Bacteria Associated with Acute Oak Decline: Where Did They Come From? We Know Where They Go

Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated with the lesions-Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and Lonsdalea Britannica-although an epi-/endophytic lifestyle has also been suggested for these bacteria. However, little is known about their environmental reservoirs or their pathway to endophytic colonisation. This work aimed to investigate the ability of the four AOD-associated bacterial species to survive for prolonged periods within rhizosphere soil, leaves and acorns in vitro, and to design an appropriate method for their recovery. This method was trialled on field samples related to healthy and symptomatic oaks. The in vitro study showed that the majority of these species could survive for at least six weeks within each sample type. Results from the field samples demonstrated that R. victoriana and G. quercinecans appear environmentally widespread, indicating multiple routes of endophytic colonisation might be plausible. B. goodwinii and L. britannica were only identified from acorns from healthy and symptomatic trees, indicating they may be inherited members of the endophytic seed microbiome and, despite their ability to survive outside of the host, their environmental occurrence is limited. Future research should focus on preventative measures targeting the abiotic factors of AOD, how endophytic bacteria shift to a pathogenic cycle and the identification of resilient seed stock that is less susceptible to AOD.

Description of Dryocola gen. nov. and two novel species, Dryocola boscaweniae sp. nov. and Dryocola clanedunensis sp. nov. isolated from the rhizosphere of native British oaks

While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4^T = CCUG 76177^T = LMG 32610^T) and Dryocola clanedunesis sp. nov. (type strain H11S18^T = CCUG 76181^T = LMG 32611^T).

Description of a novel species of Leclercia, Leclercia tamurae sp. nov. and proposal of a novel genus Silvania gen. nov. containing two novel species Silvania hatchlandensis sp. nov. and Silvania confinis sp. nov. isolated from the rhizosphere of oak

BACKGROUND

Acute Oak Decline (AOD) is a decline disease first reported on native oaks in the UK, but in recent years reports from further afield such as Europe and the Middle East, indicate that the distribution and host range is increasing at an alarming rate. The stem weeping symptoms of the disease partially develop due to polymicrobial-host interaction, caused by several members of the order Enterobacterales. While investigating the rhizosphere soil of AOD-unaffected trees, termed 'healthy' trees, and diseased oaks suffering from Acute Oak Decline (AOD), an enrichment method designed for enhanced recovery of Enterobacterales led to the recovery of several isolates that could not be classified as any existing species. These isolates showed a close relationship to the genus Leclercia, of which both species are of clinical importance, but the type species Leclercia adecarboxylata also displays plant growth-promoting properties in the rhizosphere.

RESULTS

Partial sequencing of four housekeeping genes revealed similarity to the genus Leclercia with varying degrees of relatedness. As such a complete polyphasic approach was used to determine the true taxonomic position of these isolates. This involved whole genome sequencing, phylogenomic analysis, phylogenetic analysis of both the 16S rRNA and four housekeeping gene sequences, combined with phenotypic testing and fatty acid analysis. Both the phylogenomic and phylogenetic analyses separated the isolates into four clusters, two of which were contained in the Leclercia clade. The remaining two clusters formed a separate lineage far removed from any currently defined species. Further investigation into the role of the isolates as plant growth-promoting bacteria as well as plant pathogens was investigated computationally, revealing a number of plant growth-promoting traits as well as virulence genes related to motility, adhesion and immune modulation.

CONCLUSION

Based on the genotypic and phenotypic data presented here, these isolates could be differentiated from each other and their closest neighbours. As such we propose the description of Leclercia tamurae sp. nov. (type strain H6S3^T = LMG 32609^T = CCUG 76176^T), Silvania gen. nov., Silvania hatchlandensis sp. nov. (type strain H19S6^T = LMG 32608^T = CCUG 76185^T) and Silvania confinis sp. nov. (type strain H4N4^T = LMG 32607^T = CCUG 76175^T). Due to their interesting protein annotations and alignments, these species warrant further investigation for their role in relation to plant health.

Transfer of Erwinia toletana and Erwinia iniecta to a novel genus Winslowiella gen. nov. as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov. and description of Winslowiella arboricola sp. nov., isolated from bleeding cankers on broadleaf hosts

Following a screening campaign of bleeding cankers of broadleaf hosts in Great Britain, numerous bacterial strains were isolated, identified by 16S rRNA and protein-coding gene sequencing and ultimately classified. During the course of the study, several Gram-negative, facultatively anaerobic strains were isolated from bleeding Platanus x acerifolia (London plane) and Tilia x europaea (common lime) cankers that could not be assigned to an existing species. Partial 16S rRNA gene sequencing placed these strains in the genus Erwinia, as a close phylogenetic relative of Erwinia toletana. In an effort to determine the taxonomic position of the strains, a polyphasic approach was followed including genotypic, genomic, phenotypic, and chemotaxonomic assays. Multilocus sequence analysis based on four protein-coding genes (gyrB, rpoB, infB, and atpD) confirmed the phylogenetic position of the strains as a novel taxon of subgroup 3 of the genus Erwinia, along with E. toletana and E. iniecta, and furthermore, provided support for their reclassification in a novel genus. Whole genome comparisons allowed the delimitation of the novel species and also supported the proposed transfer of subgroup 3 species to a novel genus in the Erwiniaeae. Phenotypically the novel species could be differentiated from E. toletana and E. iniecta, and the novel genus could be differentiated from the closely related genera Erwinia and Mixta. Therefore, we propose (1) the reclassification of E. toletana and E. iniecta in a novel genus, Winslowiella gen. nov., as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov., with W. toletana comb. nov. as the type species (type strain A37T = CFBP 6631T = ATCC 700880T = CECT 5263T), and (2) classification of the novel strains as Winslowiella arboricola sp. nov. (type strain BAC 15a-03bT = LMG 32576T = NCPPB 4696T).

Description of three novel species of Scandinavium: Scandinavium hiltneri sp. nov., Scandinavium manionii sp. nov. and Scandinavium tedordense sp. nov., isolated from the oak rhizosphere and bleeding cankers of broadleaf hosts

While investigating the bacterial populations of environmental samples taken from a mix of healthy and Acute Oak Decline afflicted Quercus robur (pedunculate or English oak) rhizosphere soil samples and swabs of bleeding lesions on Tilia spp. (lime) and Quercus rubra (red oak) trees, several strains belonging to the order Enterobacterales were isolated using selective media and enrichment broth. Seven strains from the Q. robur rhizosphere, three strains from Tilia spp. and one from Q. rubra were investigated, with their taxonomic status determined via a polyphasic taxonomic approach. Initially stains were identified as potential members of the recently described genus Scandinavium, based on the partial sequencing of three housekeeping genes. Further analysis of phenotypic traits, including fatty acid profiles, coupled with 16S rRNA gene and phylogenomic analysis of whole genome sequences were applied to a subset of the strains. Phylogenetic and phylogenomic analysis repeatedly placed the isolates in a monophyletic clade within Scandinavium, with four distinct clusters observed, one of which corresponded to Scandinavium goeteborgense, the type species of the genus. The remaining three clusters could be phenotypically and genotypically differentiated from each other and S. goeteborgense. As such, we describe three novel species of the genus, for which we propose the names Scandinavium hiltneri sp. nov. (type strain H11S7^T = LMG 32612^T = CCUG 76179^T), Scandinavium manionii sp. nov. (type strain H17S15^T = LMG 32613^T = CCUG 76183^T) and Scandinavium tedordense sp. nov. (type strain TWS1a^T = LMG 32614^T = CCUG 76188^T). Additionally, the descriptions of the genus Scandinavium and the type species, S. goeteborgense, are emended.

Brenneria tiliae sp. nov., isolated from symptomatic Tilia × moltkei and Tilia × europaea trees in the UK

Several strains of a previously undescribed bacterial species were isolated from mature Tilia hybrid trees suffering from bleeding cankers at various geographic locations in the UK. The strains were Gram-negative, facultatively anaerobic, and partial sequencing of the gyrB gene revealed that the strains belong to the genus Brenneria with the closest phylogenetic neighbours being Brenneria corticis and Brenneria nigrifluens. Further investigation using a polyphasic approach was undertaken to determine the taxonomic position of the novel species. Phylogenies based on the 16S rRNA gene and multilocus sequence analysis of partial housekeeping gene sequences of gyrB, rpoB, infB and atpD revealed that the strains formed an independent cluster within the genus Brenneria. The phenotypic and chemotaxonomic assays demonstrated that the strains could be differentiated from the closest relatives. Genome analysis of representative strains revealed in silico DNA-DNA hybridization values below the threshold for species delimitation, although the average nucleotide identity values obtained when compared to B. corticis (95.9-96%) were slightly higher than the suggested cut-off value of 95%. However, as all other data suggests that the strains belong to a novel taxon that can be differentiated from the closest relatives, we propose that the strains represent a novel species in the genus Brenneria, Brenneria tiliae sp. nov. (type strain WC1b.1^T=LMG 32575^T=NCPPB 4697^T).

Brenneria goodwinii growth in vitro is improved by competitive interactions with other bacterial species associated with Acute Oak Decline

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Mutually competitive interactions prevail in pairwise cultures of AOD bacteria.

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In vitro growth of brenneria goodwinii is improved by bacterial competition.

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Co-culturing of AOD bacteria indicates evolving improved fitness of B. goodwinii.

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B. goodwinii and R. victoriana can collaborate in vitro to outcompete G. quercinecans.

Brenneria goodwinii, Rahnella victoriana and Gibbsiella quercinecans are three bacterial species frequently isolated together from oak displaying symptoms of Acute Oak Decline (AOD), which include weeping patches on trunks. All three bacterial species play a role in lesion formation in the current episode of AOD in Britain, although B. goodwinii is the most dominant. The ongoing research into stem lesion formation characteristic of this polybacterial syndrome has been focussed primarily on the pathogenicity, identification and taxonomy of these bacteria. As all three species were newly classified within the past ten years, there are many unanswered questions regarding their ecology and interactions with each other. To determine the effect of bacterial interactions on fitness in vitro, we examined pairwise (diculture) and multispecies (triculture) interactions between B. goodwinii, R. victoriana and G. quercinecans in oak leaf media microcosms. Additionally, the effect of co-culturing on the evolution of these species was determined and the evolved B. goodwinii strains were examined further by whole genome sequencing. Our results indicate that B. goodwinii thrived in monoculture with significantly higher viable cell counts than the other two species. Additionally, B. goodwinii performed well in pairwise culture with mutually competitive interactions observed between B. goodwinii and R. victoriana, and between B. goodwinii and G. quercinecans. In the multispecies triculture, B. goodwinii and R. victoriana appeared to exhibit co-ordinated behaviour to outcompete G. quercinecans. After four weeks B. goodwinii grown in co-culture with the other two species developed greater evolved fitness than the strain grown in monoculture as reflected by the increased viable cell counts. The competitive interactions taking place between the threes species indicated evolving improved fitness of B. goodwinii in vitro, that gave it a growth advantage over both R. victoriana and G. quercinecans which showed no significant changes in fitness. Overall, B. goodwinii gains greater benefit in terms of fitness from in vitro competitive interaction with the other two species.

Rahnella perminowiae sp. nov., Rahnella bonaserana sp. nov., Rahnella rivi sp. nov. and Rahnella ecdela sp. nov., isolated from diverse environmental sources, and emended description of the genus Rahnella

Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus Rahnella based on partial housekeeping gene sequences and/or fatty acid analysis. However, many strains could not be assigned to any existing Rahnella species. Additionally, strains isolated from creek water and oak as well as a strain with bioremediation properties were assigned to Rahnella based on partial housekeeping gene sequences. The taxonomic status of these 21 strains was investigated using multilocus sequence analysis, whole genome analyses, phenotypic assays and fatty acid analysis. Phylogenetic and phylogenomic analyses separated the strains into five clusters, one of which corresponded to Rahnella aceris. The remaining four clusters could be differentiated both genotypically and phenotypically from each other and existing Rahnella species. Based on these results, we propose the description of four novel species: Rahnella perminowiae sp. nov. (type strain SL6^T=LMG 32257^T=DSM 112609^T), Rahnella bonaserana sp. nov. (H11b^T=LMG 32256^T=DSM 112610^T), Rahnella rivi sp. nov. (FC061912-K^T=LMG 32259^T=DSM 112611^T) and Rahnella ecdela sp. nov. (FRB 231^T=LMG 32255^T=DSM 112612^T).

Pseudomonas kirkiae sp. nov., a novel species isolated from oak in the United Kingdom, and phylogenetic considerations of the genera Pseudomonas, Azotobacter and Azomonas

As the current episode of Acute Oak Decline (AOD) continues to affect native British oak in the United Kingdom, ongoing isolations from symptomatic and healthy oak have yielded a large Pseudomonas species population. These strains could be divided into taxa representing three potential novel species. Recently, two of these taxa were described as novel Pseudomonas species in the Pseudomonas fluorescens lineage. Here, we demonstrate using a polyphasic approach that the third taxon represents another novel Pseudomonas species. The 16S rRNA gene sequencing assigned the strains to the Pseudomonas aeruginosa lineage, while multilocus sequence analysis (based on partial gyrB, rpoB and rpoD sequences) placed the 13 strains in a single cluster on the border of the Pseudomonas stutzeri group. Whole genome intra-species comparisons (based on average nucleotide identity and in silico DNA-DNA hybridization) confirmed that the strains belong to a single taxon, while the inter-species comparisons with closest phylogenetic relatives yielded similarity values below the accepted species threshold. Therefore, we propose these strains as a novel species, namely Pseudomonas kirkiae sp. nov., with the type strain FRB 229^T (P4C^T=LMG 31089^T=NCPPB 4674^T). The phylogenetic analyses performed in this study highlighted the difficulties in assigning novel species to the genus Pseudomonas due to its polyphyletic nature and close relationship to the genus Azotobacter. We further propose that a thorough taxonomic re-evaluation of the genus Pseudomonas is essential and should be performed in the near future.

Pseudomonas daroniae sp. nov. and Pseudomonas dryadis sp. nov., isolated from pedunculate oak affected by acute oak decline in the UK

Twenty-two cream-coloured bacterial strains were isolated from oak trees affected by acute oak decline (AOD) in Southern England. Isolates were Gram-negative, motile, slightly curved rods, aerobic, non-spore-forming, catalase positive and oxidase positive. 16S rRNA gene sequence analysis placed the strains in two separate phylogenetic clusters in the Pseudomonas straminea group, with Pseudomonas flavescens as the closest phylogenetic relative. Multilocus sequence analyses of the gyrB, rpoD and rpoB genes supported the delineation of the strains into two separate taxa, which could be differentiated phenotypically and chemotaxonomically from each other, and their closest relatives. Average nucleotide identity and in silico DNA-DNA hybridization values revealed percentages of genome similarity below the species threshold (95 and 70 %, respectively) between the two taxa and the closest relatives, confirming their novel species status. Therefore, on the basis of this polyphasic approach we propose two novel Pseudomonas species, Pseudomonasdaroniae sp. nov. (type strain FRB 228^T=LMG 31087^T=NCPPB 4672^T) and Pseudomonasdryadis sp. nov. (type strain FRB 230^T=LMG 31087^T=NCPPB 4673^T).

Exploring the Interface of Oncology and Palliative Care in Ireland

Aims To explore the integration and delivery of oncology led referrals to palliative care (PC) by examining physician attitudes and referral practices. Methods An online survey was circulated to oncologists and PC physicians in Ireland. Results The study (N = 100) comprised sixty-nine oncologists (69%) and thirty-one PC physicians (31%). Ninety-two(92%) believe patients with advanced cancer should receive concurrent treatment, however only 53% of oncologists(N = 37) routinely refer. Regarding end-of-life (EOL) care: 81% of oncologists (N = 55) are directly involved in its administration, despite 84% (N = 53) agreeing patients benefit when PC specialists coordinate EOL care. Conclusion The gulf between positive attitudes and limited implementation suggests the need for interdisciplinary changes to facilitate integration of PC in clinical practice in Ireland.

Taxonomy and identification of bacteria associated with acute oak decline

Acute oak decline (AOD) is a relatively newly described disorder affecting native oak species in Britain. Symptomatic trees are characterised by stem bleeds from vertical fissures, necrotic lesions in the live tissue beneath and larval galleries of the two spotted oak buprestid (Agrilus biguttatus). Several abiotic and biotic factors can be responsible for tree death, however the tissue necrosis and stem weeping is thought to be caused by a combination of bacterial species. Following investigations of the current episode of AOD which began in 2008, numerous strains belonging to several different bacteria in the family Enterobacteriaceae have been consistently isolated from symptomatic tissue. The majority of these enterobacteria were found to be novel species, subspecies and even genera, which have now been formally classified. The most frequently isolated species from symptomatic oak are Gibbsiella quercinecans, Brenneria goodwinii and Rahnella victoriana. Identification of these bacteria is difficult due to similarities in colony morphology, phenotypic profile and 16S rRNA gene sequences. Current identification relies heavily on gyrB gene amplification and sequencing, which is time consuming and laborious. However, newer techniques based on detection of single nucleotide polymorphisms show greater promise for rapid and reliable identification of the bacteria associated with AOD.

Rapid identification of bacteria associated with Acute Oak Decline by high-resolution melt analysis

Two Gram-negative Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are frequently isolated from oak suffering from Acute Oak Decline. These two species are difficult to identify based on colony morphology, carbohydrate utilization or 16S rRNA gene sequence, and identification using gyrB gene sequencing is time-consuming and laborious. A rapid identification technique, based on high-resolution melt analysis of the atpD gene, was designed to efficiently process numerous isolates from an increasing number of affected woodlands and parks. Principal component analysis of the resulting melt curves from strains of G. quercinecans, B. goodwinii and their close phylogenetic relatives allowed differentiation into distinct clusters based on species or subspecies identity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Acute Oak Decline is an increasing threat to Britain's native oak population. Two novel bacterial species both belonging to the family Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are thought to play an important role in symptom development. Here, we describe a rapid identification technique using high-resolution melt analysis of the atpD gene able to assign isolates to either G. quercinecans or B. goodwinii in a single assay, greatly reducing the time taken to identify if either or both of these species are present in symptomatic oak.

A Fuller Picture: Evaluating an Art Therapy Programme in a Multi-disciplinary Mental Health Service

Art therapy has a long history in mental health care but requires an enhanced evidence based in order to better identify its precise role in contemporary services. This paper describes an evaluation of an art therapy programme in an acute adult psychiatry admission unit in Ireland. A mixed method research design was used. Quantitative data were collected through a survey of 35 staff members and 11 service-users. Qualitative data included free-text comments collected in the survey and individual feedback from service-users. Both methods aimed to assess the role of art therapy as part of a multidisciplinary mental health service. Thematic content analysis was employed to analyse qualitative data. Staff demonstrated overwhelming support for art therapy as one element within multidisciplinary services available to patients in the acute psychiatry setting, qualitative feedback associated art therapy with improvements in quality of life and individual support, and emphasised its role as a nonverbal intervention, especially useful for those who find talking therapy difficult. Creative self-expression is valued by staff and service-users as part of the recovery process. Recommendations arising from the research include continuing the art therapy service, expanding it to include rehabilitation patients, provision of information and education sessions to staff and further research to identify other potential long-term effects. The low response of staff and small sample in this study, however, must be noted as limitations to these findings.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Investigation of in-feed organic acids as a low cost strategy to combat Salmonella in grower pigs

Salmonella carriage in pigs is a significant food safety issue. Dietary supplementation with organic acids has previously been shown to reduce shedding and transmission of Salmonella. Therefore, this study aimed to examine the effect of three commercially available organic acid-based products on Salmonella levels in grower pigs, using a model of experimental infection that closely mimics natural exposure to the organism. Seven week old trial pigs (n=40) with a mean weight of 14.7kg were placed in one of four pens with 10 pigs/pen. Pens had previously been contaminated with Salmonella Typhimurium 4,[5],12;i;- via seeder pigs. Trial pigs received one of four diets for 28days: 1, control diet; 2, sodium butyrate supplemented diet; 3, benzoic acid supplemented diet and 4, formic-citric acid supplemented diet. A further 10 pigs were placed in a Salmonella-free pen receiving the control diet. Pigs were weighed and blood sampled on days 0 and 28. Faeces was collected on day 0, 2, 3, 5, 7, 14, 21 and 28 and examined for Salmonella. On day 28, 5 pigs/group were euthanised and ileocaecal lymph nodes (ILN) and caecal contents sampled for culture. The remaining 5 pigs/pen were then fed the control diet and faeces were collected on days 35 and 42. On day 42 pigs were euthanised and ILN and caecal contents tested for Salmonella levels. The trial was repeated once. Within the first two days of exposure to the contaminated environment, 96% (77/80) of pigs became infected. Most pigs shed Salmonella at levels of between 10⁰-10³ CFU/g faeces for at least 7days post-exposure. A significant reduction in Salmonella faecal concentration was observed after supplementation with sodium butyrate (p=0.001) and a formic citric acid blend (p<0.0001). Average daily weight gain (ADWG) was significantly increased in all groups fed the supplemented feed when compared to the positive control group. The use of sodium butyrate or a blend of formic and citric acid in feed could be considered a cost-effective control measure to reduce Salmonella faecal shedding and improve ADWG in Salmonella infected herds.

A regional analysis of epidermal growth factor receptor (EGFR) mutated lung cancer for HSE South

BACKGROUND

EGFR mutated lung cancer represents a subgroup with distinct clinical presentations, prognosis, and management requirements. We investigated the survival, prognostic factors, and real-world treatment of NSCLC patients with EGFR mutation in clinical practice.

METHODS

A retrospective review of all specimens sent for EGFR analysis from December 2009 to September 2015 was performed. Patient demographics, specimen type, EGFR mutation status/type, stage at diagnosis, treatment, response rate, and survival data were recorded.

RESULTS

27/334 (8%) patient specimens sent for EGFR testing tested positive for a sensitising EGFR mutation. The median age was 65 years (40-85 years). Exon 19 deletion represented the most commonly detected alteration, accounting for 39% (n = 11). First-line treatment for those with Exon 18, 19, or 21 alterations (n = 24) was with an EGFR tyrosine kinase inhibitor (TKI) in 79% (n = 19). Objective response rate among these patients was 74% and median duration of response was 13 months (range 7-35 months).

CONCLUSION

The incidence of EGFR mutation in our cohort of NSCLC is 9% which is consistent with mutation incidence reported in other countries. The rate of EGFR mutation in our population is slightly below that reported internationally, but treatment outcomes are consistent with published data. Real-world patient data have important contributions to make with regard to quality measurement, incorporating patient experience into guidelines and identifying safety signals.

Vinorelbine induced perforation of a metastatic gastric lesion

Background

Breast carcinoma metastasis to the gastrointestinal tract is rare and more frequently associated with lobular than ductal carcinoma (Borst and Ingold, Surg 114(4):637–641 [1]). The purpose of this article is to present a case based review of a unique gastrointestinal metastasis and literature review.

Methods

A 46 year old lady with metastatic invasive ductal breast cancer was admitted to A&E with sudden onset of epigastric and left shoulder pain. She completed the first cycle of capecitabine/vinorelbine 1 week previously. Clinical examination revealed a tender epigastrium with rigidity in the upper abdomen. Free air under the diaphragm and a positive Rigler’s sign was radiologically identified. A laparoscopy demonstrated a fibrinous exudate in the left upper quadrant consistent with a walled off lesser curvature gastric perforation. A subsequent oesophagogastroduodenoscopy (OGD) demonstrated a healed gastric ulcer of benign appearance; however the pathology confirmed metastatic breast carcinoma.

Results

Literature review confirmed no previously reported cases of vinorelbine induced gastric perforation. Four cases of metastatic breast cancer with gastric metastasis presenting with perforation were identified; three of these cases (Fra et al., Presse Med 25(26):1215 (1996) [2], Solis-Caxaj et al., Gastroenterol Clin Biol 28(1):91–92 (2004) [3], Ghosn et al., Bull Cancer 78(11):1071–1073 (1991) [4]), were in the French medical literature, including one male patient (Fra et al., Presse Med 25(26):1215 (1996) [2]) and at least one ductal breast carcinoma (Solis-Caxaj et al., Gastroenterol Clin Biol 28(1):91–92 (2004) [3]). The fourth case (van Geel et al., Ned Tijdschr Geneeskd 144(37):1761–1763 (2000) [5]), was in the Dutch medical literature and a lobular breast carcinoma.

Conclusion

This case represents a rare complication of breast cancer chemotherapy, the subsequent significant benefit the patient received from treatment is consistent with the chemosensitivity to therapy that also resulted in gastric perforation. Five years after gastric perforation she resumed palliative chemotherapy after progression on sequential hormonal therapies.

Limited HLA sequence variation outside of antigen recognition domain exons of 360 10 of 10 matched unrelated hematopoietic stem cell transplant donor-recipient pairs

Traditional DNA-based typing focuses primarily on interrogating the exons of human leukocyte antigen (HLA) genes that form the antigen recognition domain (ARD). The relevance of mismatching donor and recipient for HLA variation outside the ARD on hematopoietic stem cell transplantation (HSCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in 10 of 10 (HLA-A, -B, -C, -DRB1, -DQB1) matched unrelated donor transplant pairs (n = 360). Next-generation DNA sequencing was used to characterize both HLA exons and introns for HLA-A, -B, -C alleles; exons 2, 3 and the intervening intron for HLA-DRB1 and exons only for HLA-DQA1 and -DQB1. Over 97% of alleles at each locus were matched for their nucleotide sequence outside of the ARD exons. Of the 4320 allele comparisons overall, only 17 allele pairs were mismatched for non-ARD exons, 41 for noncoding regions and 9 for ARD exons. The observed variation between donor and recipient usually involved a single nucleotide difference (88% of mismatches); 88% of the non-ARD exon variants impacted the amino acid sequence. The impact of amino acid sequence variation caused by substitutions in exons outside ARD regions in D-R pairs will be difficult to assess in HSCT outcome studies because these mismatches do not occur very frequently.

GvHD after umbilical cord blood transplantation for acute leukemia: an analysis of risk factors and effect on outcomes

Using the Center for International Blood and Marrow Transplant Research (CIBMTR) registry, we analyzed 1,404 UCBT patients [single (< 18 years) = 810, double (≥ 18 years) = 594] with acute leukemia to define the incidence of acute and chronic graft-vs.-host disease (GVHD), analyze clinical risk factors and investigate outcomes. After single UCBT, 100-day incidence of grades II–IV aGVHD was 39% (95% CI, 36–43%), grades III–IV aGVHD was 18% (95% CI, 15–20%), and 1-year cGVHD was 27% (95% CI, 24–30%). After double UCBT, 100-day incidence of grades II–IV aGVHD was 45% (95% CI, 41%–49%), grades III–IV aGVHD was 22% (95% CI, 19–26%), and 1-year cGVHD was 26% (95% CI, 22–29%). For single UCBT, multivariate analysis showed that absence of anti-thymocyte globulin (ATG) was associated with aGVHD, whereas prior aGVHD was associated with cGVHD. For double UCBT, absence of ATG and myeloablative conditioning were associated with aGVHD, while prior aGVHD predicted for cGVHD. Grades III–IV aGVHD led to worse survival whereas cGVHD had no significant effect on disease-free or overall survival. GVHD is prevalent after UCBT with severe aGVHD leading to higher mortality. Future research in UCBT should prioritize prevention of GVHD.

Gibbsiella papilionis Kim et al. 2013 is a later heterotypic synonym of Gibbsiella dentisursi Saito et al. 2013

Synonymy of Gibbsiella dentisursi DSM 23818T ( = NUM 1720T) and Gibbsiella papilionis JCM 18389T ( = LEN33T) was suspected following multilocus sequence analysis (MLSA) of both type strains in a previous classification study, where they were found to share >99.6 % gene sequence similarity. The taxonomic relationship between these two strains was re-examined here using a polyphasic approach. A DNA-DNA hybridization value of 98 % confirmed that the two type strains belong to a single taxon, while the phenotypic profiles were found to be nearly identical. Therefore we propose Gibbsiella papilionis as a later heterotypic synonym of Gibbsiella dentisursi, with the type strain as NUM 1720T ( = DSM 23818T = JCM 17201T).

Empathy and the wounded healer: a mixed-method study of patients and doctors views on empathy

Empathy is increasingly being recognized as a crucial component for an effective doctor-patient relationship. Using a mixed method approach, we surveyed 125 patients and 361 medical practitioners (doctors and medical students) views of the doctor-patient relationship. We qualitatively assessed patients' views of what constituted a good doctor and qualitatively measured empathy using a validated scale in medical practitioners. Patients desire a doctor that is both clinically proficient 66 (55%) and caring 32 (27%). Doctors who have a personal experience of illness have a statistically higher empathy score. These doctors may be well placed to help develop and foster empathy in our profession.

Gibbsiella greigii sp. nov., a novel species associated with oak decline in the USA

In 2010, cream-coloured, Gram-negative staining, facultatively anaerobic enterobacteria were isolated from a single black oak tree (Quercus kelloggii) exhibiting decline symptoms in southern California, USA. These 12 isolates were tentatively identified as Gibbsiella quercinecans based on partial gyrB sequencing. Closer examination of the strains using multilocus sequence analysis, based on partial sequences of gyrB, rpoB, infB and atpD genes, and almost complete 16S rRNA gene sequencing suggested that the isolates belong to a novel taxon within the genus Gibbsiella with G. quercinecans as their closest phylogenetic relative. DNA-DNA relatedness studies confirmed that the strains belong to a single taxon in Gibbsiella, which can be differentiated from other members of the genus by several phenotypic traits. Therefore, the name Gibbsiella greigii sp. nov. is proposed for this novel species isolated from symptomatic Q. kelloggii in the USA with FRB 224(T) (=LMG 27716(T)=NCPPB 4583(T)) as the type strain.

Non-ribosomal phylogenetic exploration of Mollicute species: new insights into haemoplasma taxonomy

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The first gapA and dnaK phylogenetic analysis of Mollicute species.

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Analysis includes a wide range of haemoplasmas species.

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Analysis supports that haemoplasmas reside within a single clade.

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Evidence of phylogenetic distance between the haemoplasmas and Mycoplasma species.

Nine species of uncultivable haemoplasmas and several Mycoplasma species were examined by partial sequencing of two protein-encoding housekeeping genes. Partial glyceraldehyde-3-phosphate dehydrogenase (gapA) and heat shock protein 70 (dnaK) gene sequences were determined for these Mollicute species; in total nine gapA sequences and ten dnaK sequences were obtained. Phylogenetic analyses of these sequences, along with those of a broad selection of Mollicute species downloaded from GenBank, for the individual genes, and for the gapA and dnaK concatenated data set, revealed a clear separation of the haemoplasmas from other species within the Mycoplasma genus; indeed the haemoplasmas resided within a single clade which was phylogenetically detached from the pneumoniae group of Mycoplasmas. This is the first report to examine the use of gapA and dnaK, as well as a concatenated data set, for phylogenetic analysis of the haemoplasmas and other Mollicute species. These results demonstrate a distinct phylogenetic separation between the haemoplasmas and Mycoplasmas that corresponds with the biological differences observed in these species, indicating that further evaluation of the haemoplasmas’ relationship with the Mycoplasma genus is required to determine whether reclassification of the haemoplasmas is necessary.

Inducing apoptosis of cancer cells using small-molecule plant compounds that bind to GRP78

Background:

Glucose regulated protein 78 (GRP78) functions as a sensor of endoplasmic reticulum (ER) stress. The aim of this study was to test the hypothesis that molecules that bind to GRP78 induce the unfolded protein response (UPR) and enhance cell death in combination with ER stress inducers.

Methods:

Differential scanning calorimetry (DSC), measurement of cell death by flow cytometry and the induction of ER stress markers using western blotting.

Results:

Epigallocatechin gallate (EGCG), a flavonoid component of Green Tea Camellia sinensis, and honokiol (HNK), a Magnolia grandiflora derivative, bind to unfolded conformations of the GRP78 ATPase domain. Epigallocatechin gallate and HNK induced death in six neuroectodermal tumour cell lines tested. Levels of death to HNK were twice that for EGCG; half-maximal effective doses were similar but EGCG sensitivity varied more widely between cell types. Honokiol induced ER stress and UPR as predicted from its ability to interact with GRP78, but EGCG was less effective. With respect to cell death, HNK had synergistic effects on melanoma and glioblastoma cells with the ER stress inducers fenretinide or bortezomib, but only additive (fenretinide) or inhibitory (bortezomib) effects on neuroblastoma cells.

Conclusion:

Honokiol induces apoptosis due to ER stress from an interaction with GRP78. The data are consistent with DSC results that suggest that HNK binds to GRP78 more effectively than EGCG. Therefore, HNK may warrant development as an antitumour drug.

The impact of rolling theatre closures on core urology training

Since 2008, government funding of the Health Service Executive (HSE) has decreased significantly. Our hospital, Cork University Hospital (CUH), implemented "cost saving" measures including scheduled operating theatre closures. We studied their affect on urological surgical activity at the hospital. A retrospective review was performed using theatre log books and theatre records to determine the number, type and training status of procedures performed for years 2009 and 2011. Scheduled theatre closures in 2011 resulted in 33 more theatre session cancelations compared to 2009. There was a reduction in the total number of procedures performed from 555 cases in 2009 to 443 in 2011 a 20.2(%) reduction. The number of "training" cases reduced from 325 (58.9%) in 2009 to 216 (48.7%) in 2011 a 10.2% reduction (Table 2). Eight out of the nine "core urology training" procedures reduced in number from 2009 to 2011 (Table 1). We have shown that scheduled theatre closures have reduced the number of procedures performed and have impacted on urology training. Scheduled theatre closures are expected to become more frequent in the future. Potential solutions to lessen the impact include providing simulation training using the Royal College of Surgeons in Ireland (RCSI) mobile skills unit during these theatre closures.

Brenneria goodwinii sp. nov., associated with acute oak decline in the UK

A group of nine Gram-negative staining, facultatively anaerobic bacterial strains isolated from native oak trees displaying symptoms of acute oak decline (AOD) in the UK were investigated using a polyphasic approach. 16S rRNA gene sequencing and phylogenetic analysis revealed that these isolates form a distinct lineage within the genus Brenneria , family Enterobacteriaceae , and are most closely related to Brenneria rubrifaciens (97.6 % sequence similarity to the type strain). Multilocus sequence analysis based on four housekeeping genes (gyrB, rpoB, infB and atpD) confirmed their position within the genus Brenneria , while DNA–DNA hybridization indicated that the isolates belong to a single taxon. The isolates can be differentiated phenotypically from their closest phylogenetic neighbours. The phylogenetic and phenotypic data demonstrate that these isolates from oak with symptoms of AOD represent a novel species in the genus Brenneria , for which the name Brenneria goodwinii sp. nov. (type strain FRB 141T  = R-43656T  = BCC 845T  = LMG 26270T  = NCPPB 4484T) is proposed.

Distribution of Lesions in Fetal Brains Following Experimental Infection of Pregnant Sheep With Toxoplasma gondii

Six ovine fetal brains were harvested 33 to 35 days postchallenge from 5 ewes, each of which was given 3000 Toxoplasma gondii oocysts on day 90 of pregnancy. Histopathologic examination of transverse sections taken at 13 levels in the fetal brains revealed the presence of toxoplasmosis-related lesions in all 6 brains. However, lesions were not randomly distributed ( P = .007); they were most numerous at the level of the optic tract, the rostral margin of the pons, and 4 mm caudal to the ansate sulcus and were absent in all sections at the level of the caudal cerebellum. Lesion distribution may be due to hemodynamic factors, differences in the expression of endothelial surface receptor molecules at the level of the blood-brain barrier, or the presence of localized permissive/inhibitory factors within the brain. The results have implications for the selection of areas of brain from aborted ovine fetuses to be examined histopathologically for laboratory diagnosis.

Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position for these isolates in the genera Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (>99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences indicated that the strains constituted a single novel species in the genus Erwinia. The strains showed general phenotypic characteristics typical of the genus Erwinia and whole genome DNA-DNA hybridization data confirmed that they represented a single novel species of the genus Erwinia. The strains showed DNA G+C contents ranging from 54.7 to 54.9 mol%. They could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, l-rhamnose and d-arabitol, but not glycerol, inositol or d-sorbitol. The name Erwinia oleae sp. nov. (type strain DAPP-PG 531(T)= LMG 25322(T) = DSM 23398(T)) is proposed for this novel taxon.

Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline

Gram-negative, facultatively anaerobic bacterial strains were consistently isolated from oak trees displaying symptoms of extensive stem bleeding. In Britain, this disorder is called Acute Oak Decline (AOD). A similar condition has been noted on species of Mediterranean oak in Spain. The identity of bacterial isolates from symptomatic trees in both countries was investigated using molecular techniques and phenotypic assays. 16S rRNA gene sequencing indicated that the strains were most closely related to the genera Serratia, Kluyvera, Klebsiella and Raoultella (all>97%). Phylogenetic analysis revealed that the strains formed a distinct lineage within the family Enterobacteriaceae, which was confirmed by both gyrB- and rpoB-gene sequencing. DNA-DNA hybridization confirmed that the strains belonged to a single taxon which could also be differentiated phenotypically from its closest phylogenetic neighbours. The phylogenetic and phenotypic data both demonstrated that the strains isolated from oak represented a novel genus and species within the family Enterobacteriaceae for which the name Gibbsiella quercinecans gen. nov., sp. nov. (type strain=FRB 97(T)=LMG 25500(T)=NCPPB 4470(T)) is proposed.

Rating the extent of surface scratches on photostimulable storage phosphor plates in a dental school environment

OBJECTIVE

The aims of this study were (1) to subjectively quantify the degree of scratching and smudging that had taken place in the junior clinic in the 9 months following the implementation of digital radiology; (2) to compare the findings with a previously published report; and (3) to identify areas in the protocol and training that can be refined to minimize future scratching and smudging.

METHODS

Seven sets of blank clinical photostimulable storage phosphor (PSP) plates were scanned after exposing them at 65 kV and 7 mA for 0.80 s. Scanned plates were lightly wiped with a soft cloth and alcohol, repackaged in plastic sleeves, re-exposed and rescanned. The two sets of resulting images were subjectively rated independently by two investigators for artefacts and placed in five categories.

RESULTS

Of all the images, approximately 75% were rated in the top 3 categories (most readable), leaving 17% and 8% in the poor and unsatisfactory categories, respectively. Mean rated values of the two image sets (before and after wiping) were not statistically different, but ratings slightly improved after cleaning the plates.

CONCLUSIONS

Wiping all plates to remove surface contamination may not always be necessary or desirable. Systems that are designed to minimize handling of the plates may help minimize scratching of them.

Relationships between clinical signs, pathological changes and tissue distribution of Mycobacterium avium subspecies paratuberculosis in 21 cows from herds affected by Johne's disease

Twenty-one cows from eight herds affected by Johne's disease were assigned to four groups: seven were not thriving and had persistent diarrhoea, six were not thriving and had intermittent diarrhoea, four were not thriving but did not have diarrhoea, and four were clinically normal. Postmortem, macroscopic lesions consistent with Johne's disease were identified in 17 of the cows and Mycobacterium avium subspecies paratuberculosis (MAP) was isolated from all of them. However, except for the fact that diarrhoea was correlated with the presence of lesions in the large intestine there was little correlation between the presence or absence of clinical signs and the lesions associated with Johne's disease. The tissue distribution of MAP was also poorly correlated with either the clinical signs or the lesions. The organism was widely distributed in 17 of the 21 cows, including three of the clinically normal animals, and was present in the mammary tissues of seven cows including two of the clinically normal animals. Three distinct histopathological patterns were observed in the affected intestines: infiltration of the lamina propria with giant cells, tuberculoid lesions, and lepromatous lesions; the lepromatous lesions were associated with extensive pathological changes.