Respiratory tract infections (bovine respiratory disease) are a major concern in calf rearing. and detection of BCV by antigen ELISA on feces in calves in the last year [OR = 3.6 (1.2C11.1)]. {A seasonal effect was shown for bRSV only A seasonal effect was shown for bRSV only in winter compared with autumn [OR = 10 more.3 (2.8C37.5)]. Other factors associated with bRSV were PI-3 detection [OR = 13.4 (2.1C86.0)], prevalence of calves with respiratory disease [OR = 1.02 (1.00C1.04) per 1% increase], and number of days with respiratory signs before sampling [OR = 0.99 (0.98C0.99) per day increase]. Next to its association with BCV, was more frequently detected in herds with 5 to 10 animals per pen [OR = 8.0 (1.4C46.9)] compared with <5 animals, and in herds with sawdust as bedding [OR = 18.3 (1.8C191.6)]. Also, for is recognized as a primary pathogen increasingly, although this remains controversial in the scientific community (Calcutt et al., 2018). Despite the importance of BRD, most available studies on pathogen identification in live animals are limited in number of herds and pathogens studied (Autio et al., 2007; Pardon et al., 2011; Murray et al., 2018). Also, most of them involve intensive systems such as feedlots or veal calves, which are confronted with respiratory disease year round at a predictable moment in the production cycle (Pardon et al., 2011; Timsit et al., 2017). In contrast, pathogens involved in the classic epidemic respiratory disease outbreaks in winter in the most frequent European farming system of family-owned medium-sized dairy and beef farms are hardly Columbianadin documented (O'Neill et al., 2014). To justify antimicrobial customize and use prevention and control measures, sampling of the respiratory tract is recommended in more and more European countries (KNMVD, 2015; EMA/EFSA, 2017; AMCRA, 2019). Different sampling methods are available, of which deep nasopharyngeal swabs, transtracheal washes, and nonendoscopic broncho-alveolar lavage (nBAL) have found their way into practice (Doyle et Mouse monoclonal to CD3/CD19/CD45 (FITC/PE/PE-Cy5) al., 2017; Timsit et al., 2017; Van Driessche et al., 2017). Next to classic bacterial susceptibility and culture testing, PCR is increasingly popular (O’Neill et al., 2014; DGZ, 2016). According to practitioners, the main advantage is that many different pathogens, both bacteria and viruses, are tested and that the high sensitivity makes it possible to test pooled samples, which complies well with their desire to obtain a group diagnosis (O’Neill et al., 2014). Also, contamination of the sample does not interfere with the test result as much as with culture. Main disadvantages are the lack of antimicrobial susceptibility testing and difficulties in Columbianadin the interpretation of detection of opportunistic pathogens such as (Fulton and Confer, 2012). Many risk factors for RTI have been identified in multiple studies, but they all used a wide variety of case definitions, covered by the BRD concept. With the exception of (Gille et al., 2018; Schibrowski et al., 2018), hardly any scholarly studies explored pathogen-specific risk factors for detection of the pathogen itself. In bovine mastitis, identification of pathogen-group-specific risk factors has led to targeted prevention and control, which is economically more efficient than a standard approach (Passchyn et al., 2014; Tolosa et al., 2015). Also, for respiratory pathogens, the eliciting risk factors may be different, enabling the Columbianadin possibility for customized advice of the current general approaches instead, conferring multiple and expensive changes on farm often. Additionally, being able Columbianadin to predict the most likely pathogen (virus, gene), bovine parainfluenzavirus type 3 (gene), bovine coronavirus (gene), (target gene = (((< 0.2 were maintained for the multivariable model. Next, the multivariable model backward was built stepwise, excluding nonsignificant variables gradually. A variable was considered a confounder if it was not an intervening variable based on a causal diagram and induced changes >25% in the coefficient of another variable. For the final models, pairwise comparisons for categorical predictors were made using Bonferroni adjustments. All relevant 2-way interactions of significant fixed effects were tested biologically. Significance was set at < 0.05 and < 0.10 was considered a trend. Model fit was evaluated using the Hosmer-Lemeshow goodness-of-fit test for logistic models (Dohoo et al., 2009). Differences in management factors between dairy, dairy-mixed, and beef herds were determined by logistic regression (PROC GLIMMIX; as described above) for binary outcomes, and linear regression (PROC MIXED) for continuous outcomes. In the linear model, maximum likelihood was used, and Bonferroni corrections for multiple comparisons. Table 1 Overview of potential risk factors for respiratory pathogens, derived from a questionnaire and the national cattle registration database history (y/n)1; estimated annual.