Microbial communities and resistomes of young calf feces

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

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

Interpretive Summary:

Technical Abstract: The prevalence of antimicrobial resistance in dairy cattle is age-dependent with a higher abundance in calves than older cows. There is some evidence that the use of antimicrobials in livestock may be associated with an increase in resistant infections in humans, especially those in close contact with livestock. The current study was performed to determine if milk that contains antibiotic residues, when fed to calves influences the communities, resistomes, and antimicrobial resistance gene (ARG) abundances in those calves. Calves were fed colostrum replacer followed by milk replacer with or without (control) added trace amounts of antibiotics. All calves had access to calf starter from day 2 and were weaned on day 49. Feces were collected on days 2, 14, 49, and 70. Shotgun metagenomic libraries were made using Nextera DNA and sequenced on a NextSeq500. Reads were cleaned using Trimmomatic and BWA. Taxonomic and ARG profiles were identified using the CosmosID server. ARGs, Metal Resistance Genes (MRGs) and Biocides Resistance Genes (BRGs) were identified using AMRPlusPlus (MEGARes) and BLASTN (ResFinder). Resistomes and communities were compared between ages and treatments using ANOSIM, Kruskal-Wallis or Wilcoxon rank sum tests. Taxonomic analysis of contigs containing ARGs was conducted using Megan, BLASTX and Kaiju. Genus richness increased after 2d until 49d (P < 0.05). Communities from 49d and 70d clustered closer together than other ages (P < 0.01). Firmicutes dominated at 2d but this was soon followed by a shift towards Bacteroidetes dominance. Phenicol and fosfomycin ARGs decreased with age (P < 0.01) while MLS, aminoglycoside, fluoroquinolone, bacitracin, and B-lactam ARGs were most abundant at 2d (P < 0.01). MRG and BRG diversity and abundance changed with age (P < 0.01) and both were lowest at 49d. The presence of added antibiotics did not influence the communities or ARGs. Most contigs (61%) containing ARG, BRG or MRG were assigned to Proteobacteria while 10% were assigned to Firmicutes. The proportions of contigs assigned to Proteobacteria in feces collected at 2, 14, 49 and 70d were 55, 30, 0.5 and 15%, respectively. 52% of contigs containing any ARG, BRG, or MRG were Enterobacteriaceae, and 57% of the contigs were assigned to Enterobacteriaceae in feces from 2d. The abundance of ARGs in calf feces decreased with calf age and Proteobacteria and Firmicutes were associated with ARG carriage. Future work should identify interventions to reduce the high level of ARG carriage in young calves.