Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

Abstract

The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 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 IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli 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.

Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying blaCTX–M–15 and qnrB19 in Agricultural Soil

“…Finally, the presence of MDR pathogens displaying a broad resistome in agricultural soil could lead to contamination of vegetables and, since these foods are usually consumed raw, the risk of human exposure to antimicrobial-resistant bacteria with clinical interest increases (Reid et al, 2020;Lopes et al, 2021). Although ingestion of these bacteria may not immediately have a direct impact on health, colonization by this pathway can contribute to the horizontal gene transfer of antimicrobial resistance to the gut microbiome (Maeusli et al, 2020).…”

“…Specifically, contamination of crops by critical priority pathogens is of great concern, since these pathogens can also contaminate vegetables for consumption (Cantas et al, 2013;Araújo et al, 2017;Lopes et al, 2017;Reid et al, 2020;Lopes et al, 2021), increasing the risk of human exposure to antimicrobial-resistant bacteria, including mcr-positive strains. Despite this, little is known about the occurrence of bacteria carrying mcr-type genes in soils.…”

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

“…Recently MDR IncHI2 ST4 plasmids ranging in size from 235,260 to 356,700bp that carry mcr-1 sourced from E. coli with ST10 from pigs with post-weaning diarrhoea, and E. coli ST10 and ST351 from white storks were described in Spain [ 46 ]. ST10 and other clonal complex 10 E. coli are frequently sourced from the faeces of pigs, fresh produce, intensively reared food-production animals, and diverse environmental niche [ 46 , 47 , 48 ] and often carry MDR IncHI2 plasmids. Colistin resistance mcr genes have not been reported from Australian porcine E. coli isolates.…”

Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections

“…There are currently more than 40 identified dfr variants [80]. These are often associated with MGEs, such as plasmids and transposons, and are almost exclusively observed as resistance gene cassettes within the variable regions of class 1 and 2 integrons in human [81], animal [35,82,83] and environmental [84] E. coli isolates, resulting in their rapid spread. Seven trimethoprim-resistance genes were identified in this collection, the most common being dfrA17 (n=26; 38 %), followed by dfrA12 (n=12; 18 %).…”