BackgroundThe microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves.ResultsThe microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05).ConclusionsUsing 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0372-5) contains supplementary material, which is available to authorized users.
A 15-d-old female crossbreed calf was referred because of paraplegia since birth. Clinical examination revealed a skin defect covered by hair on the dorsal midline in the thoracic area of the spine. Thoracolumbar spinal cord neuroanatomic localization was determined based on neurologic examination. Computed tomography of the thoracolumbar spine revealed incomplete fusion of the vertebral arches from T6 to T10 and duplication of the vertebral arch of T7. At the level of T6-T7, duplication of the spinal cord with 2 segments completely separated by a septum of hyperattenuating, probably cartilaginous, tissue was noted. Histologically, the spinal segments had different degrees of duplication. Three central canals were detected in one region. Genetic investigation for the presence of methylenetetrahydrofolate reductase (MTHFR) polymorphism, which has been investigated in both human and veterinary medicine as a possible cause of neural tube defects and abortion, was carried out and was negative in both the calf and her dam.
The abuse or misuse of antimicrobials in animal production is thought to be a potential factor in the development of antimicrobial resistance in veterinary and human medicine. With this study, we wanted to quantify antimicrobial usage in beef fattening operations in northwestern Italy and to identify factors potentially influencing antimicrobial usage. The sample was composed of 26 beef fattening operations that import heifers and bulls from France. Data were extracted from the 2014 and 2015 treatment registers kept by the farmers. The mean (±SD) number of animal daily doses per animal (nADDa) per year for each farm was 3 (±2.1) during the study period (2014–2015). Group antimicrobial treatments (57.5% of all treatments) were often administered orally (70.5%) and consisted overwhelmingly of doxycycline (97%). Individual treatments (42.5% of all treatments) were administered parenterally (98.1%) and the most often used active substances were florfenicol (19.9%), marbofloxacin (19.5%), and tylosin (12.4%). There was a negative correlation between the nADDa for total and group treatments and average batch weight at arrival and between the amount of straw added per animal per day and the nADDa (p ≤ 0.05). Our data show that antimicrobials critical for human medicine were often used in beef fattening operations in northwestern Italy before the European guidelines for the prudent use of antimicrobials in veterinary medicine were issued. Additionally, the use of antimicrobials as a preventive group treatment was still widespread, mostly in lighter weight animals.
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