Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

• Published in: Frontiers in microbiology Vol. 10; p. 3050
• Main Authors: Reid, Cameron J, Blau, Khald, Jechalke, Sven, Smalla, Kornelia, Djordjevic, Steven P
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 29.01.2020
• Subjects: antimicrobial resistance; E. coli; genomic surveillance; Microbiology; produce; whole genome sequencing; whole genome sequencing; antimicrobial resistance; produce; E. coli; genomic surveillance
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2019.03050

The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection ( = 84, 70%) with multi-locus sequence types B1-ST6186 ( = 37, 31%), C-ST165 ( = 17, 14%), B1-ST58 ( = 14, 12%), B1-ST641 ( = 8, 7%), and C-ST88 ( = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS were also identified. Storage may affect the lineages of isolated, however further studies are needed. Our study indicates produce predominantly carry with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.