Gastrointestinal nematodes in German outdoor-reared pigs based on faecal egg count and next-generation sequencing nemabiome data.

BACKGROUND: There is a higher risk for nematode infections associated with outdoor-reared pigs. Next to Ascaris suum, Oesophagostomum dentatum and Trichuris suis, there is the potential of infections with other nodular worm species, Hyostrongylus rubidus, Stongyloides ransomi and Metastrongylus spp. lungworms. Next-generation sequencing methods describing the nemabiome have not yet been established for porcine nematodes. METHODS: FLOTAC was used for faecal egg counts of porcine gastrointestinal nematodes and lungworms in piglets, fatteners and adults individually. A nemabiome analyses based on ITS-2 gene region metabarcoding was used to differentiate strongyle species. Additionally, questionnaire data was analysed using mixed-effect regression to identify potential risk factors associated with parasite occurrences and egg shedding intensity. RESULTS: On 15 of 17 farms nematode eggs were detected. Ascaris suum, strongyles and T. suis were detected on 82%, 70% and 35% of the 17 farms, respectively. Lungworms were detected on one out of four farms with access to pasture. Strongyloides ransomi was not detected. 32% (CI 28-36%), 27% (24-31%), 5% (4-7%) and 3% (0.9-8%) of the samples where tested positive for strongyles, A. suum, T. suis and lungworms, respectively. The nemabiome analysis revealed three different strongyle species, with O. dentatum being the most common (mean 93.9%), followed by O. quadrispinulatum (5.9%) and the hookworm Globocephalus urosubulatus (0.1%). The bivariate and multivariate risk factor analyses showed among others that cleaning once a week compared to twice a week increased the odds significantly for being infected with A. suum (OR 78.60) and strongyles (2077.59). Access to pasture was associated with higher odds for A. suum (43.83) and strongyles (14.21). Compared to shallow litter systems, deep litter and free range systems resulted in significant higher odds for strongyles (85.74, 215.59, respectively) and T. suis (200.33, 623.08). CONCLUSIONS: Infections with A. suum, O. dentatum, O. quadrispinulatum, T. suis, Metastrongylus spp. and G. urosubulatus are present in German outdoor-reared pigs. This is the first report of G. urosubulatus in domestic pigs in Europe. Metabarcoding based on the ITS-2 region is a suitable tool to analyse the porcine nemabiome. Furthermore, management practices have the potential of reducing the risk of parasite infections.

Health Monitoring of Fattening Pigs - Use of Production Data, Farm Characteristics and On-Farm Examination.

BACKGROUND: The use of processed secondary data for health monitoring of fattening pigs has been established in various areas, such as the use of antibiotics or in the context of meat inspection. Standardized scores were calculated based on several sources of production data and can be used to describe animal health in a large collective of pig units. In the present study, the extent to which these scores are related to different farm characteristics and management decisions were investigated. In addition, slaughter scores were compared with the results of a veterinary examination on the farms. RESULTS: The comparison of the results of the uni- and multifactorial analyses revealed that almost all of the examined factors play a role in at least one of the scores when considered individually. However, when various significant influencing factors were taken into account at any one time, most of the variables lost their statistical significance due to confounding effects. In particular, production data such as production costs or daily feed intake remained in the final models of the scores on mortality, average daily gain and external lesions. Regarding the second part of the investigation, a basic technical correlation between the slaughter scores and the on-farm indicators could be established via principal component analysis. The modelling of the slaughter scores by the on-farm indicators showed that the score on external lesions could be represented by equivalent variables recorded on the farm (e.g., lesions caused by tail or ear biting). CONCLUSIONS: It has been demonstrated that the examined health scores are influenced by various farm and management characteristics. However, when several factors are taken into account, confounding occurs in some cases, which must be considered by consultants. Additionally, it was shown that on-farm examination content is related to the scores based on equivalent findings from slaughter pigs.

Application of the voluntary human approach test on commercial pig fattening farms: a meaningful tool?

BACKGROUND: A Voluntary Human Approach Test (VHAT) was performed in pig pens, and relationships between environmental conditions and welfare indicators were investigated. Five variables were measured in 1668 pens in 214 fattening pig herds in Germany: time until the first contact (touching) between a pig and the person in the pen (TUFC), time until the observer was surrounded by pigs within a radius of approximately two meters, percentage of pigs relative to group size [%] surrounding the observer after 1 min (PPSO), percentage of pigs relative to group size [%] that completely avoided contact with the observer during the entire test period, and how the pigs contacted the observer (Score 0 [no touching] - 3 [biting]). Furthermore, variables indicative of the pigs' environment (e.g., feeding system, ventilation system), management (e.g., number of usable drinkers, number of usable manipulatable materials), and welfare (e.g., tail lesions, ear lesions) were documented. RESULTS: Pigs engaging in more forceful means of contact (nibbling, biting) approached the observer faster than those exhibiting more gentle types of contact (touching). A lower TUFC was associated with more manipulatable materials present, a higher number of drinkers, and with the control position of the caretaker located inside the pen. Pigs kept in larger groups showed a lower TUFC than those in smaller groups (P = 0.0191). However, PPSO was lower in pigs kept in smaller groups (1-12 pigs per pen) with more manipulatable materials available. In groups with low PPSOs, more tail lesions were observed (P = 0.0296). No relationship between contact type and tail or ear injuries was detected. In younger pigs, PPSO was higher (49.9 ± 23.2%) than for animals in the second half of the fattening period (45.1 ± 19.9%). CONCLUSIONS: In this on-farm study, the relationships between VHAT behavior and environmental factors revealed that external factors (e.g., management practices, housing conditions) impact animals' responses to this behavioral test. Therefore, using the VHAT as an animal welfare indicator is valid only if these variables are studied as well.

Restricted Versus Unrestricted Search Space: Experience from Mining a Large Japanese Database.

The aim of this study was to investigate whether standard Big Data mining methods lead to clinically useful results. An association analysis was performed using the apriori algorithm to discover associations among co-morbidities of diabetes patients. Selected data were further analyzed by using k-means clustering with age, long-term blood sugar and cholesterol values. The association analysis led to a multitude of trivial rules. Cluster analysis detected clusters of well and badly managed diabetes patients both belonging to different age groups. The study suggests the usage of cluster analysis on a restricted space to come to meaningful results.

Clostridium difficile genotypes in piglet populations in Germany.

Clostridium difficile was isolated from 147 of 201 (73%) rectal swabs of piglets from 15 farms of Lower Saxony and North Rhine-Westphalia. In 14 farms, 14 to 100% (mean, 78%) of the animals tested were culture positive. The rate of isolation was 68% postpartum, increased to 94% in animals 2 to 14 days of age, and declined to 0% for animals 49 days of age and older. There was no link between isolation and antibiotic treatment or diarrhea of piglets. Strains were assigned to 10 PCR ribotypes, and up to 4 PCR ribotypes were found to be present at the same time on a farm. The closely related PCR ribotypes 078 (55%) and 126 (20%) were most frequently recovered and were present in 13 of the 14 positive farms. The comparison of multilocus VNTR (variable number of tandem repeats) analysis (MLVA) data from this study and previously published data on human, porcine, and bovine PCR ribotype 078 isolates from 5 European countries revealed genetic differences between strains of different geographic origin and confirmed the relatedness of human and porcine C. difficile isolates. This study demonstrated that the human-pathogenic PCR ribotypes 078 and 126 are predominant in piglets in Germany. The results suggest that presence of C. difficile is correlated with animal age but not with antibiotic treatment or clinical disease. MLVA indicated that strains of the same geographical origin are often genetically related and corroborated the hypothesis of a close epidemiological connection between human and porcine C. difficile isolates.