Purpose: This study analyzed changes to the bacterial community composition of carrots associated with different sanitizers and storage at recommended (2oC) and temperature abuse conditions (10oC).
Methods: Compost derived from manure, with and without prior antibiotic dosing to the dairy cows, was inoculated, separately, with multi-drug resistant Escherichia coli O157:H7 and Pseudomonas aeruginosa. To provide a background inoculum representing potential carryover of resistant bacteria from the field, carrots were dip-inoculated in compost slurry followed by air drying and a tap water wash with 50 ppm free chlorine or Tsunami 100 (40ppm peroxyacetic acid; 11.2% H2O2) per manufacturer’s directions. Post drying, carrots were stored at 2oC or 10oC. DNA was extracted from the carrot surface and Illumina sequencing of 16SrDNA amplicons was performed.
Results: Carrots stored at 2oC had greater species richness than carrots stored at 10oC (P<0.0001, Shannon). Carrot bacterial communities inoculated without antibiotics containing compost were more even (Chao1) compared to compost with antibiotics (P=0.0190). Compost inoculated with ARB had more species evenness (Chao1) than non-inoculated compost (P=0.0191). OTUs belonging to 10 phyla were significantly affected by compost type, storage temperature, wash type, inoculation with ABR or a combination. Storage temperature significantly increased abundance of Pseudomonadales (P=0.0274). Carrot microbiota was mainly represented by the phyla Firmicutes, Proteobacteria, Actinobacteria, Planctomycetes, and Acidobacteria.
Significance: Refrigerated storage and use of a sanitizer wash offer strategies to alter the bacterial composition on carrots. Analysis of shot-gun metagenomics sequencing data is underway to identify the relationship between phylogeny and the resistome. This study can help inform management practices for limiting the dissemination of antimicrobial resistance from farm-to-fork.