Comparasion of five gene loci (rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ) to aid the molecular identification of viridans-group streptococci and pneumococci

Viridans-group streptococci (VGS) consist of several taxa which historically have been highly diverse. However, at times it may become necessary to have a reliable scheme for the identification of these organisms to the species level. The aim of this study is to compare the ability of five gene loci, namely rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ, to speciate such organisms through a sequence typing-based approach. Reference organisms consisting of six VGS species were compared based on sequence typing, followed by comparison of 31 wild-type respiratory isolates, and showed that employment of sequence typing using the rnpB gene locus was the most specific and reliable. Therefore, the use of rnpB sequencing for the identification of VGS to species level is a reliable and feasible option, based on a single gene target.

Molecular characterisation of the quinolone resistance-determining regions (QRDR) including gyrA, gyrB, parC and parE genes in Streptococcus pneumoniae

Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP). Currently, empirical treatment with quinolones is being used due to the emergence of beta-lactam and macrolide resistance in S. pneumonaie. Although the prevalence of quinolone-resistant S. pneumoniae remains low, increasing numbers of resistant isolates are being seen. Genetic mechanisms leading to fluoroquinolone resistance in pneumococci are complex. This study aims to use molecular methods to characterise all isolates through sequence analysis of their QRDR regions. Thirty-two S. pneumoniae isolates were obtained from nasal swabs from adult and paediatric patients attending local general practices in Northern Ireland. Phenotypic minimum inhibitory concentration (MIC) was determined for Clinical and Laboratory Standards Institute (CLSI) broth microdilution against ciprofloxacin, levofloxacin and norfloxacin. Simultaneously, the QRDR regions of gyrA, gyrB, parC and parE were analysed by sequence typing for all pneumococci obtained. Only one isolate (3.1%) showed reduced susceptibility to ciprofloxacin and levofloxacin. Two amino acid positions were discordant in the S. pneumoniae R6 strain and eight (25%) and 23 (71.9%) isolates contained the mutations Ile460Val in gyrA and Lys137Asn in parC (deposited in GenBank, accession numbers GQ999587-GQ999589), respectively. No mutations were found in either the gyrB or parE loci. In conclusion, the study demonstrated increased fluoroquinolone resistance which could not be accounted for simply through QRDR mutations, and, reciprocally, that mutations in the QRDR region do not necessarily result in overt phenotypic resistance.

P3-11-06: A Pilot Study of RPFNA in Overweight and Obese Postmenopausal Women

Background: Random periareolar fine-needle aspiration (RPFNA) is a research-based procedure used to obtain breast epithelial cells and fluid. Data suggest that atypia in epithelial cells from RPFNA specimens is associated with an increased risk of breast cancer, and changes in the degree of atypia may be a viable biomarker for response to chemopreventive interventions.

Methods: We performed RPFNA on 37 overweight or obese (body mass index (BMI≥ 25.0 kg/m2) postmenopausal (50-75 y) women enrolled in a randomized clinical trial of Vitamin D vs placebo in combination with a lifestyle (diet + exercise)-based weight loss program. Eligibility criteria included serum vitamin D concentrations 10–32 ng/mL. The procedure was performed by two trained clinicians prior to randomization to assess baseline cell counts and degree of atypia. Two areas in the breast (10:00 and 2:00 positions) were infiltrated with lidocaine, and 8 to 10 aspirations of cellular material were performed using 1.5 inch, 21-gauge needles. The aspirated fluid was placed in 9 cc of Cytolyt Thinprep (Hologic Inc.) with 1 cc of 1% neutral buffered formalin and slides were prepared according to the University of Washington Department of Pathology non-gyn protocol.

Results: Thirty-seven women were included in this analysis. The mean age and BMI of study participants was 59.3 years and 32.5 kg/m2, respectively. The mean 5-year Gail risk score for study participants was 1.96%; 52% of women had a 5-year Gail risk >1.66%. Eight participants (21.6%) had >50 cells present on cytology examination. One additional participant had 10–50 cells, and one had <10 cells. No specimens showed cellular atypia. The remainder of study participants had only blood or fibroadipose tissue on cytology specimens. Women with epithelial cells present were younger (mean age 55.0 vs. 60.2 years, p=0.05). There were no significant differences in BMI or Gail risk score between those with and without epithelial cells.

Conclusions: RPFNA in our sample of overweight/obese postmenopausal women did not yield epithelial cells in a majority of participants. Younger age was associated with a greater cell count. We are planning further studies to determine whether other markers in RPFNA specimens can be used to assess breast tissue changes in response to chemopreventive interventions.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-11-06.

Impacts of maintenance dredged material disposal on macrobenthic structure and secondary productivity

The results of a monitoring programme to assess the spatial impacts associated with ongoing dredged material disposal activity at a dispersive, coastal disposal site (southwest UK) are described. Benthic impacts were assessed using benthic community structure and secondary productivity estimates. Analyses of univariate indices (including secondary production) and multivariate community structure revealed differences between stations inside and those outside the disposal site were minimal. Generally, stations within and outside the disposal site were characterised by the same species. Regression models indicated that the variability in biological structure and secondary production was predominantly accounted for by natural variables (e.g., depth, sediment granulometry) with only a small amount of residual variability being due to contaminant variables. Thus, the elevated levels of certain contaminants in the vicinity of the disposal area were not sufficient to result in significant ecological or ecotoxicological changes. We ascribe such findings partly to the dispersive nature of the disposal site.

Prevalence of clustered regulatory interspaced short palindromic repeat (CRISPR)-like sequences in mitis-group streptococci

Clustered regulatory interspaced short palindromic repeats (CRISPRs) have been discovered in many bacteria and archaea. Many CRISPR-like sequences have been identified in an increasing number of studies on the function of CRISPRs. One CRISPR-like sequence of approximately 240 base pairs has been found to be highly conserved within 11 genome sequences of Streptococcus pneumoniae. A specific CRISPR-like polymerase chain reaction (PCR) assay was designed with the novel primers CRISPR 5F (forward primer) 5'-CTA ATY TCA TAA CCA TAR GAA TC-3' and CRISPR 3R (reverse primer) 5'-GAT AAR ATC CTY TAA WCT TCT AG-3' to detect the presence of this CRISPR-like sequence in pneumococci, as well as in viridans-group streptococci (VGS). This study investigates the prevalence of this CRISPR-like sequence in S. pneumoniae and 12 viridans-group streptococcal species and shows its existence to be shared by the majority of S. pneumoniae and, to a lesser extent, S. mitis. This CRISPR-like sequence was also found in S. australis and it is highly conserved among these strains, suggesting possible biological functional differences from true CRISPR because this CRISPR-like sequence has relatively few repeat numbers, and adjacent homology of CRISPR-associated (cas) genes was absent. The sharing of this CRISPR-like sequence between pneumococci, the mitis group and other VGS, as well as its high sequence homology, may suggest close evolutionary emergence of this sequence between these species.

Omega-5 gliadin anaphylaxis: an integrated diagnostic approach

We report the case of a 62-year old man who presented a wheat-dependent, exercise-induced anaphylaxis (WDEIA). The case illustrates the usefulness of skin prick test not only with wheat extract, but also with native gliadin extract. Moreover we confirm the value of recombinant IgE dosage with rTri a 19 omega-5 gliadin in the diagnostic pathway of this condition.

Oxidation–reduction reactions of simple hydroxamic acids and plutonium(IV) ions in nitric acid

Simple hydroxamic acids such as formo- and aceto-hydroxamic acids have been proposed as suitable reagents for the separation of either Pu and/or Np from U in modified or single cycle Purex based solvent extraction processes designed to meet the emerging requirements of advanced fuel cycles. The stability of these hydroxamic acids is dominated by their decomposition through acid hydrolysis. Kinetic studies of the acid hydrolysis of formo- and aceto-hydroxamic acids are reported in the absence and the presence of Pu(IV) ions. The slow reduction of these plutonium(IV) hydroxamate complexes to Pu(III) aquo-ions has been characterised by spectrophotometry and cyclic voltammetry. The reductions of Pu(IV) in the presence of FHA and AHA are consistent with a mechanism in which free hydroxamic acid in solution is hydrolysed whilst Pu(IV) ions remain fully complexed to hydroxamate ligands; then at some point close to a 1 : 1 Pu(IV) : XHA ratio, some free Pu4+ is released from the complex and reduction is initiated. Electrochemical and kinetic data suggest that the reductant is the hydroxamic acid rather than the hydroxylamine.

Multiple novel astrovirus species in human stool

Diarrhoea remains a significant cause of morbidity and mortality in developing countries where numerous cases remain without identified aetiology. Astroviruses are a recently identified cause of animal gastroenteritis which currently includes two species suspected of causing human diarrhoea. Using pan-astrovirus RT-PCR, we analysed human stool samples from different continents for astrovirus-related RNA sequences. We identified variants of the two known human astrovirus species plus, based on genetic distance criteria, three novel astrovirus species all distantly related to mink and ovine astroviruses, which we provisionally named HMOAstV species A-C. The complete genome of species A displayed all the conserved characteristics of mammalian astroviruses. Each of the now three groups of astroviruses found in human stool (HAstV, AstV-MLB and HMOAstV) were more closely related to animal astroviruses than to each other, indicating that human astroviruses may periodically emerge from zoonotic transmissions. Based on the pathogenic impact of their closest phylogenetic relatives in animals, further investigations of the role of HMOAstV, so far detected in Nigeria, Nepal and Pakistan, in human gastroenteritis are warranted.

Preimplantation genetic diagnosis as a source of human embryonic stem cells for disease research and drug discovery

Embryos surplus to therapeutic requirements following preimplantation genetic diagnosis can be used to derive human embryonic stem cell (hESC) lines carrying mutations significant to human disease. These cells provide a powerful in vitro tool for modelling disease progression in a number of cell types as well as having the potential to revolutionise drug discovery. Robust and reproducible directed differentiation protocols are needed to maximise the potential of these cells. In this review, we explore the current use of hESC and induced pluripotent stem cells in disease-specific research and discuss the use of stem cell technology in drug discovery and toxicity testing.

Perceived concepts of continuity of care in people with colorectal and breast cancer--a qualitative case study analysis

We aimed to develop ideas on continuity of cancer care. In-depth qualitative interviews were conducted with 28 people. Seven had cancer. Each person with cancer nominated a close person and a primary and secondary health care professional. We examined from four perspectives: experiences of the initial diagnosis; subsequent treatment; views on continuity of care; information given about the illness; psychological/physical impact of cancer and communication with professionals, family and friends. Perceived continuity of care was influenced by the actions of patients', involvement of close contacts and engagement in shared decision making. Additionally communication between primary and secondary care, the role of various health professionals and hospital administrative systems strongly influenced continuity of care. Informational, management and relational continuity have been previously described. Our data uncovered the effect of patients' actions and the involvement of close friends and families on continuity of cancer care. People with cancer should be enabled to influence continuity of their care. Full recognition of the role of health professionals, different approaches to sharing information with patients and tightening of hospital administrative systems should also be considered.