Molecular characteristics and antibiotic resistance of Escherichia coli from foods based on whole genome sequencing

Abstract

ObjectiveThis study aimed to analyze the molecular characteristics and antibiotic resistance of diarrheagenic Escherichia coli （DEC） from meat and aquatic products in Shanghai City.MethodsThe DEC isolates were characterized by applying antibiotic tests and whole genome sequencing （WGS）. The BioNumerics software was used to analyze and assemble WGS data. Then， multilocus sequence typing sequencing， virulence profiles， and antibiotic-resistant genes were analyzed adopting assembled genome sequences. The antimicrobial susceptibility was investigated.ResultsIn this study， most DEC isolates were EAEC （73.2%）， and most of the EAEC isolates carried only the astA gene （90.2%）. All 56 DEC isolates have been typed as 37 STs. The resistance rate to NAL was higher （64.3%），followed by aminoglycoside， beta-lactam， and tetracycline. The multi-drug resistant DEC isolates were 48.2% resistant； furthermore， the resistance genes were detected in these DEC isolates.ConclusionEAEC isolates are dominant DEC isolates from foods in Shanghai City. Furthermore， these DEC isolates exhibited a higher resistance rate， compared with the corresponding resistance genes. These results suggest that molecular surveillance should be enhanced. Moreover， fundamental data can be obtained by employing the WGS for tracing DEC isolates and analyzing pathogenicity.

Keywords

• diarrheagenic e. coli
• enteroaggregative e. coli
• enteropathogenic e. coli
• antibiotic resistance
• resistant genes