Genomic and Transcriptomic Analysis of Biofilm Formation in Persistent and Transient Isolates from the Retail Deli Environment Does Not Yield Insight into Persistence Mechanisms.

Persistence of in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of persistence in delis across multiple states. We hypothesized that this was correlated with isolates' innate characteristics, such as biofilm-forming capacity or gene differences. To test this hypothesis, we sequenced the genomes of 21 isolates previously collected longitudinally from the retail deli environment. Isolates were chosen to represent varying attachment capacity and sanitizer tolerance as well as persistence or transience. We used single-nucleotide polymorphism analysis to characterize the isolates' genetic relationships and used BLAST to search the isolates' genomes for antibiotic resistance elements, quaternary ammonium tolerance genes, and stress survival islets. We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome with their global planktonic transcriptome. We did not find genetic content that explained persistence. The presence of stress survival islet-1 correlated to increased attachment capacity ( < 0.05), but not persistence. Further, the presence of sanitizer tolerance elements was not significantly correlated with phenotypic sanitizer tolerance. Analysis of biofilm versus planktonic gene expression did not show the expected differences in gene expression patterns. Overall, persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates' biofilm-forming capacity, sanitizer tolerance, or genomic content.