Genomic analysis of antimicrobial resistant Escherichia coli isolated from manure and manured agricultural grasslands

Abstract

Antimicrobial resistance (AMR) is a multifactorial issue involving an intertwining relationship between animals, humans and the environment. The environment can harbour bacteria that are pathogenic to human health, including Escherichia coli, an indicator of environmental faecal contamination. Through culture dependent approaches this study identified 46 E. coli isolates in porcine and bovine manure, non-manured and manured soil, and the phyllosphere of manured grass. The grass isolation highlights grass as an environmental reservoir for E. coli. Whole genome sequencing identified 11 different multi-locus sequence types. We also identified a diverse plasmidome with 23 different plasmid replicon types. The E. coli isolates were phenotypically antibiotic resistance, predominantly multidrug resistant. Additionally, whole genome sequencing identified 31 antibiotic resistance genes, and mutations in the gyrA, parC, and parE genes, conferring fluoroquinolone resistance. The main virulence genes were associated actin mediated locomotion (icsP/sopA), siderophore production and alginate production (algA), which suggest adaptation to survive in the non-gut environment or the UV environment of grass surfaces. These results suggest that E. coli in soils and grasses may adapt to their new environments evolving novel strategies. This study demonstrates grass as an understudied environmental niche of AMR E. coli, which directly links the environment to the grass grazing animal and vice-versa via the circular economy of manure application. Impact statementEscherichia coli is capable of surviving across biomes within One Health. This study sheds light on the genomic elements present in AMR E. coli in the understudied niche of agricultural grassland. Data summaryThe genome sequences have been deposited in Genbank. Bioproject number PRJNA1080214 and SRP491607 in the sequence read archive https://www.ncbi.nlm.nih.gov/sra/?term=SRP491607.