Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen.

BACKGROUND: Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows. RESULTS: Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning. CONCLUSIONS: This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host.

Evaluation of recombinant Mycoplasma hyopneumoniae P97/P102 paralogs formulated with selected adjuvants as vaccines against mycoplasmal pneumonia in pigs.

Pig responses to recombinant subunit vaccines containing fragments of eight multifunctional adhesins of the Mycoplasma hyopneumoniae (Mhp) P97/P102 paralog family formulated with Alhydrogel(®) or Montanide™ Gel01 were compared with a commercial bacterin following experimental challenge. Pigs, vaccinated intramuscularly at 9, 12 and 15 weeks of age with either of the recombinant formulations (n=10 per group) or Suvaxyn(®) M. hyo (n=12), were challenged with Mhp strain Hillcrest at 17 weeks of age. Unvaccinated, challenged pigs (n=12) served as a control group. Coughing was assessed daily. Antigen-specific antibody responses were monitored by ELISA in serum and tracheobronchial lavage fluid (TBLF), while TBLF was also assayed for cytokine responses (ELISA) and bacterial load (qPCR). At slaughter, gross and histopathology of lungs were quantified and damage to epithelial cilia in the porcine trachea was evaluated by scanning electron microscopy. Suvaxyn(®) M. hyo administration induced significant serological responses against Mhp strain 232 whole cell lysates (wcl) and recombinant antigen F3P216, but not against the remaining vaccine subunit antigens. Alhydrogel(®) and Montanide™ Gel01-adjuvanted antigen induced significant antigen-specific IgG responses, with the latter adjuvant eliciting comparable Mhp strain 232 wcl specific IgG responses to Suvaxyn(®) M. hyo. No significant post-vaccination antigen-specific mucosal responses were detected with the recombinant vaccinates. Suvaxyn(®) M. hyo was superior in reducing clinical signs, lung lesion severity and bacterial load but the recombinant formulations offered comparable protection against cilial damage. Lower IL-1ß, TNF-α and IL-6 responses after challenge were associated with reduced lung lesion severity in Suvaxyn(®) M. hyo vaccinates, while elevated pathology scores in recombinant vaccinates corresponded to cytokine levels that were similarly elevated as in unvaccinated pigs. This study highlights the need for continued research into protective antigens and vaccination strategies that will prevent Mhp colonisation and establishment of infection.

Plasmin activity in the porcine airways is enhanced during experimental infection with Mycoplasma hyopneumoniae, is positively correlated with proinflammatory cytokine levels and is ameliorated by vaccination.

In Mycoplasma hyopneumoniae (Mhp) infection of swine, the host immune response is considered a major driver of lung pathology; however the underlying inflammatory mechanisms are not well understood. The serine protease plasmin is being increasingly recognised as a significant player in inflammatory processes. Here we compare plasmin activity in tracheobronchial lavage fluid (TBLF) from pigs experimentally challenged with Mhp that were either unvaccinated (n=10), or vaccinated with the commercial vaccine Suvaxyn(®) M.hyo (n=10). TBLF collected immediately prior to challenge and at 21 d and 35 d post-challenge was also assayed for levels of proinflammatory cytokines (TNF-α, IL-1ß and IL-6), and for bacterial load (by qPCR). Clinical signs, pathology, cytokine analyses and qPCR all indicated that vaccinated pigs had significantly reduced disease relative to unvaccinated animals. Plasmin activity increased significantly in TBLF collected at 21 d post-challenge compared to pre-challenge TBLF in unvaccinated (P<0.01), but not vaccinated animals (P>0.05). A significant correlation was observed between bacterial load and plasmin activity in the 21 d (r=0.66; P<0.01) and the 35 d post-challenge samples, (r=0.62; P<0.01). Plasmin activity was also significantly correlated with levels of TNF-α, IL-1ß and IL-6 at 21 d (r=0.78, P<0.0001; r=0.77, P<0.0001; r=0.64, P<0.005) and with TNF-α and IL-1ß at 35 d post-challenge (r=0.77, P<0.0001; r=0.74, P<0.0005). Our results indicate that plasminogen is activated to plasmin in the respiratory tract of pigs as part of the host inflammatory response to Mhp infection and that this effect is ameliorated by vaccination.

Significance of Theileria orientalis types in individual affected beef herds in New South Wales based on clinical, smear and PCR findings.

Cattle within seven NSW herds with a history or risk of clinical Theileria orientalis disease associated with introductions of cattle were examined clinically and by haematological and PCR testing at sequential bleeds or at single sampling of different risk subgroups. The T. orientalis Ikeda type was detected in all herds and Chitose type was detected in six. Pale and jaundiced mucosal surfaces were associated with clinically affected groups of cattle, and herds containing cattle with ≥ 1% theilerias in erythrocytes were associated with high prevalence of Ikeda type, with or without Chitose type. In clinically normal cattle within these Ikeda-affected herds, over half of the smear negative animals were detected as infected with Ikeda type, while 90% of smear positive cases were positive for Ikeda type. Infection with Ikeda and Chitose organisms was detected in calves as young as 1-2 weeks, rapidly increased in prevalence within one month and was maintained until 4.5 months of age. In these calves Ikeda prevalence increased at a faster rate than the other MPSP types, particularly Buffeli which is generally considered to be avirulent, and suggests either an increased growth rate or rate of transmission of the Ikeda type or failure of the host immune system to clear this type. Particularly high T. orientalis prevalence rates were detected (in blood samples from a single time point) in adults that had been in direct contact with weaner cattle introduced from coastal areas; however, the lack of direct contact with affected cattle did not prevent infection with Ikeda type in some cases. Spread within previously naïve herds was variable, and results also depended on the sampling time point. In contrast, groups in which infection was already established gave repeatedly similar results at multiple samplings taken at one month intervals. Our results confirm that a large reservoir of infected but clinically normal animals exists within T. orientalis-affected cattle herds and PCR testing of EDTA bloods is more sensitive for detecting subclinical infection than blood smear examination. Direct contact with weaner cattle introduced from coastal areas appears to be a major risk factor for T. orientalis infection in adult cattle. Frequent sampling may be used to monitor spread of T. orientalis within newly affected herds, but may be unrewarding once a high prevalence is established.

Theileria orientalis MPSP types in Australian cattle herds associated with outbreaks of clinical disease and their association with clinical pathology findings.

Between September 2010 and November 2011, 350 EDTA blood samples were received from 73 Australian cattle herds, as cases suspected to be infected with Theileria orientalis. Beef cattle were predominantly affected, with Angus and Angus-crossbred cattle representing 48% of smear positive samples examined. DNA extracts were tested in conventional polymerase chain reaction (PCR) assays for genes encoding the p32, Ikeda, Chitose and Buffeli major piroplasm surface proteins (MPSP). PCR findings were compared with results of clinical pathology examinations of stained blood smears for parasitaemia and packed cell volume (PCV). PCR testing was much more sensitive than clinical pathology examinations in detecting T. orientalis infections, and concurrent testing of neat and diluted extracts gave significantly more PCR positive results than testing of neat extract alone. Significant associations and correlations were shown between PCR results of p32 and Ikeda assays with PCV levels indicative of anaemia, and with the level of parasitaemia estimated by smears. A high proportion of samples had concurrent Ikeda and Chitose infection, and significantly more clinical cases of theileriosis were associated with the Ikeda MPSP type as the sole infection, compared with sole infection with types Chitose or Buffeli. The findings indicate Ikeda type organisms were significantly associated with clinical parameters of theileriosis in cattle herds in eastern Australia, and that this type is most likely to be responsible for outbreaks of theileriosis experienced in affected Australian herds. In New South Wales, 11 of 14 regulatory districts yielded Ikeda positive samples, with five (Mid-Coast, Cumberland, Central North, Hume and Lachlan) containing 234/307 (76%) of the Ikeda positive samples.

Evaluation of clinical, histological and immunological changes and qPCR detection of Mycoplasma hyopneumoniae in tissues during the early stages of mycoplasmal pneumonia in pigs after experimental challenge with two field isolates.

Differences in Mycoplasma hyopneumoniae strain virulence and infection patterns will affect experimental challenge systems used to evaluate vaccine efficacy. Two strains (Hillcrest and Beaufort) were assessed by experimental pig challenge for their ability to induce clinical and pathological lesions and cytokine responses. Tracheobronchial lavage fluid (TBLF) was collected before and 17-18 days after challenge with Hillcrest (n=8), Beaufort (n=8) or no organisms (n=3). Coughing was assessed twice daily, and at slaughter 21 (n=9) or 28 (n=10) days post-challenge, gross and histopathology of lungs were quantified and a quantitative PCR (mhp183 qPCR) was applied to detect M. hyopneumoniae DNA in tissues and TBLF. Hillcrest was clearly superior to Beaufort in its ability to induce coughing and pneumonic lesions. At 17-18 days, interleukin (IL)-1ß and IL-6 concentrations in TBLF were only significantly higher (8.7 and 5.1 fold respectively) than controls (P<0.001) in Hillcrest-challenged pigs. Lungs of all Hillcrest-challenged pigs were qPCR positive at either slaughter date, but only at day 28 in Beaufort-challenged pigs. M. hyopneumoniae DNA was highest in concentration in lungs 21 days after Hillcrest challenge, and was detected in the spleen, kidney and/or liver of Hillcrest-challenged pigs, but not in Beaufort pigs. While M. hyopneumoniae DNA concentration in TBLF was elevated following Hillcrest and Beaufort challenge, there was no significant difference in mean mycoplasmal DNA concentration detected in TBLF from pigs challenged with either isolate (P>0.05). Thus a suitable challenge strain, coupled with lung pathology and cytokine assays, are valuable in assessing post-challenge responses. Assessment of M. hyopneumoniae DNA in lung and abdominal tissues by mhp183 qPCR, in conjunction with histopathology, were valuable in confirming M. hyopneumoniae infection.

Mycobacterium avium subspecies paratuberculosis cultured from the feces of a Southern black rhinoceros (Diceros bicornis minor) with diarrhea and weight loss.

Abstract: Mycobacterium avium paratuberculosis (Map) was cultured from the feces of a wild-caught, female, adult Southern black rhinoceros. The animal, which presented with a 4-mo history of diarrhea and weight loss, was prescribed a course of antimycobacterial drugs. The clinical signs resolved, and the feces were repeatedly culture negative thereafter. Although the Rhinocerotidae are likely to be resistant to Johne's disease, this case raises the possibility that they can become transiently infected with the causative organism.

Mhp182 (P102) binds fibronectin and contributes to the recruitment of plasmin(ogen) to the Mycoplasma hyopneumoniae cell surface.

Mycoplasma hyopneumoniae is a major, economically damaging respiratory pathogen. Although M. hyopneumoniae cells bind plasminogen, the identification of plasminogen-binding surface proteins and the biological ramifications of acquiring plasminogen requires further investigation. mhp182 encodes a highly expressed 102 kDa protein (P102) that undergoes proteolytic processing to generate surface-located N-terminal 60 kDa (P60) and C-terminal 42 kDa (P42) proteins of unknown function. We show that recombinant P102 (rP102) binds plasminogen at physiologically relevant concentrations (K(D) ~ 76 nM) increasing the susceptibility of plasmin(ogen) to activation by tissue-specific plasminogen activator (tPA). Recombinant proteins constructed to mimic P60 (rP60) and P42 (rP42) also bound plasminogen at physiologically significant levels. M. hyopneumoniae surface-bound plasminogen was activated by tPA and is able to degrade fibrinogen, demonstrating the biological functionality of M. hyopneumoniae-bound plasmin(ogen) upon activation. Plasmin(ogen) was readily detected in porcine ciliated airways and plasmin levels were consistently higher in bronchoalveolar lavage fluid from M. hyopneumoniae-infected animals. Additionally, rP102 and rP42 bind fibronectin with K(D) s of 26 and 33 nM respectively and recombinant P102 proteins promote adherence to porcine kidney epithelial-like cells. The multifunctional binding ability of P102 and activation of M. hyopneumoniae-sequestered plasmin(ogen) by an exogenous activator suggests P102 plays an important role in virulence.

Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium subsp. paratuberculosis in cattle.

Dilution rates for pooled faecal culture (PFC) and direct IS900 polymerase chain reaction (D-PCR) tests were evaluated on faecal samples from infected cows mixed with uninfected faeces in dilutions from 1 in 5 to 1 in 50. PFC was performed by radiometric culture, with confirmation by IS900 PCR and restriction endonuclease analysis (PCR/REA) on growth, and by mycobactin dependency testing on solid medium. Using 37 culture positive faecal samples from 12 subclinical cows, 83.8% and 94.6% of samples were confirmed positive in the PFC assay at dilutions of 1 in 50 and 1 in 30, respectively. Lower dilutions (1 in 5 to 1 in 20) provided only marginally better sensitivity, and confirmation of PFC growth by PCR/REA was significantly more sensitive than mycobactin dependency. D-PCR had significantly lower sensitivity than PFC confirmed by PCR/REA, with pools of 1 in 50, 30, 10 and 5 yielding positive results in 64.9%, 70.3%, 78.4% and 83.8% of samples, respectively. Cattle considered to be shedding 1.5 x 10(6) viable M. avium subsp. paratuberculosis (Map)/g faeces (on the basis of estimated losses in processing and growth rates in radiometric broth) were positive at dilutions up to 1 in 50 in the PFC and D-PCR. Those shedding 5 x 10(5) viable Map/g were positive in the PFC at dilutions up to 1 in 40, but required a 1 in 10 dilution or less for D-PCR. The results suggest that for cattle shedding relatively high concentrations of Map in faeces (>2 x 10(5) viable Map/g), maximal dilutions of 1 in 30 for PFC and 1 in 10 for D-PCR would be applicable.

Sampling and repeatability of radiometric faecal culture in bovine Johne's disease.

The repeatability of detection of Mycobacterium avium subsp. paratuberculosis (Map) within and between samplings from 16 paratuberculous dairy cows (13 subclinical; 3 clinical) was investigated by radiometric culture of quadrants of faecal dung pats collected on four to seven occasions over a 10-16-day period. Results were compared to serological status and to pathological and bacteriological findings in multiple tissues obtained at slaughter from 15 of the animals 2-6 weeks after the faecal samplings. From faecal samples taken on 77 occasions over the 2-week period, 296/308 (96%) quadrants were culture positive, with samples from all cattle showing evidence of faecal shedding of Map. Histological lesions typical of paratuberculosis were present in 14 of the 15 cows examined at slaughter, varying in severity from mild (two animals) to moderate (4) and advanced (8), and all predilection tissue sites yielded Map. The negative faecal samples were derived from a single animal that was culture positive in two quadrants on each of the first two (of four) sampling occasions (i.e. culture positive in only 4 of 16 collected quadrants). This animal was found to be histologically negative at slaughter, and culture positive from three of five predilection tissue sites. Faecal samples from cows with subclinical and clinical paratuberculosis, with lesion severity ranging from mild to severe at multiple predilection sites, produced faeces with relatively consistent concentrations of Map within samples. There was significant variation in concentrations of Map between samples in individual animals over a period of 2 weeks, but this did not affect the dichotomous positive-negative culture status for 15 of the 16 cattle. A faecal sample collected non-randomly per rectum thus provides a representative specimen for detection of Map by radiometric culture on a single sampling occasion.

A study of the foodborne pathogens: Campylobacter, Listeria and Yersinia, in faeces from slaughter-age cattle and sheep in Australia.

In a study of faeces from 475 slaughter-age cattle and sheep from 19 herds or flocks, Campylobacter species (C. jejuni and C. coli) were cultured from all production systems studied and from 73.7 per cent (14/19) of herds or flocks. Within individual properties there was a higher prevalence in cattle than in sheep, with Campylobacter being most commonly isolated from feedlot cattle. The median prevalences and ranges were: for dairy cattle, six per cent (0-24%), feedlot beef cattle, 58 per cent (12-92%) pasture beef cattle, two per cent (0-52%), mutton sheep, 0 per cent (0-4%) and prime lambs eight per cent. Listeria ivanovii was cultured from one dairy cow but Yersinia enterocolitica was not cultured from any animal. Campylobacter is the leading bacterial causative agent of acute diarrhoea in humans in many industrialised countries. While the role of cattle and sheep in producing human campylobacteriosis either directly or via contaminated food, remains to be epidemiologically clarified, this study suggests that the production system, particularly for cattle, may be an important consideration.