Genomic analysis of plasmid content in food isolates of E. coli, strongly supports its role as a reservoir for virulence and antibiotic resistance genes
2022
Balbuena-Alonso, María G. | Cortés-Cortés, Gerardo | Kim, Jaeyoun | Lozano-Zarain, Patricia | Camps, Manel | del Carmen Rocha-Gracia, Rosa
Escherichia coli is ubiquitous in the environment, foods, and mammalian hosts. It can cause disease and exhibits high rates of antibiotic resistance. This study examines the possible role of food strains of E. coli as reservoirs of clinical outbreaks using a genomic approach. We gather a database of fully assembled genomic sequences from E. coli isolated from food (n = 77) and clinical samples (n = 649) deposited in the GenBank by December 2020. We classify the host based on genomic markers and annotate genomic indicators of plasmid content using the most up-to-date genomic analysis pipelines. Once annotated, we look for biases in the representation of these markers; we reasoned that the stronger the bias, the lower the probability of consistent genetic exchange between the two populations. We confirm differences in the lineages present in each bacterial subpopulation. However, food and clinical plasmids present extensive structural similarities, including a similar fraction of transferable plasmids. Food plasmids often carry antimicrobial resistance genes (ARGs) and frequently virulence genes. A replicon enrichment analysis identified IncR as a specialized replicon in food strains, disseminating resistance and virulence genes. IncH1A, I2A, IA replicons exhibit a narrower cargo preference, largely disseminating drug resistance in food strains. IncH1B, Col, IncX4 and pO1, by contrast, preferentially spread virulence genes. Finally, we identified a small subset of replicons that appears to be shuttling between the food and the clinic. Overall, our analysis provides strong genomic evidence that plasmids in E. coli contaminating foods represent a significant reservoir of ARGs and virulence factors.
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