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peer-reviewed, Background and Aims: Inclusion of the mesentery during resection for colorectal cancer is associated with improved outcomes but has yet to be evaluated in Crohn’s disease. This study aimed to determine the rate of surgical recurrence after inclusion of mesentery during ileocolic resection for Crohn’s disease. Methods: Surgical recurrence rates were compared between two cohorts. Cohort A [n = 30] underwent conventional ileocolic resection where the mesentery was divided flush with the intestine. Cohort B [n = 34] underwent resection which included excision of the mesentery. The relationship between mesenteric disease severity and surgical recurrence was determined in a separate cohort [n = 94]. A mesenteric disease activity index was developed to quantify disease severity. This was correlated with the Crohn’s disease activity index and the fibrocyte percentage in circulating white cells. Results: Cumulative reoperation rates were 40% and 2.9% in cohorts A and B [P = 0.003], respectively. Surgical technique was an independent determinant of outcome [P = 0.007]. Length of resected intestine was shorter in cohort B, whilst lymph node yield was higher [12.25 ± 13 versus 2.4 ± 2.9, P = 0.002]. Advanced mesenteric disease predicted increased surgical recurrence [Hazard Ratio 4.7, 95% Confidence Interval: 1.71–13.01, P = 0.003]. The mesenteric disease activity index correlated with the mucosal disease activity index [r = 0.76, p < 0.0001] and the Crohn’s disease activity index [r = 0.70, p < 0.0001]. The mesenteric disease activity index was significantly worse in smokers and correlated with increases in circulating fibrocytes. Conclusions: Inclusion of mesentery in ileocolic resection for Crohn’s disease is associated with reduced recurrence requiring reoperation., PUBLISHED, peer-reviewed

peer-reviewed, Crohn’s disease (CD) displays mesenteric disease manifestations such as fat wrapping and mesenteric thickening. The frequency at which these occur in CD point to a pathobiological relevance. Fat wrapping in particular has been suggested to play a role in disease progression [1]. This study aimed to evaluate the relationship between mesenteric disease and other manifestations of CD and to examine the significance of advanced mesenteric disease., ACCEPTED, peer-reviewed

peer-reviewed, The mesentery in Crohn’s disease frequently displays disease manifestations, such as mesenteric thickening and fat wrapping. Fibrocytes are a precursor cell type that can differentiate into fibroblasts or adipocytes [1]. They have previously been identified in the mesentery in inflammatory conditions such as mesenteric panniculitis [2]. This study aimed to investigate the role of fibrocytes in Crohn’s mesenteric disease manifestations., ACCEPTED, peer-reviewed

peer-reviewed, Background: Recent advances in our understanding of mesenteric anatomy have shown that the mesentery is continuous along the intestinal tract at vascular, lymphatic and connective tissue levels [1]. Thus, the mesentery represents a conduit which may propagate disease [2]. This study aimed to investigate abnormalities of the mesentery in Crohn's disease (CD) at a histological level., ACCEPTED, peer-reviewed

peer-reviewed, Background Carbapenemase-producing Enterobacteriaceae (CPE) can cause healthcare–associated infections with high mortality rates. New Delhi metallo-beta-lactamase-1 (NDM-1) is amongst the most recently discovered carbapenemases. Aim To report the first outbreak of NDM-1 CPE in Ireland, including microbiological and epidemiological characteristics, and assessing the impact of infection prevention and control measures. Methods Retrospective microbiological and epidemiological review. Cases were defined as patients with a CPE positive culture. Contacts were designated as roommates or ward mates. Findings This outbreak involved ten patients, with a median age of 71 years (range 45-90 years), located in three separate but affiliated healthcare facilities. One patient was infected (the index case); the nine others were colonised. Nine NDM-1-producing Klebsiella pneumoniae, a NDM-1-producing Escherichia coli and a K. pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae were detected between week 24 2014 and week 37 2014. Pulsed field gel electrophoresis demonstrated similarity. NDM-1 positive isolates were meropenem resistant with MICs ranging from 12 to 32 μg/ml. All were tigecycline susceptible (MICs ≤1 μg/ml). One isolate was colistin resistant (MIC 4.0 μg/ml; mcr-1 gene not detected). In 2015, four further NDM-1 isolates were detected. Conclusions The successful management of this outbreak was achieved via the prompt implementation of enhanced infection prevention and control practices to prevent transmission. These patients did not have a history of travel outside of Ireland, but a number had frequent hospitalisations in Ireland, raising concerns regarding the possibility of increasing but unrecognised prevalence of NDM-1 and potential decline in value of travel history a marker of colonisation risk., ACCEPTED, peer-reviewed

peer-reviewed, Background The Mid-West of Ireland has higher than average national rates of invasive extended-spectrum beta-lactamase (ESBL) bloodstream infections and carbapenemase-producing Enterobacteriaceae (CPE), with increasing numbers of ESBL isolates detected in community-dwelling patients. Aims To conduct a point prevalence study in a convenience sample of the Mid-West population with the aim of determining the extent of ESBL colonisation Methods Utilising anonymised community stool samples that had completed routine analysis, we conducted a point prevalence study over a four-week period on all samples that met defined inclusion and exclusion criteria. Limited epidemiological data was recorded: (1) age of patient, (2) gender, (3) sender location. From these stool specimens, rectal swabs were inoculated (eSwab™ 480CE, Copan, Italy), which were subsequently cultured on selective chromogenic agar (Colorex™ ESBL). Culture plates were incubated aerobically at 37˚C for 24 hours. Results Of 195 samples processed, 58% (n=112) were from females. The median patient age was 62.4 years (range 20-94 years). 186 samples (95%) originated from general practitioner clinics. During the study period, only nine eligible stool samples were received from LTCF (6 public). From 195 Colorex™ ESBL chromogenic agar plates cultured, no ESBL-producing organisms were detected. Conclusions This community point prevalence study did not identify ESBL-colonisation despite high numbers of patients with invasive ESBL bloodstream infections presenting for admission in our institution. We believe this may be because of our small sample size. Data regarding antimicrobial exposure and other risk factors for ESBL-colonisation was also not available. We remain vigilant for ESBL-producing organisms., ACCEPTED, peer-reviewed

peer-reviewed, Rapid detection of patients with carbapenem-producing Enterobacteriaceae (CPE) is essential for the prevention of nosocomial cross-transmission, allocation of isolation facilities and to protect patient safety. Here, we aimed to design a new laboratory work-flow, utilising existing laboratory resources, in order to reduce time-to-diagnosis of CPE. A review of the current CPE testing processes and of the literature was performed to identify a real-time commercial polymerase chain reaction (PCR) assay that could facilitate batch testing of CPE clinical specimens, with adequate CPE gene coverage. Stool specimens (210) were collected; CPE-positive inpatients (n=10) and anonymised community stool specimens (n=200). Rectal swabs (eSwab™) were inoculated from collected stool specimens and a manual DNA extraction method (QIAamp® DNA Stool Mini Kit) was employed. Extracted DNA was then processed on the Check-Direct CPE® assay. The three step process of making the eSwab™, extracting DNA manually and running the Check-Direct CPE® assay, took <5 minutes, 1 hour 30 minutes and 1 hour 50 minutes, respectively. It was time efficient with a result available in under 4 hours, comparing favourably with the existing method of CPE screening; average time-to-diagnosis of 48/72 hours. Utilising this CPE work-flow would allow a ‘same-day’ result. Antimicrobial susceptibility testing results, as is current practice, would remain a ‘next-day’ result. In conclusion, the Check-Direct CPE® assay was easily integrated into a local laboratory work-flow and could facilitate a large volume of CPE screening specimens in a single batch, making it cost-effective and convenient for daily CPE testing., ACCEPTED, peer-reviewed

peer-reviewed, Background and Aims: Faecal diversion is associated with improvements in Crohn’s disease but not ulcerative colitis, indicating that differing mechanisms mediate the diseases. This study aimed to investigate levels of systemic mediators of inflammation, including fibrocytes and cytokines, [1] in patients with Crohn’s disease and ulcerative colitis preoperatively compared with healthy controls and [2] in patients with Crohn’s disease and ulcerative colitis prior to and following faecal diversion. Methods: Blood samples were obtained from healthy individuals and patients with Crohn’s disease or ulcerative colitis. Levels of circulating fibrocytes were quantified using flow cytometric analysis and their potential relationship to risk factors of inflammatory bowel disease were determined. Levels of circulating cytokines involved in inflammation and fibrocyte recruitment and differentiation were investigated. Results: Circulating fibrocytes were elevated in Crohn’s disease and ulcerative colitis patients when compared with healthy controls. Smoking, or a history of smoking, was associated with increases in circulating fibrocytes in Crohn’s disease, but not ulcerative colitis. Cytokines involved in fibrocyte recruitment were increased in Crohn’s disease patients, whereas patients with ulcerative colitis displayed increased levels of pro-inflammatory cytokines. Faecal diversion in Crohn’s disease patients resulted in decreased circulating fibrocytes, pro-inflammatory cytokines, and TGF-β1, and increased IL-10, whereas the inverse was observed in ulcerative colitis patients. Conclusions: The clinical effect of faecal diversion in Crohn’s disease and ulcerative colitis may be explained by differing circulating fibrocyte and cytokine responses. Such differences aid in understanding the disease mechanisms and suggest a new therapeutic strategy for inflammatory bowel disease.

peer-reviewed, Crohn’s disease (CD) is a debilitating inflammatory bowel condition of unknown aetiology that is growing in prevalence globally. Large-scale studies have determined associations between female obesity or low body mass index (BMI) with risk of CD at all ages or 8–< 40 years, respectively. For males, low BMI entering adult life is associated with increased incidence of CD or ulcerative colitis up to 40 years later. Body composition analysis has shown that combinations of lean tissue loss and high visceral fat predict poor CD outcomes. Here, we assessed dietary intake, physical activity and whole or regional body composition of patients with CD relapse or remission. This anthropometric approach found people with CD, irrespective of relapse or remission, differed from a large representative healthy population sample in exhibiting elevated gynoid fat and reduced android fat. CD is associated with mesenteric adipose tissue, or “creeping fat”, that envelops affected intestine exclusive of other tissue; that fat is localised to the android region of the body. In this context, CD mesenteric adiposity represents a stark juxtaposition of organ-specific and regional adiposity. Although our study population was relatively small, we suggest tentatively that there is a rationale to refer to Crohn’s disease as a fatty intestine condition, akin to fatty liver conditions. We suggest that our data provide early insight into a subject that potentially warrants further investigation across a larger patient cohort

peer-reviewed, Background: Positive expiratory pressure (PEP) devices are an important element of the management of cystic fibrosis, and of other respiratory diseases. Whereas there have been reports in the literature of contamination of airway clearance devices and their surfaces by microbial pathogens, there is little evidence available regarding such contamination and its contribution to respiratory infection. Aim: To establish whether pathogenic bacteria can contaminate PEP devices in the con text of normal cleaning and maintenance practices. Methods: Patients’ home-use clearance devices were brought to a routine clinic appointment and collected for microbiology sampling and analysis. The patients were provided with replacement devices. Nineteen such devices were collected from 17 patients, reflecting use of multiple devices by some patients. Swabs were taken and cultured from each patient’s used device, the patient’s airway, as well as from new unopened and unused devices that acted as controls. Results: Seven of 19 devices (37%) tested positive for presence of pathogenic bacteria. Device-cleaning methods varied among patients and non-sterilization methods were found to be ineffective at removing pathogens. Microbial species found on the devices did not correlate with those identified from airway swabs. Conclusion: This study demonstrates the presence of pathogens on positive expiratory pressure devices. The potential for transmission of these pathogens to the patient’s airway and the risk of infection remains unclear and requires further study.

peer-reviewed, Background: Improved diagnostic biomarkers are required for acute appendicitis. The circulating fibrocyte percentage (CFP) is increased in inflammatory states, but has not been studied in acute appendicitis. This study aimed to determine CFP in acute appendicitis and compare diagnostic accuracy with standard serological biomarkers. Methods: A prospective cohort study was carried out between June2015 and February2016 at University Hospital Limerick. The CFP was determined by dual-staining peripheral venous samples for CD45 and collagen I using fluorescence-activated cell sorting, and correlated with histopathological diagnoses. The accuracy of CFP in determining histological acute appendicitis was characterized and compared with the white cell count, C-reactive protein concentration, neutrophil count, lymphocyte count and neutrophil:lymphocyte ratio. Results: Of 95 adults recruited, 15 were healthy individuals and 80 had suspected appendicitis at presentation. Forty-six of these 80 patients had an appendicectomy, of whom 34 had histologically confirmed appendicitis. The CFP was statistically higher in patients with pathologically proven acute appendicitis than in healthy controls(median6⋅1 (i.q.r.1⋅6–11⋅6)versus2⋅3(0 ⋅9–3⋅4)percent respectively; P = 0⋅008). The diagnostic accuracy of CFP, as determined using the area under the receiver operating characteristic(ROC)curve, was similar to that of standard biomarkers. In multinomial regression analysis, only raised CFP was retained as an independent prognostic determinant of acute appendicitis (odds ratio 1⋅57, 95 per cent c.i. 1⋅05 to 2⋅33; P = 0⋅027). Conclusion: The CFP is increased in histologically confirmed acute appendicitis and is as accurate as standard serological biomarkers in terms of diagnosis

peer-reviewed, Artificial Insemination (AI) is the single most important tool in facilitating the genetic improvement of dairy cows. Both frozen and liquid semen are used in AI, however the majority (~95%) of insemination doses worldwide (and in Ireland) employ use of frozen semen (Vishwanath & Shannon, 2000). Only 5% of insemination doses used in Ireland are liquid semen, however, during peak breeding season of April and May, this number could rise to 25%. Use of frozen semen in AI has the benefit of long term storage as it causes the biochemical and developmental changes in sperm to stop, however, after the freeze thaw process, more than 50% of sperm cells are damaged (Vishwanath & Shannon, 2000), meaning a higher concentration of sperm cells per dose is required and therefore, less insemination doses per ejaculate are achieved. The use of stored fresh semen would remove this problem of damaged sperm cells after a freeze thaw process. Liquid semen would also allow a lower concentration of sperm cells per insemination dose, thereby, maximising the use of semen from high genetic merit bulls. It has been reported that although liquid bull semen maintains motility for up to 4 weeks post collection, in vivo fertility declines significantly after 4-5 days post collection (Vishwanath & Shannon, 1997). The reason for this sudden drop in fertility remains to be elucidated; however, it could be attributed to a number of factors, such as changes in the lipid profile and a subsequent loss in cell membrane fluidity, perhaps due to attack from reactive oxygen species (ROS). The addition of long chain fatty acids to bull sperm in vitro may have a stabilising effect on the sperm membrane, through fatty acids constituents being incorporated into the sperm cell membrane, as reported in a study by Neill & Masters (1971) or by inhibiting or reducing the lipid peroxidation (LPO) of the sperm membrane, which is high in polyunsaturated fatty acids.

peer-reviewed, Artificial Insemination (AI) is the single most important tool in facilitating the genetic improvement of dairy cows. Both frozen and liquid semen are used in AI, however the majority (~95%) of insemination doses worldwide (and in Ireland) employ use of frozen semen (Vishwanath & Shannon, 2000). Only 5% of insemination doses used in Ireland are liquid semen, however, during peak breeding season of April and May, this number could rise to 25%. Use of frozen semen in AI has the benefit of long term storage as it causes the biochemical and developmental changes in sperm to stop, however, after the freeze thaw process, more than 50% of sperm cells are damaged (Vishwanath & Shannon, 2000), meaning a higher concentration of sperm cells per dose is required and therefore, less insemination doses per ejaculate are achieved. The use of stored fresh semen would remove this problem of damaged sperm cells after a freeze thaw process. Liquid semen would also allow a lower concentration of sperm cells per insemination dose, thereby, maximising the use of semen from high genetic merit bulls. It has been reported that although liquid bull semen maintains motility for up to 4 weeks post collection, in vivo fertility declines significantly after 4-5 days post collection (Vishwanath & Shannon, 1997). The reason for this sudden drop in fertility remains to be elucidated; however, it could be attributed to a number of factors, such as changes in the lipid profile and a subsequent loss in cell membrane fluidity, perhaps due to attack from reactive oxygen species (ROS). The addition of long chain fatty acids to bull sperm in vitro may have a stabilising effect on the sperm membrane, through fatty acids constituents being incorporated into the sperm cell membrane, as reported in a study by Neill & Masters (1971) or by inhibiting or reducing the lipid peroxidation (LPO) of the sperm membrane, which is high in polyunsaturated fatty acids.

peer-reviewed, Background and Aims: Mesenteric lymph nodes are sites in which translocated bacteria incite and progress immunological responses. For this reason, understanding the microbiome of mesenteric lymph nodes in inflammatory bowel disease is important. The bacterial profile of Crohn’s disease mesenteric lymph nodes has been analysed using culture-independent methods in only one previous study. This study aimed to investigate the mesenteric lymph node microbiota from both Crohn’s disease and ulcerative colitis patients. Methods: Mesenteric lymph nodes were collected from Crohn’s disease and ulcerative colitis patients undergoing resection. Total DNA was extracted from mesenteric lymph nodes and assessed for the presence of bacterial DNA [16S]. All work was completed in a sterile environment using aseptic techniques. Samples positive for 16S DNA underwent next-generation sequencing, and the identity of bacterial phyla and species were determined. Results: Crohn’s disease mesenteric lymph nodes had a distinctly different microbial profile to that observed in ulcerative colitis. The relative abundance of Firmicutes was greater in nodes from ulcerative colitis patients, whereas Proteobacteria were more abundant in Crohn’s disease. Although species diversity was reduced in the mesenteric lymph nodes of patients with Crohn’s disease, these lymph nodes contained greater numbers of less dominant phyla, mainly Fusobacteria. Conclusion: This study confirms that there are distinct differences between the Crohn’s disease and ulcerative colitis mesenteric lymph node microbiomes. Such microbial differences could aid in the diagnosis of Crohn’s disease or ulcerative colitis, particularly in cases of indeterminate colitis at time of resection, or help explain their mechanisms of development and progression.

peer-reviewed, Crohn's disease is hallmarked by mesenteric abnormalities including thickening, shortening and extension ofmesenteric fat over the intestinal surface (“fat wrapping” or “creeping fat”) (Coffey et al., 2016; Peyrin-Biroulet et al., 2007; Sheehan et al., 1992; Crohn et al., 1932). Mesenteric and submucosal mesenchymal abnormalities overlap in histological appearance and both inflammatory fronts meet to generate transmural inflammation (Coffey and O'leary, 2016).

peer-reviewed, Rationale: There is limited evidence supporting the routine use of palivizumab in paediatric cystic fibrosis (CF) patients to reduce respiratory syncytial virus (RSV) infection and related hospitalisation. Despite this, anti-RSV prophylaxis is increasingly common. This is the first report from Ireland regarding palivizumab outcomes for children with CF, under 2 years old, despite the greatest prevalence of CF globally. Methods: An audit was performed at a tertiary hospital in Ireland’s mid-West to document all children with CF, <24 months old, who received palivizumab over a five year period and comparision made with all eligible children for the prior five year period who had not received the product (also CF patients). Palivizumab was administered to both cohorts in their first year of life. Hospitalisation rates were compared using Fisher’s exact test. Incidence of RSV and Pseudomonas aeruginosa infection was recorded. Results: A total of 19 patients who received palivizumab were included in the study; comparision was made with a retrospective control group of 30 patients. Prophylactic palivizumab did not prevent hospitalisation for 10/19 patients, 3 of whom were affected by RSV. This was significantly greater than in the control group, where no hospitalisations were recorded (p < 0.0001). P. aeruginosa was isolated in one case from the study cohort, while no P. aeruginosa was detected in the control group. Conclusions: This study, the first of its kind from Ireland where CF prevalence is highest, does not provide unequivocal support for prophylactic use of palivizumab in CF patients under 2 years. Despite being derived from a small sample size, based on these data and complementary clinical observation, we have discontinued such prophylaxis. However, should reported incidence of RSV-related hospitalisation increase, there is scientific plausibility for appropriately powered, randomised, controlled trials of palivizumab.

peer-reviewed, Background: Pseudomonas aeruginosa is a pathogen associated with cystic fibrosis that has potential to decrease lung function and cause respiratory failure. Paranasal sinuses are increasingly recognised as potential reservoirs for intermittent colonisation by P. aeruginosa. This case documents investigation and outcome of P. aeruginosa recurrence in a male paediatric patient over an eight year period. Case presentation: A 12 year old Irish male paediatric cystic fibrosis patient experienced intermittent culturing of P. aeruginosa from the oropharyngeal region, indicating chronic infection of the sinuses despite absence of symptoms, retaining good lung function, and normal bronchoscopy and bronchoalveloar lavage. However, P. aeruginosa was isolated from a sinus wash-out and was identified as a unique strain of P. aeruginosa that was also cultured from cough swabs. Despite treatment, successful eradication from the paranasal sinuses was not achieved. Conclusions: Few reports have addressed the paranasal sinuses as a reservoir for lung infection in cystic fibrosis patients despite increased recognition of the need to investigate this niche. In this case, attempts at eradication of P. aeruginosa present in paranasal sinuses including oral and nebulised antimicrobials proved unsuccessful. However, detection of P. aeruginosa in the paranasal sinuses instigated antimicrobial treatment which may have contributed to prevention of migration to the lower airways. Our outcome provides additional insight and may indicate utility of nasal lavage or nasal endoscopy in paediatric cystic fibrosis patients’ annual review clinic visits.

peer-reviewed, Artificial Insemination (AI) is the single most important tool in facilitating the genetic improvement of dairy cows. Both frozen and liquid semen are used in AI, however the majority (~95%) of insemination doses worldwide (and in Ireland) employ use of frozen semen (Vishwanath & Shannon, 2000). Only 5% of insemination doses used in Ireland are liquid semen, however, during peak breeding season of April and May, this number could rise to 25%. Use of frozen semen in AI has the benefit of long term storage as it causes the biochemical and developmental changes in sperm to stop, however, after the freeze thaw process, more than 50% of sperm cells are damaged (Vishwanath & Shannon, 2000), meaning a higher concentration of sperm cells per dose is required and therefore, less insemination doses per ejaculate are achieved. The use of stored fresh semen would remove this problem of damaged sperm cells after a freeze thaw process. Liquid semen would also allow a lower concentration of sperm cells per insemination dose, thereby, maximising the use of semen from high genetic merit bulls. It has been reported that although liquid bull semen maintains motility for up to 4 weeks post collection, in vivo fertility declines significantly after 4-5 days post collection (Vishwanath & Shannon, 1997). The reason for this sudden drop in fertility remains to be elucidated; however, it could be attributed to a number of factors, such as changes in the lipid profile and a subsequent loss in cell membrane fluidity, perhaps due to attack from reactive oxygen species (ROS). The addition of long chain fatty acids to bull sperm in vitro may have a stabilising effect on the sperm membrane, through fatty acids constituents being incorporated into the sperm cell membrane, as reported in a study by Neill & Masters (1971) or by inhibiting or reducing the lipid peroxidation (LPO) of the sperm membrane, which is high in polyunsaturated fatty acids.