Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota

The view on antimicrobials has dramatically changed due to the increased knowledge on the importance of microbiota composition in different body parts. Antimicrobials can no longer be considered only beneficial, but also potentially deleterious for favourable bacterial populations. Still, the use of metaphylactic antimicrobial treatment at early stages of life is a practice in use in porcine production. Many reports have shown that antibiotics can critically affect the gut microbiota, however the effect of perinatal antimicrobial treatment on the nasal microbiota has not been explored yet. To gain insights on the potential changes in nasal microbial composition due to antimicrobial treatments, piglets from two different farms were sampled at weaning. The nasal microbiota was analysed when antimicrobial treatment was used early in life, and later, when no antimicrobial treatment was used during the lactation period. Removal of perinatal antimicrobials resulted in an increased bacterial diversity in nasal microbiota at weaning. Concurrently, elimination of antimicrobials produced an increase in the relative abundance of Prevotella and Lactobacillus, and a decrease in Moraxella and Bergeyella. These changes in microbiota composition were accompanied by an improvement of the piglets' health and a higher productivity in the nursery phase

Similar frequency of Porcine circovirus 3 (PCV‐3) detection in serum samples of pigs affected by digestive or respiratory disorders and age‐matched clinically healthy pigs

Porcine circovirus 3 (PCV‐3) has been identified in pigs affected by different disease conditions, although its pathogenicity remains unclear. The objective of the present study was to assess the frequency of PCV‐3 infection in serum samples from animals suffering from post‐weaning respiratory or digestive disorders as well as in healthy animals. A total of 315 swine serum samples were analysed for PCV‐3 DNA detection by conventional PCR; positive samples were further assayed with a quantitative PCR and partially sequenced. Sera were obtained from 4 week‐ to 4 month‐old pigs clinically diagnosed with respiratory (n = 129) or digestive (n = 126) disorders. Serum samples of age‐matched healthy animals (n = 60) served as negative control. Pigs with clinical respiratory signs had a wide variety of pulmonary lesions including suppurative bronchopneumonia, interstitial pneumonia, fibrinous‐necrotizing pneumonia and/or pleuritis. Animals with enteric signs displayed histopathological findings like villus atrophy and fusion, catarrhal enteritis and/or catarrhal colitis. Overall, PCV‐3 DNA was detected in 19 out of 315 analysed samples (6.0%). Among the diseased animals, PCV‐3 was found in 6.2% (8 out of 129) and 5.6% (7 out of 126) of pigs with respiratory and digestive disorders, respectively. The frequency of PCV‐3 PCR positive samples among healthy pigs was 6.7% (4 out of 60). No apparent association was observed between PCR positive cases and any type of histopathological lesion. The phylogenetic analysis of the partial genome sequences obtained showed high identity among viruses from the three groups of animals studied. In conclusion, PCV‐3 was present in the serum of diseased and healthy pigs to similar percentages, suggesting that this virus does not seem to be causally associated with respiratory or enteric disorders.info:eu-repo/semantics/acceptedVersio

A Shift in Porcine Circovirus 3 (PCV-3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population

The identification of a new circovirus (Porcine circovirus 3, PCV-3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV-3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV-3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV-3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10-10 substitution/site/year) than the PCV-2 one. Accordingly, the action of selective pressures on PCV-3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV-2, suggesting either a reduced PCV-3 plasticity or a less efficient host-induced natural selection. A complex and not-directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium

Frequency of Detection and Phylogenetic Analysis of Porcine circovirus 3 (PCV-3) in Healthy Primiparous and Multiparous Sows and Their Mummified Fetuses and Stillborn

Porcine circovirus 3 (PCV-3) has been suggested as a putative causal agent of swine reproductive disease. A number of different studies have pointed out this association, but there is still a lack of information regarding the normal rates of PCV-3 infection in farms with normal reproductive parameters. The objective of the present study was to assess the frequency of PCV-3 detection in primiparous and multiparous sows and in tissues from their respective fetuses from farms with average reproductive parameters. Sera from 57 primiparous and 64 multiparous sows from 3 different farms were collected at two time points. Brain and lung tissues from 49 mummies and 206 stillborn were collected at farrowing. Samples were tested by PCR, and when positive, quantified by quantitative PCR. Thirty-nine complete genomes were obtained and phylogenetically analyzed. All sera from multiparous sows were negative, while 19/57 (33.3%) primiparous sows were PCV-3 PCR positive. From the 255 tested fetuses, 86 (33.7%) had at least one tissue positive to PCV-3. The frequency of detection in fetuses from primiparous sows (73/91, 80.2%) was significantly higher than those from multiparous ones (13/164, 7.9%). It can be concluded that PCV-3 is able to cause intrauterine infections in absence of overt reproductive disorders.info:eu-repo/semantics/publishedVersio

Retrospective detection of Porcine circovirus 3 (PCV-3) in pig serum samples from Spain

Porcine circovirus 3 (PCV‐3) is an emerging circovirus species that has recently been reported in different countries around the world, suggesting a widespread circulation. In this study, sera samples originating from 654 pigs of different production phases and clinical/pathological conditions, submitted for diagnostic purposes between 1996 and 2017, were randomly selected. Detection of PCV‐3 genome in such samples was attempted with a previously described PCR method, and the partial genome sequence was obtained from selected PCV‐3‐positive samples from different years. Compiled data confirmed that PCV‐3 has been circulating in the Spanish pig population since 1996. The overall frequency of PCV‐3 PCR‐positive samples in the study period was 11.47% (75 of 654). Phylogenetic analysis of twelve PCV‐3 partial sequences obtained showed a high nucleotide identity with the already known PCV‐3 sequences, with minor variations among years. No significant correlation was found between the detection of PCV‐3 and any production phase nor clinical/pathological condition. These results confirm PCV‐3 circulation at least since 1996 in the Spanish pig population with a low/moderate frequency. Although the information obtained was limited, PCV‐3 did not appear to be linked to any specific pathological condition or age group.info:eu-repo/semantics/publishedVersio

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids

This study was supported by the Ministry of Economy and Competitiveness (MINECO) from the Spanish Government (grant number AGL2016-78160-C2-1-R). The authors are also grateful to the Centres de Recerca de Catalunya (CERCA) Programme and Global Alliance for Research on African swine fever (GARA). The authors thank Frederic Paboeuf and Audrey Fougeroux for providing SPF and domestic pig samples.Most of the microorganisms living in a symbiotic relationship in different animal body sites (microbiota) reside in the gastrointestinal tract (GIT). Several studies have shown that the microbiota is involved in host susceptibilities to pathogens. The fecal microbiota of domestic and wild suids was analyzed. Bacterial communities were determined from feces obtained from domestic pigs (Sus scrofa) raised under different conditions: specific-pathogen-free (SPF) pigs and domestic pigs from the same bred, and indigenous domestic pigs from a backyard farm in Kenya. Secondly, the fecal microbiota composition of the African swine fever (ASF) resistant warthogs (Phacochoerus africanus) from Africa and a European zoo was determined. African swine fever (ASF) is a devastating disease for domestic pigs. African animals showed the highest microbial diversity while the SPF pigs the lowest. Analysis of the core microbiota from warthogs (resistant to ASF) and pigs (susceptible to ASF) showed 45 shared OTUs, while 6 OTUs were exclusively present in resistant animals. These six OTUs were members of the Moraxellaceae family, Pseudomonadales order and Paludibacter, Anaeroplasma, Petrimonas, and Moraxella genera. Further characterization of these microbial communities should be performed to determine the potential involvement in ASF resistance

Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota

The view on antimicrobials has dramatically changed due to the increased knowledge on the importance of microbiota composition in different body parts. Antimicrobials can no longer be considered only beneficial, but also potentially deleterious for favourable bacterial populations. Still, the use of metaphylactic antimicrobial treatment at early stages of life is a practice in use in porcine production. Many reports have shown that antibiotics can critically affect the gut microbiota, however the effect of perinatal antimicrobial treatment on the nasal microbiota has not been explored yet. To gain insights on the potential changes in nasal microbial composition due to antimicrobial treatments, piglets from two different farms were sampled at weaning. The nasal microbiota was analysed when antimicrobial treatment was used early in life, and later, when no antimicrobial treatment was used during the lactation period. Removal of perinatal antimicrobials resulted in an increased bacterial diversity in nasal microbiota at weaning. Concurrently, elimination of antimicrobials produced an increase in the relative abundance of Prevotella and Lactobacillus, and a decrease in Moraxella and Bergeyella. These changes in microbiota composition were accompanied by an improvement of the piglets' health and a higher productivity in the nursery phase