Prevalence of enteric pathogens in diarrheic and non-diarrheic samples from pig farms with neonatal diarrhea in the North East of Spain

Transmissible Gastroenteritis Virus (TGEV) and Porcine Respiratory Coronavirus (PRCV): Epidemiology and Molecular Characteristics-An Updated Overview

Transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV) are enveloped, single-stranded RNA viruses belonging to the genus Alphacoronavirus in the family Coronaviridae. PRCV, a TGEV mutant with a spike(S) gene deletion, exhibits altered tissue tropism. TGEV replicates mainly in the intestines and causes severe diarrhea and high mortality in piglets, whereas PRCV replicates mainly in the respiratory tract. PRCV causes mild or subclinical respiratory infections but may contribute to respiratory disease syndrome in pigs infected with other respiratory pathogens. As PRCV and TGEV continuously evolve, monitoring these viruses is important for disease prevention and control. In this review, we provide updated information on the prevalence and genetic characteristics of TGEV/PRCV and their phylogenetic relationships. We also discuss the impact of mutations, deletions and recombination on the virulence and tissue tropism of TGEV/PRCV and highlight the possible zoonotic potential of these viruses.

Identification of a potential interspecies reassortant rotavirus G and avastrovirus 2 co-infection from black-headed gull (Chroicocephalus ridibundus) in Hungary

The black-headed gull is the most common nesting gull species in Hungary. Based on the lifestyle and feeding habits of the black-headed gull, which is highly adapted to the human environment, they can be carriers and spreaders of potential human and other animal pathogens. Between 2014 and 2018 within the framework of the "Life Bird Ringing program" a total of 7 faecal samples were collected from gulls and one sample (MR04) was randomly selected for viral metagenomics and mass sequencing. 95.4% and 4% of the reads were classified into family Seadornaviridae and Astroviridae, respectively, and then were verified by RT-PCR method. In this study, the complete genome of a potential interspecies reassortant rotavirus (RV) strain gull/MR04_RV/HUN/2014 (PP239049-PP239059) and the partial ORF1ab, complete ORF2 of a novel avian nephritis virus strain gull/MR04_AAstV/HUN/2014 (PP239060) was discussed. The strain gull/MR04_RV/HUN/2014 was closely related to rotavirus G (RVG) viruses based on the proteins VP1-VP3, VP6, NSP2, NSP3, and NSP5, but it was more related to the human rotavirus B (RVB) strain Bang373 based on the NSP1, NSP4 and VP7, VP4 proteins, which is assumed to be the result of reassortment between different RVG-RVB rotavirus species. The strain gull/MR04_AAstV/HUN/2014 belonged to the genus Avastrovirus species avastrovirus 2 (AAstV-2) and is related to members of group 6 of avian nephritis viruses (ANVs), but based on the genetic distances it may be the first representative of a separate group. Additional gull samples were found to be negative by RT-PCR. Gulls, which are well adapted to the human environment, could potentially spread enterically transmitted viral pathogens like interspecies reassortant rotaviruses (RVG/RVB), but further molecular surveillance is needed to explore more deeply the viral communities of gulls or other related species adapted to human environments.

Data recording and use of data tools for pig health management: perspectives of stakeholders in pig farming

Introduction

Data-driven strategies might combat the spreading of infectious pig disease and improve the early detection of potential pig health problems. The current study aimed to explore individual views on data recording and use of data tools for pig health management by recruiting stakeholders (N = 202) in Spain, Ireland, and the Netherlands.

Methods

Questionnaire focused on current on-farm challenges, current status of data recording on farms, and evaluation of the two mock data tools. Particularly, "benchmarking tool" was designed to visualize individual farm's pig mortality, targeting the management of infectious respiratory and gastrointestinal diseases; and "early-warning tool" was designed to generate an alarm through monitoring coughs in pigs, targeting the management of infectious respiratory diseases.

Results

Results showed that respiratory and gastrointestinal diseases and aggressive behaviors were the most frequently mentioned health challenge and welfare challenge, respectively. Most of the data was more frequently recorded electronically than on paper. In general, the "benchmarking tool" was perceived as useful for the management of infectious respiratory and gastrointestinal diseases, and the "early-warning tool" was evaluated as useful for the management of infectious respiratory diseases. Several barriers to the perceived usefulness of these two tools were identified, such as the lack of contextual information, inconvenience of data input, limited internet access, reliance on one's own experience and observation, technical hurdles, and mistrust of information output. The perceived usefulness of both tools was higher among highly educated participants, and those who reported being integrators and positive toward technology for disease control. Female participants and those who came from integrated farms evaluated the "early-warning tool" as more useful compared to their counterparts. The perceived usefulness of the "early-warning tool" was negatively affected by age and work experience, but positively affected by extensiveness of data recording, positive attitude toward technology, and the current use of technology.

Discussion

In summary, participants showed optimistic views on the use of data tools to support their decision-making and management of infectious pig respiratory and gastrointestinal diseases. It is noteworthy that data tools should not only convey the value of data for informed decision-making but also consider stakeholders' preconditions and needs for data tools.

Control of Neonatal Diarrhea in Piglets with Reduced Antibiotic Use by Application of a Complementary Feed-A Randomized Controlled Farm Trial

The objective of this farm trial was to investigate if the consumption of antibiotics could be reduced when piglets showing early signs of neonatal diarrhea were treated with an oral dose of tannin extract derived from sweet chestnut wood. The farm had a very high incidence of neonatal diarrhea among gilt litters. Gilts were randomized into test or control groups in a 1:1 ratio to compare the consumption of antibiotics used for piglets and piglet mortality during the four-week trial period. Control litters were treated with the oral antibiotic paromomycin, while test litters were treated with the complementary feed O-Nella-Protect. The farm trial included 18 gilt litters comprising 254 piglets. In the control group, 100% of the piglets received antibiotic treatment. In the test group, consumption of antibiotics used against diarrhea was reduced by 84% (p = 0.001) and consumption of antibiotics used for other illnesses was reduced by 45% (p = 0.045). In both test and control groups, six piglets died. Microbiological analysis identified both potential bacterial and viral pathogens. In conclusion, the farm trial indicates that even under the challenge of potentially serious bacterial and viral pathogens, a complimentary feed containing a tannin extract can support piglet health and reduce antibiotic consumption.

Effect of Vaccination Against E. coli, C. perfringens Type A/C on Piglet Productive and Clinical Parameters Under Field Conditions

Background: One of the main strategies to control neonatal porcine diarrhoea (NPD) is through vaccination of the sows. This study aimed to compare the efficacy of two commercial vaccination schemes under field conditions on a farm where a C. perfringens type A cpb2-positive strain was implicated in NPD. Methods: This study was performed in a farrow-to-wean herd with 5500 sows, already using an E. coli and C. perfringens vaccine but still suffering NPD. Where the presence of a C. perfringens type A cpb2-positive strain was confirmed, Enteroporc Coli AC® (Ceva) was administrated to the sows in group A according to the manufacturer's instructions. Sows in group B were vaccinated using two other combined commercial vaccines. In each group, piglets from 10 litters were ear-tagged and individually weighed at birth and at 8 and 22 days of age. The incidence of diarrhoea, general piglet body condition, and antimicrobial treatment were recorded within 10 consecutive days after birth. Results: A total of 234 piglets (119 in group A and 115 in group B) were included. The mean weight gain of piglets from birth to 22 days of age was significantly higher in group A (4.99 kg) than in group B (4.66 kg) (p = 0.039). The rest of the recorded parameters such as the presence of diarrhoea, the piglet's body condition score, and the number of days with antimicrobial treatment did not differ significantly between groups. Conclusions: This study confirmed the efficiency of the Enteroporc Coli AC® vaccine in reducing clinical symptoms of diarrhoea in piglets, which was comparable with the other vaccines used in the study. The positive effect on piglets' productive performance during the lactation phase was observed.

Differences in enteric pathogens and intestinal microbiota between diarrheic weaned piglets and healthy penmates

Postweaning diarrhea (PWD) is a multifactorial disease caused by different aetiological agents, like viruses or bacteria and where the role of the microbiota remains unclear. The aim of this study was to assess differences between healthy and diarrheic weaned pigs concerning the prevalence of pathogens and changes in the intestinal microbiota. Eighteen farms with PWD were selected and 277 fecal samples were collected (152 diarrheic vs 125 healthy). Presence of Rotavirus A (RVA), B (RVB), C (RVC) and Porcine Epidemic Diarrhea Virus (PEDV), virulence factors of Escherichia coli and Clostridioides difficile were analyzed by PCR. Finally, the microbiota composition was also study by 16 S rRNA sequencing on 148 samples (102 diarrheic vs 46 healthy). RVA (53.95 % vs 36 %, p=0.04) and RVB (49.67 % vs 28.8 %, p<0.001) were more frequent in diarrheic animals. Furthermore, RVA viral load was higher in diseased animals. VT2 toxin was significantly associated with diarrhea, whereas other virulence factors were not. Presence of C. difficile and PEDV was almost negligible. Regarding microbiota changes, Fusobacteriota phylum was more frequent in diarrheic samples and Ruminococcaceae family in healthy penmates. During the first week postweaning, Enterobacteriace and Campylobacteria were enriched in animals presenting diarrhea. Furthermore, Lactobacillus was detected in those individuals with no RVA infection. In conclusion, RVA seems to play a primary role in PWD. Classic E. coli virulence factors were not associated with diarrhea, indicating the need for revising their implication in disease. Moreover, Lactobacillus was found frequently in animals negative for RVA, suggesting some protective effect.

Nucleotide metabolism-related host proteins RNA polymerase II subunit and uridine phosphorylase 1 interacting with porcine epidemic diarrhea virus N proteins affect viral replication

Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that targets pig intestines to cause disease. It is globally widespread and causes huge economic losses to the pig industry. PEDV N protein is the protein that constitutes the core of PEDV virus particles, and most of it is expressed in the cytoplasm, and a small part can also be expressed in the nucleus. However, the role of related proteins in host nucleotide metabolic pathways in regulating PEDV replication have not been fully elucidated. In this study, PEDV-N-labeled antibodies were co-immunoprecipitated and combined with LC-MS to screen for host proteins that interact with N proteins. Bioinformatics analyses showed that the selected host proteins were mainly enriched in metabolic pathways. Moreover, co-immunoprecipitation and confocal microscopy confirmed that the second-largest subunit of RNA polymerase II (RPB2) and uridine phosphorylase 1 (UPP1) interacted with the N protein. RPB2 is the main subunit of RNA polymerase II and plays an important role in eukaryotic transcription. UPP1 is an enzyme that catalyzes reversible phosphorylation of uridine to uracil and ribo-1-phosphate to promote catabolism and bio anabolism. RPB2 overexpression significantly promoted viral replication, whereas UPP1 overexpression significantly inhibited viral replication. Studies on interactions between the PEDV N and host proteins are helpful in elucidating the pathogenesis and immune escape mechanism of PEDV.

Molecular characterization of Escherichia coli virulence markers in neonatal and postweaning piglets from major pig-producing districts of Uganda

BACKGROUND

Piggery production is highly constrained by diseases, with diarrhoea in piglets being a major cause of economic losses to smallholder farmers in Uganda. Enterotoxigenic Escherichia coli (ETEC) is thought to be one of the major etiologies of this diarrhoea. A cross-sectional study was carried out in two high pig-producing districts of Uganda with the aim of determining the significance of piglet diarrhoea and the pathogenic determinants of causative E. coli.

METHODOLOGY

A total of 40 households with piglets were visited in each district for a questionnaire survey and faecal sample collection. The questionnaire-based data collected included; demographic data and pig management practices. E. coli were isolated from diarrheic (43) and non-diarrheic (172) piglets and were subjected to antimicrobial susceptibility testing against nine commonly used antimicrobial agents. The E. coli isolates were further screened for the presence of 11 enterotoxin and fimbrial virulence gene markers using multiplex polymerase chain reaction. Data entry, cleaning, verification and descriptive statistics were performed using Microsoft Excel. Statistical analysis to determine any association between the presence of virulence markers and diarrhea in piglets was done using SPSS software (Version 23), with a p value of less than 0.05 taken as a statistically significant association.

RESULTS

Escherichia coli were recovered from 81.4% (175/215) of the faecal samples. All the isolates were resistant to erythromycin, and most showed high resistance to tetracycline (71%), ampicillin (49%), and trimethoprim sulfamethoxazole (45%). More than half of the isolates (58.3%) carried at least one of the 11 virulence gene markers tested. EAST1 was the most prevalent virulence marker detected (35.4%), followed by STb (14.8%). Expression of more than one virulence gene marker was observed in 6.2% of the isolates, with the EAST1/STa combination being the most prevalent. Three adhesins; F17 (0.6%), F18 (6.3%) and AIDA-I (0.6%) were detected, with F18 being the most encountered. There was a statistically significant association between the occurrence of piglet diarrhoea and the presence of the AIDA-1 (p value = 0.037) or EAST1 (p value = 0.011) gene marker among the isolates.

CONCLUSION AND RECOMMENDATION

The level of antimicrobial resistance among E. coli isolates expressing virulence markers were high in the sampled districts. The study established a significant association between presence of EAST1 and AIDA-I virulence markers and piglet diarrhea. Further studies should be carried out to elucidate the main adhesins borne by these organisms in Uganda and the actual role played by EAST1 in the pathogenesis of the infection since most isolates expressed this gene.

Lipidomics reveals the significance and mechanism of the cellular ceramide metabolism for rotavirus replication

As one of the most important causative agents of severe gastroenteritis in children, piglets, and other young animals, species A rotaviruses have adversely impacted both human health and the global swine industry. Vaccines against rotaviruses (RVs) are insufficiently effective, and no specific treatment is available. To understand the relationships between porcine RV (PoRV) infection and enterocytes in terms of the cellular lipid metabolism, we performed an untargeted liquid chromatography mass spectrometry (LC-MS) lipidomics analysis of PoRV-infected IPEC-J2 cells. Herein, a total of 451 lipids (263 upregulated lipids and 188 downregulated lipids), spanning sphingolipid, glycerolipid, and glycerophospholipids, were significantly altered compared with the mock-infected group. Interestingly, almost all the ceramides among these lipids were upregulated during PoRV infection. LC-MS analysis was used to validated the lipidomics data and demonstrated that PoRV replication increased the levels of long-chain ceramides (C16-ceramide, C18-ceramide, and C24-ceramide) in cells. Furthermore, we found that these long-chain ceramides markedly inhibited PoRV infection and that their antiviral actions were exerted in the replication stage of PoRV infection. Moreover, downregulation of endogenous ceramides with the ceramide metabolic inhibitors enhanced PoRV propagation. Increasing the levels of ceramides by the addition of C6-ceramide strikingly suppressed the replication of diverse RV strains. We further found that the treatment with an apoptotic inhibitor could reverse the antiviral activity of ceramide against PoRV replication, demonstrating that ceramide restricted RV infection by inducing apoptosis. Altogether, this study revealed that ceramides played an antiviral role against RV infection, providing potential approaches for the development of antiviral therapies.IMPORTANCERotaviruses (RVs) are among the most important zoonosis viruses, which mainly infected enterocytes of the intestinal epithelium causing diarrhea in children and the young of many mammalian and avian species. Lipids play an essential role in viral infection. A comprehensive understanding of the interaction between RV and lipid metabolism in the enterocytes will be helpful to control RV infection. Here, we mapped changes in enterocyte lipids following porcine RV (PoRV) infection using an untargeted lipidomics approach. We found that PoRV infection altered the metabolism of various lipid species, especially ceramides (derivatives of the sphingosine). We further demonstrated that PoRV infection increased the accumulation of ceramides and that ceramides exerted antiviral effects on RV replication by inducing apoptosis. Our findings fill a gap in understanding the alterations of lipid metabolism in RV-infected enterocytes and highlight the antiviral effects of ceramides on RV infection, suggesting potential approaches to control RV infection.

Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions

A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome changes were associated with differences in performance regardless of sanitary conditions or diets. Since piglets often become mixed in multiple-site production systems and facility hygiene is also often neglected, this study suggests that increased Trp, Thr, and Met (AA+) dietary supplementation could contribute to mitigating the side effects of these harmful risk factors in modern pig farms.

Genomic diversity of group A rotaviruses from wild boars and domestic pigs in Japan: wide prevalence of NSP5 carrying the H2 genotype

Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.

The vaccination changed the profile of rotavirus infection with the increase of non-rotavirus A species diagnosis in one-week-old diarrheic piglets

Porcine rotavirus (RV) is a major viral agent associated with severe diarrhea in newborn piglets. RVA, RVB, RVC, and RVH are RV species that have already been identified in pigs. RVA is considered the most prevalent and relevant virus in pig production worldwide. This study aimed to evaluate the frequency of RV infection associated with diarrhea in suckling piglets from regular RVA-vaccinated Brazilian pig herds between 2015 and 2021. Therefore, 511 diarrheic fecal samples were collected from suckling piglets aged up to 3 weeks from 112 pig farms located in three main Brazilian pork production regions. All piglets were born to RVA-vaccinated sows. The nucleic acids of RVA, RVC, and RVH were investigated by RT-PCR assays and RVB by semi-nested RT-PCR assay. Of the diarrheic fecal samples analyzed, 221/511 (43.3%) were positive for at least one of the RV species. Regarding the distribution of RV species among the positive fecal samples that presented with only one RV species, 99 (44.8%), 63 (28.5%), and 45 (20.4%) were identified as RVB, RVC, and RVA, respectively. RVH was not identified in diarrheic piglets with a single infection. More than one RV species was identified in 14/221 (6.3%) of the diarrheic fecal samples evaluated. Co-detection of RVB + RVH (11/221; 5.0%), RVA + RVB (1/221; 0.4%), RVA + RVC (1/221; 0.4%), and RVB + RVC (1/221; 0.4%) was identified in fecal samples. The results demonstrated a significant increase in the RVC and, mainly, RVB detection rates in single infections. This study allowed us to characterize the importance of other RV species, in addition to RVA, in the etiology of neonatal diarrhea in piglets from pig herds with a regular vaccination program for RVA diarrhea control and prophylaxis.

Characterization of Antimicrobial Resistance in Escherichia coli Isolated from Diarrheic and Healthy Weaned Pigs in Catalonia

Postweaning diarrhea (PWD) is a multifactorial concern in the swine industry that leads to high antibiotic consumption, usually without testing susceptibility, increasing the risk of the selection of Escherichia coli-resistant strains. In this study, 251 E. coli strains isolated from fecal samples of diarrheic (n = 148) and apparently healthy piglets (n = 103) in farms in Catalonia were tested against their susceptibility to fourteen different antimicrobials. The phenotypic antimicrobial resistance (AMR) testing revealed high levels of AMR, with 41.4% of the isolates presenting a multidrug-resistant (MDR) profile. More specifically, resistance to class D (prudence) antimicrobials such as erythromycin (99.6%), amoxicillin (95.2%), streptomycin (91.6%), tetracycline (88.8%), lincospectin (64.5%), and sulfamethoxazole/trimethoprim (60%) was very high, as well as to class C (caution) antimicrobials such as florfenicol (45%). A special concern was observed for antimicrobial category B (restrict), like quinolones and colistin, that both presented a high rate of resistance. Colistin use was substantially reduced in Spain, but resistance is still present in weaned pigs, presenting a MIC90 of 4 μg/mL. This suggests that reducing antibiotic use is not enough to eliminate this AMR. Finally, it was found that piglets suffering diarrhea were more commonly carriers of MDR strains than the healthy ones (49.3% vs. 35%, p = 0.031). Therefore, given the high rates of resistance to the most commonly used antimicrobials, especially in diseased pigs, a new non-antibiotic-based approach should be implemented for the management of PWD.

Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs

Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.

Clostridioides difficile in Pigs and Dairy Cattle in Northern Italy: Prevalence, Characterization and Comparison between Animal and Human Strains

It has been observed that novel strains of Clostridioides difficile can rapidly emerge and move between animal and human hosts. The aim of this study was to investigate the prevalence of C. difficile in pigs and dairy cattle in northern Italy and to characterize and compare C. difficile animal strains with those from patients from the same geographical area. The C. difficile strains were isolated from animals from farms and slaughterhouses (cross-sectional studies) and from neonatal animals with enteric disorders in routine diagnostic investigations (passive surveillance). Samples positive for C. difficile were found in 87% of the pig farms and in 40% of the cattle farms involved in the cross-sectional studies, with a 20% prevalence among suckling piglets and 6.7% prevalence in neonatal calves, with no significant difference between animals with and without diarrheal symptoms. The prevalence of C. difficile in older animal categories was significantly lower. This result suggests that young age is an important risk factor for C. difficile colonization. In cross-sectional studies at slaughterhouses, in both the heavy pigs and dairy cows examined, only 2% of the intestinal content samples were positive for C. difficile and no contamination was found on the surface of the carcasses. Considering passive surveillance, the prevalence rates of positive samples were 29% in piglets and 1.4% in calves. Overall, 267 strains of animal origin and 97 from humans were collected. In total, 39 ribotypes (RTs) were identified, with RT 078 and RT 018 being predominant among animals and humans, respectively. Several RTs overlapped between animals and patients. In particular, RT 569 was identified as an emergent type in our country. Resistance to erythromycin and moxifloxacin was widely diffused among C. difficile strains, regardless of origin. This study supports C. difficile as a pathogen of one-health importance and highlights the need for a collaborative approach between physicians and veterinarians to control and prevent infections that are able to cross species and geographical barriers.

Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain

BACKGROUND

The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized.

RESULTS

PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (> 90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries.

CONCLUSIONS

Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered.

Coinfection with porcine epidemic diarrhea virus and Clostridium perfringens type A enhances disease severity in weaned pigs

Clostridium perfringens is a constituent of the normal gut microbiome in pigs; however, it can potentially cause pre- and post-weaning diarrhea. Nevertheless, the importance of this bacterium as a primary pathogen of diarrhea in piglets needs to be better understood, and the epidemiology of C. perfringens in Korean pig populations is unknown. To study the prevalence and typing of C. perfringens, 203 fecal samples were collected from diarrheal piglets on 61 swine farms during 2021-2022 and examined for the presence of C. perfringens and enteric viruses, including porcine epidemic diarrhea virus (PEDV). We determined that the most frequently identified type of C. perfringens was C. perfringens type A (CPA; 64/203, 31.5%). Among the CPA infections, single infections with CPA (30/64, 46.9%) and coinfections with CPA and PEDV (29/64, 45.3%) were the most common in diarrheal samples. Furthermore, we conducted animal experiments to investigate the clinical outcome of single infections and coinfections with highly pathogenic (HP)-PEDV and CPA in weaned piglets. The pigs infected with HP-PEDV or CPA alone showed mild or no diarrhea, and none of them died. However, animals that were co-inoculated with HP-PEDV and CPA showed more-severe diarrheal signs than those of the singly infected pigs. Additionally, CPA promoted PEDV replication in coinfected piglets, with high viral titers in the feces. A histopathological examination revealed more-severe villous atrophy in the small intestine of coinfected pigs than in singly infected pigs. This indicates a synergistic effect of PEDV and CPA coinfection on clinical disease in weaned piglets.

Detection of Enterotoxigenic Escherichia coli and Clostridia in the Aetiology of Neonatal Piglet Diarrhoea: Important Factors for Their Prevention

This study aimed to research the involvement of enterotoxigenic E. coli (ETEC) and C. difficile or C. perfringens type C in the aetiology of neonatal piglet diarrhoea in Greece and to identify preventive factors for them. A total of 78 pooled faecal samples were collected randomly from 234 suckling piglets (1-4 days of age) with diarrhoea from 26 pig farms (3 piglets × 3 litters × 26 farms = 234 piglets = 78 faecal pool samples). The collected samples were initially screened for the presence of E. coli and C. difficile or C. perfringens via cultivation on MacConkey and anaerobic blood agar, respectively. Subsequently, the samples were pooled on ELUTE cards. From samples tested, 69.23% of those in the farms were ETEC F4-positive, 30.77% were ETEC F5-positive, 61.54% ETEC were F6-positive, 42.31% were ETEC F4- and E. coli enterotoxin LT-positive, 19.23% were ETEC F5- and LT-positive, 42.31% were ETEC F6- and LT-positive, while LT was found in 57.69% of those in the farms. C. difficile was involved in many cases and identified as an emerging neonatal diarrhoea etiological agent. Specifically, Toxin A of C. difficile was found in 84.62% and Toxin B in 88.46% of those in the farms. Antibiotic administration to sows in combination with probiotics or acidifiers was revealed to reduce the detection of antigens of ETEC and the enterotoxin LT of E. coli.

Microbiological Findings and Associated Histopathological Lesions in Neonatal Diarrhoea Cases between 2020 and 2022 in a French Veterinary Pig Practice

This retrospective study described the aetiologies of neonatal diarrhoea cases and their associations with histological findings. A total of 106 diarrhoeic neonatal piglets were selected. Cultures, MALDI typings, PCRs and evaluation of intestinal lesions were performed. A total of 51 cases (48.1%) were positive for only one pathogen and 54 (50.9%) were positive for more than one pathogen. Clostridium perfringens type A was the most frequently detected pathogen (61.3%), followed by Enterococcus hirae (43.4%), rotavirus type A (38.7%), rotavirus type C (11.3%) and enterotoxigenic Escherichia coli (3.8%). Only lesions in the small intestine were correlated with detected pathogens. The detection of rotavirus was associated with an increased probability of observing villous atrophy (p < 0.001), crypt hyperplasia (p = 0.01) and leucocyte necrosis in the lamina propria (p = 0.05). The detection of Clostridium perfringens type A was associated with an increased probability of observing bacilli in close proximity to the mucosa (p < 0.001) and a decreased probability of observing epithelial necrosis (p = 0.04). Detection of Enterococcus hirae was associated with an increased probability of observing enteroadherent cocci (p < 0.001). Multivariate regression logistic models revealed that epithelial necrosis was more likely to occur in Enterococcus hirae-positive piglets (p < 0.02) and neutrophilic infiltrate was more likely to occur in Clostridium perfringens type A- and Enterococcus hirae-positive piglets (p = 0.04 and p = 0.02, respectively).

Diagnostic Approach to Enteric Disorders in Pigs

The diagnosis of enteric disorders in pigs is extremely challenging, at any age. Outbreaks of enteric disease in pigs are frequently multifactorial and multiple microorganisms can co-exist and interact. Furthermore, several pathogens, such as Clostridium perfrigens type A, Rotavirus and Lawsonia intracellularis, may be present in the gut in the absence of clinical signs. Thus, diagnosis must be based on a differential approach in order to develop a tailored control strategy, considering that treatment and control programs for enteric diseases are pathogen-specific. Correct sampling for laboratory analyses is fundamental for the diagnostic work-up of enteric disease in pigs. For example, histology is the diagnostic gold standard for several enteric disorders, and sampling must ensure the collection of representative and optimal intestinal samples. The aim of this paper is to focus on the diagnostic approach, from sampling to the aetiological diagnosis, of enteric disorders in pigs due to different pathogens during the different phases of production.

Genetic Diversity of Porcine Group A Rotavirus Strains from Pigs in South Korea

Porcine group A rotavirus (PoRVA; family, Reovirideae) strains cause acute viral gastroenteritis in piglets (especially suckling and weaned pigs), resulting in significant economic losses. In this study, we analyzed the VP7 and VP4 genes of PoRVA isolated between 2014 and 2018 from domestic pigs in South Korea to investigate the prevalence of predominant circulating genotypes (G and P types). The prevalence of the PoRVA antigen in the diarrheic fecal samples was 14.1% (53/377). Further genetic characterization of the VP7 and VP4 genes of 53 PoRVA isolates identified six different G-genotypes and five different P genotypes. The G4 and G9 genotypes were the most common (each 39.6%) in PoRVA-positive pigs, followed by P[7] and P[6] (33.9% and 30.1%, respectively). Because the G5 and G9 genotype vaccines are currently mainly used in South Korea, this result provides valuable epidemiological information about the genetic characteristics of PoRVA circulating on domestic pig farms. Development of a novel PoRVA vaccine that targets the current strains circulating in South Korea may be required for more effective virus control on pig farms.

A TaqMan Probe-Based Multiplex Real-Time PCR for Simultaneous Detection of Porcine Epidemic Diarrhea Virus Subtypes G1 and G2, and Porcine Rotavirus Groups A and C

Porcine viral diarrhea diseases affect the swine industry, resulting in significant economic losses. Porcine epidemic diarrhea virus (PEDV) genotypes G1 and G2, and groups A and C of the porcine rotavirus, are major etiological agents of severe gastroenteritis and profuse diarrhea, particularly among piglets, with mortality rates of up to 100%. Based on the high prevalence rate and frequent co-infection of PEDV, RVA, and RVC, close monitoring is necessary to avoid greater economic losses. We have developed a multiplex TaqMan probe-based real-time PCR for the rapid simultaneous detection and differentiation of PEDV subtypes G1 and G2, RVA, and RVC. This test is highly sensitive, as the detection limits were 20 and 100 copies/μL for the G1 and G2 subtypes of PEDV, respectively, and 50 copies/μL for RVA and RVC, respectively. Eighty-eight swine clinical samples were used to evaluate this new test. The results were 100% in concordance with the standard methods. Since reassortment between porcine and human rotaviruses has been reported, this multiplex test not only provides a basis for the management of swine diarrheal viruses, but also has the potential to impact public health as well.

On the Infectious Causes of Neonatal Piglet Diarrhoea—A Review

The aim of this paper is to review current knowledge on the relationship between presumptive infectious agents and neonatal porcine diarrhoea (NPD). The literature provides information on the rationale for this causation, including the first mention, main understandings gained with respect to, e.g., pathogenesis, and the knowledge to date on the specific relationships. Further, surveys on the presence and relative importance of these pathogens in NPD are included and the methodology used to identify the causation are discussed.

The Status of Pig Welfare in Selected Districts of Uganda: Implications for Health and Productivity Interventions

We conducted a pig welfare survey in four high pig producing districts in central Uganda, namely Masaka, Mukono, Mpigi, and Wakiso in 2021. Data were collected from 270 pig farms, and a total of 3,561 pigs, and consisted of resource-based (housing and water supply), animal-based (pig body condition and physical injuries), and management-based (records of morbidity and mortality) indicators of pig health and welfare. Data on animal and resource-based indicators were obtained from physical assessments of pigs and farm facilities, while management indicators and demographic details were collected by farmer interview. Across all farms, sow mortality in the last 12 months was reported to be 2.5% (95% Confidence Interval: 1.7, 4.8%). Animal-based indicators identified 9% (6.1, 13.7%) of sows with scouring/diarrhea, 7.6% (4.7, 11.5%) with lameness and 92% (85.1, 96.7%) of dry or lactating sows were found to be “skinny” with a body condition score of 1 or 2. In addition, piglet mortality was as high as 10.2% (8.5, 12.9%). A total of 19% of sows were partially or completely restricted from free movement inside pens. Ninety-three per cent of sows had continuous access to water, but only 48.8% of the water supplies were clean. Twenty per cent of farms reported sows experiencing stillbirths , 15% reported ill thrift, 12.5% reported respiratory disease and 10.8% reported gastrointestinal disease. Wakiso district registered the lowest pig mortality which was significantly lower compared to the other three districts. This study reveals that Ugandan pigs are exposed to severe undernutrition, dirty water, high mortality, physical injuries, poor housing, and health challenges (stillbirth, ill thrift, and Gastrointestinal disorders). Meaningful change to farmer livelihoods and pig welfare can be made by designing simple interventions that target improve housing structures, provision of cooling facilities especially during hot periods (heat stress) and bedding materials. The findings also represent a benchmark for the assessment of the effect of such interventions designed to improve farm health and productivity.

Assessing the Epidemiology of Rotavirus A, B, C and H in Diarrheic Pigs of Different Ages in Northern Italy

Rotaviruses are classified in 10 groups (A to J), where rotavirus A (RVA) is the major cause of diarrhea in humans and animals. With some exceptions, there is scarce information on the epidemiology of non-A rotaviruses in human and animal hosts. Currently, five species (A, B, C, E and H) have been identified in pigs. In the present study we investigated the prevalence of RVA, RVB, RVC and RVH among diarrheic pigs of different ages, in different seasons and in the presence of co-infections. Two molecular assays were developed for the detection of porcine RVA, RVB, RVC and RVH and were used to screen 962 stool specimens from suckling, weaning and fattening pigs with acute enteritis. Overall, rotaviruses were detected in a high percentage of samples (78%), with RVA being predominant (53%), followed by RVC (45%), RVB (43%) and RVH (14%). RVA was more common in the suckling (58%) and weaning cohorts (64%), while RVB, RVC and RVH were also frequently detected in fattening pigs. Only RVA and RVB infections followed a seasonal trend and exhibited age-related differences. Rotavirus infections were frequently present in combination with other pathogens. The present study depicts a portrait of rich rotavirus diversity in porcine herds, identifying seasonal and age-related patterns of circulation of the different rotavirus species in the surveyed areas.

Pathogens Detected in 205 German Farms with Porcine Neonatal Diarrhea in 2017

Neonatal diarrhea (ND) is still a frequently observed problem in modern industrial pig production. ND is predominantly caused by bacterial and viral pathogens. The objective of this study was to give an overview of different pathogens involved in ND in Germany. In 2017, a total number of 555 litters from 205 German pig farms with clinical ND were sampled with pooled fecal samples. All samples were analyzed regarding bacterial pathogens by culture and viral pathogens by polymerase chain reaction (PCR). Isolated strains of Clostridium (C.) perfringens, Escherichia (E.) coli, and C. difficile were further characterized by molecular techniques (e.g., PCR). There were 200 litters (36%), out of 555 sampled litters of 205 farms, which were positive for at least one, while most of them were positive for two or more pathogens. Toxin-producing C. perfringens type A could be detected in 122 farms (59.2%), C. difficile in 116 (56.1%), pathogenic E. coli in 79 (38.6%), and Rotavirus type A in 72 (35%). Among E. coli isolates, enterotoxigenic (8.8%) (F4 fimbriae positive (60.0%)) and necrotoxigenic E. coli (5.3%) were the most frequently detected pathotypes. In conclusion, in most of the farms with porcine ND it turned out to be a disease mainly caused by multiple pathogens, predominantly C. perfringens type A, pathogenic E. coli, and Rotavirus type A. Nevertheless, C. difficile and necrotoxigenic E. coli might be emerging pathogens in ND.

Occurrence of Rotavirus A Genotypes and Other Enteric Pathogens in Diarrheic Suckling Piglets from Spanish Swine Farms

Simple Summary

Neonatal diarrhea is a major cause of economic losses in the swine industry worldwide and has significant impact in Spain, which is one of the biggest pork producers globally. Multiple infectious agents can contribute to this condition, with some viruses such as species A rotavirus (RVA) playing a major role. Studies on their occurrence and genetic diversity are essential for development of RVA vaccines. In this study, fecal samples from diarrheic suckling piglets originating from farms distributed throughout Spain were analyzed for RVA and four other common enteric pathogens using molecular methods. The individual prevalence was 89.4%, 64.4%, 44.9%, 33.7% and 4.4% for Clostridiumperfringens, Clostridioides (formerly Clostridium) difficile, species A rotavirus, species C rotavirus and porcine epidemic diarrhea virus, respectively. Most specimens (96.9%) were positive for at least one of the target pathogens and concurrent infections were common. The molecular characterization of RVA positive specimens of specific genes used for genotyping revealed the extensive genetic diversity of RVA strains circulating in swine herds in Spain. Comparison with genotypes contained in the commercial vaccine available in Spain showed differences in the identity of the predominant RVA genotypes from diarrheic piglets in the sampled pig farms. These findings contribute to the surveillance of RVA strains circulating in swine herds in Spain and may help optimize target vaccine design.

Abstract

Species A rotavirus (RVA) is a major viral pathogen causing diarrhea in suckling piglets. Studies on its genetic heterogeneity have implications for vaccine efficacy in the field. In this study, fecal samples (n = 866) from diarrheic piglets younger than 28 days were analyzed over a two-year period (2018–2019). Samples were submitted from 426 farms located in 36 provinces throughout Spain and were tested using real-time PCR (qPCR) and reverse transcription real-time PCR (RT-qPCR) for five enteric pathogens. The individual prevalence was 89.4%, 64.4%, 44.9%, 33.7% and 4.4% for Clostridiumperfringens, Clostridioides (formerly Clostridium) difficile, species A rotavirus, species C rotavirus and porcine epidemic diarrhea virus, respectively. Most specimens (96.9%) were positive for at least one of the target pathogens, and more than 80% of samples harbored mixed infections. Nucleotide sequencing of 70 specimens positive for RVA revealed the presence of the VP7 genotypes G4, G9, G3, G5, G11 and the VP4 genotypes P7, P23, P6 and P13, with the combinations G4P7 and G9P23 being the most prevalent, and especially in the areas with the highest pig population. The study shows the extensive genetic diversity of RVA strains as well as discrepancies with the genotypes contained in the vaccine available in Spain, and multiple amino acid differences in antigenic epitopes of different G- and P- genotypes with the vaccine strains. Further investigations are needed to determine the efficacy of the vaccine to confer clinical protection against heterologous strains.

Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome

A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.

Cross-sectional study on risk factors associated with porcine epidemic diarrhea virus infection in pig farms in Junan county, China

Porcine epidemic diarrhea (PED) is a highly contagious, intestinal infectious disease in pigs, characterized by severe diarrhea, vomiting and dehydration. PED is widely epidemic in China as well as in many eastern Asian and America countries, causing tremendous losses in pig industry. However, little was known about the disease frequency and the associated risk factors of PED in pig farms. A cross-sectional study was conducted to estimate the herd prevalence and to identify the potential risk factors of porcine epidemic diarrhea virus (PEDV) infection of pig farms (≥100 pigs) in Junan county, China. A two-stage random sampling strategy was adopted, and a total of 751 fecal samples from suckling piglets of 82 farms were collected and tested by RT-PCR and sequencing for PEDV. Meanwhile, information on the putative risk factors of PEDV infection of those farms were collected in forms of questionnaires, followed by a descriptive analysis, univariable and multivariable logistic regression analysis. The results showed that the herd-level true prevalence of PEDV infection of pig farms in Junan was 35.16 % (95 %CI: 22.91-53.89); there were two variables significantly associated with PEDV infection, which were 'having more than 1000 slaughter pigs per annum' (OR = 5.42, 95 %CI: 1.19-24.72), and 'Weaning at 21-25 days' old' (OR = 4.50, 95 %CI:1.25-16.20). The research suggested that PED was highly endemic in pig farms in Junan county; larger herd size and weaning at an earlier age were potential risk factors associated with PEDV infection in pig farms in Junan. This study set an example in the research on herd-level prevalence of PEDV infection and risk factors associated with PEDV infection, and the results were of practical significance for the future planning of prevention and control of PED in Junan or other areas of China.

Extended-Spectrum β-Lactam Resistant Klebsiella pneumoniae and Escherichia coli in Wild European Hedgehogs (Erinaceus europeus) Living in Populated Areas

Simple Summary

The alarming emergence of antimicrobial resistance (AMR) in human and veterinary medicine has activated awareness for monitoring the levels of AMR pollution in the environment and wildlife. European hedgehogs (Erinaceus europaeus) are common wild species habiting urban areas in Europe. In this study, the occurrence and distribution of extended-spectrum β-lactam (ESBL) resistant enterobacteria and AMR genes were assessed in wild European hedgehogs in Catalonia, NE Spain. The results showed that 36.8% of the animals were detected as carriers of β-lactamase/carbapenemase resistance genes, with a special occurrence of human nosocomial bacteria such as Klebsiella pneumoniae, Escherichia coli, and Citrobacter freundii. In addition, more than half of the enterobacteria presented a multidrug resistance (MDR) phenotype and 31% of the isolates had an extended XDR profile. No differences in the spatial distribution of animals with AMR genes were observed within the study region. The results of this study suggest that the close contact with human areas predispose the transmission of AMR genes to wild hedgehogs because they either inhabit and/or feed in an anthropogenic environment. In conclusion, hedgehogs could be good sentinels or bioindicators of AMR environmental pollution, especially in highly populated areas with high human activity.

Abstract

Wildlife has been suggested to be a good sentinel of environmental health because of its close interaction with human populations, domestic animals, and natural ecosystems. The alarming emergence of antimicrobial resistance (AMR) in human and veterinary medicine has activated/triggered the awareness of monitoring the levels of AMR pollution in wildlife. European hedgehogs (Erinaceus europaeus) are common wild species habiting urban areas in Europe. However, there are few studies conducted in hedgehogs as reservoirs of AMR bacteria or genes. The aim of this study was to assess the occurrence and distribution of ESBL, AmpC, and carbapenem-resistant enterobacteria and AMR genes in wild European hedgehogs in Catalonia, a densely populated region of NE Spain. A total of 115 hedgehogs admitted at the Wildlife Rehabilitation Center of Torreferrussa were studied. To our knowledge, this is the first description of β-lactam resistant enterobacteria in wild hedgehogs. Interestingly, 36.8% (42/114) of the animals were detected as carriers of β-lactamase/carbapenemase resistance genes. Klebsiella spp. (59.6%), and specifically K. pneumoniae (84.6%), were the bacteria with the highest proportion of resistance genes, followed by E. coli (34.6%) and C. freundii (5.8%). The most frequently detected genetic variants were blaCTX-M-15 (19.3%), blaSHV-28 (10.5%), blaCMY-1 (9.7%), blaCMY-2 (8.8%), and blaOXA-48 (1.7%). In addition, 52% (27/52) of the isolates presented a multidrug resistance (MDR) phenotype and 31% had an extended drug resistance (XDR) profile. No clustering of animals with AMR genes within the study region was shown in the spatial analysis, nor differences in the proportion of positive animals among regions, were detected. The results of this study suggest that wild European hedgehogs could be good sentinels of AMR environmental pollution, especially in areas with a high human population density, because they either inhabit and/or feed in an anthropogenic environment. In conclusion, it is crucial to raise awareness of the strong interconnection between habitats and compartments, and therefore this implies that AMR issues must be tackled under the One Health approach.

Ligilactobacillus salivarius Strains Isolated From the Porcine Gut Modulate Innate Immune Responses in Epithelial Cells and Improve Protection Against Intestinal Viral-Bacterial Superinfection

Previously, we constructed a library of Ligilactobacillus salivarius strains from the intestine of wakame-fed pigs and reported a strain-dependent capacity to modulate IFN-β expression in porcine intestinal epithelial (PIE) cells. In this work, we further characterized the immunomodulatory activities of L. salivarius strains from wakame-fed pigs by evaluating their ability to modulate TLR3- and TLR4-mediated innate immune responses in PIE cells. Two strains with a remarkable immunomodulatory potential were selected: L. salivarius FFIG35 and FFIG58. Both strains improved IFN-β, IFN-λ and antiviral factors expression in PIE cells after TLR3 activation, which correlated with an enhanced resistance to rotavirus infection. Moreover, a model of enterotoxigenic E. coli (ETEC)/rotavirus superinfection in PIE cells was developed. Cells were more susceptible to rotavirus infection when the challenge occurred in conjunction with ETEC compared to the virus alone. However, L. salivarius FFIG35 and FFIG58 maintained their ability to enhance IFN-β, IFN-λ and antiviral factors expression in PIE cells, and to reduce rotavirus replication in the context of superinfection. We also demonstrated that FFIG35 and FFIG58 strains regulated the immune response of PIE cells to rotavirus challenge or ETEC/rotavirus superinfection through the modulation of negative regulators of the TLR signaling pathway. In vivo studies performed in mice models confirmed the ability of L. salivarius FFIG58 to beneficially modulate the innate immune response and protect against ETEC infection. The results of this work contribute to the understanding of beneficial lactobacilli interactions with epithelial cells and allow us to hypothesize that the FFIG35 or FFIG58 strains could be used for the development of highly efficient functional feed to improve immune health status and reduce the severity of intestinal infections and superinfections in weaned piglets.

Detection of Beta-Lactam-Resistant Escherichia coli and Toxigenic Clostridioides difficile Strains in Wild Boars Foraging in an Anthropization Gradient

Disease transmission among wild boars, domestic animals and humans is a public health concern, especially in areas with high wild boar densities. In this study, fecal samples of wild boars (n = 200) from different locations of the Metropolitan Area of Barcelona were analyzed by PCR to explore the frequency of β-lactamases and extended cephalosporin and carbapenem resistance genes (ESBLs) in Escherichia coli strains and the presence of toxigenic Clostridioides difficile. The prevalence of genes conferring resistance to β-lactam antimicrobials was 8.0% (16/200): bla_CMY-2 (3.0%), bla_TEM-1b (2.5%), bla_CTX-M-14 (1.0%), bla_SHV-28 (1.0%), bla_CTX-M-15 (0.5%) and bla_CMY-1 (0.5%). Clostridioides difficile TcdA+ was detected in two wild boars (1.0%), which is the first report of this pathogen in wild boars in Spain. Moreover, the wild boars foraging in urban and peri-urban locations were more exposed to AMRB sources than the wild boars dwelling in natural environments. In conclusion, the detection of E. coli carrying ESBL/AmpC genes and toxigenic C. difficile in wild boars foraging in urban areas reinforces the value of this game species as a sentinel of environmental AMRB sources. In addition, these wild boars can be a public and environmental health concern by disseminating AMRB and other zoonotic agents. Although this study provides the first hints of the potential anthropogenic sources of AMR, further efforts should be conducted to identify and control them.

Intestinal Viral Loads and Inactivation Kinetics of Livestock Viruses Relevant for Natural Casing Production: a Systematic Review and Meta-Analysis

Animal intestines are the source of edible sausage casings, which are traded worldwide and may come from areas where notifiable infectious animal diseases are prevalent. To estimate the risks of virus contamination, knowledge about the quantity of virus and decimal reduction values of the standard preservation method by salting is of great importance. A literature search, based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, was performed in search engine CAB Abstracts to determine the viral load of 14 relevant animal viruses in natural casings or intestines. Only a very limited number of scientific publications per virus were found and viral loads in the intestines varied from high for ASFV (five publications), BVDV (3), CSFV (6), PPRV (3), RPV (2) and TGEV (3) to moderate for PEDV (2) and SVDV (3), low for HEV (2) and FMDV (5), very low for VESV (1) and negative for PrV (2) and VSV (1). PRRSV was found in intestines, however, viral titers were not published. Three viruses (BVDV, CSFV and PPRV) with high viral loads were selected to search for their inactivation kinetics. For casings, no inactivation data were found, however, thermal inactivation data of these viruses were available, but differed in quantity, quality and matrices. In conclusion, important data gaps still exist when it comes to the quantitative inactivation of viruses in sausage casings or livestock intestines.

Rapid and sensitive detection of rotavirus by surface-enhanced Raman scattering immunochromatography

A surface-enhanced Raman scattering (SERS) immunochromatographic assay (ICA) has been developed for rapid, ultrasensitive, and quantitative detection of rotavirus in feces using double Raman molecule-labeled Au-core Ag-shell nanoparticles. The Raman signals are generated by 5,5'-dithiobis-(2-nitrobenzoic acid) and the intensity of the characteristic peak at 1334^-1 cm was detected as the analytical signal. The Raman signals were enhanced by the SERS-enhanced effect of both Au and Ag, the large amount of Raman molecules, and the hot-spot effect in the narrow gap between the Au core and Ag shell. The SERS ICA can quantitatively detect rotavirus in a concentration range of 8- 40,000 pg/mL, with detection limits of 80 pg/mL and 8 pg/mL based on naked eye observation and SERS signal detection, respectively. No cross-reaction was observed from other common pathogens. The standard deviation of the intra- and inter-batch repetitive tests is less than 10%, and the coincidence between SERS ICA and RT-qPCR as well as commercial colloidal gold ICA is 100%. The results indicated that this SERS ICA is able to quantitatively detect rotavirus in feces in 20 min with high sensitivity, selectivity, reproducibility, and accuracy and might be a promising method for the early detection of rotavirus in clinical analysis.

Prevalence and genome characterization of porcine rotavirus A in southern Mozambique

Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.

Pigs are not susceptible to SARS-CoV-2 infection but are a model for viral immunogenicity studies

Conventional piglets were inoculated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) through different routes, including intranasal, intratracheal, intramuscular and intravenous ones. Although piglets were not susceptible to SARS‐CoV‐2 and lacked lesions or viral RNA in tissues/swabs, seroconversion was observed in pigs inoculated parenterally (intramuscularly or intravenously).

A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput characterization of the swine sperm microbiome remains scarce. We carried RNA-seq on 40 ejaculates each from a different Pietrain boar and found that a proportion of the sequencing reads did not map to the Sus scrofa genome. The current study aimed at using these reads not belonging to pig to carry a pilot study to profile the boar sperm bacterial population and its relation with 7 semen quality traits. We found that the boar sperm contains a broad population of bacteria. The most abundant phyla were Proteobacteria (39.1%), Firmicutes (27.5%), Actinobacteria (14.9%) and Bacteroidetes (5.7%). The predominant species contaminated sperm after ejaculation from soil, faeces and water sources (Bacillus megaterium, Brachybacterium faecium, Bacillus coagulans). Some potential pathogens were also found but at relatively low levels (Escherichia coli, Clostridioides difficile, Clostridium perfringens, Clostridium botulinum and Mycobacterium tuberculosis). We also identified 3 potential antibiotic resistant genes from E. coli against chloramphenicol, Neisseria meningitidis against spectinomycin and Staphylococcus aureus against linezolid. None of these genes were highly abundant. Finally, we classified the ejaculates into categories according to their bacterial features and semen quality parameters and identified two categories that significantly differed for 5 semen quality traits and 13 bacterial features including the genera Acinetobacter, Stenotrophomonas and Rhodobacter. Our results show that boar semen contains a bacterial community, including potential pathogens and putative antibiotic resistance genes, and that these bacteria may affect its reproductive performance.

Antimicrobial Resistance Profiles and Characterization of Escherichia coli Strains from Cases of Neonatal Diarrhea in Spanish Pig Farms

Escherichia coli is considered one of the most common agents associated with neonatal diarrhea in piglets. The aim of this work was to characterize the pathogenic and antimicrobial resistance (AMR) profiles of 122 E. coli strains isolated from pigs suffering diarrhea (n = 94) and pigs without diarrhea (n = 28) of 24 farms in Spain. Virulence factors, toxins and AMR (ESBL and colistin) genes and AMR phenotypes of E. coli isolates were analyzed. Low prevalence of pathogenic E. coli strains (26%) was found in both groups. However, ETEC and VTEC strains were more frequently isolated from diarrheic piglets. Irrespectively of diarrhea occurrence, 97.5% of the strains showed a multidrug-resistance (MDR) profile to aminopenicillins, sulfonamides and tetracyclines. It was found that 22% of E. coli was CTX-M+, with CTX-M-14 being the principal allelic variant. Remarkably, 81.5% of CTX-M+ strains were isolated from diarrheic animals and presented an extended MDR profile to aminopenicillins, quinolones and aminoglycosides. Finally, low frequencies of colistin resistance genes mcr-1 (4/122) and mcr-4 (1/122) were found. MDR E. coli strains are circulating in pig farms of Spain, representing a serious threat to animal and public health. More appropriate diagnostic approaches (genetic and AMR phenotypic analysis) should be implemented in animal health to optimize antibiotic treatments.

Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018

Background

In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. To investigate the prevalence and genetic evolution of diarrhea-associated viruses responsible for the outbreaks, a total of 2987 field diarrheal samples collected from 168 pig farms in five provinces in Southern China during 2012–2018 were tested.

Results

Porcine epidemic diarrhea virus (PEDV) was most frequently detected virus with prevalence rates between 50.21 and 62.10% in samples, and 96.43% (162/168) in premises, respectively. Porcine deltacoronavirus (PDCoV) was the second prevalent virus with prevalence rates ranging from 19.62 to 29.19% in samples, and 70.24% (118/168) in premises, respectively. Both transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PoRV) were detected at low prevalence rates of < 3% in samples and 10.12% in premises. In this study, we identified a newly emerged swine acute diarrhea syndrome coronavirus (SADS-CoV) in diarrheal samples of piglets from Fujian province in Southern China, and the prevalence rate of SADS-CoV was 10.29% (7/68). Co-infections of these diarrhea-associated viruses were common. The most frequent co-infection was PEDV with PDCoV, with an average detection rate of 12.72% (380/2987, ranging from 8.26–17.33%). Phylogenetic analysis revealed that PEDVs circulating in Southern China during the last 7 years were clustered with the variant strains of PEDV in genotype IIa. The most frequent mutations were present in the collagenase equivalent (COE) and epitope regions of the spike gene of the PEDVs currently circulating in the field. Genetic relationships of PDCoVs were closely related with Chinese strains, other than those present in the USA, South Korea, Thailand and Lao’s public.

Conclusions

The findings of this study indicated that variant PEDV, PDCoV, and SADS-CoV were leading etiologic agents of porcine diarrhea, and either mono-infections or co-infections of pathogenic enteric CoVs were common in pigs in Southern China during 2012–2018. Thus, significant attention should be paid in order to effectively prevent and control porcine viral diarrhea.