Genetic diversity of multi-drug resistant and antibiotic susceptible Escherichia coli from dairy cows and calves

Authors: Haley, Bradd; KIM, SEON-WOO - University Of Maryland; SALAHEEN, SERAJUS - University Of Maryland; Van Kessel, Jo Ann

Submitted to: American Society for Microbiology Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2018
Publication Date: 6/8/2018
Citation: Haley, B.J., Kim, S., Salaheen, S., Van Kessel, J.S. 2018. Genetic diversity of multi-drug resistant and antibiotic susceptible Escherichia coli from dairy cows and calves. American Society for Microbiology Annual Meeting. p. 1.

Interpretive Summary:

Technical Abstract: Dairy calf and cow feces are reservoirs of antibiotic resistant bacteria that can potentially contaminate meat, pre-pasteurized milk, the environment, wildlife, and other dairy animals. Escherichia coli, a minor constituent of the bovine fecal community, is known to often encode multiple antibiotic resistance mechanisms and studies have shown that pre-weaned calves more frequently shed resistant E. coli than do lactating cows. To evaluate the genetic diversity of both antibiotic susceptible and antibiotic resistant E. coli from pre-weaned calves and lactating cows, we sequenced the genomes of 169 isolates collected from composite manure samples on commercial dairy farms in Pennsylvania. Genome sequencing was conducted on an Illumina NextSeq 500 platform. Raw Reads were trimmed and curated using trimmomatic and Deconseq and subsequently assembled using SPAdes. For each isolate, the phylogenetic group and sequence type was determined in silico and virulence genes associated with the major E. coli pathotypes were determined using BLAST. The most frequently detected phylogenetic groups among all isolates were B1 and A. Of the multi drug resistant (MDR) calf isolates, 28% were phylogenetic group A and 42% were phylogenetic group B1, while 21% and 50% of the susceptible isolates were phylogenetic groups A and B1, respectively. Interestingly, 21% of the susceptible calf isolates were phylogenetic group E while only 1% of the MDR calf isolates were phylogenetic group E. In both groups of calf isolates, 32 sequence types were identified. The most frequently detected group among the calf MDR E. coli was ST10, while ST2521 was the most frequently detected susceptible E. coli from this age group. Among the lactating cattle, 75% and 11% of the isolates were phylogenetic groups B1 and A, respectively, while 53% of the MDR isolates were phylogenetic group B1. Within these groups the most frequently detected ST was ST88 among the MDR isolates and ST58 among the susceptible isolates. Virulence genes from most pathotypes were detected, with individual isolates encoding between 0 and 14 of these virulence factors. For all groups, the average number of virulence genes for each isolate was four except among the susceptible isolates recovered from lactating cows which encoded an average of 2.5 virulence factors per isolate. Results of this study indicate that MDR and antibiotic susceptible E. coli are both highly diverse groups. Further, multiple virulence factors involved in the infection processes of the major pathotypes were detected among the strains, with some of these strains being MDR members of the STs known to be involved in severe human infections.