Pathological and bacteriological characterization of neonatal porcine diarrhoea of uncertain aetiology

Antimicrobial resistance in Escherichia coli from Swedish piglets with diarrhoea and associations with potential risk factors

BACKGROUND

Antibiotic treatments of diarrhoea in suckling piglets and in pigs after weaning are common worldwide and contribute to antimicrobial resistance (AMR) in Escherichia coli from pigs. In Sweden, during the last decades, resistance to trimethoprim-sulphonamide and ampicillin has increased markedly in E. coli from routine clinical samples from piglets with diarrhoea, hereafter referred to as "clinical submissions". This has occurred despite a comparatively low use of antibiotics in Swedish pig production. However, clinical submissions might be biased towards farms with treatment failures and therefore overestimate occurrence of AMR. To explore the representativeness of data from such samples we compared occurrence of AMR in E. coli from clinical submissions and from concurrent samples collected from piglets with diarrhoea by convenience, referred to as "study samples". We also investigated associations between farm-related potential risk factors and AMR using farm data collected through a questionnaire. Data were evaluated using univariable and multivariable statistical models, as well as a multivariate model.

RESULTS

In all, 158 study samples from 97 herds and questionnaires from 83 herds were analysed. Resistance to streptomycin (37%), trimethoprim-sulphonamide (32%), ampicillin (30%), and tetracycline (18%) were the most frequent traits. Occurrence of AMR in 158 E. coli isolates from study samples was not significantly different from occurrence in 57 isolates from concurrent clinical submissions (P > 0.05). In 70% of herds, more than 10% of the sows were treated with antibiotics in the first week after farrowing, and trimethoprim-sulphonamide was the most common first choice antibiotic. Trimethoprim-sulphonamide resistance was associated with the proportion of sows receiving post-farrowing treatment. Resistance to ampicillin, tetracycline, and streptomycin resistances were indirectly associated with sow treatments, likely via co-resistance to trimethoprim-sulphonamide. There was no significant association between high dose zinc oxide supplementation and AMR (P > 0.05).

CONCLUSIONS

Clinical submissions do not overestimate occurrence of AMR in E. coli from Swedish piglets with diarrhoea and are therefore relevant for AMR monitoring. Even at low treatment rates, post-farrowing treatment of sows increases the risk for AMR in piglets. This applies especially for trimethoprim-sulphonamide resistance, but also for resistance to other antibiotics, and indicates that antibiotic use must be reduced substantially to achieve a reduction of AMR.

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.

Antimicrobial resistance- and pathogen patterns in the fecal microbiota of sows and their offspring in German commercial pig farms

Reducing antibiotic use is one of the biggest challenges in pig farming, as antibiotics have been used for years to control typical problems such as newborn or post-weaning diarrhea. The pressure a one health approach has created on animal production regarding antimicrobial resistance is an opportunity to find other strategies against enterobacterial pathogens in suckling and weaned piglets. A farm-specific approach could have a good success due to the individual farm structures in Germany and other countries. In this study, non-metric multidimensional scaling, hierarchical clustering, and latent class analysis were used to determine the impact of antibiotic use on antibiotic resistance patterns and pathogen prevalence in 20 German pig farms. This may help to develop individualized health strategies. 802 fresh fecal samples were collected from sows and piglets from 20 piglet production and rearing farms at different production times (sows antepartum and postpartum, suckling piglets, weaned piglets). In addition, the use of antibiotics was recorded. DNA extracts were subjected to quantitative real-time qPCR with primers specific for antibiotic resistance genes (int1, sul1-3, dfrA1, mcr-1, blaCTX-M), and virulence factors of relevant bacteria (C. difficile, C. perfringens, Salmonella, Escherichia/Shigella/Hafnia, E. coli). Linear and logistic regression models were used to analyze the relationship between different antibiotics and the major genes contributing to the clustering of observations for the different animal groups. Clustering revealed different farm clusters for sows, suckling piglets, and weaned piglets, with the most remarkable diversity in antibiotic use among weaned piglets. Amoxicillin, lincomycin, and enrofloxacin were identified as the most probable cause of increased odds of the presence of relevant antibiotic resistance genes (mcr1, dfrA1, blaCTX-M). Still, direct effects of a specific antibiotic on its associated resistance gene were rare. Enrofloxacin and florfenicol favored the occurrence of C. difficile in sows. The E. coli fimbriae genes were less affected by antibiotic use in sows and piglets, but the F4 fimbriae gene could be associated with the integrase 1 gene in piglets. The results confirm that multidrug-resistant enterobacteria are widespread in German pig farms and give awareness of the impact of current antibiotic use while searching for alternative health strategies.

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).

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.

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.

Microbial content of non-fermented liquid feed consumed by sows affects the occurrence of neonatal diarrhoea in their piglets: A case-control study

BACKGROUND

Microbial colonisation of piglets' intestines starts at birth, especially from contact with sow's faeces. Piglet microbiota could therefore be influenced by the sow's diet. The objective of this study was to evaluate whether the microbiological flora of liquid feed for sows can be associated with the development of neonatal diarrhoea.

METHODS

This study was carried out on 10 case farms with neonatal diarrhoea and 10 control farms without neonatal diarrhoea. On each farm, a microbiological analysis of gestating and lactating liquid feed was performed. A generalised linear model was used to study the impact of the liquid feed microbiological counts and pH on the probability of neonatal diarrhoea developing.

RESULTS

For thermotolerant coliforms, sulphite-reducing bacteria, heterotrophic bacteria and lactic-acid bacteria counts, there was no significant difference between case and control farms. The higher the count of total coliforms, enterococci and yeasts in sow non-fermented liquid feed, the greater the probability of observing neonatal diarrhoea. Moreover, taking into account total coliforms and yeasts counts together is highly predictive of neonatal diarrhoea risk.

CONCLUSION

This study offers new perspectives of investigation and understanding of neonatal diarrhoea in breeding farms feeding sows with a non-fermented liquid feed.

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

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Multiple pathogens were found in all neonatal diarrhea outbreaks.

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RVA was the most frequent agent associated with diarrheic cases.

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Other enteric pathogens can be involved in some neonatal diarrhea outbreaks.

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The multifactorial origin of pig diarrhea requires a personalized farm diagnosis.

Diarrhea is one of the major causes of neonatal mortality in pigs. In the present study, 31 pig farms with outbreaks of neonatal diarrhea were investigated in Catalonia (NE Spain) from February 2017 until June 2018. Two hundred and fifteen diarrheic samples from 1 to 7 days old piglets were tested for a panel of enteric pathogens. In 19 of the studied farms additional fecal samples from apparently healthy pen-mates were collected and tested for the same panel of infectious agents. Samples were bacteriologically cultured and tested by PCR for E. coli virulence factors genes, C. perfringens types A and C toxins (Cpα, Cpβ, Cpβ2) and C. difficile toxins (TcdA, TcdB). Moreover, Rotavirus A (RVA), Rotavirus B (RVB), Rotavirus C (RVC), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) were also determined by RT-qPCR. More than one pathogen could be detected in all of the outbreaks. Nevertheless, RVA was the only agent that could be statistically correlated with the outcome of diarrhea. For the other viruses and bacteria analyzed significant differences between the diseased pigs and the controls were not found. In spite of this, the individual analysis of each of the studied farms indicated that other agents such as RVB, RVC, toxigenic C. difficile or pathogenic E. coli could play a relevant role in the outbreak of diarrhea. In conclusion, the large diversity of agent combinations and disease situations detected in neonatal diarrhea outbreaks of this study stand for a more personalized diagnosis and management advice at a farm level.

Diversity analysis of intestinal microflora between healthy and diarrheal neonatal piglets from the same litter in different regions

Though the problem of neonatal piglet diarrhea is well known, the differences in the bacterial diversity and community composition between healthy and diarrheal piglets are still unknown. We investigated these differences in neonatal piglets from Jiangxi Province, China. Healthy (H, n = 20) and diarrheal (D, n = 20) piglets were selected from six regions. The fecal microbial communities were analyzed by sequencing the V3V4 region of 16S rRNA gene. We found the ratio of major phyla (Fusobacteria, Bacteroidetes, Firmicutes and Proteobacteria) was >99% of 7 phyla. The overall alpha diversity indices, such as chao, sobs, coverage and Shannon, were not significantly different. Moreover, the relative abundance of the predicted functions was highly similar in the two groups. Our results indicated that Clostridium was divided into two major groups: Clostridium sensu stricto_1 and stricto_2. Sensu stricto_2 was highly abundant in the D group and low abundance in the H group, whereas the results of sensu stricto_1 were opposite. Comparative analyses within the H or D groups showed that Escherichia-Shigella and Streptococcus at the genus level and unclassified Lactobacillus at the species level were significant difference. Comparative analyses of the two groups showed that unclassified Prevotellaceae at the genus level and Fusobacterium mortifierum were significantly different and had high linear discriminant analysis (LDA) scores. The significantly different microbes composition results also existed in the same litter, based on excluding regions influence. These results suggested that piglet diarrhea was closely associated with these microbes. This study provides insights into gut microbial interactions and prevention of piglet diarrhea.

Diarrhoea in neonatal piglets: a case control study on microbiological findings

Background

Many factors can influence the occurrence of neonatal diarrhoea in piglets. Currently, well-known pathogens such as enterotoxigenic Escherichia coli and Clostridium perfringens type C appear to play a minor role in development of disease. Other infectious pathogens may be involved. In this study, we aimed to investigate the presence of selected infectious pathogens in neonatal piglets with clinical and pathological signs of enteric disease. The association between rotavirus A, Enterococcus hirae, Clostridium difficile and Clostridium perfringens type A/C and diarrhoea was investigated in a case control study on piglet level. The possible role of E. coli virulence factors was investigated in a multistep-procedure using herd-pools of E.coli isolates to screen for their presence.

Results

Rotavirus A was detected more often in cases (25%) than in controls (6%) (P < 0.001). The detection rate of Enterococcus hirae, Clostridium difficile and C. perfringens type A positive for beta2 genes was the same in the two groups of piglets. C. perfringens type C was not detected in the study. Investigations on E. coli virulence factors showed a high prevalence of EAST1 toxin genes (55% of tested case piglets were positive) and AIDA-1 adhesin genes (63% of toxin positive case piglets were positive) in case piglets.

Conclusions

Detection of rotavirus A was statistically significantly associated with neonatal piglet diarrhoea.

An aetiologic role of E. coli carrying virulence factors EAST1 and AIDA-1 needs further investigation as the study points out these two factors as possible causative factors in neonatal diarrhoea.

Detection of E.hirae, C.difficile and C. perfringens type A carrying beta 2 genes was not associated with neonatal piglet diarrhoea. However, the study suggested that massive overgrowth by E. hirae could be part of the pathogenesis in some cases of neonatal diarrhoea.

Electronic supplementary material

The online version of this article (10.1186/s40813-018-0094-5) contains supplementary material, which is available to authorized users.

Viral and bacterial investigations on the aetiology of recurrent pig neonatal diarrhoea cases in Spain

Background

Neonatal diarrhoea represents a major disease problem in the early stages of animal production, increasing significantly pre-weaning mortality and piglets weaned below the target weight. Enteric diseases in newborn piglets are often of endemic presentation, but may also occur as outbreaks with high morbidity and mortality. The objective of this study was to assess the frequency of different pathogens involved in cases of recurrent neonatal diarrhoea in Spain.

Results

A total of 327 litters from 109 sow farms located in Spain with neonatal recurrent diarrhoea were sampled to establish a differential diagnosis against the main enteric pathogens in piglets. In total, 105 out of 109 (96.3%) case submissions were positive to one of the examined enteric organisms considered potentially pathogenic (Escherichia coli, Clostridium perfringens types A and C, Transmissible gastroenteritis virus [TGEV], Porcine epidemic diarrhoea virus [PEDV] or Rotavirus A [RVA]). Fifty-eight out of 109 (53.2%) submissions were positive for only one of these pathogens, 47 out of 109 (43.1%) were positive for more than one pathogen and, finally, 4 out of 109 (3.7%) were negative for all these agents. Escherichia coli strains were isolated from all submissions tested, but only 11 of them were classified into defined pathotypes. Clostridium perfringens type A was detected in 98 submissions (89.9%) and no C. perfringens type C was found. Regarding viruses, 47 (43.1%) submissions were positive for RVA, 4 (3.7%) for PEDV and none of them for TGEV.

Conclusion

In conclusion, C. perfringens type A, E. coli and RVA were the main pathogens found in faeces of neonatal diarrheic piglets in Spain.

Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets

Diarrhea is a leading cause of increased mortality in neonatal and young piglets. Aberration of the gut microbiota is one important factor in the etiology of piglet diarrhea. However, information regarding the structure and function of the gut microbiome in diarrheic neonatal piglets is limited. To investigate the composition and functional potential of the fecal microbiota in neonatal piglets, we performed 16S rRNA gene sequencing on 20 fecal samples from diarrheic piglets and healthy controls, and metagenomics sequencing on a subset of six samples. We found striking compositional and functional differences in fecal microbiota between diarrheic and healthy piglets. Neonatal piglet diarrhea was associated with increases in the relative abundance of Prevotella, Sutterella, and Campylobacter, as well as Fusobacteriaceae. The increased relative abundance of Prevotella was correlated with the reduction in Escherichia coli and the majority of beneficial bacteria that belonging to the Firmicutes phylum (e.g., Enterococcus, Streptococcus, Lactobacillus, Clostridium, and Blautia) in diarrheic piglets. The differentially functional gene abundances in diarrheic piglets were an increase in bacterial ribosome, and contributed primarily by the genera Prevotella, this indicates a growth advantage of the Prevotella in diarrheic conditions. Additional functional gene sets were associated with the reduction of polyamine transport, monosaccharide and sugar-specific PTS transport, amino acid transport, and two-component regulatory system. These profiles likely impact the ability to transport and uptake nutrients, as well as the ability to fight microbial infections in the piglet gut ecosystem. This work identifies a potential role for Prevotella in the community-wide microbial aberration and dysfunction that underpins the pathogenesis of piglet diarrhea. Identification of these microbial and functional signatures may provide biomarkers of neonatal piglet diarrhea.

Rethinking the role of alpha toxin in Clostridium perfringens-associated enteric diseases: a review on bovine necro-haemorrhagic enteritis

Bovine necro-haemorrhagic enteritis is an economically important disease caused by Clostridium perfringens type A strains. The disease mainly affects calves under intensive rearing conditions and is characterized by sudden death associated with small intestinal haemorrhage, necrosis and mucosal neutrophil infiltration. The common assumption that, when causing intestinal disease, C. perfringens relies upon specific, plasmid-encoded toxins, was recently challenged by the finding that alpha toxin, which is produced by all C. perfringens strains, is essential for necro-haemorrhagic enteritis. In addition to alpha toxin, other C. perfringens toxins and/or enzymes might contribute to the pathogenesis of necro-haemorrhagic enteritis. These additional virulence factors might contribute to breakdown of the protective mucus layer during initial stage of pathogenesis, after which alpha toxin, either or not in synergy with other toxins such as perfringolysin O, can act on the mucosal tissue. Furthermore, alpha toxin alone does not cause intestinal necrosis, indicating that other virulence factors might be needed to cause the extensive tissue necrosis observed in necro-haemorrhagic enteritis. This review summarizes recent research that has increased our understanding of the pathogenesis of bovine necro-haemorrhagic enteritis and provides information that is indispensable for the development of novel control strategies, including vaccines.

Farm characteristics and management routines related to neonatal porcine diarrhoea: a survey among Swedish piglet producers

Background

In recent years reports from a number of countries, including Sweden, describe problems with diarrhoea in newborn piglets despite the use of previously effective preventive measures. This seemingly altered disease pattern of neonatal porcine diarrhoea (NPD) warrants investigations on the magnitude and manifestation of the problem. The aim of the present study was to investigate the herd-level prevalence of NPD in Sweden and to describe disease characteristics and intervention strategies used in affected herds. To obtain this information a questionnaire was developed and sent out to 170 randomly selected herds. The presence of NPD in the herds was specified as “Yes”, “No” or “Occasional cases” during the preceding year.

Results

A response rate of 58% (98/170) was achieved. The total prevalence of farmer experienced NPD, including occasional cases was 79.6% (95% CI 70.6–86.4%). Most herds (85%; 83/98) employed maternal vaccination against enterotoxigenic Escherichia coli (ETEC). The most common treatment regimens used in affected herds included antimicrobials only (43%; 18/42) or antimicrobials in combination with supplementary fluids (33%; 14/42). Trimethoprim in combination with a sulphonamide was the drug of choice in 57% (24/42) of the affected herds whereas the remaining herds used a broad range of other antimicrobials (neomycin, amoxicillin, fluoroquinolones, penicillin, and tylosin). Furthermore, the risk of experiencing NPD was found to be higher in herds with >200 sows (OR = 4.0) compared to herds with <200 sows and in herds where more ambitious efforts (such as providing supplemental colostrum or practicing split-suckling) were made to save weak-born piglets (OR = 4.4).

Conclusions

The results of the present study indicate that Swedish farmers commonly experience NPD in their herds, often despite vaccination against ETEC. Considering the extent of this problem and its contribution to antimicrobial usage, improving alternative control strategies for NPD needs to be prioritized.

Electronic supplementary material

The online version of this article (doi:10.1186/s13028-016-0261-0) contains supplementary material, which is available to authorized users.

Prevalence of adhesin and toxin genes in E. coli strains isolated from diarrheic and non-diarrheic pigs from smallholder herds in northern and eastern Uganda

Background

Enterotoxigenic E. coli (ETEC) significantly contribute to diarrhea in piglets and weaners. The smallholder pig producers in Uganda identified diarrhea as one of the major problems especially in piglets. The aim of this study was to; i) characterize the virulence factors of E. coli strains isolated from diarrheic and non-diarrheic suckling piglets and weaners from smallholder herds in northern and eastern Uganda and ii) identify and describe the post-mortem picture of ETEC infection in severely diarrheic piglets. Rectal swab samples were collected from 83 piglets and weaners in 20 herds and isolated E. coli were characterized by PCR, serotyping and hemolysis.

Results

The E. coli strains carried genes for the heat stable toxins STa, STb and EAST1 and adhesins F4 and AIDA-I. The genes for the heat labile toxin LT and adhesins F5, F6, F18 and F41 were not detected in any of the E. coli isolates. Where the serogroup could be identified, E. coli isolates from the same diarrheic pig belonged to the same serogroup. The prevalence of EAST1, STb, Stx2e, STa, AIDA-I, and F4 in the E. coli isolates from suckling piglets and weaners (diarrheic and non-diarrheic combined) was 29, 26.5, 2.4, 1.2, 16, and 8.4 %, respectively. However the prevalence of F4 and AIDA-I in E. coli from diarrheic suckling piglets alone was 22.2 and 20 %, respectively. There was no significant difference in the prevalence of the individual virulence factors in E. coli from the diarrheic and non-diarrheic pigs (p > 0.05). The main ETEC strains isolated from diarrheic and non-diarrheic pigs included F4/STb/EAST1 (7.2 %), F4/STb (1.2 %), AIDA/STb/EAST1 (8 %) and AIDA/STb (8 %). At post-mortem, two diarrheic suckling piglets carrying ETEC showed intact intestinal villi, enterocytes and brush border but with a layer of cells attached to the brush border, suggestive of ETEC infections.

Conclusion

This study has shown that the F4 fimbriae is the most predominant in E. coli from diarrheic piglets in the study area and therefore an F4-based vaccine should be considered one of the preventive measures for controlling ETEC infections in the piglets in northern and eastern Uganda.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0796-2) contains supplementary material, which is available to authorized users.

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets

Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24–48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.