Design of a High-Throughput Real-Time PCR System for Detection of Bovine Respiratory and Enteric Pathogens

Comparative Insights into Acute Gastroenteritis in Cattle Caused by Bovine Rotavirus A and Bovine Coronavirus

Acute gastroenteritis (AGE) in cattle significantly impacts the economy due to relatively high morbidity and mortality and decreased production. Its multifactorial nature drives its global persistence, involving enteric viruses, bacteria, protozoa, and environmental factors. Bovine Rotavirus A (BoRVA) and bovine coronavirus (BCoV) are among the most important enteric RNA viruses causing AGE in cattle. These viruses infect intestinal enterocytes, leading to cell damage and consequently to malabsorption and diarrhea. BoRVA primarily affects calves under 14 days old with gastrointestinal clinical signs, while BCoV affects all ages, causing gastrointestinal and respiratory distress. The economic impact of BoRVA and BCoV, along with their interspecies transmission potential, warrants attention. This concise review discusses the molecular structure, epidemiology, pathogenesis, clinical signs, diagnosis, treatment, and preventive measures of BoRVA and BCoV while providing a comparative analysis. By offering practical guidance on managing such viral infections in cattle, these comparative insights may prove valuable for veterinarians in clinical practice.

Frequency of Bovine Respiratory Disease Complex Bacterial and Viral Agents Using Multiplex Real-Time qPCR in Quebec, Canada, from 2019 to 2023

The bovine respiratory disease complex (BRD) is a multifactorial disease caused by various bacterial and viral pathogens. Using rapid pathogen detection techniques is helpful for tailoring therapeutic and preventive strategies in affected animals and herds. The objective of this study was to report the frequency of 10 pathogens by multiplex RT-qPCR on samples submitted for BRD diagnosis to a diagnostic laboratory (Biovet Inc., QC, Canada) in the Province of Quebec, Eastern Canada. From the 1st of January 2019 to the 31st of December 2023, a total of 1875 samples were analyzed. Most samples collected were individual samples (1547 of 1860 samples for which information was available (83.17%)), and the rest were from pooled samples of 2 (8.55%, n = 159) or ≥3 specimens (8.28%, n = 154). In 19.3% of the samples (n = 362), no pathogen was found, whereas 54.1% of samples had two or more different pathogens. Among the viruses, bovine coronavirus (BCV) was the most commonly found (27.5% of samples, n = 516), followed by bovine respiratory syncytial virus (BRSV) (17.7%, n = 332), whereas, for bacteria, Pasteurella multocida (50.1%, n = 940) and Mannheimia haemolytica (26.9%, n = 505) were the most common. The frequency of samples positive for Histophilus somni, Mycoplasmopsis bovis, influenza type D virus (IDV), bovine parainfluenza virus type 3 (BPI3V), bovine herpesvirus type 1 (BHV1), and bovine viral diarrhea virus (BVDV) was 22.6%, 22.4%, 4.6%, 4.3%, 2.7%, and 0.9%, respectively. In the multivariable Poisson regression model, the total number of pathogens increased with the number of animals in the pool, with an incidence risk ratio (IRR) of 1.15 (95% CI 1.02-1.29) and 1.32 (1.18-1.47) for 2 individuals in the pool and ≥3 individuals vs. individual samples, respectively. An increased number of pathogens were isolated in the winter season (IRR = 1.28 (95% CI 1.17-1.40)) compared to fall, and a lower number of pathogens were isolated in the summer compared to fall (IRR = 0.82 (95% CI 0.73-0.92)). These seasonal differences were mostly driven by the number of viruses isolated. This study gives interesting insights on the circulation of BRD pathogens in cattle from Eastern Canada.

High-throughput screening for respiratory pathogens within pigs in Denmark; analysis of circulating porcine respiratory coronaviruses and their association with other pathogens

Porcine respiratory coronavirus (PRCV) typically causes subclinical or mild respiratory infections in pigs, but may lead to more severe disease with other factors. PRCV infection in Denmark was initially detected in 1984, but data are lacking about its current prevalence and diversity. Antibodies against PRCV were detected in about 75 % of recent pig sera from Denmark. In addition, pig nasal swab samples were screened for PRCV and 12 other respiratory pathogens using a high-throughput RT-qPCR system. All targeted pathogens were detected but at different prevalences. Significant associations were found between the presence of PRCV and certain other pathogens. From PRCV positive samples, partial spike gene sequences and complete nucleocapsid coding sequences were determined. In phylogenetic analyses, these PRCVs clustered with earlier European PRCVs and were distinct from transmissible gastroenteritis virus. We conclude that PRCV is widespread within the pig population in Denmark. Further studies on the significance of PRCV are warranted.

Exploring the Genetic Diversity of Mycoplasma hyopneumoniae in Pigs with Pneumonia and Pleurisy at Slaughter

Mycoplasma (M.) hyopneumoniae is the key pathogen of the porcine respiratory disease complex (PRDC) and contributes to pleurisy in pigs. Due to its limited metabolism and laborious cultivation, molecular tools are useful for diagnosis. This study investigated the genetic diversity of M. hyopneumoniae in slaughter pigs with pneumonia and pleurisy, and it assessed co-infections by Pasteurella multocida type A (PM), Actinobacillus pleuropneumoniae (APP), and swine influenza virus A (sIVA). Lungs (n = 70) with different pleurisy scores and lesions compatible with M. hyopneumoniae infection were collected for convenience. Macroscopic and microscopic evaluations were performed. M. hyopneumoniae was detected using qPCR, and MLST was used for genetic characterization. Co-infections with PM and APP were also evaluated by qPCR, while the immunohistochemistry assessed sIVA infection. All lungs were positive for M. hyopneumoniae. Histopathology confirmed M. hyopneumoniae-associated lesions. MLST characterization was possible in 25 lungs and revealed 10 distinct allelic profiles, with none matching known sequence types in the public database. Co-infections were detected in 40% of the samples with APP and 32% with PM, with 12% showing both pathogens and 52% of the samples presenting microscopic lesions compatible with sIVA infection. The diverse genetic profiles found underscore the need for research on isolation and potential pathogenic variations.

Bovine Respiratory Disease (BRD) in Post-Weaning Calves with Different Prevention Strategies and the Impact on Performance and Health Status

Our study aimed to compare Bovine Respiratory Disease (BRD) morbidity, mortality, and growth in dairy and dairy beef cross-bred calves during the commingle period, 81-120 days of age, using two different BRD prevention strategies. The calves (n = 1799) were randomly assigned into groups: (1) Control (CON; received no vaccine or metaphylaxis); (2) Tulathromycin metaphylaxis (TUL; IncrexxaTM, Elanco Animal Health Inc., Greenfield, IN, USA); and (3) Mannheimia haemolytica vaccine (VACC; Nuplura® PH, Elanco Animal Health Inc., Greenfield, IN, USA). Calves were individually weighed three times during the study to estimate average daily gain (ADG). Deep nasopharyngeal swabs, thoracic ultrasonography, health scores, and treatment records were collected during the study. Ultrasound and health score results were not different across treatments. In this study, the TUL group had a lower cumulative BRD incidence than CON. The cumulative incidence and 95% CI of BRD during the commingle period, 81-120 days of age for CON, TUL, and VACC were 0.43 (0.38 to 0.47), 0.36 (0.38 to 0.40), and 0.39 (0.35 to 0.43), respectively. The ADG for CON, TUL, and VACC were 0.25 ± 0.15, 0.32 ± 0.15, and 0.17 ± 0.15 kg, respectively. There was no difference among the treatment groups for ADG. Management and environmental conditions were variable at this operation throughout the study period and likely impacted the calves. Earlier interventions may be needed when the BRD incidence is elevated in high-risk calves.

Comparing Occurrence of Bovine Respiratory Pathogens Detected by High-Throughput Real-Time PCR in Nasal Swabs and Non-Endoscopic Bronchoalveolar Lavage Samples from Dairy and Veal Calves

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.

Development of a 1-step TaqMan real-time PCR method for detection of the Bovine Group A Rotavirus

BACKGROUND

The purpose of this study was to develop a 1-step real-time quantitative fluorescence polymerase chain reaction (QF-PCR) method for detecting Bovine Group A Rotavirus (BRVA). The primers and probe were designed targeting the VP6 gene of BRVA. The standard substance was obtained through in vitro transcription. The primers, probe concentration, and annealing temperatures were optimized to determine the optimal system and conditions for the reaction. The specificity, sensitivity, and repeatability of the method were assessed and compared with a reported real-time QF-PCR method for clinical samples.

RESULTS

The results indicated that the detection method can achieve a sensitivity of 3.47 copies/μL and exhibit good specificity by exclusively detecting BRVA without cross-reactivity to other common pathogens in cattle and sheep. The standard curve exhibited a robust linear correlation, and the amplification efficiency was calculated to be 105%. The intra-group and inter-group coefficients of variation were less than 2%. A total of 96 clinical samples were tested and compared with the real-time QF-PCR method that was reported. The coincidence rate was 90.63% (87/96). Furthermore, the clinical samples revealed that the prevalence of BRV in cattle from Fujian Province was 85.42% (82/96).

CONCLUSION

This study has successfully developed a 1-step real-time QF-PCR method for BRVA, which offers an efficient and sensitive technical support for the rapid diagnosis and epidemiological investigation of BRVA.

Development of real-time RT-PCR systems for detection and quantitation of bovine enteric viral pathogens

The enteric viruses in animals are responsible for severe and devastating losses to the livestock owners with a profound negative impact on animal, health, welfare, and productivity. These viruses are usually transmitted via the feco-oral route and primarily infect the digestive tract of the humans, bovines and different mammals as well as birds. Some of the important enteric viruses in ruminants are: Rotavirus A (RVA), Peste des petits virus (PPRV), Norovirus (NV), Bovine corona virus (BoCV) and Bluetongue virus (BTV). In the present study, sensitive, specific and reliable TaqMan probe-based RT-qPCRs were developed and standardized for the rapid detection and quantification of enteric viruses from fecal samples. The assays result in efficient amplification of the RVA, BTV and BoCV RNA with a limit of detection (LoD) of 5, 5 and 4 copies, respectively, which is 1000 times more sensitive than the traditional gel-based RT-PCR. The reproducibility of each assay was satisfactory, thus allowing for a sensitive and accurate measurement of the viral RNA load in clinical samples. In conclusion, real time PCR developed for these viruses are highly specific and sensitive technique for the detection of diarrheic viral pathogens of cattle and buffalo.

Monitoring bovine dairy calf health and related risk factors in the first three months of rearing

BACKGROUND

Rearing replacement heifers is pivotal for the dairy industry and is associated with high input costs for the preweaned calves, due to their higher susceptibility to diseases. Ensuring calf health and viability calls for systematic approaches in order to mitigate the costs induced by managing sick calves and to ensure animal welfare. The objective of this study was to develop a systematic and feasible health-monitoring tool for bovine dairy calves based on repeated clinical observations and diagnostic results of calves at three time points; the 1st (T0), the 3rd (T1) and the 12th (T3) week of age. The study included observations from 77 dairy heifer calves in nine Danish commercial dairy herds. Immunisation status was assessed by serum Brix% at T0. Clinical scoring included gastrointestinal disease (GD) and respiratory disease (RD). The average daily weight gain (ADWG) was estimated from heart-girth measurements. Pathogen detection from nasal swabs and faecal samples were analysed for 16 respiratory and enteric pathogens by means of high-throughput real time-PCR. All measures obtained in each herd were visualised in a panel to follow the health status of each calf over time.

RESULTS

The individual clinical observations combined with diagnostic information from immunisation and pathogen detection form each enrolled calf are presented in a herd dashboard illustrating the health status over the study period. This monitoring revealed failure of passive transfer (Brix% < 8.1) in 31% of the 77 enrolled calves, signs of severe GD peaked at T0 with 20% affected calves, while signs of severe RD peaked at T2 with 42% affected calves. ADWG over the first eight weeks was estimated to be 760 g (± 190 g). Pathogen profiles varied between herds.

CONCLUSIONS

The large variation in both clinical disease and pathogen occurrence across herds emphasizes the need for herd specific monitoring. Combining the results of the present study from measures of immunisation, health and growth from individual calves in one visualisation panel allowed for the detection of patterns across age groups in the specific herds, showing promising potential for early detection and interventions that can lead to enhanced calf health and welfare.

Gastro-intestinal lesions are not relatable to diarrhoea or specific pathogens in post-weaning diarrhoea (PWD) in pigs

BACKGROUND

Post-weaning diarrhoea (PWD) is a multifactorial condition and the most well documented infectious cause is enterotoxigenic Escherichia coli. The objective of the study was to investigate possible associations between pathological manifestations and pathogens in pigs with and without PWD. The study was conducted as a case-control study and included a total of 173 pigs from 9 different commercial intensive indoor production herds in eastern Denmark.

RESULTS

Based on clinical examination, a total of 89 piglets with PWD (cases) and 84 piglets without PWD (controls) were included. Most of the pigs (n = 105/173) presented gastric lesions, which were more frequently observed in the control group. The odds of gastric ulcers were lower among pigs with PWD compared to pigs without PWD with an odds ratio (OR) of 0.2 (0.0; 0.7). Abnormal content in the colon was associated with PWD, with an OR of 6.5 (3.2; 14.3). No apparent association was found between lesions and the various pathogens or a combination of these. The odds of neutrophilic granulocyte infiltration were lower in the jejunum among pigs with PWD (OR 0.3 [0.1; 0.6]) compared to pigs without PWD. The association between neutrophilic granulocyte infiltration in jejunum and PWD differed between the herds (P = 0.03). Furthermore, the associations between PWD and hyperleukocytosis (P = 0.04) or infiltration of eosinophilic granulocytes (P = 0.04) in ileum were also herd dependent. Histopathology revealed several lesions not relatable to PWD.

CONCLUSION

The association between lesions and specific pathogens or PWD is more complex than anticipated.

Lesions and pathogens found in pigs that died during the nursery period in five Danish farms

BACKGROUND

Diagnosing and treatment of diseases in pigs are important to maintain animal welfare, food safety and productivity. At the same time antimicrobial resistance is increasing, and therefore, antibiotic treatment should be reserved for individuals with a bacterial infection. The aim of the study was to investigate gross and histological lesions and related pathogens in pigs that died during the nursery period in five Danish farms. In addition, high throughput, real-time qPCR monitoring of specific porcine pathogens in fecal sock and oral fluid samples were carried out to investigate the between-farm and between-batch variation in the occurrence of pathogens.

RESULTS

Twenty-five batches of nursery pigs from five intensive, indoor herds were followed from weaning (approximately four weeks) to the end of nursery (seven to eight weeks post weaning). Gross and histological evaluation of 238 dead and 30 euthanized pigs showed the highest prevalence of lesions in the skin, respiratory system, gastrointestinal tract, and joints. Gross and histological diagnoses of lung and joint lesions agreed in 46.5% and 62.2% of selected pigs, respectively. Bacteriological detection of Escherichia coli, Streptococcus suis or Staphylococcus aureus infections in joints, lungs and livers was confirmed as genuine infection on immunohistochemical staining in 11 out of 70 tissue sections. The real-time qPCR analysis of pooled samples showed that most pathogens detected in feces and in oral fluid in general followed the same shedding patterns in consecutive batches within herds.

CONCLUSIONS

Gross assessment should be supplemented with a histopathological assessment especially when diagnosing lesions in the lungs and joints. Moreover, microbiological detection of pathogens should optimally be followed up by in situ identification to confirm causality. Furthermore, routine necropsies can reveal gastric lesions that may warrant a change in management. Real-time qPCR testing of fecal sock samples and oral fluid samples may be used to monitor the infections in the individual herd and testing one batch seems to have a good predictive value for subsequent batches within a herd. Overall, optimal diagnostic protocols will provide a more substantiated prescription of antibiotics.

Current and Emerging Diagnostic Approaches to Bacterial Diseases of Ruminants

The diagnostic approaches and methods to detect bacterial pathogens in ruminants are discussed, with a focus on cattle. Conventional diagnostic methods using culture, isolation, and characterization are being replaced or supplemented with new methods. These include molecular diagnostics such as real-time polymerase chain reaction and whole-genome sequencing. In addition, methods such as matrix-assisted laser desorption ionization-time-of-flight mass spectrometry enable rapid identification and enhanced pathogen characterization. These emerging diagnostic tools can greatly enhance the ability to detect and characterize pathogens, but performance and interpretation vary greatly across sample and pathogen types, disease syndromes, assay performance, and other factors.

Characterization of Influenza D Virus in Danish Calves

Influenza D virus (IDV) was first described in 2011 and has been found to mainly circulate among cattle and swine populations worldwide. Nasal swab samples were collected from 100 Danish calf herds (83 dairy and 17 veal herds) from 2018-2020. Influenza D virus was detected in 12 of the herds. Samples with the lowest cycle quantification value were selected for full genome sequencing. A hemagglutinin-esterase fusion (HEF) gene sequence from a Danish IDV collected in 2015 was also included in this study. Phylogenetic analysis showed that viruses from seven of the IDV-positive herds belonged to the D/OK lineage and clustered together in the HEF tree with the IDV collected in 2015. Viruses from the four other herds belonged to the D/660 lineage, where three of the viruses clustered closely together, while the fourth virus was more phylogenetically distant in all gene segments. The high level of genetic similarity between viruses from two different herds involved in calf trading suggests that transmission occurred through the movement of calves. This study is, to our knowledge, the first to describe the characterization of IDV in calves in Denmark.