Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments

BACKGROUND

The global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets' health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.

RESULTS

The control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.

CONCLUSIONS

Overall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.

Invasive Streptococcus suis isolated in Spain contain a highly promiscuous and dynamic resistome

Introduction

Streptococcus suis is a major pathogen for swine and human. Here we aimed to know the rates of antimicrobial resistance (AMR) in invasive S. suis isolates recovered along Spain between 2016 - 2021 and elucidate their genetic origin.

Methods

Antibiotic susceptibility testing was performed for 116 isolates of different genetic backgrounds and geographic origins against 18 antibiotics of 9 families. The association between AMR and genotypes and the origin of the isolates were statistically analyzed using Pearson´s chi-square test and the likelihood ratio. The antimicrobial resistant genes were identified by whole genome sequencing analysis and PCR screenings.

Results

High AMR rates (>80%) were detected for tetracyclines, spectinomycin, lincosamides, and marbofloxacin, medium (20-40%) for sulphonamides/trimethoprim, tiamulin, penicillin G, and enrofloxacin, and low (< 20%) for florfenicol, and four additional β-lactams. The occurrence of multidrug resistance was observed in 90% of isolates. For certain antibiotics (penicillin G, enrofloxacin, marbofloxacin, tilmicosin, and erythromycin), AMR was significantly associated with particular sequence types (STs), geographic regions, age of pigs, and time course. Whole genome sequencing comparisons and PCR screenings identified 23 AMR genes, of which 19 were previously reported in S. suis (aph(3')-IIIa, sat4, aadE, spw, aac(6')-Ie-aph(2'')-Ia, fexA, optrA, erm(B), mef(A/E), mrs(D), mph(C), lnu(B), lsa(E), vga(F), tet(M), tet(O), tet(O/W/32/O), tet(W)), and 4 were novel (aph(2'')-IIIa, apmA, erm(47), tet(T)). These AMR genes explained the AMR to spectinomycin, macrolides, lincosamides, tiamulin, and tetracyclines. Several genes were located on mobile genetic elements which showed a variable organization and composition. As AMR gene homologs were identified in many human and animal pathogens, the resistome of S. suis has a different phylogenetic origin. Moreover, AMR to penicillin G, fluoroquinolones, and trimethoprim related to mutations in genes coding for target enzymes (pbp1a, pbp2b, pbp2x, mraY, gyrA, parC, and dhfr). Bioinformatic analysis estimated traits of recombination on target genes, also indicative of gene transfer events.

Conclusions

Our work evidences that S. suis is a major contributor to AMR dissemination across veterinary and human pathogens. Therefore, control of AMR in S. suis should be considered from a One Health approach in regions with high pig production to properly tackle the issue of antimicrobial drug resistance.

The Susceptibility Trends of Respiratory and Enteric Porcine Pathogens to Last-Resource Antimicrobials

Monitoring the antimicrobial susceptibility of last-resource antimicrobials for veterinary pathogens is urgently needed from a one-health perspective. The objective of this study was to analyze the antimicrobial susceptibility trends of Spanish porcine bacteria to quinolones, cephalosporins, and polymyxins. Isolates of Actinobacillus pleuropneumoniae, Pasteurella multocida, and Escherichia coli were isolated from sick pigs from 2019 to 2022. An antimicrobial susceptibility test was determined based on the minimal inhibitory concentration (MIC) following an internationally accepted methodology. The MIC categorization was based on distributing the range of MIC values in four categories, with category one being the most susceptible (lowest MIC value) and category four the least susceptible (highest MIC value). Moreover, clinical susceptibility (susceptible/non-susceptible) was also determined according to the CLSI and EUCAST clinical breakpoints. A logistic and multinomial logistic regression model was used to analyze the susceptibility data for dichotomized and categorized MIC data, respectively, for any pair of antimicrobial/microorganism. In general terms, the antimicrobial susceptibility of pig bacteria to these antimicrobials remained stable or increased in the last four years in Spain. In the case of A. pleuropneumoniae and quinolones, a significant temporal trend was observed where isolates from 2020 had significantly increased odds of being more susceptible than isolates from 2019. In the case of E. coli and polymyxins, a significant temporal trend was observed where isolates from 2020 and 2021 had significantly increased odds of being more susceptible than isolates from 2019 and 2020, respectively. Finally, significant odds of being less susceptible were only observed for cephalosporins and E. coli for 2020 versus 2019, stagnating for the rest of study period. These results provide sound data on critically important antimicrobials in swine medicine.

Susceptibility trends of swine respiratory pathogens from 2019 to 2022 to antimicrobials commonly used in Spain

BACKGROUND

Antimicrobial resistance is one of the most important health challenges in humans and animals. Antibiotic susceptibility determination is used to select the most suitable drug to treat animals according to its success probability following the European legislation in force for these drugs. We have studied the antibiotic susceptibility pattern (ASP) of Actinobacillus pleuropneumoniae (APP) and Pasteurella multocida (PM) isolates, collected during the period 2019-2022 in Spain. ASP was measured by determining minimum inhibitory concentration using standardized laboratory methods and its temporal trend was determined by logistic regression analysis of non-susceptible/susceptible isolates using clinical breakpoints.

RESULTS

It was not observed any significant temporal trends for susceptibility of Actinobacillus pleuropneumoniae to ceftiofur, florfenicol, sulfamethoxazole/trimethoprim, tulathromycin and tildipirosin during the study period (p > 0.05). Contrarily, a significant temporal trend (p < 0.05) was observed for quinolones (enrofloxacin and marbofloxacin), tetracyclines (doxycycline and oxyteracycline), amoxicillin, tiamulin and tilmicosin. On the other hand, it was not observed any significant temporal trends for susceptibility of Pasteurella multocida to quinolones (enrofloxacin and marbofloxacin), amoxicillin, ceftiofur, florfenicol and macrolides (tildipirosin, tulathromycin and tilmicosin) during the study period (p > 0.05). Contrarily, a significant temporal trend (p < 0.05) was observed for tetracyclines (oxyteracycline), tiamulin and sulfamethoxazole/trimethoprim.

CONCLUSIONS

In general terms, pig pathogens (APP and PM) involved in respiratory diseases analysed herein appeared to remain susceptible or tended to increase susceptibility to antimicrobials over the study period (2019-2022), but our data clearly showed a different pattern in the evolution of antimicrobial susceptibility for each combination of drug and microorganism. Our results highlight that the evolution of antimicrobial susceptibility must be studied in a case-by-case situation where generalization for drug families and bacteria is not possible even for bacteria located in the same ecological niche.

Key performance indicators used by dairy consultants during the evaluation of reproductive performance during routine visits

Dairy farms need thorough and efficient reproduction control. Consultants specialized in reproduction use key performance indicators (KPI) to monitor the reproductive performance of farms and must be able to decipher between the approach in a first visit and routine visits. A total of 49 consultants specialized in dairy reproduction from 21 countries responded to an online survey conducted to determine the most suitable parameters during routine visits every 2 to 4 weeks. The survey was comprised of 190 questions, 178 of them rated from 0 (irrelevant) to 10 (maximum importance) points. The questions were divided into five sections: (1) consultant and farm model, (2) general data of the farm, (3) cow reproduction, (4) postpartum and metabolic disease, and (5) heifer reproduction. The median, interquartile range, minimum and maximum values, and 95% confidence interval were determined for each question. Afterward, a multivariate analysis, using between-group linkage via Ward's hierarchical clustering was conducted to generate clusters of consultants according to their response pattern. Finally, a chi-square test was conducted to assess the association between years of experience of the consultant and farm size within the clusters generated in each section of the questionnaire. The majority of the consultants considered 34 parameters to be highly important (rated 8-10) to analyze during routine visits. The consultants used several KPI (in variable quantitative range) to evaluate any of the presented sections and considered that all the five sections are critical to control. They are aware of using KPI that reflect heat detection, fertility, and farming efficiency as well as KPI that can provide information on reproductive efficiency in the near future for cows, such as postpartum and metabolic diseases. However, parameters that are relatively old and ineffective, in terms of reproductive performance control, are still highly regarded by the majority of consultants in a routine-visit scenario. Farm size and years of experience of the consultant did not influence the type or number of parameters chosen as KPI during routine visits. The parameters rated with the highest importance (rate 10) that could be considered for an easy, fast, and universal use in routine visits to assess the reproductive status were: First service CR (%), Overall pregnancy rate (%) for cows, and age at first calving (d) for heifers.

How Streptococcus suis escapes antibiotic treatments

Streptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.

Technological Tools for the Early Detection of Bovine Respiratory Disease in Farms

Simple Summary

The inclusion of remote automatic systems that use continuous learning technology are of great interest in precision livestock cattle farming, since the average size of farms is increasing while time for individual observation is decreasing. Bovine respiratory disease is a main concern in both fattening and heifer rearing farms due to its impact on antibiotic use, loss of performance, mortality, and animal welfare. Much scientific literature has been published regarding technologies for continuous learning and monitoring of cattle’s behavior and accurate correlation with health status, including early detection of bovine respiratory disease. This review summarizes the up-to-date technologies for early diagnosis of bovine respiratory disease and discusses their advantages and disadvantages under practical conditions.

Abstract

Classically, the diagnosis of respiratory disease in cattle has been based on observation of clinical signs and the behavior of the animals, but this technique can be subjective, time-consuming and labor intensive. It also requires proper training of staff and lacks sensitivity (Se) and specificity (Sp). Furthermore, respiratory disease is diagnosed too late, when the animal already has severe lesions. A total of 104 papers were included in this review. The use of new advanced technologies that allow early diagnosis of diseases using real-time data analysis may be the future of cattle farms. These technologies allow continuous, remote, and objective assessment of animal behavior and diagnosis of bovine respiratory disease with improved Se and Sp. The most commonly used behavioral variables are eating behavior and physical activity. Diagnosis of bovine respiratory disease may experience a significant change with the help of big data combined with machine learning, and may even integrate metabolomics as disease markers. Advanced technologies should not be a substitute for practitioners, farmers or technicians, but could help achieve a much more accurate and earlier diagnosis of respiratory disease and, therefore, reduce the use of antibiotics, increase animal welfare and sustainability of livestock farms. This review aims to familiarize practitioners and farmers with the advantages and disadvantages of the advanced technological diagnostic tools for bovine respiratory disease and introduce recent clinical applications.

A genome-wide screen for resilient responses in growing pigs

Background

There is a growing interest to decipher the genetic background of resilience and its possible improvement through selective breeding. The objective of the present study was to provide new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. Commercial Duroc pigs were challenged with an attenuated Aujeszky vaccine at 12 weeks of age. Two resilience indicators were used: deviation from the expected body weight at 16 weeks of age given the growth curve of non-vaccinated pigs (∆BW) and the increase in acute-phase protein haptoglobin at four days post-vaccination (∆HP). Genome-wide association analyses were carried out on 445 pigs, using genotypes at 41,165 single nucleotide polymorphisms (SNPs) and single-marker and Bayesian multiple-marker regression approaches.

Results

Genomic regions on pig chromosomes 2, 8, 9, 11 (∆BW) and 8, 9, 13 (∆HP) were found to be associated with the resilience indicators and explained high proportions of their genetic variance. The genomic regions that were associated explained 27 and 5% of the genetic variance of ∆BW and ∆HP, respectively. These genomic regions harbour promising candidate genes that are involved in pathways related to immune response, response to stress, or signal transduction (CD6, PTGDR2, IKZF1, RNASEL and MYD88), and growth (GRB10 and LCORL).

Conclusions

Our study identified novel genomic regions that are associated with two resilience indicators (∆BW and ∆HP) in pigs. These associated genomic regions harbour potential candidate genes involved in immune response and growth pathways, which emphasise the strong relationship between resilience and immune response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00739-1.

Key Performance Indicators Used by Dairy Consultants During the Evaluation of Reproductive Performance in a First Visit

Reproduction plays a fundamental role in the profitability of dairy farms. Consultants use key performance indicators (KPI) to monitor the reproductive performance of the farms. They must decipher between the most suitable ones to face two different scenarios that may need the analysis of different parameters: (1) approach in a first visit, and (2) routine visits. Forty-nine consultants specialized in dairy reproduction from 21 countries responded to an online survey conducted to determine the most suitable parameters in a first visit approach. The survey was comprised of 190 questions, 178 of them rated from 0 (irrelevant) to 10 (maximum importance) points. The questions were divided into 5 sections: (1) consultant and farm model, (2) general data of the farm, (3) cow reproduction, (4) postpartum and metabolic disease, and (5) heifer reproduction. The median, interquartile range, minimum and maximum values, and 95% confidence interval (CI) were determined for each question. Afterward, a multivariate analysis, using between-group linkage via Ward's hierarchical clustering was conducted to generate clusters of consultants according to their response pattern. Lastly, a Chi-square test was conducted to assess the association between the years of experience of the consultant and farm size within the clusters generated in each section of the questionnaire. Most of the consultants considered 27 parameters to be highly important to analyze during the first visit. Consultants use several KPIs (in variable quantitative range) to evaluate any of the presented sections. Moreover, consultants preferred parameters focused on heat detection, fertility, and pregnancy achievement regarding the production cycle of a dairy cow. Consultants also showed high interest in obtaining a general overview of milk production, farming efficiency, and the heifer rearing process; but the farm size and the years of experience of the consultant influenced the type and number of parameters chosen as KPI. The parameters rated with the highest importance (rate 10) that could be considered for an easy, fast, and universal first visit to assess the reproductive status were: first service conception rate, overall pregnancy rate, and 21d pregnancy rate for cows, and age at first calving for heifers.

Porcine Reproductive and Respiratory Syndrome Surveillance in breeding Herds and Nurseries Using Tongue Tips from Dead Animals

The detection capacity of Porcine Reproductive and Respiratory Syndrome virus (PRRSV) in tongues from dead animals in breeding herds (stillborns and piglets dying during the lactating period) and nursery farms (naturally dead animals) for PRRSV surveillance was evaluated. The samples were selected if pairs of serum and tongues were available from 2018 to 2020. Serum (pools of five) and exudate from tongues (one bag) were analyzed by PRRSV RT-PCR. The agreement between the serum sample procedure versus tongues exudate was assessed using a concordance test (Kappa statistic) at batch level. A total of 32 submissions, corresponding to 14 farms, had PRRSV diagnostic information for serum and tongues exudate. The overall agreement of batch classification as positive or negative, based on RT-PCR PRRSV results, between serum and tongue exudate of the 32 pairs was 76.9%. Cohen's Kappa was 0.55. The main discrepancy came from the presence of positive samples in tongues exudate and not in serum, suggesting that tongue exudate to monitor PRRSV seems to be more sensitive than serum. These results suggest that this sample procedure could be also used for PRRSV surveillance and monitoring.

A Methodology to Quantify Resilience in Growing Pigs

Simple Summary

The concept of resilience can be defined as the ability of animals to maintain their productivity despite the stressors that might occur during the rearing period. Despite the growing interest in the genetic determinism of resilience and its possible inclusion in selection objectives, there is no straightforward method to measure this trait. Several quantifying methods estimate resilience based on productivity such as body weight or milk production, or non-productivity related traits such as immunity or stress responses. The objective of this study was to elaborate novel resilience indicators in growing pigs based on both productivity (body weight) and non-productivity (acute-phase proteins) related traits. We propose the deviation from the expected growth curve and the increment of the acute-phase protein haptoglobin, after applying a common vaccine, as resilience indicators in growing pigs under standard rearing conditions. We showed that the suggested resilience indicators are under a genetic control, show a substantial variability in the population, and may be improved through selection.

Abstract

There is a growing concern about the genetic determinism of resilience and its possible implementation in breeding programs. The objective of our study was to elaborate novel resilience indicators in growing pigs based on the deviation from the expected growth curve and the increment of the acute-phase protein haptoglobin (HP) after applying a common vaccine. A total of 445 pigs were vaccinated with an attenuated Aujeszky vaccine at 12 weeks of age. Deviation from the expected body weight (ΔBW) given the growth curve of unvaccinated pigs at 28 days post-vaccination (DPV) and the increment of HP at 4 DPV (ΔHP) were suggested as resilience indicators. Challenged pigs that maintained their productivity and had a minor activation of HP were deemed resilient, whereas pigs that had low ∆BW values and a high activation of HP were deemed susceptible. Pigs were also classified based on ∆BW and ∆HP relative to the expected BW at 28 DPV and to the basal level of HP, respectively. The concordance was high between both methods, indicating that ΔBW and ΔHP are not sensitive to the animal’s expected BW nor the basal level of HP. The heritability estimates were moderate for ∆BW (0.33) and low-to-moderate for ∆HP (0.16). Our study suggests ΔBW and ΔHP as novel resilience indicators in pigs. The suggested indicators capture different aspects of resilience, are easy to measure, and are genetically controlled. Thus, they may be improved through selective breeding. Further analyses are needed to validate our findings.

Modelling the SARS-CoV-2 outbreak: Assessing the usefulness of protective measures to reduce the pandemic at population level

A new bioinspired computational model was developed for the SARS-CoV-2 pandemic using the available epidemiological information, high-resolution population density data, travel patterns, and the average number of contacts between people. The effectiveness of control measures such as contact reduction measures, closure of communities (lockdown), protective measures (social distancing, face mask wearing, and hand hygiene), and vaccination were modelled to examine possibilities for control of the disease under several protective vaccination levels in the population. Lockdown and contact reduction measures only delay the spread of the virus in the population because it resumes its previous dynamics as soon as the restrictions are lifted. Nevertheless, these measures are probably useful to avoid hospitals being overwhelmed in the short term. Our model predicted that 56% of the Spanish population would have been infected and subsequently recovered over a 130 day period if no protective measures were taken but this percentage would have been only 34% if protective measures had been put in place. Moreover, this percentage would have been further reduced to 41.7, 27.7, and 13.3% if 25, 50 and 75% of the population had been vaccinated, respectively. Finally, this percentage would have been even lower at 25.5, 12.1 and 7.9% if 25, 50 and 75% of the population had been vaccinated in combination with the application of protective measures, respectively. Therefore, a combination of protective measures and vaccination would be highly efficacious in decreasing not only the number of those who become infected and subsequently recover, but also the number of people who die from infection, which falls from 0.41% of the population over a 130 day period without protective measures to 0.15, 0.08 and 0.06% if 25, 50 and 75% of the population had been vaccinated in combination with protective measures at the same time, respectively.

Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis

Fibrinous polyserositis in swine farming is a common pathological finding in nursery animals. The differential diagnosis of this finding should include Glaesserella parasuis (aetiological agent of Glässer's disease) and Mycoplasma hyorhinis, among others. These microorganisms are early colonizers of the upper respiratory tract of piglets. The composition of the nasal microbiota at weaning was shown to constitute a predisposing factor for the development of Glässer's disease. Here, we unravel the role of the nasal microbiota in the subsequent systemic infection by M. hyorhinis, and the similarities and differences with Glässer's disease. Nasal samples from farms with recurrent problems with polyserositis associated with M. hyorhinis (MH) or Glässer's disease (GD) were included in this study, together with healthy control farms (HC). Nasal swabs were taken from piglets in MH farms at weaning, before the onset of the clinical outbreaks, and were submitted to 16S rRNA gene amplicon sequencing (V3-V4 region). These sequences were analyzed together with sequences from similar samples previously obtained in GD and HC farms. Animals from farms with disease (MH and GD) had a nasal microbiota with lower diversity than those from the HC farms. However, the composition of the nasal microbiota of the piglets from these disease farms was different, suggesting that divergent microbiota imbalances may predispose the animals to the two systemic infections. We also found variants of the pathogens that were associated with the farms with the corresponding disease, highlighting the importance of studying the microbiome at strain-level resolution.

Modeling of Vaccination and Contact Tracing as Tools to Control the COVID-19 Outbreak in Spain

We developed an agent-based stochastic model, based on P Systems methodology, to decipher the effects of vaccination and contact tracing on the control of COVID-19 outbreak at population level under different control measures (social distancing, mask wearing and hand hygiene) and epidemiological scenarios. Our findings suggest that without the application of protection social measures, 56.1% of the Spanish population would contract the disease with a mortality of 0.4%. Assuming that 20% of the population was protected by vaccination by the end of the summer of 2021, it would be expected that 45% of the population would contract the disease and 0.3% of the population would die. However, both of these percentages are significantly lower when social measures were adopted, being the best results when social measures are in place and 40% of contacts traced. Our model shows that if 40% of the population can be vaccinated, even without social control measures, the percentage of people who die or recover from infection would fall from 0.41% and 56.1% to 0.16% and 33.5%, respectively compared with an unvaccinated population. When social control measures were applied in concert with vaccination the percentage of people who die or recover from infection diminishes until 0.10% and 14.5%, after vaccinating 40% of the population. Vaccination alone can be crucial in controlling this disease, but it is necessary to vaccinate a significant part of the population and to back this up with social control measures.

Using PRRSV-Resilient Sows Improve Performance in Endemic Infected Farms with Recurrent Outbreaks

Simple Summary

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease responsible for huge economic losses to the pig industry. The selection of PRRSV resilient sows has been proposed as a strategy to control this disease. A simulation model was developed to test the differences in reproductive performance and economic outcome of resilient or susceptible sows under farm PRRSV endemic conditions with or without recurrent PRRSV outbreaks. The data from phenotyped sows came from a PRRSV-positive farm with 1500 sows that suffered a PRRSV outbreak that lasted 24 weeks within three years. The reproductive parameters were generally better for resilient than for susceptible sows in PRRSV-positive farms suffering recurrent PRRSV outbreaks. Consequently, the piglet production cost was lower for resilient than for susceptible sows in any condition but showed only significant differences in PRRSV endemic farms suffering recurrent outbreaks. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows under endemic conditions with or without recurrent outbreaks. Thus, the selection of PRRSV resilient sows is always a profitable approach for producers supporting the control of this disease.

Abstract

The selection of porcine reproductive and respiratory syndrome (PRRS) resilient sows has been proposed as a strategy to control this disease. A discrete event-based simulation model was developed to mimic the outcome of farms with resilient or susceptible sows suffering recurrent PRRSV outbreaks. Records of both phenotypes were registered in a PRRSV-positive farm of 1500 sows during three years. The information was split in the whole period of observation to include a PRRSV outbreak that lasted 24 weeks (endemic/epidemic or En/Ep) or only the endemic phase (En). Twenty simulations were modeled for each farm: Resilient/En, Resilient/En_Ep, Susceptible/En, and Susceptible/En_Ep during twelve years and analyzed for the productive performance and economic outcome, using reference values. The reproductive parameters were generally better for resilient than for susceptible sows in the PRRSV En/Ep scenario, and the contrary was observed in the endemic case. The piglet production cost was always lower for resilient than for susceptible sows but showed only significant differences in the PRRSV En/Ep scenario. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows for the PRRSV endemic (12%) and endemic/epidemic scenarios (17%). Thus, the selection of PRRSV resilient sows is a profitable approach for producers to improve disease control.

A Cow-Calf Farming System Fully Adapted to Elevation and Harsh Conditions in Andorra (Europe)

The use of natural resources is an important topic to optimize the efficiency of cattle production. The purpose of this work is to describe the project of the Bruna d'Andorra; a local cow breed under an extensive cow-calf system in Andorra (Europe), as an example of local farming and marketing of its meat products in an area with adverse environmental conditions. This breed is located in Andorra, a microstate that consists predominantly of rugged mountains and harsh weather conditions. The cow-calf Bruna d'Andorra extensive system is thoroughly described and productive and reproductive performance, compiled over 21 years (2000-2020), has been analyzed by years with the Chi-square test or ANOVA to compare proportions or means, respectively, and regression analysis was used to decipher evolution across years. The results show a population with a census large and stable enough to avoid inbreeding. Moreover, a sustained improvement of the productive performance and maternal fitness has been observed along the studied period for Bruna d'Andorra. The work concludes that local breeds can achieve sustainable animal production, especially when farmers, public administration and commercial circuits in the area agree to cooperate on such projects. The study also concludes that the Bruna d'Andorra cow breed can still improve in meat and reproductive performance.

Angular momentum generation in nuclear fission

When a heavy atomic nucleus splits (fission), the resulting fragments are observed to emerge spinning¹; this phenomenon has been a mystery in nuclear physics for over 40 years^2,3. The internal generation of typically six or seven units of angular momentum in each fragment is particularly puzzling for systems that start with zero, or almost zero, spin. There are currently no experimental observations that enable decisive discrimination between the many competing theories for the mechanism that generates the angular momentum^4-12. Nevertheless, the consensus is that excitation of collective vibrational modes generates the intrinsic spin before the nucleus splits (pre-scission). Here we show that there is no significant correlation between the spins of the fragment partners, which leads us to conclude that angular momentum in fission is actually generated after the nucleus splits (post-scission). We present comprehensive data showing that the average spin is strongly mass-dependent, varying in saw-tooth distributions. We observe no notable dependence of fragment spin on the mass or charge of the partner nucleus, confirming the uncorrelated post-scission nature of the spin mechanism. To explain these observations, we propose that the collective motion of nucleons in the ruptured neck of the fissioning system generates two independent torques, analogous to the snapping of an elastic band. A parameterization based on occupation of angular momentum states according to statistical theory describes the full range of experimental data well. This insight into the role of spin in nuclear fission is not only important for the fundamental understanding and theoretical description of fission, but also has consequences for the γ-ray heating problem in nuclear reactors^13,14, for the study of the structure of neutron-rich isotopes^15,16, and for the synthesis and stability of super-heavy elements^17,18.

Antimicrobial Stewardship for Respiratory Pathogens in Swine

The aim of this study was to set up antimicrobial stewardship for swine respiratory pathogens following the recommendation from the European Medicine Agency. The obtained antimicrobial susceptibility pattern recommended using antimicrobial stewardship for each clinical case instead of treatment guidelines focused on pathogens. Thus, the bacteria are isolated and the MIC values, the clinical interpretation for each antimicrobial (susceptible or resistant), additional information about the distance between the MIC obtained and the clinical breakpoint, and set up for each drug, are represented in the report provided for veterinarians. A graph from green (susceptible) to red (resistant) is enclosed for each antimicrobial and microorganism in the report. The greener, the more susceptible is the strain, and the redder, the less susceptible is the strain for each particular antimicrobial. This information could help veterinarians to select the most suitable antimicrobial from first, second, or last option antimicrobials. Thus, veterinarians should choose the antimicrobial, inside each option, with the best antimicrobial susceptibility pattern that corresponds with the greener status in the report. The information provided in the report could be useful for all clinical cases, caused by a certain bacterium within the same pig production system, if an epidemiological link could be established.

Identification of a Newly Conserved SLA-II Epitope in a Structural Protein of Swine Influenza Virus

Despite the role of pigs as a source of new Influenza A Virus viruses (IAV) potentially capable of initiating human pandemics, immune responses to swine influenza virus (SwIV) in pigs are not fully understood. Several SwIV epitopes presented by swine MHC (SLA) class I have been identified using different approaches either in outbred pigs or in Babraham large white inbred pigs, which are 85% identical by genome wide SNP analysis. On the other hand, some class II SLA epitopes were recently described in outbred pigs. In this work, Babraham large white inbred pigs were selected to identify SLA II epitopes from SwIV H1N1. PBMCs were screened for recognition of overlapping peptides covering the NP and M1 proteins from heterologous IAV H1N1 in IFNγ ELISPOT. A novel SLA class II restricted epitope was identified in NP from swine H1N1. This conserved novel epitope could be the base for further vaccine approaches against H1N1 in pigs.

Antimicrobial Resistance Genes in Porcine Pasteurella multocida Are Not Associated with Its Antimicrobial Susceptibility Pattern

Forty-eight Pasteurella multocida isolates were recovered from porcine pneumonic lungs collected from farms in “Castilla y León” (north-western Spain) in 2017–2019. These isolates were characterized for their minimal inhibition concentrations to twelve antimicrobial agents and for the appearance of eight resistance genes: tetA, tetB, bla_ROB1, bla_TEM, ermA, ermC, mphE and msrE. Relevant resistance percentages were shown against tetracyclines (52.1% for doxycycline, 68.7% for oxytetracycline), sulphamethoxazole/trimethoprim (43.7%) and tiamulin (25.0%), thus suggesting that P. multocida isolates were mostly susceptible to amoxicillin, ceftiofur, enrofloxacin, florfenicol, marbofloxacin and macrolides. Overall, 29.2% of isolates were resistant to more than two antimicrobials. The tetracycline resistance genes (tetA and tetB) were detected in 22.9% of the isolates, but none were positive to both simultaneously; bla_ROB1 and bla_TEM genes were found in one third of isolates but both genes were detected simultaneously in only one isolate. The ermC gene was observed in 41.7% of isolates, a percentage that decreased to 22.9% for msrE; finally, ermA was harbored by 16.7% and mphE was not found in any of them. Six clusters were established based on hierarchical clustering analysis on antimicrobial susceptibility for the twelve antimicrobials. Generally, it was unable to foresee the antimicrobial susceptibility pattern for each family and the association of each particular isolate inside the clusters established from the presence or absence of the resistance genes analyzed.

Vaccination Is a Suitable Tool in the Control of Aujeszky's Disease Outbreaks in Pigs Using a Population Dynamics P Systems Model

Simple Summary

Maximizing the efficiency of pork production in line with sustainability and environmental restrictions presents a challenge for the pig industry in the coming years. It is necessary to develop practices based on cost/benefit analyses of the effects of disease on animal performance. Diseases can be controlled in various ways, such as vaccination programs and management protocols, among others, to control pathogens. We have developed a model to disentangle the effects of management and vaccination strategies to control one of the most important pig viral diseases, Aujeszky disease. Our results suggest that after confirming the diagnosis, early vaccination of most of the population is critical to decrease the spread of the virus and minimize its impact on pig productivity. However, the effect of management is negligible for the control of this virus. Thus, this model can be used to evaluate preventive medicine programs in the control of known diseases and for new ones that could appear in the future.

Abstract

Aujeszky’s disease is one of the main pig viral diseases and results in considerable economic losses in the pork production industry. The disease can be controlled using preventive measures such as improved stock management and vaccination throughout the pig-rearing period. We developed a stochastic model based on Population Dynamics P systems (PDP) models for a standard pig production system to differentiate between the effects of pig farm management regimes and vaccination strategies on the control of Aujeszky’s disease under several different epidemiological scenarios. Our results suggest that after confirming the diagnosis, early vaccination of most of the population (>75%) is critical to decrease the spread of the virus and minimize its impact on pig productivity. The direct economic cost of an outbreak of Aujeszky’s disease can be extremely high on a previously uninfected farm (from 352–792 Euros/sow/year) and highlights the positive benefits of investing in vaccination measures to control infections. We demonstrate the usefulness of computational models as tools in the evaluation of preventive medicine programs aimed at limiting the impact of disease on animal production.

A probabilistic Poisson-based model to detect PRRSV recirculation using sow production records

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease associated with a decrease in the number of born alive piglets (NBA) and an increase in the number of lost piglets (NLP) per farrowing. Under practical conditions, it is critical to assess whether a farm is suffering PRRSV recirculation in the sow herd as soon as possible. The aim of this research work was to develop a new method to detect potential PRRSV recirculation in sow production farms. Sow reproductive performance records from one farm (farm T) were used to set up the method and records from ten additional farms (farms V1 to V10) were used for validation. A conditional Poisson model of NLP on NBA was proposed to fit the data. A three-step procedure was implemented to detect potential PRRSV recirculation: (i) computation of the maximum-likelihood estimates of the expected values of NBA and NLP in a PRRSV non-recirculating scenario; (ii) calculation, for each farrowing, of the p-value associated with the probability of jointly observing deviations towards decreased NBA and increased NLP. The detection of a potential PRRSV recirculation was based on (iii) the combined p-value resulting from weighing the p-values of the last N farrowings by the chi-square-inverse method. In order to gain specificity, a displacement on the expected non-recirculating NBA and NLP values was used for tuning purposes. With this approach, two PRRSV circulating periods were detected in farm T, which were confirmed with standard laboratorial diagnostic techniques. The method was subsequently validated in farms V1 to V10, where ten PRRSV-recirculating time episodes had been diagnosed. The method proposed here was able to detect the ten PRRSV recirculations using a relatively small set of contiguous farrowings, with only two mismatched weeks, one as a false negative, in farm V1, and one as a false positive, in farm V4. It is concluded that a conditional Poisson-based model of NLP on NBA can be a useful tool for routinely detecting PRRSV recirculation in sow herds.

Near Real-Time Monitoring of Clinical Events Detected in Swine Herds in Northeastern Spain

Novel techniques of data mining and time series analyses allow the development of new methods to analyze information relating to the health status of the swine population in near real-time. A swine health monitoring system based on the reporting of clinical events detected at farm level has been in operation in Northeastern Spain since 2012. This initiative was supported by swine stakeholders and veterinary practitioners of the Catalonia, Aragon, and Navarra regions. The system aims to evidence the occurrence of endemic diseases in near real-time by gathering data from practitioners that visited swine farms in these regions. Practitioners volunteered to report data on clinical events detected during their visits using a web application. The system allowed collection, transfer and storage of data on different clinical signs, analysis, and modeling of the diverse clinical events detected, and provision of reproducible reports with updated results. The information enables the industry to quantify the occurrence of endemic diseases on swine farms, better recognize their spatiotemporal distribution, determine factors that influence their presence and take more efficient prevention and control measures at region, county, and farm level. This study assesses the functionality of this monitoring tool by evaluating the target population coverage, the spatiotemporal patterns of clinical signs and presumptive diagnoses reported by practitioners over more than 6 years, and describes the information provided by this system in near real-time. Between January 2012 and March 2018, the system achieved a coverage of 33 of the 62 existing counties in the three study regions. Twenty-five percent of the target swine population farms reported one or more clinical events to the system. During the study period 10,654 clinical events comprising 14,971 clinical signs from 1,693 farms were reported. The most frequent clinical signs detected in these farms were respiratory, followed by digestive, neurological, locomotor, reproductive, and dermatological signs. Respiratory disorders were mainly associated with microorganisms of the porcine respiratory disease complex. Digestive signs were mainly related to colibacilosis and clostridiosis, neurological signs to Glässer's disease and streptococcosis, reproductive signs to PRRS, locomotor to streptococcosis and Glässer's disease, and dermatological signs to exudative epidermitis.

Salmonella Infection in Mesenteric Lymph Nodes of Breeding Sows

Salmonellosis is one of the main foodborne diseases worldwide. Breeding sows asymptomatically infected with Salmonella can transmit the pathogen to piglets and humans. The isolation of Salmonella from mesenteric lymph nodes (MLNs) is considered a demonstration of asymptomatic infection in swine. As previous breeding sow studies have been performed using feces, the aim of this work was to study the occurrence of Salmonella infections by sampling MLNs, in comparison to their serological status. First, Salmonella fecal shedding was studied in 12/16 large breeding farms to establish the framework of study. Then, MLN (n = 264) and blood (n = 237) samples were obtained at an abattoir from sows of 15 of these 16 breeding farms. Additionally, risk factors associated with Salmonella MLN infection were analyzed. A total of 6.1% (16/264) sows, distributed in 40% (6/15) of the farms, had the pathogen in MLN. Salmonella Typhimurium was the most frequent serovar isolated. Interestingly, 43.8% (7/16) of MLN isolates were susceptible to all the antimicrobials tested and were found distributed throughout all farms with at least one sow positive. As well, one isolate of the emerging DT195 clone was detected and found to be resistant to six antibiotic families (ASSuTNx-Cfx). The serovars and the resistance profiles of the Salmonella isolates from feces were completely different to those obtained from MLNs. The seroprevalence (41.8% of sows and 100% of farms) was higher than that of MLN infections, showing no concordance (k = 0.15) between these two diagnostic tests in sows. Strategies directed to correct two risk factors (i.e., administration of dry food and old premises) would most likely help to reduce Salmonella infections in breeding sows.

Serum-Derived Extracellular Vesicles from African Swine Fever Virus-Infected Pigs Selectively Recruit Viral and Porcine Proteins

: African swine fever is a devastating hemorrhagic infectious disease, which affects domestic and wild swines (Susscrofa) of all breeds and ages, with a high lethality of up to 90-100% in naïve animals. The causative agent, African swine fever virus (ASFV), is a large and complex double-stranded DNA arbovirus which is currently spreading worldwide, with serious socioeconomic consequences. There is no treatment or effective vaccine commercially available, and most of the current research is focused on attenuated viral models, with limited success so far. Thus, new strategies are under investigation. Extracellular vesicles (EVs) have proven to be a promising new vaccination platform for veterinary diseases in situations in which conventional approaches have not been completely successful. Here, serum extracellular vesicles from infected pigs using two different ASFV viruses (OURT 88/3 and Benin ΔMGF), corresponding to a naturally attenuated virus and a deletion mutant, respectively, were characterized in order to determine possible differences in the content of swine and viral proteins in EV-enriched fractions. Firstly, EVs were characterized by their CD5, CD63, CD81 and CD163 surface expression. Secondly, ASFV proteins were detected on the surface of EVs from ASFV-infected pig serum. Finally, proteomic analysis revealed few specific proteins from ASFV in the EVs, but 942 swine proteins were detected in all EV preparations (negative controls, and OURT 88/3 and Benin ΔMGF-infected preparations). However, in samples from OURT 88/3-infected animals, only a small number of proteins were differentially identified compared to control uninfected animals. Fifty-six swine proteins (Group Benin) and seven proteins (Group OURT 88/3) were differentially detected on EVs when compared to the EV control group. Most of these were related to coagulation cascades. The results presented here could contribute to a better understanding of ASFV pathogenesis and immune/protective responses in the host.

Effect of Porcine circovirus 2 (PCV-2) maternally derived antibodies on performance and PCV-2 viremia in vaccinated piglets under field conditions

Background

Nowadays, the most common presentation of PCV-2 is the subclinical infection in piglets after weaning. The success of PCV-2 vaccination is associated with the control of the clinical disease as well as the improvement of production parameters. In consequence, the objective of the present study was to analyse the effect of PCV-2 maternally derived antibody (MDA) levels on vaccine efficacy in piglets vaccinated at three weeks of age with a commercial PCV-2 subunit vaccine. The study was performed analysing a database with 6112 wean-to-slaughter piglets from 4 different European regions.

Results

Results showed that the use of the vaccine was able to decrease the PCV-2 viremia calculated as area under the curve (AUC = 60.29 ± 3.73), increase average daily weight gain (ADWG = 0.65 ± 0.01 kg/day) and reduce mortality (7%) in vaccinated piglets compared to non-vaccinated ones (AUC of 198.27 ± 6.14, 0.62 ± 0.01 kg/day and 11% respectively). The overall difference of ADWG between both groups was close to 30 g per day (p < 0.05), also when they were split for low and high levels of MDA titres. Moreover, the animals with the highest ADWG were observed in the group of piglets vaccinated with high or extremely high antibody titres (0.66 and 0.65 kg/day respectively). Considering only animals with extremely high antibody titres, both study groups performed similar, however there was a numerical difference of 10 g/day in favour of vaccinated piglets. Likewise, lack of correlation between ADWG and MDA was observed suggesting that no maternal antibody interference was present with the tested vaccine because the vaccinated animals grew faster compared to unvaccinated control animals, regardless of the level of maternal antibodies present at the time of vaccination.

Conclusions

The results of the present study demonstrated that the MDA against PCV-2 transferred through the colostrum intake has a protective effect against this viral infection. The vaccine used in the present study (Ingelvac CircoFLEX®) was effective when applied at three weeks of age and was not affected by the level of MDA at the time of vaccination.

Improving the management procedures in farms infected with the Porcine Reproductive and Respiratory Syndrome virus using PDP models

Pig meat production need to be built up in the future due to the increase of the human population worldwide. To address this challenge, there is plenty of room for improvement in terms of pig production efficiency that could be severely hampered by the presence of diseases. In this sense, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is one of the most costly disease present in industrial pork production in Europe and North America. We have developed a model to analyze the effect of different management procedures to control this important virus in different epidemiological scenarios. Our results clearly suggest that no cross-fostering during lactation and the maintaining of litter integrity significantly decrease the number of sick and dead animals during the rearing period compared to scenarios where cross-fostering and no litter integrity are practiced. These results highlight the relevance of different management strategies to control PRRSV and quantify the effect of limiting cross-fostering and avoiding mixing animals from different litters in PRRSV positive farms to optimize animal production. Our findings will allow pig farmers to apply these management procedures to control this disease under field conditions in a very cost-effective way.

Identification of resilient sows in Porcine Reproductive and Respiratory Syndrome virus infected farms

The identification of resilient sows can improve reproductive performance in farms exposed to multiple challenges. A common challenge is the porcine reproductive and respiratory syndrome virus (PRRSV). A key issue to deal with disease resilience is to set up a feasible phenotyping strategy. Our aim was to develop a phenotyping criterion to discriminate susceptible from resilient sows in PRRSV-infected farms. A total of 517 Landrace x Large White gilts were classified as resilient (R) or susceptible (S) to PRRSV virus, following vaccination with MLV-PRRSV at 6-7 wk of age, in a PRRSV negative multiplication farm. Female piglets were phenotyped as R if their serum was negative to PRRSV at 7 and 21 d post-vaccination (DPV) or as S if their serum was positive at 7 and/or 21 DPV. Amongst them, 382 gilts were transferred to a PRRSV-positive production farm, where the number of piglets born alive (NBA), stillborn (NSB), mummified (NMU), lost (NLP=NSB+NMU) and total born (NTB = NBA+NLP) were recorded for almost three years. Data were collected during two periods according to the PRRSV farm health status, which were confirmed as either PRRSV-positive stable (endemic) or inestable (epidemic). Analyses were carried out under a Bayesian approach. The heritability for the resilience criterion was estimated using a threshold model. A linear (for NTB and NBA) and a binomial model (for NSB, NMU and NLP) on the resilience criterion by the farm health status were used to assess the difference between R and S sows. The heritability of the resilience criterion was 0.46 (SD 0.06). The probability of a piglet being lost was greater (≥0.97) in S than in R litters, regardless of whether the delivery occurred during a PRRSV outbreak (20.5% vs 17.0%) or not (15.8% vs 13.7%). The lower piglet mortality rate in R sows was due to NSB, in the endemic phase (13.0% vs 15.0% of NTB, with a posterior probability of 98% of S sows showing higher NSB than R sows), and to NMU, in the epidemic phase (4.0% vs 8.4% of NTB, with a posterior probability of >99% of S sows showing higher NMU than R sows). During a PRRSV outbreak, the S sows were twice as likely to give birth to a mummified piglet as compared to R sows. These findings provide evidence that the described phenotyping scheme has a potential use as a PRRSV resilience criterion.

Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV)

The porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine diseases in the world. It is causing an enormous economic burden due to reproductive failure in sows and a complex respiratory syndrome in pigs of all ages, with mortality varying from 2 to 100% in the most extreme cases of emergent highly pathogenic strains. PRRSV displays complex interactions with the immune system and a high mutation rate, making the development, and implementation of control strategies a major challenge. In this review, the biology of the virus will be addressed focusing on newly discovered functions of non-structural proteins and novel dissemination mechanisms. Secondly, the role of different cell types and viral proteins will be reviewed in natural and vaccine-induced immune response together with the role of different immune evasion mechanisms focusing on those gaps of knowledge that are critical to generate more efficacious vaccines. Finally, novel strategies for antigen discovery and vaccine development will be discussed, in particular the use of exosomes (extracellular vesicles of endocytic origin). As nanocarriers of lipids, proteins and nucleic acids, exosomes have potential effects on cell activation, modulation of immune responses and antigen presentation. Thus, representing a novel vaccination approach against this devastating disease.

Targeted-pig trial on safety and immunogenicity of serum-derived extracellular vesicles enriched fractions obtained from Porcine Respiratory and Reproductive virus infections

The Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the etiological agent of one of the most important swine diseases with a significant economic burden worldwide. Unfortunately, available vaccines are partially effective highlighting the need of novel approaches. Previously, antigenic viral proteins were described in serum-derived extracellular vesicles (EVs) from pigs previously infected with PRRSV. Here, a targeted-pig trial was designed to determine the safety and immunogenicity of such extracellular vesicles enriched fractions. Our results showed that immunizations with EV-enriched fractions from convalescence animals in combination with montanide is safe and free of virus as immunizations with up-to two milligrams of EV-enriched fractions did not induce clinical symptoms, adverse effects and detectable viral replication. In addition, this vaccine formulation was able to elicit specific humoral IgG immune response in vaccinated animals, albeit variably. Noticeably, sera from vaccinated animals was diagnosed negative when tested for PRRSV using a commercial ELISA test; thus, indicating that this new approach differentiates vaccinated from infected animals. Lastly, after priming animals with EV-enriched fractions from sera of convalescence animals and boosting them with synthetic viral peptides identified by mass spectrometry, a distinctive high and specific IFN-γ response was elicited. Altogether, our data strongly suggest the use of serum EV-enriched fractions as a novel vaccine strategy against PRRSV.

Descriptive study for culling and mortality in five high-producing Spanish dairy cattle farms (2006-2016)

Background

High turnover rate in dairy farms due to culling and mortality is associated with poor animal welfare, an increase in production costs and lower economic benefits for the dairy farm. Understanding cow elimination better would help to formulate specific prevention measures and improve the efficiency of milk production in dairy farms. Culling and mortality data from five standard high-producing dairy farms in Spain were analysed over a period of 11 years (2006–2016). Data were collected by the same veterinary team and using the same software system.

Results

Significant between-herd differences in eliminated cows were observed for type of elimination (slaughter or death on the farm), age at elimination, cause of elimination, number of lactations and production parameters, such as total days in milk, life milk yield, litres per day of productive life and litres per day of life. Culling and mortality were higher during the hot season and for cows of second and third parities. Between-herd differences were observed. Reproductive disorders (30.2%) were the most frequent reason for elimination, with low production (23.4%) being the second most frequent reason. Accidents on the farm (7.7%) were a more frequent cause of elimination than metabolic diseases (7.2%), locomotor disorders (2.4%) and obstetrics (2.4%).

Conclusions

Veterinary teams or farmers’ associations can use culling and mortality information for benchmarking cow farms if data collection and analysis is standardised for comparability. The analysis of culling and mortality information should help farmers to improve efficiency.

Electronic supplementary material

The online version of this article (10.1186/s13028-018-0399-z) contains supplementary material, which is available to authorized users.

Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period

Antimicrobials have been used in a prophylactic way to decrease the incidence of digestive disorders during the piglet post-weaning period. Nowadays, it is urgent to reduce their consumption in livestock to address the problem of antimicrobial resistance. In this study, the effect of a product on piglet microbiota has been investigated as an alternative to antimicrobials. Three groups of ten post-weaning pigs were sampled at 0, 15 and 30 days one week post-weaning; the control, antibiotic and feed additive group received a standard post-weaning diet without antibiotics or additives, the same diet as the control group but with amoxicillin and colistin sulphate and the same diet as the control group but with a feed additive (Sanacore-EN, Nutriad International N.V.), respectively. The total DNA extracted from faeces was used to amplify the 16S RNA gene for massive sequencing under manufacturer’s conditions. Sequencing data was quality filtered and analyzed using QIIME software and suitable statistical methods. In general terms, age modifies significantly the microbiota of the piglets. Thus, the oldest the animal, the highest bacterial diversity observed for the control and the feed additive groups. However, this diversity was very similar in the antibiotic group throughout the trial. Interestingly, a clear increase in abundance of Bacillus and Lactobacillus spp was detected within the feed additive group versus the antibiotic and control groups. In conclusion, the feed additive group had a positive effect in the endogenous microbiota of post-weaning pigs increasing both, the diversity of bacterial families and the abundance of lactic acid bacteria during the post-weaning period.

African swine fever virus infection in Classical swine fever subclinically infected wild boars

BACKGROUND

Recently moderate-virulence classical swine fever virus (CSFV) strains have been proven capable of generating postnatal persistent infection (PI), defined by the maintenance of viremia and the inability to generate CSFV-specific immune responses in animals. These animals also showed a type I interferon blockade in the absence of clinical signs. In this study, we assessed the infection generated in 7-week-old CSFV PI wild boars after infection with the African swine fever virus (ASFV). The wild boars were divided in two groups and were infected with ASFV. Group A comprised boars who were CSFV PI in a subclinical form and Group B comprised pestivirus-free wild boars. Some relevant parameters related to CSFV replication and the immune response of CSFV PI animals were studied. Additionally, serum soluble factors such as IFN-α, TNF-α, IL-6, IL-10, IFN-γ and sCD163 were analysed before and after ASFV infection to assess their role in disease progression.

RESULTS

After ASFV infection, only the CSFV PI wild boars showed progressive acute haemorrhagic disease; however, the survival rates following ASFV infection was similar in both experimental groups. Notwithstanding, the CSFV RNA load of CSFV PI animals remained unaltered over the study; likewise, the ASFV DNA load detected after infection was similar between groups. Interestingly, systemic type I FN-α and IL-10 levels in sera were almost undetectable in CSFV PI animals, yet detectable in Group B, while detectable levels of IFN-γ were found in both groups. Finally, the flow cytometry analysis showed an increase in myelomonocytic cells (CD172a⁺) and a decrease in CD4⁺ T cells in the PBMCs from CSFV PI animals after ASFV infection.

CONCLUSIONS

Our results showed that the immune response plays a role in the progression of disease in CSFV subclinically infected wild boars after ASFV infection, and the immune response comprised the systemic type I interferon blockade. ASFV does not produce any interference with CSFV replication, or vice versa. ASFV infection could be a trigger factor for the disease progression in CSFV PI animals, as their survival after ASFV was similar to that of the pestivirus-free ASFV-infected group. This fact suggests a high resistance in CSFV PI animals even against a virus like ASFV; this may mean that there are relevant implications for CSF control in endemic countries. The diagnosis of ASFV and CSFV co-infection in endemic countries cannot be ruled out and need to be studied in greater depth.

Carotenoid intake and SCD genotype exert complementary effects over fat content and fatty acid composition in Duroc pigs

Nutritional and genetic strategies are needed to enhance intramuscular fat (IMF) and MUFA content without altering carcass leanness. Dietary vitamin A restriction has been suggested to specifically promote IMF, whereas a polymorphism of the () gene has shown to specifically increase MUFA. The purpose of this study was to investigate the combined effects of provitamin A (PVA) carotenoid intake and genotype (>) on hepatic retinoid content and on the liver, muscle (LM and gluteus medius [GM]), and subcutaneous fat (SF) content and fatty acid composition. Following a split-plot design, 32 castrated Duroc pigs, half of each of the 2 homozygous genotypes (CC and TT), were subjected from 165 to 195 d of age to 2 finishing diets differing in the PVA carotenoid content (an enriched-carotene diet [C+] and a control diet [C-]). Both diets were identical except for the corn line used in the feed. The C+ was formulated with 20% of a carotenoid-fortified corn (M37W-Ph3) whereas the C- instead used 20% of its near isogenic M37W line, which did not contain PVA carotenoids. No vitamin A was added to the diets. The C- was estimated to provide, at most, 1,300 IU of vitamin A/kg and the C+ to supply an extra amount of at least 800 IU vitamin A/kg. Compared with the pigs fed the C-, pigs fed with C+ had 3-fold more retinoic acid ( < 0.01) and 4-fold more gene expression in the liver ( = 0.06). The diet did not affect performance traits and backfat thickness, but pigs fed the C+ had less fat (4.0 vs. 5.0%; = 0.07) and MUFA (18.3 vs. 22.5%; = 0.01) in the liver, less IMF (5.4 vs. 8.3%; = 0.04) in the GM, and more fat content (90.4 vs. 87.9%; = 0.09) and MUFA (48.0 vs. 46.6%; = 0.04) in SF. The TT genotype at the gene increased MUFA ( < 0.05) in all tissues (21.4 vs. 19.5% in the liver, 55.0 vs. 53.1% in the LM, 53.9 vs. 51.7% in the GM, and 48.0 vs. 46.7% in SF for TT and CC genotypes, respectively). Liver fat and MUFA content nonlinearly declined with liver all- retinoic acid, indicating a saturation point at relatively low all- retinoic acid content. The results obtained provide evidence for a complementary role between dietary PVA and genotype, in the sense that the TT pigs fed with a low-PVA diet are expected to show higher and more monounsaturated IMF without increasing total fat content.

A bivalent dendrimeric peptide bearing a T-cell epitope from foot-and-mouth disease virus protein 3A improves humoral response against classical swine fever virus

Three dendrimeric peptides were synthesized in order to evaluate their immunogenicity and their potential protection against classical swine fever virus (CSFV) in domestic pigs. Construct 1, an optimized version of a previously used dendrimer, had four copies of a B-cell epitope derived from CSFV E2 glycoprotein connected to an also CSFV-derived T-cell epitope through maleimide instead of thioether linkages. Construct 2 was similarly built but included only two copies of the B-cell epitope, and in also bivalent construct 3 the CSFV T-cell epitope was replaced by a previously described one from the 3A protein of foot-and-mouth disease virus (FMDV). Animals were inoculated twice with a 21-day interval and challenged 15days after the second immunization. Clinical signs were recorded daily and ELISA tests were performed to detect antibodies against specific peptide and E2. The neutralising antibody response was assessed 13days after challenge. Despite the change to maleimide connectivity, only partial protection against CSFV was again observed. The best clinical protection was observed in group 3. Animals inoculated with constructs 2 and 3 showed higher anti-peptide humoral response, suggesting that two copies of the B-cell epitope are sufficient or even better than four copies for swine immune recognition. In addition, for construct 3 higher neutralizing antibody titres against CSFV were detected. Our results support the immunogenicity of the CSFV B-cell epitope and the cooperative role of the FMDV 3A T-cell epitope in inducing a neutralising response against CSFV in domestic pigs. This is also the first time that the FMDV T-cell epitope shows effectivity in improving swine immune response against a different virus. Our findings highlight the relevance of dendrimeric peptides as a powerful tool for epitope characterization and antiviral strategies development.

Potential use of local and systemic humoral immune response parameters to forecast Mycoplasma hyopneumoniae associated lung lesions

Immunopathological events are key for the development of enzootic pneumonia (EP), which is macroscopically observed as cranioventral pulmonary consolidation (CVPC). This study aimed to investigate the putative association between the humoral immune response against Mycoplasma hyopneumoniae (M. hyopneumoniae) and prevalence and extension of CVPC in 1) experimentally infected pigs, 2) slaughtered pigs and 3) sequentially necropsied pigs in a longitudinal study. CVPC was scored by means of the European Pharmacopoeia recommended methodology. Specific IgG, IgG1 and IgG2 antibodies were assessed in serum. In addition, mucosal IgG and IgA antibodies were analyzed in broncho-alveolar lavage fluid (BALF) from experimentally challenged pigs. The systemic humoral immune response in experimentally infected pigs was delayed in onset whereas humoral respiratory mucosal immune response appeared more rapidly but declined earlier. Although low, BALF IgG antibodies showed the highest correlation with CVPC scores (r = 0.49, p<0.05). In slaughter-aged pigs, both percentage of lungs with CVPC and mean lung lesion score were significantly higher in M. hyopneumoniae seropositive farms compared to the seronegative ones (p<0.001). Similarly, seropositive sequentially necropsied pigs showed more severe CVPC than seronegative ones. Overall, mean serological values might help to forecast prevalence and severity of EP-like lung lesions using a population based approach. Remarkably, the specific systemic humoral immune response was found to be predominated by the IgG2 subclass, suggesting a dominant Th1-mediated immune response to M. hyopneumoniae.

Biochemical and proteomic analyses of the physiological response induced by individual housing in gilts provide new potential stress markers

Background

The objective assessment of animal stress and welfare requires proper laboratory biomarkers. In this work, we have analyzed the changes in serum composition in gilts after switching their housing, from pen to individual stalls, which is generally accepted to cause animal discomfort.

Results

Blood and saliva samples were collected a day before and up to four days after changing the housing system. Biochemical analyses showed adaptive changes in lipid and protein metabolism after the housing switch, whereas cortisol and muscular markers showed a large variability between animals. 2D-DIGE and iTRAQ proteomic approaches revealed variations in serum protein composition after changing housing and diet of gilts. Both techniques showed alterations in two main homeostatic mechanisms: the innate immune and redox systems. The acute phase proteins haptoglobin, apolipoprotein A-I and α1-antichymotrypsin 3, and the antioxidant enzyme peroxiredoxin 2 were found differentially expressed by 2D-DIGE. Other proteins related to the innate immune system, including lactotransferrin, protegrin 3 and galectin 1 were also identified by iTRAQ, as well as oxidative stress enzymes such as peroxiredoxin 2 and glutathione peroxidase 3. Proteomics also revealed the decrease of apolipoproteins, and the presence of intracellular proteins in serum, which may indicate physical injury to tissues.

Conclusions

Housing of gilts in individual stalls and diet change increase lipid and protein catabolism, oxidative stress, activate the innate immune system and cause a certain degree of tissue damage. We propose that valuable assays for stress assessment in gilts may be based on a score composed by a combination of salivary cortisol, lipid metabolites, innate immunity and oxidative stress markers and intracellular proteins.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0887-1) contains supplementary material, which is available to authorized users.

Serum-derived exosomes from non-viremic animals previously exposed to the porcine respiratory and reproductive virus contain antigenic viral proteins

PRRSV is the etiological agent of one of the most important swine diseases with a significant economic burden worldwide and limitations in vaccinology. Exosomes are 30-100 nm vesicles of endocytic origin. Remarkably, immunizations with exosomes containing antigens from tumors or pathogens are capable of eliciting protective immune responses, albeit variably, in cancer and infectious diseases. Here we describe the isolation, molecular composition and immunogenicity of serum-derived exosomes from naïve animals, from PRRSV viremic animals and from animals previously PRRSV infected but already free of viruses (non viremic). Exosomes were isolated through size exclusion chromatography and characterized by different methodologies. Exosome-enriched fractions from naïve and natural infected animals contained classical tetraspanin exosomal markers (CD63 and CD81) and high concentrations of particles in the size-range of exosomes as detected by nanoparticle tracking analysis and cryo-TEM. NanoLC-MS/MS was used to identify viral antigens associated to exosomes. PRRSV-proteins were detected in serum samples from only viremic animals and from animals previously infected already free of viruses (non-viremic), but not in controls. Moreover, immune sera from pigs previously exposed to PRRSV specifically reacted against exosomes purified from non-viremic pig sera in a dose-dependent manner, a reactivity not detected when naïve sera was used in the assay. To facilitate future studies, a scaling-up process was implemented. To the best of our knowledge, this is the first molecular characterization of serum-derived exosomes from naïve pigs and pigs actively or previously infected with PRRSV. The presence of antigenic viral proteins in serum-derived exosomes free of virus, suggest their use as a novel vaccine approach against PRRSV.

Piglet nasal microbiota at weaning may influence the development of Glässer's disease during the rearing period

BACKGROUND

The microbiota, the ensemble of microorganisms on a particular body site, has been extensively studied during the last few years, and demonstrated to influence the development of many diseases. However, these studies focused mainly on the human digestive system, while the populations in the respiratory tract have been poorly assessed, especially in pigs. The nasal mucosa of piglets is colonized by an array of bacteria, many of which are unknown. Among the early colonizers, Haemophilus parasuis also has clinical importance, since it is also the etiological agent of Glässer's disease. This disease produces economical losses in all the countries with pig production, and the factors influencing its development are not totally understood. Hence, the purpose of this work was to characterize the nasal microbiota composition of piglets, and its possible role in Glässer's disease development.

RESULTS

Seven farms from Spain (4 with Glässer's disease and 3 control farms without any respiratory disease) and three farms from UK (all control farms) were studied. Ten piglets from each farm were sampled at 3-4 weeks of age before weaning. The total DNA extracted from nasal swabs was used to amplify the 16S RNA gene for sequencing in Illumina MiSeq. Sequencing data was quality filtered and analyzed using QIIME software. The diversity of the nasal microbiota was low in comparison with other body sites, showing a maximum number of operational taxonomic units (OTUs) per pig of 1,603, clustered in five phyla. Significant differences were found at various taxonomical levels, when the microbiota was compared regarding the farm health status. Healthy status was associated to higher species richness and diversity, and UK farms demonstrated the highest diversity.

CONCLUSIONS

The composition of the nasal microbiota of healthy piglets was uncovered and different phylotypes were shown to be significantly altered in animals depending on the clinical status of the farm of origin. Several OTUs at genus level were identified over-represented in piglets from control farms, indicating their potential as probiotics. Although we provide relevant data, fully metagenomic approaches could give light on the genes and metabolic pathways involved in the roles of the nasal microbiota to prevent respiratory diseases.

Shedding of cephalosporin resistant Escherichia coli in pigs from conventional farms after early treatment with antimicrobials

This study assessed the dynamics of cephalosporin resistant (CR) E. coli populations during the life cycle of pigs treated early in life with ceftiofur or tulathromycin. The study was conducted at eight conventional pig farms; four for each treatment with ceftiofur or tulathromycin. At each farm, 70 7-day-old piglets were divided into two groups: a control group (n = 30) and a treatment group (n = 40). Faecal samples were collected on day 0 and on days 2, 7 and 180 post-treatment. Sows were also sampled on day 0. CR E. coli were selected on MacConkey agar with ceftriaxone. On five farms, 7-day-old piglets excreted CR E. coli before treatment associated with the presence of CR E. coli in sows. The occurrence of CR E. coli positive animals decreased with increasing piglet age. The remaining three farms tested negative for CR E. coli during the study period. Results demonstrated great variability in the frequency of CR E. coli positive animals between farms, independent of treatment. Treatment with ceftiofur resulted in a transitory increase in the counts of CR E. coli after 48 h. However, other risk factors including the presence of CR E. coli in sows and animal age were more important than antimicrobial treatment. Accordingly, intervention strategies targeting sows would likely have a beneficial effect in reducing the occurrence of antimicrobial resistance in primary pig production.

Assessment of Mycoplasma hyopneumoniae-induced Pneumonia using Different Lung Lesion Scoring Systems: a Comparative Review

Mycoplasma hyopneumoniae is the primary aetiological agent of swine enzootic pneumonia (EP) and one of the major contributors to the porcine respiratory disease complex (PRDC). Gross lung lesions in pigs affected by EP consist of cranioventral pulmonary consolidation (CVPC), usually distributed bilaterally in the apical, intermediate, accessory and cranial parts of the diaphragmatic lobes. Several lung scoring methods are currently in place for the evaluation of CVPC. The aims of this study were (1) to review the lung lesion scoring systems used to assess pneumonia associated with M. hyopneumoniae infection, and (2) to evaluate eight of these scoring systems by applying them to the lungs of 76 pigs with experimentally-induced M. hyopneumoniae pneumonia. A significant correlation between all lung lesion scoring systems was observed and the coefficients of determination in a regression analysis were very high between each pair-wise comparison, except for a unique scoring system based on image analysis. A formula of equivalence between lung scoring methods was developed in order to compare the results obtained with these methods. The present review provides a basis for comparison (even retrospectively) of lesions evaluated using different lung scoring systems.

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper

Extracellular vesicles (EVs), such as exosomes and microvesicles, are released by different cell types and participate in physiological and pathophysiological processes. EVs mediate intercellular communication as cell-derived extracellular signalling organelles that transmit specific information from their cell of origin to their target cells. As a result of these properties, EVs of defined cell types may serve as novel tools for various therapeutic approaches, including (a) anti-tumour therapy, (b) pathogen vaccination, (c) immune-modulatory and regenerative therapies and (d) drug delivery. The translation of EVs into clinical therapies requires the categorization of EV-based therapeutics in compliance with existing regulatory frameworks. As the classification defines subsequent requirements for manufacturing, quality control and clinical investigation, it is of major importance to define whether EVs are considered the active drug components or primarily serve as drug delivery vehicles. For an effective and particularly safe translation of EV-based therapies into clinical practice, a high level of cooperation between researchers, clinicians and competent authorities is essential. In this position statement, basic and clinical scientists, as members of the International Society for Extracellular Vesicles (ISEV) and of the European Cooperation in Science and Technology (COST) program of the European Union, namely European Network on Microvesicles and Exosomes in Health and Disease (ME-HaD), summarize recent developments and the current knowledge of EV-based therapies. Aspects of safety and regulatory requirements that must be considered for pharmaceutical manufacturing and clinical application are highlighted. Production and quality control processes are discussed. Strategies to promote the therapeutic application of EVs in future clinical studies are addressed.

Virological and serological characterization of vaccinated and non-vaccinated piglet subpopulations coming from vaccinated and non-vaccinated sows

The present study describes the virological and serological profiles of PCV2 vaccinated (V) and non-vaccinated (NV) piglet subpopulations coming from V and NV sows in a PCV2 subclinically infected farm. Four hundred seventy-six piglets born from V or NV sows were further subdivided in a total of four groups: NV sows-NV pigs (NV-NV), NV sows-V pigs (NV-V); V sows-NV pigs (V-NV) and V sows-V pigs (V-V). Seventy-five pigs were randomly selected at the beginning of the trial from each group and they were bled at 4, 8, 12, 16, 21 and 25 weeks of age. All animals included in the trial were weighed at 4 and 25 weeks of age and their average daily weight gain (ADWG) was calculated. Serum samples obtained at different time points were used to assess PCV2 infection (viremia) and the level of antibodies by means of immunoperoxidase monolayer assay (IPMA) against this pathogen. IPMA titers (classified in high, medium or low) and PCR results (positive or negative) were analyzed using a multiple correspondence and K-means cluster analysis. According to these tests, animals included in the study were classified into the following four clusters: (1) 93 piglets that were viremic mainly from 12 to 25 weeks of age and with PCV2 antibody titers increasing over time; (2) 75 piglets with late PCV2 infection and seroconversion (later than 16 weeks of age); (3) 26 piglets with high but decreasing PCV2 antibody titers and low percentages of PCV2 PCR positive serum samples; and (4) 105 piglets with medium and high IPMA titers throughout the trial and sporadic PCR positive samples. The defined subpopulations of piglets were observed in all experimental groups (NV-NV, NV-V, V-NV and V-V) although in variable percentages. Thus, animals from clusters 1 and 2 belonged mainly to the NV-NV and V-NV groups and animals from clusters 3 and 4 were distributed mainly into the NV-V and V-V groups. Finally, the ADWG of pigs belonging to clusters 3 and 4 was significantly higher (p=0.02) than that of pigs belonging to clusters 1 and 2. Within each cluster, no statistically significant differences were found in ADWG between treatment groups.

Serum haptoglobin dynamics in pigs vaccinated or not vaccinated against porcine circovirus type 2

The present work describes the serum haptoglobin (Hp) dynamics in piglets vaccinated and non-vaccinated with a commercial porcine circovirus type 2 (PCV2) vaccine at 3 weeks of age, and its relationship with the average daily weight gain (ADWG). The field study was carried out on two farms (A and B) with a previous clinical history of PCV2-systemic disease (PCV2-SD). The aim of the study was to assess whether Hp could be used as a surrogate marker of PCV2 vaccine efficacy. PCV2 infection was confirmed by quantitative real time PCR (qPCR) in pigs from both farms, but PCV2-SD was only diagnosed in farm A. No statistically significant relation was found between serum Hp concentration and the percentage of qPCR positive animals and the treatment applied (PCV2 vaccination) in both farms. On the other hand, using linear regression analysis, a significant negative correlation between the area under the curve of Hp (AUC_Hp) and ADWG was observed for farm A (p < 0.00001) and B (p = 0.01). Based on the obtained determination coefficient (R²) values, AUC_Hp explained 20.0 and 11.6% of the observed ADWG for farms A and B, respectively. The present study supports that the measurement of acute phase proteins may be an indicator of ADWG in pig farms, but it was not apparently feasible to use the serum Hp concentration as a surrogate marker of PCV2 vaccine efficacy.