Leveraging artificial intelligence and software engineering methods in epidemiology for the co-creation of decision-support tools based on mechanistic models.

Epidemiological modeling is a key lever for infectious disease control and prevention on farms. It makes it possible to understand the spread of pathogens, but also to compare intervention scenarios even in counterfactual situations. However, the actual capability of decision makers to use mechanistic models to support timely interventions is limited. This study demonstrates how artificial intelligence (AI) techniques can make mechanistic epidemiological models more accessible to farmers and veterinarians, and how to transform such models into user-friendly decision-support tools (DST). By leveraging knowledge representation methods, such as the textual formalization of model components through a domain-specific language (DSL), the co-design of mechanistic models and DST becomes more efficient and collaborative. This facilitates the integration of explicit expert knowledge and practical insights into the modeling process. Furthermore, the utilization of AI and software engineering enables the automation of web application generation based on existing mechanistic models. This automation simplifies the development of DST, as tool designers can focus on identifying users' needs and specifying expected features and meaningful presentations of outcomes, instead of wasting time in writing code to wrap models into web apps. To illustrate the practical application of this approach, we consider the example of Bovine Respiratory Disease (BRD), a tough challenge in fattening farms where young beef bulls often develop BRD shortly after being allocated into pens. BRD is a multi-factorial, multi-pathogen disease that is difficult to anticipate and control, often resulting in the massive use of antimicrobials to mitigate its impact on animal health, welfare, and economic losses. The DST developed from an existing mechanistic BRD model empowers users, including farmers and veterinarians, to customize scenarios based on their specific farm conditions. It enables them to anticipate the effects of various pathogens, compare the epidemiological and economic outcomes associated with different farming practices, and decide how to balance the reduction of disease impact and the reduction of antimicrobial usage (AMU). The generic method presented in this article illustrates the potential of artificial intelligence (AI) and software engineering methods to enhance the co-creation of DST based on mechanistic models in veterinary epidemiology. The corresponding pipeline is distributed as an open-source software. By leveraging these advancements, this research aims to bridge the gap between theoretical models and the practical usage of their outcomes on the field.

Identifying and addressing barriers and opportunities for bovine respiratory disease complex vaccination: a consensus paper on practical recommendations for best practise vaccination.

Many questions are raised, and challenges faced in the new era of (intranasal) bovine respiratory disease complex vaccination. An increase in vaccination rate is expected, due to its positive impact on cattle health, reduction of antimicrobial use and economic factors. However, engagement of farmers and veterinarians with regard to vaccination is often affected by limitations, resulting in the development of barriers to vaccination, but also opportunities to overcome these. The objective of the report is to provide practical recommendations and a consensus on best practises for BRDC vaccination, addressing barriers faced by veterinarians and farmers. The report combines an evidence review with expert opinions and includes discussions on different vaccination approaches, such as intranasal and systemic protocols. As result of the discussions, several barriers to BRDC vaccination were identified, including a lack of knowledge or visibility of the disease's impact, the preference for blanket antibiotic use over vaccination, resistance to change, the need for visible success, uncertainty about the best time to vaccinate, and concerns about adverse reactions and vaccine efficacy in the presence of maternal antibodies. While these barriers seem substantial, they provide opportunities for the veterinary sector. Indeed, veterinarians are encouraged to use the argumentation presented, along with local case studies and diagnostic testing to highlight the impact of disease, while conducting calf health audits, ensuring expectations are managed to achieve visible success. Overall, this consensus paper aims to provide practical recommendations and support for veterinarians and farmers to overcome barriers and increase BRDC vaccination rates in cattle.

Modeling the effects of farming practices on bovine respiratory disease in a multi-batch cattle fattening farm.

Bovine Respiratory Disease (BRD) affects young bulls, causing animal welfare and health concerns as well as economical costs. BRD is caused by an array of viruses and bacteria and also by environmental and abiotic factors. How farming practices influence the spread of these causal pathogens remains unclear. Our goal was to assess the impact of zootechnical practices on the spread of three causal agents of BRD, namely the bovine respiratory syncytial virus (BRSV), Mannheimia haemolytica and Mycoplasma bovis. In that extent, we used an individual based stochastic mechanistic model monitoring risk factors, infectious processes, detection and treatment in a farm possibly featuring several batches simultaneously. The model was calibrated with three sets of parameters relative to each of the three pathogens using data extracted from literature. Separated batches were found to be more effective than a unique large one for reducing the spread of pathogens, especially for BRSV and M.bovis. Moreover, it was found that allocating high risk and low risk individuals into separated batches participated in reducing cumulative incidence, epidemic peaks and antimicrobial usage, especially for M. bovis. Theses findings rise interrogations on the optimal farming practices in order to limit BRD occurrence and pave the way to models featuring coinfections and collective treatments p { line-height: 115%; margin-bottom: 0.25 cm; background: transparent}a:link { color: #000080; text-decoration: underline}a.cjk:link { so-language: zxx}a.ctl:link { solanguage: zxx}.

Modelling the effects of antimicrobial metaphylaxis and pen size on bovine respiratory disease in high and low risk fattening cattle.

Bovine respiratory disease (BRD) dramatically affects young calves, especially in fattening facilities, and is difficult to understand, anticipate and control due to the multiplicity of factors involved in the onset and impact of this disease. In this study we aimed to compare the impact of farming practices on BRD severity and on antimicrobial usage. We designed a stochastic individual-based mechanistic BRD model which incorporates not only the infectious process, but also clinical signs, detection methods and treatment protocols. We investigated twelve contrasted scenarios which reflect farming practices in various fattening systems, based on pen sizes, risk level, and individual treatment vs. collective treatment (metaphylaxis) before or during fattening. We calibrated model parameters from existing observation data or literature and compared scenario outputs regarding disease dynamics, severity and mortality. The comparison of the trade-off between cumulative BRD duration and number of antimicrobial doses highlighted the added value of risk reduction at pen formation even in small pens, and acknowledges the interest of collective treatments for high-risk pens, with a better efficacy of treatments triggered during fattening based on the number of detected cases.

Ultrasonography of the cranial part of the thorax is a quick and sensitive technique to detect lung consolidation in veal calves.

BACKGROUND: In the veal calf industry, bovine respiratory disease is the main cause of morbidity and mortality. Lung ultrasonography (LUS) is an accurate technique to diagnose bronchopneumonia in calves. Due to the economic constraints faced by the industry, a screening technique able to rapidly examine large numbers of calves is required. OBJECTIVE: To determine if lung ultrasonography focusing on the cranial part of the thorax (1st to 2nd intercostal space (ICS) on the right and 2nd to 3rd on the left) and/or on the middle part of the thorax (3rd to 5th ICS on the right and 4th to 5th on the left) (alternative techniques) are rapid screening techniques as sensitive as LUS of the entire lung (reference technique) to identify calves with lung consolidation lesions. METHODS: Data on 300 veal calves aged 33.1 ± 8.0 days and weighing on average 67.5 ± 4.0 kg at LUS from two farms were analysed. Systematic LUS of the entire lung was performed on all calves and a lung consolidation score was given to different parts of the thorax. Agreements between the alternative and the reference techniques were measured by Cohen's κ, McNemar's test and weighted κ. RESULTS: Agreement between LUS focusing on the cranial + middle part or on the cranial part only of the thorax and the reference technique were almost perfect with a cutoff of 1 cm. The relative sensitivity of these two alternative techniques was high (> 93%). CONCLUSION: Lung ultrasonography of the cranial + middle part or on the cranial part only of the thorax are quick and sensitive techniques to identify veal calves with lung consolidation lesions shortly after arrival at the facility.

To Vaccinate or Not: Impact of Bovine Viral Diarrhoea in French Cow-Calf Herds.

Bovine viral diarrhoea (BVD) remains an issue despite control programs implemented worldwide. Virus introduction can occur through contacts with neighbouring herds. Vaccination can locally protect exposed herds. However, virus spread depends on herd characteristics, which may impair vaccination efficiency. Using a within-herd epidemiological model, we compared three French cow-calf farming systems named by their main breed: Charolaise, Limousine, and Blonde d'Aquitaine. We assessed vaccination strategies of breeding females assuming two possible protections: against infection or against vertical transmission. Four commercial vaccines were considered: Bovilis®, Bovela®, Rispoval®, and Mucosiffa®. We tested various virus introduction frequency in a naïve herd. We calculated BVD economic impact and vaccination reward. In Charolaise, BVD economic impact was 113€ per cow over 5 years after virus introduction. Irrespective of the vaccine and for a high enough risk of introduction, the yearly expected reward was 0.80€ per invested euro per cow. Vaccination should not be stopped before herd exposure has been decreased. In contrast, the reward was almost nil in Blonde d'Aquitaine and Limousine. This highlights the importance of accounting for herd specificities to assess BVD impact and vaccination efficiency. To guide farmers' vaccination decisions against BVD, we transformed this model into a French decision support tool.

Infectious Bovine Respiratory Diseases in Adult Cattle: An Extensive Necropsic and Etiological Study.

In young cattle, bovine respiratory disease (BRD) is a major cause of death and Mannheimia haemolytica is a frequent pathogen. Knowledge of fatal BRD in adult cattle is more limited. We assessed the importance of infectious BRD as a cause of death in adult cattle and determined the associated pathogens. We analyzed data from 737 adult cattle necropsies at the Pathology Unit for Large Animals at Oniris, Nantes, France over a 6 year period (2013-2019). Each carcass was subjected to a complete necropsy. Lungs showing macroscopic lesions were classified into three categories: infectious primary pulmonary (IPP) lesions, thromboembolic pneumonia (TEP) and others (aspiration pneumonia, verminous pneumonia, and local extension of an extra-pulmonary inflammatory process). Half of the lungs with IPP macroscopic lesions were sampled for histology and submitted for polymerase chain reaction. BRD was the second leading cause of death (15.7%) after digestive diseases (32.2%). A strong predominance of IPP lesions (42.3%) and TEP lesions (39.6%) was also demonstrated. In IPP macroscopic lesions, fibrinous, hemorrhagic and/or hecrotic (FHN) bronchopneumonia accounted for 77.6% of macroscopic lesions. Mannheimia haemolytica was significantly associated with FHN bronchopneumonia macroscopic lesions. This study suggests that Mannheimia haemolytica should be included in the differential diagnosis of BRD in adult cattle.

Appeasing Pheromones against Bovine Respiratory Complex and Modulation of Immune Transcript Expressions.

Bovine respiratory disease is still a major concern and has major economic impact. Another consequence of respiratory infections is the use of antimicrobial molecules to control bacterial pathogens. This can participate in the emergence and shedding of antimicrobial resistance that can threaten animal as well as human health. Appeasing pheromones with their capacity to reduce stress and thus their ability to preserve the functions of the immune system have been proposed to reduce the use of antimicrobial substances. In this study, we assessed the effect of appeasing pheromone administration on bovine health and performance during the fattening period. Zootechnical and health parameters and whole blood immune transcript expressions were measured over four weeks in bulls to determine the effect of the pheromone. We observed increased clinical signs on Day 8 (D8) and decreased clinical signs on D30 in bulls who received the pheromone and a higher expression of interleukin 8 transcripts in this group than in the control group on D8. Our results are overall in line with previous reports in livestock species. Further studies are needed to shed more light on the effect of appeasing pheromones and decipher their exact mechanisms of action.

Minimizing the number of origins in batches of weaned calves to reduce their risks of developing bovine respiratory diseases.

Bovine respiratory diseases (BRD) are a major concern for the beef cattle industry, as beef calves overwhelmingly develop BRD symptoms during the first weeks after their arrival at fattening units. These cases occur after weaned calves from various cow-calf producers are grouped into batches to be sold to fatteners. Cross-contaminations between calves from different origins (potentially carrying different pathogens), together with increased stress because of the process of batch creation, can increase their risks of developing BRD symptoms. This study investigated whether reducing the number of different origins per batch is a strategy to reduce the risk of BRD cases. We developed an algorithm aimed at creating batches with as few origins as possible, while respecting constraints on the number and breed of the calves. We tested this algorithm on a dataset of 137,726 weaned calves grouped into 9701 batches by a French organization. We also computed an index assessing the risks of developing BRD because of the batch composition by considering four pathogens involved in the BRD system. While increasing the heterogeneity of batches in calf bodyweight, which is not expected to strongly impact the performance, our algorithm successfully decreased the average number of origins in the same batch and their risk index. Both this algorithm and the risk index can be used as part of decision tool to assess and possibly minimize BRD risk at batch creation, but they are generic enough to assess health risk for other production animals, and optimize the homogeneity of selected characteristics.

To what extent does the composition of batches formed at the sorting facility influence the subsequent growth performance of young beef bulls? A French observational study.

To meet the demands of the beef cattle sector in France, weaned beef calves are transported to sorting facilities and sorted into batches composed of animals of similar body weight (BW) before the beginning of the fattening period. This procedure aims to facilitate animal management. However, it leads to practices that affect animal welfare, health and performance, such as transporting weaned beef calves over long distances and mixing animals originating from different cow/calf farms. In contrast, other potentially beneficial practices, such as pre-weaning vaccination against bovine respiratory diseases (BRD), are seldom taken into consideration when batches are formed. This observational study, based on field data from 15,735 Charolais bulls, aimed to investigate which criteria should be favored for batch constitution by quantifying the effect of batch characteristics on the growth performance of young bulls during the fattening period. Clustering analysis was used to group young bulls exhibiting similar batch characteristics and define batch types. Associations between batch characteristics/batch types and individual growth performance/homogeneity of growth performance (mean and standard deviation (SD) of average daily gain (ADG) and fattening period duration) were studied using linear mixed models. The mean BW and the percentage of animals vaccinated against BRD before weaning were positively associated with ADG (+35 g/d for each additional 50 kg and +28 g/d for a high percentage of vaccinated animals, P < 0.05). In contrast, transportation distance was negatively associated with ADG (-12 g/d for each additional 120 km travelled). Mixing animals and BW homogeneity did not affect growth performance (P > 0.05). Only the mean BW and mixing animals negatively influenced the homogeneity of ADG (P < 0.01). The clustering analysis revealed that batches with the most BW heterogeneity, the least mixing, the shortest transportation distance and a high percentage of pre-weaning animals vaccinated against BRD had better growth performance compared to batches with the opposite characteristics (+61 g/d, P < 0.001). Our results suggest that major improvements of growth performance of fattening young bulls could be obtained by minimizing transportation distance, providing vaccination programs against BRD before weaning, and maintaining groups from the same cow/calf farm instead of constituting groups of animals with similar BW at the beginning of fattening.

Extracellular DNA: A Nutritional Trigger of Mycoplasma bovis Cytotoxicity.

Microbial access to host nutrients is a key factor of the host-pathogen interplay. With their nearly minimal genome, wall-less bacteria of the class Mollicutes have limited metabolic capacities and largely depend on host nutrients for their survival. Despite these limitations, host-restricted mycoplasmas are widely distributed in nature and many species are pathogenic for humans and animals. Yet, only partial information is available regarding the mechanisms evolved by these minimal pathogens to meet their nutrients and the contribution of these mechanisms to virulence. By using the ruminant pathogen Mycoplasma bovis as a model system, extracellular DNA (eDNA) was identified as a limiting nutrient for mycoplasma proliferation under cell culture conditions. Remarkably, the growth-promoting effect induced by supplementation with eDNA was associated with important cytotoxicity for actively dividing host cells, but not confluent monolayers. To identify biological functions mediating M. bovis cytotoxicity, we produced a library of transposon knockout mutants and identified three critical genomic regions whose disruption was associated with a non-cytopathic phenotype. The coding sequences (CDS) disrupted in these regions pointed towards pyruvate metabolism as contributing to M. bovis cytotoxicity. Hydrogen peroxide was found responsible for eDNA-mediated M. bovis cytotoxicity, and non-cytopathic mutants were unable to produce this toxic metabolic compound. In our experimental conditions, no contact between M. bovis and host cells was required for cytotoxicity. Further analyses revealed important intra-species differences in eDNA-mediated cytotoxicity and H2O2 production, with some strains displaying a cytopathic phenotype despite no H2O2 production. Interestingly, the genome of strains PG45 and HB0801 were characterized by the occurrence of insertion sequences (IS) at close proximity to several CDSs found disrupted in non-cytopathic mutants. Since PG45 and HB0801 produced no or limited amount of H2O2, IS-elements might influence H2O2 production in M. bovis. These results confirm the multifaceted role of eDNA in microbial communities and further identify this ubiquitous material as a nutritional trigger of M. bovis cytotoxicity. M. bovis may thus take advantage of the multiple sources of eDNA in vivo to modulate its interaction with host cells, a way for this minimal pathogen to overcome its limited coding capacity.

Atypical actinobacillosis affecting hind limbs and lungs in a single beef cattle herd.

Actinobacillosis usually is a sporadic infection that affects the tongue in cattle ("wooden tongue") with possible spread to the digestive tract. Two 4-year-old Rouge-des-Prés cows from a single French beef herd were referred for chronic (2-6 months) swelling and cutaneous nodules in the distal hind limbs. In addition to cutaneous signs, physical examination disclosed cachexia, lameness, lymphadenitis of the hind limbs, and pneumonia in both cows. Cytologic examination of direct skin smears was inconclusive, and no parasites were observed in examination of multiple skin scrapings. Histopathological examination of skin and lung biopsy specimens identified chronic, diffuse, severe pyogranulomatous dermatitis, associated with Splendore-Hoeppli phenomenon and intralesional Gram-negative bacteria. Cultures from skin, lymph nodes, and lungs (both cows were euthanized for welfare reasons) identified a Pasteurellaceae organism, confirmed as Actinobacillus lignieresii by partial sequencing of the rpoB gene. This report emphasizes that actinobacillosis can appear as a small outbreak in cattle with cutaneous and respiratory signs.

Implementing Precision Antimicrobial Therapy for the Treatment of Bovine Respiratory Disease: Current Limitations and Perspectives.

The therapeutic efficacy of an early treatment protocol with an infection-stage adjusted fluoroquinolone regimen was evaluated in a field study on young bulls (YBs) presenting signs of bovine respiratory disease (BRD). A total of 195 YB (Charolais, Limousin, and Rouge-des-Prés breeds) from 6 farms implementing or not prophylactic antimicrobial treatments (PROPHY or absence) were randomly assigned to 1 of 2 experiment groups based on time of detection of BRD and first-line marbofloxacin regimen, early adjusted dose [Early 2 (E2)] or late standard dose [Late 10 (L10)]. Each YB was administered orally a reticulo-rumen bolus, allowing continuous monitoring of ruminal temperature. In the E2 group, YB presenting early signs of BRD, i.e., an increase in ruminal temperature over 40.2°C and persisting more than 12 h, confirmed by a clinical examination showing no or mild signs of BRD, were given 2 mg/kg of marbofloxacin. In the L10 group, YBs presenting moderate or severe signs of BRD at visual inspection, confirmed at clinical examination, were given 10 mg/kg of marbofloxacin. If needed, YBs were given a relapse treatment. The YBs were followed for 30 days. The proportions of first and relapse treatments were calculated, as well as the therapeutic efficacy at day 10. In the E2 group, the first-line treatments' proportion was significantly higher (P < 0.05), while the relapse treatments' proportion tended to be higher (P = 0.08), than in the L10 group. Evolution of clinical scores (CSs) of diseased YB was followed for 10 days. In both groups, CS and rectal temperature decreased significantly 24 h after treatment (P < 0.05). Treatment incidences (TI) representing antimicrobial consumption assessed on used daily doses (UDD) were calculated. Antimicrobial consumption of marbofloxacin and relapse treatments were not significantly different between the groups. These values were strongly influenced by the recourse to a prophylactic antimicrobial treatment, accounting for more than 90% of the antimicrobial amount in the herds implementing prophylaxis. The higher number of treatments in the groups treated on the basis of ruminal temperature monitoring, the accuracy of the detection method, and the necessary conditions to implement precision antimicrobial therapy in the field are discussed in this article.

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations.

In the context of requested decrease of antimicrobial use in veterinary medicine, our objective was to assess the impact of two doses of marbofloxacin administered on young bulls (YBs) and veal calves (VCs) treated for bovine respiratory disease, on the total population of Enterobacteriaceae in gut flora and on the emergence of resistant Enterobacteriaceae. In two independent experiments, 48 YBs from 6 commercial farms and 33 VCs previously colostrum deprived and exposed to cefquinome were randomly assigned to one of the three groups LOW, HIGH, and Control. In LOW and HIGH groups, animals received a single injection of, respectively, 2 and 10 mg/kg marbofloxacin. Feces were sampled before treatment, and at several times after treatment. Total and resistant Enterobacteriaceae enumerating were performed by plating dilutions of fecal samples on MacConkey agar plates that were supplemented or not with quinolone. In YBs, marbofloxacin treatment was associated with a transient decrease in total Enterobacteriaceae count between day (D)1 and D3 after treatment. Total Enterobacteriaceae count returned to baseline between D5 and D7 in all groups. None of the 48 YBs harbored marbofloxacin-resistant Enterobacteriaceae before treatment. After treatment, 1 out of 20 YBs from the Control group and 1 out of 14 YBs from the HIGH group exhibited marbofloxacin-resistant Enterobacteriaceae. In VCs, the rate of fluoroquinolone-resistant Enterobacteriaceae significantly increased after low and high doses of marbofloxacin treatment. However, the effect was similar for the two doses, which was probably related to the high level of resistant Enterobacteriaceae exhibited before treatment. Our results suggest that a single treatment with 2 or 10 mg/kg marbofloxacin exerts a moderate selective pressure on commensal Enterobacteriaceae in YBs and in VCs. A fivefold decrease of marbofloxacin regimen did not affect the selection of resistances among commensal bacteria.

Impact of Timing and Dosage of a Fluoroquinolone Treatment on the Microbiological, Pathological, and Clinical Outcomes of Calves Challenged with Mannheimia haemolytica.

The efficacy of an early and low inoculum-adjusted marbofloxacin treatment was evaluated on microbiological and clinical outcomes in calves infected with 4.10(7) CFU of Mannheimia haemolytica A1. Twenty-two calves were included based on their rectal temperature rise in the 10 h after challenge and allocated in four groups, receiving a single intramuscular injection of saline (CON), 2 mg/kg marbofloxacin 2-4 h after inclusion (early treatment, E2), 2 or 10 mg/kg marbofloxacin 35-39 h after inclusion (late treatments, L2, L10). In CON calves, M. haemolytica DNA loads in bronchoalveolar lavages continuously increased from inclusion to day 4, and were associated with persistent respiratory clinical signs and lung lesions. At times of early and late treatments, M. haemolytica loads ranged within 3.5-4 and 5.5-6 log10 DNA copies/mL, respectively. Early 2 mg/kg marbofloxacin treatment led to rapid and total elimination of bacteria in all calves. The late treatments induced a reduction of bacterial loads, but 3 of 6 L2 and 1 of 6 L10 calves were still positive for M. haemolytica at day 4. Except for CON calves, all animals exhibited clinical improvement within 24 h after treatment. However, early 2 mg/kg treatment was more efficacious to prevent pulmonary lesions, as indicated by the reduction of the extension and severity of gross lesions and by the histopathological scores. These results demonstrated for the first time that a reduced antibiotic regimen given at an early stage of the disease and targeting a low bacterial load could be efficacious in a natural bovine model of pneumonia.

Disruption of Bcchs4, Bcchs6 or Bcchs7 chitin synthase genes in Botrytis cinerea and the essential role of class VI chitin synthase (Bcchs6).

Chitin synthases play critical roles in hyphal development and fungal pathogenicity. Previous studies on Botrytis cinerea, a model organism for necrotrophic pathogens, have shown that disruption of Bcchs1 and more particularly Bcchs3a genes have a drastic impact on virulence (Soulié et al., 2003, 2006). In this work, we investigate the role of other CHS including BcCHS4, BcCHS6 and BcCHS7 during the life cycle of B. cinerea. Single deletions of corresponding genes were carried out. Phenotypic analysis indicates that: (i) BcCHS4 enzyme is not essential for development and pathogenicity of the fungus; (ii) BcCHS7 is required for pathogenicity in a host dependant manner. For Bcchs6 gene disruption, we obtained only heterokaryotic strains. Indeed, sexual or asexual purification assays were unsuccessful. We concluded that class VI chitin synthase could be essential for B. cinerea and therefore BcCHS6 represents a valuable antifungal target.

Transmission dynamics of Mycoplasma bovis in newly received beef bulls at fattening operations.

Mycoplasma bovis is an important cause of bovine respiratory disease (BRD) in newly received cattle at fattening operations. However, little information on its within-pen transmission dynamics during a BRD outbreak is available. Such information is nevertheless crucial to adapt control measures during M. bovis-associated BRD outbreaks. The objective of the current study was to determine whether single or multiple clones of M. bovis are present within a pen during a BRD outbreak that occurs early in the feeding period. Sixteen BRD outbreaks that naturally occurred in 12 pens of 8-12 bulls each (n = 112) newly received at 3 fattening operations were investigated. Two hundred and thirty-nine transtracheal aspirations (TTA) were performed during the outbreaks, and the M. bovis isolates obtained were characterized by pulsed-field gel electrophoresis (PFGE). Mycoplasma bovis isolates were recovered from TTA in 8 of the 16 BRD outbreaks that occurred. The within-pen prevalence of bulls positive for M. bovis during these outbreaks ranged from 8% to 100%. The PFGE analysis revealed that, even though bulls came from multiple origins, a single clone of M. bovis was present within a pen during BRD outbreaks with a high prevalence of M. bovis infection. The study therefore indicates that, even if M. bovis can recrudesce from carriers after stressful events such as transportation and commingling, the increased prevalence of M. bovis pulmonary infection observed during BRD outbreaks that are early occurring in the feeding period seems primarily due to the horizontal transmission of only 1 clone among cattle.

Early detection of bovine respiratory disease in young bulls using reticulo-rumen temperature boluses.

The use of reticulo-rumen temperature boluses to detect bovine respiratory disease (BRD) was investigated in young bulls following their entry into a fattening unit. Twenty-four bulls received a bolus at entry and were observed for 40 days. As soon as a reticulo-rumen hyperthermia (RH) episode was detected using the bolus, clinical examination was performed by a veterinarian and then repeated every 12-24h until the end of RH episode. Fifty-two RH episodes were detected in 22 animals. High rectal temperatures (40.1±0.6°C) were observed during these episodes. BRD was diagnosed on the basis of clinical examination during 38/52 RH episodes in 21 animals (positive predictive value 73%). The onset of BRD signs always occurred after the onset of RH episodes, with a time-lag from 12 to 136 h, depending on BRD signs. Monitoring reticulo-rumen temperature permits early detection of BRD; however, clinical examination is required to confirm BRD.

Evaluation of a commercial real-time reverse transcription polymerase chain reaction kit for the diagnosis of Bovine respiratory syncytial virus infection.

Recently a commercial real-time reverse transcription polymerase chain reaction (RT-PCR) kit has been marketed for the detection of Bovine respiratory syncytial virus (BRSV). However, diagnostic interpretation of the results of this kit requires its comparison to commonly used methods. Therefore, the objective of this study was to evaluate the performance of this kit in comparison with the conventional direct fluorescent antibody test (FAT). Twenty BRSV strains and 14 heterologous bovine viruses were used to check the kit's sensitivity and specificity. The efficiency and detection limit of the kit were determined by testing dilution series of a BRSV strain. The comparison between real-time RT-PCR kit and FAT was performed with 94 clinical samples from calves with clinical signs of respiratory disease including lung tissues (n = 55), transtracheal aspiration samples (n = 20), and nasal swab samples (n = 19). All of the BRSV strains tested were detected by real-time RT-PCR. No cross-reaction was shown with the 14 heterologous bovine viruses. The real-time RT-PCR was 99.3% efficient with a detection limit of 0.1 TCID(50) (50% tissue culture infective dose). The results of real-time RT-PCR and FAT were concordant for 65 of the 94 clinical samples tested. The remaining 29 clinical samples were positive by real-time RT-PCR and negative by FAT, demonstrating the higher sensitivity of real-time RT-PCR. In conclusion, the kit evaluated in this study was sensitive, specific, and had a low threshold of detection. Furthermore, the use of this kit instead of FAT allows an improvement of the sensitivity for the detection of BRSV in clinical samples.

Management- and housing-related risk factors of respiratory disorders in non-weaned French Charolais calves.

Our aim was to determine at calf-batch level the management- and housing-related risk factors of respiratory disorders in non-weaned Charolais calves. Farmers recorded cases according to the definition provided i.e. the association of at least one respiratory sign and, in the same calf or another calf of the same batch, at least one general sign on the same day or the day before. During farm visits, quality of farmers' records was checked and questionnaires were applied to gather farm and herd characteristics and to describe farming practices and housing facilities. Data were suitable for analysis for 172 batches where no metaphylactic treatment was implemented. Batches had great disparity in incidence of respiratory disorders. In the 120 batches with at least one case, the quartiles of incidence rate were, respectively, 0.95, 2.15 and 3.59 cases per 1000 calf-days at-risk. For risk-factor analysis, the statistical unit was the calf-batch located in a given batch. We used a ZINB model because (i) there was significant overdispersion of incidence rates of respiratory disorders (overdispersion test statistic of O=1049 (P<0.001)), (ii) probability was high that a two-group modelling process existed (Vuong statistic of V=2.44 (P=0.0073)) and (iii) the ZINB model fit significantly better than the ZIP model (likelihood-ratio statistic of 340.14 (P<0.001)). The risk was higher in open-fronted barns or in open barns compared to closed ones (incidence-rate ratios (IRRs): 1.9 and 1.8), in barns where no annual disinfection was implemented (IRR: 1.5) and in part slope with straw/part scraped and in part straw-bedded/part scraped barns compared to completely straw-bedded barns (IRRs: 1.9 and 1.6). Larger calf-batches were more at-risk than smaller batches (OR for the effect of an increase of 10 calves on the probability of a 0 count: 0.5).