Microbial resistance to processing treatments poses a food safety concern as treatment tolerant pathogens can emerge. Occasional foodborne outbreaks caused by pathogenic E. coli have led to human and economic losses. Therefore, this study screened for the extreme heat resistance (XHR) phenotype as well as one known genetic marker, the Locus of Heat Resistance (LHR), in 4123 E. coli isolated from diverse meat animals at different processing stages. Prevalence of XHR and LHR amongst the meat-borne E. coli was found to be 10.3% and 11.4% respectively, with 19% agreement between the two. Finished meat products showed the highest LHR prevalence (24.3%) compared to other processing stages (0-0.6%). None of the LHR+ E. coli in this study would be considered pathogens based on screening for virulence genes. Four high-quality genomes were generated by whole genome sequencing of representative LHR+ isolates. Nine horizontally acquired LHRs were identified and characterized, four plasmid-borne and five chromosomal. Nine newly identified LHRs belong to ClpK1 LHR or ClpK2 LHR variants sharing 61-68% nucleotide sequence identity, while one LHR appears to be a hybrid. Our observations suggest positive correlation between number of LHR regions present in isolates and the extent of heat resistance. The isolate exhibiting the highest degree of heat resistance possessed 4 LHRs belonging to three different variant groups. Maintenance of as many as 4 LHRs in a single genome emphasizes the benefits of the LHR in bacterial physiology and stress-response.
IMPORTANCE Currently, a “multiple-hurdle” approach based on a combination of different antimicrobial interventions including heat are being utilized during meat processing to control the burden of spoilage and pathogenic bacteria. Our recent study suggests U.S. beef cattle harbor E. coli that possess the Locus of Heat Resistance (LHR). LHR seemingly contributes to the global stress tolerance in bacteria, hence poses a food safety concern. Therefore, it is important to understand the distribution of the LHR amongst meat-borne bacteria identified at different stages of different meat processing systems. Complete genome sequencing and comparative analysis of selected heat resistant bacteria provides a clearer understanding of stress and heat resistance mechanisms. Further, sequencing data may offer a platform to gain further insights into genetic background that provides optimal bacterial tolerance against heat and other processing treatments.