Purpose: We analyzed and compared the genomes of Escherichia coli from soils fertilized with litter of chickens fed with or without tetracycline-supplemented diet to determine their antimicrobial resistance, virulence and persistence.
Methods: The genomes of 13 E. coli strains collected over several months (8 from soil fertilized with litter of tetracycline-fed chickens and 5 from that of control diet) were sequenced by Illumina MiSeq. Sequence processing and assembly were performed using Spades, before annotating them using RAST. Known virulence and antibiotic resistance genes were detected by BLASTN. A whole-genome phylogenetic tree was built to define the relationships among strains.
Results: The genome size ranged from 5.0 to 5.3 Mbp, with a G+C content of 50.4 to 51.2%. The number of protein-coding genes and mobile genetic elements varied from 4905 to 5357, and 40 to 136, respectively. All 13 E. coli strains harbored tetD, blaCMY-2 and ampC genes while tetA or tetB and blaTEM were the most frequently found genes in strains recovered from the tetracycline treatment regardless of the collection time (August - March). Strains isolated at different months appeared to contain similar resistance genes, suggesting their maintenance over time. Virulence genes such as malX, ompT, traT and iss were found in all 13 strains. Furthermore, our data point toward possible horizontal genes transfer. Phylogenetic analysis showed genetic relationships between strains, indicating their persistence in soils over time.
Significance: Our results reveal that E. coli strains from chicken litter harboring multiple antibiotic resistance and virulence genes persist in agricultural soils regardless of tetracycline feed-supplementation. Such E. coli could constitute a reservoir of antibiotic resistance/virulence genes and present a food safety risk.