Determining the Effect of Varied Proportions of Cohort Administered Tulathromycin at Arrival on Nasopharyngeal Microbiota and Performance Characteristics in Yearling Steers in the First 56 Days on Feed

Abstract

Metaphylaxis or treating the entire population of cattle at arrival with an antimicrobial has been studied extensively in the cattle industry; however, little information is available on the impacts of treating only a proportion of the population with antimicrobials at arrival. The study objective was to determine potential associations between the proportion of animals in a pen treated with antimicrobial therapy with pen performance and nasopharyngeal microbiome. Yearling steers (n = 160) were randomly allocated to study pens (n = 40) and pens were systematically randomized to one of two antimicrobial treatments (META: all four head received tulathromycin; MIXED: two of four head randomly selected to receive tulathromycin). The study was conducted in conjunction with an essential oil feeding trial. Deep nasal pharyngeal (DNP) swabs were collected from every steer at Days 0, 14, 28, and 56. All DNP swabs were individually cultured for Pasteurella multocida and Mannheimia haemolytica. Samples of DNA were extracted from DNP swabs, pooled by pen, and analyzed by metagenomic shotgun sequencing to compare nasopharyngeal microbiome composition and quantity of resistance genes between test groups. Neither antimicrobial nor essential oil treatment groups had any significant associations with performance or DNP microbiome. Sampling day was significantly associated with alpha and beta diversity at the species level. Shannon's diversity and Inverse Simpson diversity were significantly lower on Day 14 versus both Day 0 and Day 56. These data indicated a shift in microbial populations across study days; however, the microbiome diversity and relative abundance were not significantly different between antimicrobial treatment groups.

Keywords: bovine respiratory disease; growth performance; nasal microbiota; tulathromycin.

Figure 1

Boxplots illustrating the distribution of read counts by sampling day for (A) raw reads and (B) nonhost reads. Each sample is represented by a dot plotted with horizontal jitter to minimize overlap. Post hoc pairwise comparisons with significant adjusted P values are indicated by horizontal lines with asterisks (* = <0.05 and ** = <0.01).

Figure 2

Alpha diversity boxplots. Comparison of (A) observed, (B) Shannon, and (C) Inverse Simpson alpha diversity metrics among samples from Days 0, 14, and 56. Post hoc pairwise comparisons with significant adjusted p values are indicated by horizontal lines with asterisks (* = <0.05, ** = <0.01, and *** = <0.001).

Figure 3

Species beta diversity. NMDS plots of species beta diversity by (A) sampling day, or (B) antimicrobial treatment. Ellipses denote 95% confidence intervals. Pairwise PERMANOVA analysis indicates significant differences in beta diversity for all pairwise comparisons of sampling day: Day 0–Day 14, R² = 0.075, adjusted p = 0.003; Day 0–Day 56, R² = 0.052, adjusted p = 0.003; Day 14–Day 56, R² = 0.159, adjusted p = 0.003. There is no significant difference between antibiotic treatment groups (R² = 0.017, p = 0.133).

Figure 4

Species relative abundance. Relative abundance of species in samples grouped by (A) sampling day or (B) antimicrobial treatment. Panels are labeled by group: Day 0, 14, and 56 in A and half and meta in B. Each vertical bar represents one sample. Species are color-coded according to the accompanying key, with species with relative abundance under 0.005 grouped as “low-abundance species”.

Figure 5

Differential species abundance by day. Feature plots of relative abundance by sampling day for the four species with statistically significant differential abundance between sampling days (A) Moraxella bovoculi, (B) Moraxella bovis, (C) Pasteurella multocida, and (D) Mesomycoplasma dispar. Significant differences in abundance (after Holm–Bonferroni correction) are indicated by horizontal lines with asterisks (* = <0.05 and *** = <0.001).