survival of enterobacteria in the gastrointestinal tract of the host and allowing the invasion of microvascular endothelial cells in the brain [70,71].…”

Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

“…We observed similar communities and reported the presence of pathogens, that could infect humans and animals, associated with rotting grapes, such as C. sakazakii SRG2, K. pneumoniae SRG3, and S. gigas SRG18. C. sakazakii is an emerging opportunistic foodborne pathogen with the potential to cause meningitis, bacteremia, and necrotizing enterocolitis, particularly in infants (Drudy et al, 2006;Aly et al, 2019). K. pneumoniae is an important conditional pathogenic and iatrogenic infectious bacterium.…”

Helicobacter pylori Virulence Factors Exploiting Gastric Colonization and its Pathogenicity

“…In recent years, the whole genome sequencing (WGS)-based approach from cultured bacterial isolates has emerged as one of the most comprehensive tools for surveillance study, drug resistance determination, and evolutionary analysis of infectious diseases [219,220,221,222,223,224]. This is due to improved sequencing technologies, the user friendly nature, easy availability of reagents, improved accuracy of up to 93%, reasonably lower costs (150EUR per 5 MB genome by Illumina MiSeq), and faster results (nine days versus 21 days) compared to traditional DNA sequencing [221,222,225,226,227].…”

“…Similarly, another study was conducted by Edwards et al to characterize the putative virulence factors in Plesiomonas shigelloides [228]. Furthermore, Aly et al used a WGS-based study to identify genes associated with biofilm formation, antibiotic resistance, and pathogenicity [224]. The results of these studies clearly suggest that WGS-based approaches are an advancement over traditional Sanger sequencing.…”