Microbiological Profile of the Upper and Lower Respiratory Tract of Suckling and Weaned Dairy Calves with Acute Respiratory Disease

Simple Summary Bovine respiratory disease (BRD) is a significant health issue affecting calves in dairy herds worldwide. BRD is caused by viruses and bacteria affecting the upper (URT) and lower respiratory tracts (LRT). The microbiological profile of BRD can vary widely, so it is important to understand the causes of outbreaks to treat and prevent them effectively. This study examined the microbiological profile of nine BRD outbreaks in dairy calves from Paran & aacute;, southern Brazil. An analysis was conducted on lung tissue (LRT n = 12) and deep nasopharyngeal swab (URT n = 24) samples. Three herds showed a viral etiology, mainly bovine viral diarrhea virus (BVDV). In three herds, the cause was bacterial (Mycoplasma bovis), while in one herd, a mixed infection of BVDV and M. bovis was found. In two outbreaks, no primary agents for BRD were identified; only bacteria were identified as secondary agents. Viral and single infections were more common in the LRT, causing pneumonia and deaths. Mixed bacterial infections predominated in the URT, involving more than one species of bacteria or bacteria and viruses. In the assessed region, it is recommended that calves receive sufficient levels of passive immunity to BVDV. In cases of BRD, antibiotics targeting M. bovis are recommended for treatment.Abstract Bovine respiratory disease (BRD) is a significant global health issue in cattle farming, leading to substantial economic losses. This study analyzed the microbiological profiles of BRD outbreaks in nine dairy cattle herds in southern Brazil. We examined 36 biological samples, including 24 deep nasopharyngeal swabs (NS) and 12 lung tissue, from 29 suckling and 7 weaned heifer calves with acute BRD. PCR and RT-PCR techniques were used to partially amplify the genes of five viruses and four respiratory bacteria. A total of 8 different microorganisms, 4 viruses (bovine viral diarrhea virus, n = 5; bovine coronavirus, n = 3; bovine alphaherpesvirus 1, n = 3; and bovine parainfluenza virus 3, n = 2), and 4 bacteria (Pasteurella multocida, n = 16; Mycoplasma bovis, n = 8; Histophilus somni, n = 7; and Mannheimia haemolytica, n = 4) were identified in 29 (80.5%) samples. Seven samples (four lung tissue and three NS) were negative for all the microorganisms. Mixed infections were more common (62.1%) than single infections (37.9%). Bacterial nucleic acids were more commonly co-detected in NS than in lung tissue. Nucleic acids from a single pathogen were more frequently detected in lung tissues than in NS. M. bovis was the only bacterium detected in the lower respiratory tract. Understanding the microbiological profiles of the respiratory tracts of dairy calves with clinical signs of BRD is crucial for implementing effective biosecurity measures to prevent BRD in suckling and weaned dairy heifer calves.