Development of DNA probes to detect Cronobacter sakazakii based on comparative genomics and its application in food samples

The objective of this study was to develop new primer-probe set to detect Cronobacter sakazakii based on comparative genomics. Among 16 candidates of gene clusters from the results of panX analysis, gene annotated as type 1 fimbrial protein was selected as target of primer and sensitivity/selectivity of designed primer were confirmed with 59 strains. When tryptic soy broth (TSB), phosphate-buffered saline (PBS), Enterobacteriaceae Enrichment (EE), and Escherichia coli DNA were used as interference material, compounds except 50% EE had no significant effect on the detection of C. sakazakii . Moreover, it was verified that the detection efficiency of PCR analysis using designed primer in food samples such as powdered infant formula (PIF), PIF containing Lactobacillus , and milk was not significantly different from conventionally used selective media. These results implicated that designed primer based on comparative genomics can be used effectively for detection of C. sakazakii in various food products. • Comparative genomics was applied to design the primer-probe sets for C. sakazakii. • Gene annotated as type 1 fimbrial protein was selected as target of primer. • Sensitivity and selectivity of the designed primer were evaluated. • Effect of interference materials were investigated. • Applicability in food samples were validated with powdered infant formula and milk samples.