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Associations between animal and herd management factors, serological response to three respiratory pathogens and pluck lesions in finisher pigs on a farrow-to-finish farm
No full textBackground
Serological screening is a common method to monitor antibody response to pathogen exposure, but results could vary due to several factors. This study aimed to quantify animal and management related factors associated with variation in antibody levels in finisher pigs at slaughter, in an Irish farrow-to-finish farm endemically infected with Actinobacillus pleuropneumonia (App), Mycoplasma hyopneumoniae (Mhyo) and swine influenza virus (SIV). A second objective was to estimate differences in antibody levels in pigs presenting pluck lesions. This was an observational study whereby pigs were managed as per routine farm practice. Data on sow parity, number of born alive (NBA) pigs per litter, cross-fostering status, birth and weaning body weight were recorded from 1016 pigs born from one farrowing batch. At slaughter, blood samples were collected for serological analysis and pigs were inspected for presence of enzootic pneumonia (EP)-like lesions, pleurisy, pericarditis and heart condemnations. Pigs were retrospectively classified into three production flows, depending on time spent in each production stage: flow 1 (F1; pigs followed the normal production flow); flow 2 (F2; pigs which were delayed by 1 week from advancing forward); and flow 3 (F3; pigs delayed by > 1 week from advancing forward). A nested case-control design was applied by matching pigs from each flow by sow parity, birth weight and NBA.
Results
Pigs born from primiparous sows had higher antibody levels for App than those born to parity ≥5 sows (P 0.05). Pigs in F1 had lower antibody levels for App but higher antibody levels for SIV than F2 and F3 pigs (P 0.05), except for increased antibody levels for Mhyo when EP-like lesions were present (P = 0.006).
Conclusion
Results indicate that offspring from primiparous sows develop higher antibody levels for App IV toxin when exposed to this disease and that enforcement of a strict all-in/all-out production system would reduce on-farm disease circulation. A high percentage of pigs were affected with EP-like lesions which were associated with higher antibody levels for Mhyo
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation
No full textSince the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed
MAP, Johne’s disease and the microbiome; current knowledge and future considerations
No full textMycobacterium avium subsp. paratuberculosis is the causative agent of Johne’s disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne’s disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne’s disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne’s disease
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens
No full textBackground
The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual’s core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible.
Results
Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media.
Conclusions
We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers.
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Conserved and breed-specific differences in the cervical transcriptome of sheep with divergent fertility at the follicular phase of a natural oestrus cycle
No full textBackground
The outcome of cervical artificial insemination (AI) with frozen-thawed semen in sheep is limited by the inability of sperm to traverse the cervix of some ewe breeds. Previous research has demonstrated that cervical sperm transport is dependent on ewe breed, as sperm can traverse the cervix in greater numbers in some higher fertility ewe breeds. However, the molecular mechanisms underlying ewe breed differences in sperm transport through the cervix remain unknown. In this study, we aimed to characterise the cervical transcriptome of four European ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen at the follicular phase of a natural oestrous cycle. Cervical post mortem tissue samples were collected from two Irish ewe breeds (Belclare and Suffolk; medium and low fertility, respectively) and from two Norwegian ewe breeds (Norwegian White Sheep (NWS) and Fur; high fertility compared to both Irish breeds) at the follicular phase of a natural oestrous cycle (n = 8 to 10 ewes per breed).
Results
High-quality RNA extracted from biopsies of the mid-region of the cervix was analysed by RNA-sequencing and Gene Ontology (GO). After stringent filtering (P 1.5), a total of 11, 1539 and 748 differentially expressed genes (DEGs) were identified in Belclare, Fur and NWS compared to the low fertility Suffolk breed, respectively. Gene ontology analysis identified significantly enriched biological processes involved in muscle contraction, extracellular matrix (ECM) development and the immune response. Gene co-expression analysis revealed similar patterns in muscle contraction and ECM development modules in both Norwegian ewe breeds, which differed to the Irish ewe breeds.
Conclusions
These breed-specific biological processes may account for impaired cervical sperm transport through the cervix in sheep during the follicular phase of the reproductive cycle. This novel and comprehensive dataset provides a rich foundation for future targeted initiatives to improve cervical AI in sheep
Horn bud size of dairy-bred and suckler-bred calves at time of disbudding
No full textBackground
Hot-iron disbudding is a common management procedure to prevent horn growth in calves. The study objective was to examine effect of age, breed and sex on horn bud size of dairy-bred and suckler-bred calves at time of disbudding.
Results
The left and right horn bud size (diameter and height in mm) of 279 calves, including dairy-bred Holstein-Friesian (Male (M) = 88) and 191 suckler-bred (86 Charolais, CH; (M = 39, Female (F) = 47), 67 Limousin, LM; (M = 32, F = 35) and 38 Simmental, SI; (M = 22, F = 16) sired)) was measured using a digital calliper at time of disbudding. Calves were retrospectively assigned to two age categories at time of disbudding: 1), 14 to 28 days (d) old and 2), 29 to 60 d old. Holstein-Friesian M calves had a greater horn bud diameter (16.97 v.14.45 mm) and height (7.79 v. 5.00 mm) compared to suckler-bred M calves (P 0.05) among the suckler-bred calves. Suckler-bred M calves had a greater horn bud diameter (14.46 vs 13.29 mm) and height (5.01 vs 3.88 mm) compared to suckler-bred F calves (P < 0.05).
The slopes of the lines of best fit show that horn bud diameter and height increased with age (P 0.05) for CH and LM male calves, or for SI and LM female calves. Linear regression of age with diameter and with height for each breed and sex showed high variability in the data as indicated by R-squared values ranging from 0.003–0.41 indicating that in the case of the diameter and the height, the weight of the fitting effect was poor.
Conclusions
Calf age is not a good predictor of horn bud size and recommendations for the disbudding of calves should be based on horn bud size and not on age. The implications of these findings are that calves should be disbudded while horn development is still at the bud stage and when the bud is large enough to be easily palpable/visible, but not so large that disbudding could lead to severe tissue trauma
Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. is influenced by production system, antimicrobial use, and biosecurity measures on Spanish pig farms
No full textBackground
Antimicrobial resistance (AMR) is a global public health threat consequence of antimicrobial use (AMU) in human and animal medicine. In food-producing animals factors such as management, husbandry or biosecurity may impact AMU. Organic and extensive Iberian swine productions are based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the AMR in indicator bacteria. Here, we evaluate the usefulness of commensal Escherichia coli and Enterococcus spp. isolates as AMR bioindicators when comparing 37 Spanish pig farms from both intensive and organic-extensive production systems, considering the effect of AMU and biosecurity measures, the last only on intensive farms.
Results
The production system was the main factor contributing to explain the AMR differences in E. coli and Enterococcus spp. In both bacteria, the pansusceptible phenotype was more common (p < 0.001) on organic-extensive farms when compared to intensive herds. The microbiological resistance in commensal E. coli was, for most of the antimicrobials evaluated, significantly higher (p < 0.05) on intensive farms. In enterococci, the lincosamides usage revealed the association between AMR and AMU, with an increase in the AMR for erythromycin (p < 0.01), quinupristin-dalfopristin (p < 0.01) and the multidrug-resistant (MDR) phenotype (p < 0.05). The biosecurity measures implemented on intensive farms influenced the AMR of these bioindicators, with a slightly lower resistance to sulfamethoxazole (p < 0.01) and the MDR phenotype (p < 0.05) in E. coli isolated from farms with better cleaning and disinfection protocols. On these intensive farms, we also observed that larger herds had a higher biosecurity when compared to smaller farms (p < 0.01), with no significant associations between AMU and the biosecurity scores.
Conclusions
Overall, this study evidences that the production system and, to a lesser extent, the biosecurity measures, contribute to the AMR development in commensal E. coli and Enterococcus spp., with antimicrobial usage as the main differential factor, and demonstrates the potential value of these bacteria as bioindicators on pig farms in AMR surveillance programs
"The world is losing this little girl": An exploration of hospital-based Children\u27s End of Life Care through a Narrative Lens
No full textThe death of a child is a profound and life-changing loss for all families. The majority of children continue to die in hospital due to the nature of the child\u27s illness, the suddenness of their deterioration, and, at times, parental choice. The lack of research in this field in Ireland was one of the motivations for this study. Based in an acute children\u27s hospital during a period of transition and amalgamation into a larger entity, the rationale for this study was to explore the experiences of families whose child was provided End of Life Care (EOLC) in the hospital and subsequently died, and the staff who cared for them.
Using a Narrative approach, the study is framed within a social constructionist perspective on bereavement, highlighting the belief that death occurs within a social context. 15 parents who had experienced the death of a child 6 months to two and a half years prior to being interviewed, were invited to share their experience through the use of a two part in-depth interview which took place in their own home or at the research site according to their wishes. In addition, 24 staff members at the research site were interviewed in focus groups using the same approach. Reflective Thematic Analysis was used as the method of analysis across all interviews, and narrative analysis was used to identify unique and enabling experiences from the interviews.
From the analysis of the parent interviews, three major themes emerged which reflected Turner\u27s (1967) concept of "liminality" representing the changes that occur as families go through this key rite of passage. These themes convey parents\u27 experiences of separating from their known world and entering into the complex and challenging world of EOLC. The focus groups for health care professions emphasised the complexities of the work in this area as well as the personal impact on staff. Further findings from a narrative reading of the data brought relationships between parents and staff to the fore. The role of staff in enabling moments of lasting significance for parents with their children is revealed. The findings from the study have been integrated into a "Map of Narrative Practice in Children\u27s End of Life Care", highlighting the importance of relationship-based care, based on a shared sense of humanity around the tragic death of a child. This research emphasises the importance of communication and actions recognising the unique relationship between parents and their child and their deep emotional connection. By adopting a social constructionist and narrative approach, hospital-based children\u27s EOLC can provide spontaneous opportunities to promote positive adjustment and endeavouring to minimise future complications in what is one of the most difficult bereavements
A Scientific Evaluation of Traditional Chinese Medicine (TCM): Houttuynia cordata Thunb Saururaceae - A Case Study
No full textTraditional Chinese Medicine (TCM) is one of the oldest medical systems in the world, still
used for prevention or treatment of diseases in the modern China. It is a unique and holistic
system, guided by ancient Chinese philosophy. The fish mint herb Houttuynia cordata Thunb
(Yu xing cao 鱼腥草) is widely used as a TCM herb in China for the treatment of ailments
including cancer, coughs, fever, dysentery, enteritis, and cognitive deficits. The H. cordata
medicine is used as a decoction prepared by traditional aqueous extraction of the dried plant
material, which is the most used formulation in TCM. Previous studies exploring organic
solvent extracts of H. cordata have been shown to contain secondary metabolites including
flavonoids, alkaloids, phenolics and volatile components. These extracts demonstrate anti-
inflammatory, anti-obesity, and anti-cancer effects as well as activity in inflammatory bowel
disease (IBD). However, there is a big gap in studies, with few investigations into the chemical
composition and biological activity of the H. cordata traditional aqueous decoction. Therefore,
research on the chemical fingerprinting and biological studies for H. cordata traditional
aqueous extract of is demanding.
In this thesis, sixteen H. cordata samples purchased from three different geographical regions
(Sichuan, Hubei, Anhui) in China were investigated. Plant identity for each material was
confirmed by microscopic means in comparison with monographs. Three extraction methods
(traditional aqueous decoction extraction, phytochemical extraction, and steam distillation) of
H. cordata were carried out. The chemically fingerprints for each extract were generated using
analytical techniques including Nuclear Magnetic Resonance (NMR) spectroscopy, High
Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) and Gas
Chromatography-Mass Spectrometry (GC-MS) as appropriate. The main focus of the study
was on the aqueous extract, which corresponds to the traditional medicinal decoction of H.
cordata. Principal component analysis (PCA) based on NMR spectroscopy metabolomics was
used to analyse the metabolomic data for the aqueous and phytochemical extracts, and this
allowed us compare small differences that become clearer in the metadata.
This project is centred on the traditional aqueous decoction, and biological activities of the
corresponding aqueous extracts were assessed and correlated with the chemistry. We initially
investigate the ability of the extracts to inhibit the cholinesterase enzymes including
acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The extracts only
demonstrated significant inhibition of AChE activity. The anti-inflammatory activity of
aqueous extracts was then evaluated in vitro (TNF-α activated Caco-2 monolayers) by
assessing intestinal inflammation associated mediators (ZO-1, Occludin, EGFR, IL-1β, IL-6,
IL-10, MAPK ERK 1/2) through RT-qPCR, ELISA and Western-blot. The anti-inflammatory
role of H. cordata was then further evaluated in a DSS-induced murine colitis model in vivo.
In this model both prevention and recovery effects of the H. cordata aqueous extract were
evaluated by disease scores (weight loss, bloody stool, diarrhoea), hematoxylin and eosin
staining of colonic tissue, and mediators associated with inflammation (MPO, Occludin, TNF-
α,EGFR, IL-1β, IL-6, IL-10).
Principal component analysis (PCA) of the 1H NMR spectroscopy metadata for the 16 samples
analysed distinguished three aqueous outliers. Three outliers were also distinguished between
the samples, from their phytochemical (MeOH) extracts. The outliers identified in the two types
of extract differed from each other, showing that the plants biosynthesis different chemical
metabolites depending on their area of cultivation and methods of preparation and storing.
Fifteen compounds were identified and quantified by HPLC-MS. Using this technique
qualitative and quantitative differences between the aqueous outliers and quality control (QC)
sample can be distinguished. Twenty-eight volatile compounds were identified by GC-MS in
the essential oil recovered by steam distillation of H. cordata plant material. The main
component identified in this oil is 2-undecanone known as the ‘fish mint’ marker. H. cordata
aqueous extracts showed protective effects on the intestinal inflammation in vitro by enhancing
ZO-1, Occludin, IL-10 and suppressing EGFR, IL-1β and IL-6. A mechanism explaining this
activity via an EGFR dependent MAPK (ERK) 1/2 signalling pathway is proposed. The three
chemically different aqueous outliers, are shown to be pharmacologically different, in these
biological studies. An international Good Manufacture Practice (GMP) standardised product
of H. cordata plant material from Hubei showed more potency. A beneficial intestinal
improvement observed in vivo, was seen at a molecular level within colonic tissues for both
the prevention and recovery trial, which agrees with in vitro findings, although no apparent
enhancement in recovery symptoms was observed.
In conclusion, aqueous extracts from H. cordata sourced from different geographical regions
have been shown to be chemically different, which may be a result of biotic and abiotic factors.
these observations underpin the need for scientific evaluation of TCM herbal material to
ensure its consistent quality, safety, and efficacy. Extracts were prepared using traditional
aqueous and phytochemical extraction methods. These extracts have different chemical
fingerprints. The resulting H. cordata aqueous decoctions also demonstrated varying intensity
of pharmacological activity. Inhibition of the enzyme AChE supports the use of H. cordata in
improving cognitive health and is worthy of further study. Confirmation of the role of the
traditional decoction of H. cordata in the support of intestinal barrier integrity is very
significant and validates the traditional use of H. cordata decoction in the treatment of
inflammatory gut conditions such as inflammatory bowel disease (IBD)