Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams

Feeding waste milk (WM) to preweaning dairy calves is a common management practice that offers economic benefits but may influence the microbiome and antimicrobial resistance (AMR) due to the presence of antibiotic residues. The objective of this study was to describe longitudinal patterns in the nasopharyngeal microbiome and AMR gene profiles of dairy calves fed either nonsupplemented milk replacer or milk replacer supplemented with low-level β-lactam antibiotics to simulate WM exposure during the preweaning period. Using shotgun metagenomic sequencing, we profiled the nasopharyngeal microbiome and resistome of 11 Holstein bull calves fed milk replacer with (MR+A; n = 6) or without (MR; n = 5) low levels of β-lactam antibiotics. Antibiotic concentrations were selected to reflect residue levels reported in WM. Deep nasopharyngeal swabs were collected every 2 wk from 1 to 15 wk of age; samples from wk 3 and 15 were excluded due to elevated contaminant burden, resulting in 6 retained time points. No significant differences in microbial α-diversity, β-diversity, or community structure were detected by dietary treatment or sampling age. Tetracycline, macrolide-lincosamide-streptogramin, aminoglycoside, metal, acid, and biocide resistance classes were among the most prominent, with descriptive differences in z-score patterns between groups but no significant differences detected. Larger-scale studies are needed to evaluate the long-term effects of WM feeding on respiratory health and AMR dynamics in dairy calves.