Large scale genome-wide analysis identifies characteristics of multidrug-resistant Escherichia coli potentially associated with persistence in the dairy calf gut

Authors: Haley, Bradd; Kim, Seonwoo; HOVINGH, ERNEST - Pennsylvania State University; Van Kessel, Jo Ann

Submitted to: Microbiome
Publication Type: Abstract Only
Publication Acceptance Date: 4/14/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Dairy animals are known to harbor antimicrobial resistant bacteria in their gastrointestinal tract, with young calves carrying a significantly higher relative abundance of antimicrobial resistance genes (ARG) and organisms than older lactating and dry cows. This phenomenon is observed in the absence of antibiotic exposure, indicating that non-antibiotic and non-ARG factors are involved in the enrichment of resistant organisms in the young calf. To investigate this, we sequenced the genomes of 288 Escherichia coli isolates collected from calves and cows on dairy farms in Pennsylvania. Of these, 124 were susceptible to a panel of 8 classes of antibiotics, 120 were multi-drug resistant (MDR, resistant to > 3 classes of antibiotics), and 44 were resistant to 1 or 2 classes of antibiotics. Genomes were sequenced on a NextSeq 500. Cleaned and curated reads were assembled using SPAdes and genomes were annotated with Prokka. For each genome, resistance genes, phylogroups, plasmids replicons, sequence types (ST), and virulence factors (VFs) were identified in silico. Multiple MDR, resistant, and susceptible isolates encoded VFs that are associated with severe infections, including nine STEC. A high number of ExPEC VFs were identified among the MDR isolates, and approximately 10% of isolates were identified as major ExPEC ST (ST95, 117, 69, and 10). No associations between number of VFs and ARGs were identified. The pangenome consisting of genes identified in more than 19 genomes was identified using GET_HOMOLOGUES. ARGs were removed from this matrix and an ordination analysis of the presence/absence of these genes in susceptible and MDR isolates indicated there are slightly different suites of genes in an appreciable number of genomes from each group (MDR vs susceptible). A Fisher’s exact test with a False Discovery Rate (FDR) correction identified over 900 sequences that were enriched in either the MDR or susceptible genomes (FDR < 0.05). Of these, approximately 75% are enriched in MDR genomes. Multiple metabolic pathways such as iron-scavenging, inositol transport and metabolism, and a gene cluster annotated at ascorbate transporters and associated with exopolysaccharide production were enriched in MDR genomes. Similarly, metal and biocide resistance genes and P fimbriae genes were also enriched in the MDR genomes. Future work will focus on the roles of these enriched genes in the persistence of resistance in the calf gut, with the aim of identifying mechanisms to reduce the load of antibiotic resistance on dairy farms.