This study aimed to enhance our understanding of the agreement between two sampling methods for the detection of bovine respiratory disease (BRD) pathogens in calves using high-throughput real-time qPCR (ht-RT-qPCR). In total, 233 paired nasal swab (NS) and non-endoscopic bronchoalveolar lavage (nBAL) samples were collected from 152 calves from 12 Danish cattle herds. In 202 of the observations, the calves were examined using a standardized clinical protocol. Samples were tested for three viruses (bovine respiratory syncytial virus, bovine corona virus, and influenza D virus) and six bacteria (Histophilus somni, Mannheimia haemolytica, Mycoplasma bovis, Mycoplasma species, Pasteurella multocida, and Truepurella pyogenes). The results showed age-related differences in disease and pathogen occurrence, with the highest detection rates in calves aged 35 days or older. Poor to moderate agreement was found between the NS and nBAL results. The presence of Mannheimia haemolytica in both NS and nBAL in younger calves and in nBAL in older calves was associated with clinical BRD. There was a potential link between BRD and influenza D virus in older calves, although it was only found in one herd in a small sample size. Overall, NS was a relatively poor predictor of pathogens in the lower respiratory tract. The present study confirms the complexity of pathogen detection in BRD, with marked influences of age and the sampling method on pathogen detection and disease associations.

Several different pathogens, including Escherichia coli, are strongly associated with calf diarrhoea. The population diversity of intestinal E. coli within each diarrhetic calf and between diarrhetic calves is not well understood. In the present study, 391 faecal samples were obtained during 2023–2024 from Danish dairy calves with diarrhoea. Semi-quantified growth estimates of E. coli after culturing did not reflect the diarrhetic grade nor whether E. coli was the only pathogen observed in the sample. From each sample, five isolates were subjected to multiple-locus variable-number tandem repeat analysis (MLVA) and revealed that 70% of faecal samples contained more than one type of E. coli. Genotyping, sequence typing and in silico serotyping showed a large diversity of E. coli between faecal samples. Surprisingly, isolates with a genotype representing mixed features of Diffusely adhering E. coli/Extraintestinal pathogenic E. coli were found in 25% of the isolates, while the classic Enterotoxigenic E. coli genotype was only observed in 5% of the isolates, and only 4% of the faecal samples were positive for E. coli F5 (K99) fimbriae, as determined by PCR. In conclusion, a diverse population of (non-F5) E. coli is associated with diarrhoea in calves. High genomic diversity of E. coli within samples needs to be considered when selecting only one isolate for antimicrobial resistance profiling and vaccination measurements.

Background: Bovine respiratory disease (BRD) is a major driver of antimicrobial use in veal calf production systems. Although vaccination may reduce disease incidence and antimicrobial treatments, field evidence supporting clinically relevant reductions in antimicrobial use remains limited. This study evaluated the clinical efficacy of a combined intranasal (IN) and parenteral (subcutaneous/intramuscular; SC/IM) vaccination strategy targeting bovine respiratory syncytial virus, Histophilus somni, and Mannheimia haemolytica under commercial conditions. Methods: A randomised controlled field trial was conducted on two Danish veal calf farms between November 2019 and April 2020, including 880 calves allocated to a vaccinated group (n = 445) or an unvaccinated control group (n = 435). Health outcomes included morbidity, antimicrobial use, mortality, growth performance, and slaughterhouse pulmonary and pleural lesions and were analysed using mixed-effects models. Results: Vaccination significantly reduced BRD-associated morbidity across all evaluation periods (from day 5 after arrival to slaughter), with relative reductions of 18.8–24.6% and 30% fewer antimicrobial treatment days. Pulmonary and pleural lesions were significantly less frequent in vaccinated calves (≈36% reduction). No statistically significant differences were observed in growth performance or mortality. Conclusions: Combined IN + SC/IM vaccination was associated with lower BRD-associated morbidity, antimicrobial treatments, and slaughterhouse respiratory lesions under commercial conditions.