Towards identification of new genetic determinants for post-weaning diarrhea in piglets.

Post-weaning diarrhea in pigs is a considerable challenge in the pig farming industry due to its effect on animal welfare and production costs, as well as the large volume of antibiotics, which are used to treat diarrhea in pigs after weaning. Previous studies have revealed loci on SSC6 and SSC13 associated with susceptibility to specific diarrhea causing pathogens. This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biological determinants for diarrhea susceptibility. With the present work, we revealed a new locus for diarrhea resistance on SSC16. Furthermore, studies of metabolomics in the same pigs revealed one metabolite associated with diarrhea.

The cotton swab method: an accurate and less invasive way to assess fecal consistency in weaned pigs.

BACKGROUND: Researchers and pig veterinarians are interested in assessing pigs' fecal consistency. This study developed a standardized protocol and scale for the cotton swab method, which is a way of assessing the fecal consistency in pigs. The accuracy of the cotton swab method was evaluated in weaned pigs using fecal dry-matter analysis as a golden standard. The study also proposed fecal dry-matter percentage thresholds for the categorization of fecal consistency on a four-point scale. RESULTS: The thresholds of 10.3%, 16.6%, and 21.9% fecal dry-matter were suggested for categorization of the consistency of fecal samples on a four-point scale. The accuracy of the cotton swab method was high. The agreement to the four-point fecal consistency score derived from the fecal dry-matter percentage was almost perfect (weighted Gwet's agreement coefficient = 0.87 [95% confidence interval: 0.84; 0.91]). The cotton swab method had a sensitivity of 85.0% (95% confidence interval: 76.5; 91.4) and a specificity of 95.2% (95% confidence interval: 92.0; 97.3) when used to diagnose whether pigs had diarrhea or not. For non-diarrheic pigs, the method almost always (n = 287/289) required less handling than the collection of a fecal sample by digital rectal manipulation. CONCLUSION: The cotton swab method is an accurate way to assess fecal consistency in pigs, both on a four-point scale and as a dichotomous diarrhea score. The method is quick to perform and less invasive than methods relying on the collection of fecal samples. New fecal dry-matter thresholds between feces of different consistencies were proposed.

Easy and reliable assessment of the prevalence of porcine post-weaning diarrhoea.

Post-weaning diarrhoea is a condition of increasing importance due to recent restrictions and bans on the preventive use of antimicrobials and medicinal zinc oxide. For various purposes, it is valuable to monitor the occurrence of post-weaning diarrhoea. The aim of this paper was to propose a protocol for easy and reliable assessment of the prevalence of post-weaning diarrhoea within a section of pigs as an alternative to clinical examination of a random sample of pigs. Two datasets were collected in two different observational field investigations, including more than 4000 individual clinical examinations of newly weaned pigs. First we identified a clinical marker for post-weaning diarrhoea. Second, we drew samples by simulation from our two dataset using different simplified sampling strategies and compared these to conventional random sampling strategies. The prediction error for estimates of the diarrhoea prevalence within a section was compared for the different sampling strategies. The study showed that pigs with diarrhoea had an increased risk of displaying diarrheic soiling of the hind part as well as dull, long, and bristly hair coat, and possibly also hollow flanks and a suboptimal body condition score. Diarrheic soiling of the hind part was the best clinical predictor of diarrhoea; our best estimate of the diagnostic sensitivity was 76.1% (95% credible interval: 72.0, 79.8), and the specificity was 97.1% (95% credible interval: 96.5 0.97.7). Diarrheic soiling of the hind is only a valid clinical predictor of diarrhoea for the first 14 days after insertion into the nursery unit. The precision and accuracy of prevalence estimates were similar for haphazard sampling compared to random sampling of the pigs. Likewise, sampling from a restricted number of pens produced prediction errors similar to sampling across all pens. Yet, the study had limitations regarding sample sizes, and furthermore it is difficult to provide certainty for absence of effects. We recommend sampling pigs haphazardly within at least three randomly selected pens for post-weaning diarrhoea prevalence surveys in order to easily obtain a reliable prevalence estimate. Based on our findings, we conclude the paper by proposing a simple four-step protocol for surveys of the within-section prevalence of post-weaning diarrhoea.

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.

An observational field study of porcine post-weaning diarrhea: clinical and microbiological findings, and fecal pH-measurements as a potential diagnostic tool.

BACKGROUND: Recently, in-feed medicinal zinc has been phased out in pig production in the European Union. This makes updated knowledge about porcine post-weaning diarrhea (PWD) crucial. The objectives of the present study were to investigate (i) the clinical presentation of PWD in pigs housed in Danish herds that did not use medicinal zinc, specifically the prevalence of diarrhea and whether PWD was associated to clinical signs of dehydration or altered body temperature; (ii) which microorganism are associated to PWD; and iii) whether measurements of the fecal pH have a potential to be used diagnostically to differentiate between infectious etiologies in cases of PWD. RESULTS: The prevalence of diarrhea varied considerably between the outbreaks in the nine studied herds (median = 0.58, range = 0.10; 0.94). In a cross-sectional design (n = 923), diarrhea was associated with reduced rectal temperature and alkaline feces. Diarrhea was also associated with observably reduced skin elasticity, possibly indicating dehydration. In both diarrheic case pigs (n = 87) and control pigs (n = 86), the presence of Brachyspira pilosicoli, Clostridium perfringens, Cryptosporidium spp., Cystoisopora suis, enterotoxigenic Escherichia coli, Lawsonia intracellularis, porcine circovirus types 2 and 3, rotavirus A, B, C, and H, Samonella enterica spp. enterica, and Trichuris suis was described. PWD was associated with high levels of enterotoxigenic E. coli shedding (odds ratio versus no E. coli detection = 4.79 [CI 1.14; 12.62]). Diarrhea was associated with high levels of rotavirus A shedding (odds ratio versus no/low rotavirus A = 3.80 [CI 1.33; 7.97]). The association between microbiological findings in diarrheic pigs and fecal pH was negligible. CONCLUSIONS: Enterotoxigenic E. coli was confirmed to be a cause of PWD; however, cases of PWD where enterotoxigenic E. coli was not detected in high levels occurred commonly, and this adds to the increasing evidence suggesting that PWD is not necessarily a result of enteric colibacillosis. Rotaviral enteritis might be a differential diagnosis of PWD. pH-measurements cannot be used to differentiate between differential diagnoses for PWD.

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.

A Systematic Review: Is Porcine Kobuvirus Causing Gastrointestinal Disease in Young Pigs?

Since porcine kobuvirus (PKV) was first described in 2008, researchers have speculated whether the virus is of clinical importance. This systematic literature review answers the question: Is porcine kobuvirus a cause of gastrointestinal disease in young pigs? A case-control study showed that PKV was not associated with neonatal diarrhea. A cohort study suffered from a very small sample size (n = 5), and in an experimental trial, the effect of PKV inoculation could not be separated from the effect of being inoculated with porcine epidemic diarrhea virus. In 13 poorly defined observational studies, more than 4000 young pigs had been assigned a diarrhea status and their feces analyzed for PKV. Unfortunately, the studies lacked well-characterized unbiased samples, and thus the strongest possible inference from these studies was that a very strong association between PKV and diarrhea is unlikely. PKV was commonly detected in non-diarrheic pigs, and this could indicate that PKV is not a sufficient cause in itself or that reinfection of individuals with some immunological protection due to previous infections is common. Conclusively, there is a lack of good evidence of PKV being a cause of gastrointestinal disease, but the sparse available evidence suggests that PKV is of limited clinical importance.

Bacterial topography of the upper and lower respiratory tract in pigs.

BACKGROUND: Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing. RESULTS: The bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT. CONCLUSION: We provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.

Evidence-Based Recommendations for Herd Health Management of Porcine Post-Weaning Diarrhea.

Aided by their advising veterinarians, pig producers need to make difficult decisions regarding herd health management strategies. For instance, the preventive use of antimicrobials and medicinal zinc oxide must be substituted with more sustainable preventive approaches to porcine post-weaning diarrhea. Veterinarians and pig producers may find assistance in knowledge based on evidence in this regard; however, the overwhelming scientific literature is not always readily available. The overall aim of this paper is to suggest herd health management decision-support tools that can aid veterinary-assisted decision making in the control of porcine post-weaning diarrhea at a tactical level. The first objective was to validate the need for a herd health management concept, including two decision-support tools. The second objective was to develop evidence-based recommendations that can aid veterinary-assisted decision-making for the herd health management of post-weaning diarrhea. The first objective was investigated by a questionnaire-based study among veterinary pig practitioners in Denmark. For the second objective, we conducted a scientific summary based on scientific review papers identified through a systematic search in three databases. From the papers, we synthesized and extracted 79 specific recommendations. In this paper, we report comprehensive evidence-based recommendations for the herd health management of post-weaning diarrhea.

Post-weaning diarrhea in pigs weaned without medicinal zinc: risk factors, pathogen dynamics, and association to growth rate.

BACKGROUND: Porcine post-weaning diarrhea (PWD) has reemerged as an important topic in pig production, as common control strategies based on prophylactic use of antimicrobials and zinc oxide have been deemed unsustainable. The objectives of this study were to estimate the cumulative incidence of porcine post-weaning diarrhea with different etiologies in production systems weaning without zinc oxide and prophylactic antimicrobials, to assess risk factors for post-weaning diarrhea, and to estimate the impact of post-weaning diarrhea on growth rate. A cohort study was conducted at two commercial indoor producers weaning without medicinal zinc oxide and prophylactic antimicrobials. RESULTS: Piglets were included at birth (n = 300) and 272 survived until weaning. After insertion to the nursery units, the piglets were clinically examined every day for 14 days, and rectal swabs were collected and analyzed for enterotoxigenic Escherichia coli (ETEC) and rotavirus A. The cumulative incidences of PWD the first 14 days after insertion to the nursery units were 41.8% (CI 33.6, 50.4) and 51.1% (CI 42.3, 60.0) at the two producers, respectively. We found a low incidence of cases associated to ETEC, and detected a substantial proportion of cases associated to rotavirus. We observed a biphasic pattern in the assumed etiology with rotavirus occurring first, and then a shift towards cases associated to ETEC/non-ETEC hemolytic E. coli. Being offspring of older sows was a protective factor for the development of PWD (Hazard ratio = 0.88 [CI 0.78, 0.99] per unit increase in parity of the dam). Low birth weight reduced the post-weaning growth rate (- 5.2 g/day [CI - 7.5, - 2.9] per 100 g decrease in birthweight) and increased the hazard of developing PWD (Hazard ratio for birthweight below 1100 g: 2.30 [CI 1.41-3.74]). The combined effect of having diarrhea for 2 days or more and receiving antimicrobial treatment was associated with an increased average daily weight gain. CONCLUSIONS: This study suggests novel insights regarding pathogen dynamics and risk factors for PWD in productions not using prophylactic antimicrobials and medicinal zinc. The findings may have important implications for both antimicrobial usage and prevention strategies.