Molecular characterization of Escherichia coli isolated from hemp seeds

Hemp seeds are increasingly produced on small farms in Slovakia and used for production of food. We detected contamination of 1.4 × 107 CFU·g-1 coliform bacteria in hemp seeds from a small farm and isolated three strains of Escherichia coli. These were characterized by GTG-typing and by whole genome sequencing. The three strains were indistinguishable from each other by GTG-typing but different from a reference strain E. coli CCM 2024. They were not distinguished either by multi-locus sequence type (MLST) deduced from whole genome sequences, as all strains were of sequence type 58, or by core genome-based MLST (cgMLST), as all strains belonged to type 148521. All strains were found to be fumC4/fimH32 type and serotype H21, O-antigen was not identified. No plasmid origin was detected. No gene encoding for shiga toxin was detected. Several virulence-associated genes were detected in all three strains at high identities with sequences in the database, namely, fimH, lpfA, terC, csgA, hlyE, nlpI, yehB, yehC and yehD. Further virulence-associated genes were detected at shorter lengths, namely, fdeC, gad and yehA. Several antibiotic resistance genes were also identified. The strains were found to be virtually identical. With a probability of being a human pathogen, they need to be addressed for on-farm food production safety.