Genomic and phenotypic analysis of heat and sanitizer resistance in Escherichia coli from beef in relation to the locus of heat resistance

Citation

Yang, X., Tran, F., Zhang, P., Wang, H. (2021). Genomic and phenotypic analysis of heat and sanitizer resistance in Escherichia coli from beef in relation to the locus of heat resistance. Applied and Environmental Microbiology, [online] 87(23), http://dx.doi.org/10.1128/AEM.01574-21

Plain language summary

The locus of heat resistance (LHR) confers extreme heat resistance to E. coli. It is concerning if E. coli can survive the cooking process as some E. coli strains can cause severe illness in humans. We investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR to better understand the implications of heat resistant E. coli to beef safety. We found that the LHR-positive and LHR-negative E. coli clustered differently on the phylogenetic tree based on core genome and some of the very closely clustered LHR strains had different levels of heat resistance. Interestingly, the LHR-positive E. coli had underrepresentation of genes involved in epithelial attachment and virulence. No meaningful difference was noted between LHR-positive and LHR-negative E. coli strains in their response to sanitizers. We also noted that a commonly used enrichment method for E. coli may inadvertently select for heat resistant E. coli, leading to population bias. The findings of this study show that the genomic background, in addition to the presence of LHR, plays an important role in the degree of heat resistance in E. coli. Caution should be exercised when recovering E. coli at elevated temperatures.

Abstract

The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P, 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids. The growth rates at 42°C were 0.71 6 0.02 and 0.65 6 0.02 log(OD) h21 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.

Publication date

2021-11-01

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