The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions.

The primary objective of this cross-sectional study was to identify associations between the diversity and composition of the nasopharyngeal (NP) microbiota and pneumonia status, as diagnosed by ultrasonography (US), in preweaned dairy calves. Characteristics of the NP microbiota were compared between calves with and without pneumonia, as diagnosed by US. Secondary objectives were to compare the composition of the NP microbiota between calves by age, clinical respiratory score (CRS), and previous antibiotic therapy. Holstein heifer calves (n = 50) from a southern Wisconsin dairy were enrolled at either 3 or 6 wk of age; 4 calves were sampled at both time points. Antibiotic treatment history was also collected for the 30 d before enrollment. For the purpose of this study, pneumonia was defined as having lobar pneumonia, as diagnosed by US, in at least 1 lung lobe. Following examination by CRS and US, a deep nasopharyngeal swab was obtained for 16S rRNA amplicon sequencing. Alpha diversity was reduced in calves that were CRS positive, and beta diversity tended to be different in calves previously treated with antibiotics and in calves that were CRS positive. Microbial diversity was not different between calves with and without pneumonia. The most dominant genus identified was Mycoplasma spp.; however, there was no association between relative abundance (RA) and pneumonia status. The median RA of Mycoplasma spp. was increased by 25 (95% confidence interval, CI: 3, 40) in calves at 3 wk of age compared with 6 wk of age. The median RA of Pasteurella spp. was increased by 1.5 (95% CI: 0.1, 3) in calves with pneumonia, as diagnosed by US, compared with calves without pneumonia. Additionally, Pasteurella spp. was increased by 2.3 (95% CI: 0, 9) in CRS-positive calves compared with CRS-negative calves. The median RA of Psychrobacter spp. was increased by 2 (95% CI: 0, 12) and median RA of Chryseobacterium spp. was increased by 0.15 (95% CI: 0, 2) in calves that were not treated previously with antibiotics compared with calves previously treated with antibiotics.