Respiratory tract infections (bovine respiratory disease) are a major concern in calf rearing. The objective of this study was to identify pathogen-specific risk factors associated with epidemic respiratory disease in calves. A cross-sectional study was conducted, involving 128 outbreaks (29 dairy, 58 dairy-mixed, and 41 beef) in Belgium (2016-2018). A semiquantitative PCR for 7 respiratory pathogens was done on a pooled nonendoscopic bronchoalveolar lavage sample for each herd. Potential risk factors were collected by questionnaire and derived from the national cattle registration databank. Most outbreaks occurred between October and March, and single and multiple viral infections were detected in 58.6% (75/128) and 13.3% (17/128), respectively. Bovine coronavirus (BCV) was the most frequently isolated virus (38.4%), followed by bovine respiratory syncytial virus (bRSV; 29.4%) and parainfluenzavirus type 3 (PI-3; 8.1%). Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni were detected in 33.3, 41.2, 89.1, and 36.4% of the herds, respectively. Specific risk factors for BCV detection were detection of M. haemolytica [odds ratio (OR) = 2.8 (95% confidence interval = 1.1-7.5)], increasing herd size [OR = 1.3 (1.0-1.8) for each increase with 100 animals] and detection of BCV by antigen ELISA on feces in calves in the last year [OR = 3.6 (1.2-11.1)]. A seasonal effect was shown for bRSV only {more in winter compared with autumn [OR = 10.3 (2.8-37.5)]}. Other factors associated with bRSV were PI-3 detection [OR = 13.4 (2.1-86.0)], prevalence of calves with respiratory disease [OR = 1.02 (1.00-1.04) per 1% increase], and number of days with respiratory signs before sampling [OR = 0.99 (0.98-0.99) per day increase]. Next to its association with BCV, M. haemolytica was more frequently detected in herds with 5 to 10 animals per pen [OR = 8.0 (1.4-46.9)] compared with <5 animals, and in herds with sawdust as bedding [OR = 18.3 (1.8-191.6)]. Also, for H. somni, housing on sawdust was a risk factor [OR = 5.2 (1.2-23.0)]. Purchase of cattle [OR = 2.9 (1.0-8.0)] and housing of recently purchased animals in the same airspace [OR = 5.0 (1.5-16.5)] were risk factors for M. bovis. This study identified pathogen-specific risk factors that might be useful for the development of customized control and prevention and for the design of decision support tools to justify antimicrobial use by predicting the most likely pathogen before sampling results are available.

M. bovis is one of the leading causes of respiratory disease and antimicrobial use in cattle. The pathogen is widespread in different cattle industries worldwide, but highest prevalence is found in the veal industry. Knowledge on M. bovis strain distribution over the dairy, beef and veal industries is crucial for the design of effective control and prevention programs, but currently undocumented. Therefore, the present study evaluated the molecular epidemiology and genetic relatedness of M. bovis isolates obtained from Belgian beef, dairy and veal farms, and how these relate to M. bovis strains obtained worldwide. Full genomes of one hundred Belgian M. bovis isolates collected over a 5-year period (2014–2019), obtained from 27 dairy, 38 beef and 29 veal farms, were sequenced by long-read nanopore sequencing. Consensus sequences were used to generate a phylogenetic tree in order to associate genetic clusters with cattle sector, geographical area and year of isolation. The phylogenetic analysis of the Belgian M. bovis isolates resulted in 5 major clusters and 1 outlier. No sector-specific M. bovis clustering was identified. On a world scale, Belgian isolates clustered with Israeli, European and American strains. Different M. bovis clusters circulated for at least 1.5 consecutive years throughout the country, affecting all observed industries. Therefore, the high prevalence in the veal industry is more likely the consequence of frequent purchase from the dairy and beef industry, than that a reservoir of veal specific strains on farm would exist. These results emphasize the importance of biosecurity in M. bovis control and prevention.

Abortions and perinatal mortalities (APM) substantially affect cattle industry efficiency. Various infectious and noninfectious factors have been associated with bovine APM worldwide. Infections are often considered pivotal due to their abortifacient potential, leading laboratories to primarily investigate relevant infectious agents for APM cases. Some infectious causes, such as Brucella abortus, have also a zoonotic impact, necessitating monitoring for both animal and human health. However, underreporting of bovine APM is a global issue, affecting early detection of infectious and zoonotic causes. Previous studies identified factors influencing case submission, but regional characteristics may affect results. In Belgium, farmers are obliged to report cases of APM within the context of a national brucellosis monitoring program. The inclusion criteria for this monitoring program cover abortions (gestation length of 42-260 d) and perinatal mortalities of (pre)mature calves following a gestation length of more than 260 d, which were stillborn or died within 48 h after birth. The objective of the present study was to describe the evolution in submission of APM cases within a mandatory abortion monitoring program in relation to subsidized initiatives in the northern part of Belgium. Based on the proportion of APM submissions versus the proportion of bovine reproductive females, an APM proportion (APM_PR) was calculated, and factors at both animal and herd level that may influence this APM_PR were explored by using linear models. This evaluation revealed that the APM_PR increased with the introduction of an extensive analytical panel of abortifacient agents and a free on-farm sample collection from 0.44% to 0.94%. Additionally, an increase of the APM_PR was associated with an outbreak of an emerging abortifacient pathogen (Schmallenberg virus; 1.23%), and the introduction of a mandatory eradication program for bovine viral diarrhea virus (BVDv; 1.20%). The APM_PR was higher in beef compared with dairy cattle, and it was higher in winter compared with fall, spring, and summer. Smaller herds categorized in the first quartile had a higher APM_PR compared with larger herds. Herds that submitted an APM in the previous year had a higher APM_PR in the next year compared with herds without an APM submission. Finally, herds for which there was evidence of the presence of BVDv had a higher APM_PR compared with herds without evidence of the presence of BVDv. In conclusion, the number of APM submissions increased after the introduction of a free on-farm sample collection and an extensive pathogen screening panel. Production type (beef), season (winter), smaller herd size, previous APM, and presence of BVDv seemed to have a positive effect on APM_PR. However, even under mandatory circumstances, APM still seems to be underreported, since the APM_PR was lower than the expected minimal rate of 2%. Therefore, further research is necessary to identify the drivers that convince farmers to submit APM cases to improve submission rates and ensure an efficient monitoring program for APM and eventually associated zoonotic pathogens.

Anaplasmosis, borreliosis, rickettsiosis and babesiosis are tick-borne diseases of medical, veterinary and economic importance. In Belgium, little is known on the prevalence of these diseases in animals and previous screenings relate only to targeted geographic regions, clinical cases or a limited number of tested samples. We therefore performed the first nationwide seroprevalence study of Anaplasma spp., A. phagocytophilum, Borrelia spp., Rickettsia spp. and Babesia spp. in Belgian cattle. We also screened questing ticks for the aforementioned pathogens. ELISAs and IFATs were performed on a representative sample set of cattle sera stratified proportionally to the number of cattle herds per province. Questing ticks were collected in areas where the highest prevalence for the forenamed pathogens in cattle serum were observed. Ticks were analyzed by quantitative PCR for A. phagocytophilum (n = 783), B. burgdorferi sensu lato (n = 783) and Rickettsia spp. (n = 715) and by PCR for Babesia spp. (n = 358). The ELISA screening for antibodies to Anaplasma spp. and Borrelia spp. in cattle sera showed an overall seroprevalence of 15.6% (53/339) and 12.9% (52/402), respectively. The IFAT screening for antibodies against A. phagocytophilum, Rickettsia spp. and Babesia spp. resulted in an overall seroprevalence of 34.2% (116/339), 31.2% (99/317) and 3.4% (14/412), respectively. At the provincial level, the provinces of Liege and Walloon Brabant harboured the highest seroprevalence of Anaplasma spp. (44.4% and 42.7% respectively) and A. phagocytophilum (55.6% and 71.4%). East Flanders and Luxembourg exhibited the highest seroprevalence of Borrelia spp. (32.4%) and Rickettsia spp. (54.8%) respectively. The province of Antwerp showed the highest seroprevalence of Babesia spp. (11%). The screening of field-collected ticks resulted in a prevalence of 13.8% for B. burgdorferi s.l., with B. afzelii and B. garinii being the most common genospecies (65.7% and 17.1%, respectively). Rickettsia spp. was detected in 7.1% of the tested ticks and the only identified species was R. helvetica. A low prevalence was found for A. phagocytophilum (0.5%) and no Babesia positive tick was detected. The seroprevalence data in cattle indicate hot spots for tick-borne pathogens in specific provinces and highlights the importance of veterinary surveillance in anticipating the emergence of diseases among humans. The detection of all pathogens, with the exception of Babesia spp. in questing ticks, underlines the need of raising awareness among public and professionals on other tick-borne diseases along with lyme borreliosis.

Hepatitis E virus (HEV) is the causative agent of hepatitis E disease in humans. While sporadic HEV infections, which occur in industrialised countries and are typically due to HEV genotypes 3 or 4, are asymptomatic and self-limiting, a chronic form of the disease can lead to liver cirrhosis in immunocompromised individuals. Pigs share HEV 3 and 4 genotypes and are thus considered a major animal reservoir for human infection. A subset of animals has been shown to carry HEV particles at the age of slaughter, rendering raw or undercooked pig products potential vectors for human infection. To provide an overview of the current dissemination of HEV in Belgian pig herds, this study was designed as a randomized, robust, large-scale, cross-sectional, serological survey. HEV genotypes and subtypes recently circulating in Belgium (2020–2021) were investigated. Sample stratification as well as epidemiological investigation through the available demographic data of the sampled herds showed that HEV widely circulated in the Belgian pig population during this time and that a change in the circulating HEV strains may have occurred in the last decade. Herd size and type were identified as risk factors for HEV herd-seropositivity. Identifying farms at risk of being HEV-positive is an important step in controlling HEV spread and human infection.

Hepatitis E viruses (HEV) cause hepatitis E in humans. In industrialized countries, sporadic HEV infections, typically caused by HEV genotypes 3 or 4, can become chronic and progress to liver cirrhosis in immunocompromised individuals. Pigs are a significant animal reservoir, implicating raw or undercooked pork products as potential sources of human infection. To better understand HEV dissemination in the Belgian pig population, potential risk factors were investigated by linking farm-level HEV serological status to biosecurity questionnaire data. Farrow-to-finish herd type, free-range systems, and poor boot hygiene were significantly associated with higher within-herd prevalences. This enabled an initial risk profiling of various farming types and the development of predictions for all Belgian pig farms. When combined with the census of the Belgian wild boar population, the predicted HEV status of all professional Belgian pig farms (based on these associations) does not suggest that the proximity of wild boars is a main source of HEV in free-ranging herds. Identifying risk factors for increased circulation of HEV between and within pig farms is critical to controlling its spread and reducing human infection.