Pneumococcal Colonisation Rates in Patients Admitted to a UK Hospital with Lower Respiratory Tract Infection - a prospective case-control study

BACKGROUND Current diagnostic tests are ineffective at identifying the aetiological pathogen in hospitalised adults with lower respiratory tract infection (LRTI). The association of pneumococcal colonisation with disease has been suggested as a means to increase diagnostic precision. We compared pneumococcal colonisation rate and density of nasal pneumococcal colonisation by a) classical culture and b) quantitative real time lytA Polymerase Chain Reaction (qPCR) in patients admitted to hospital in the UK with LRTI compared to control patients. METHODS 826 patients were screened for inclusion in this prospective case-control study. 38 patients were recruited, 19 with confirmed LRTI and 19 controls with another diagnosis. Nasal wash (NW) was collected at the time of recruitment. RESULTS Pneumococcal colonisation was detected in 1 LRTI patient and 3 controls (p=0.6) by classical culture. Using qPCR pneumococcal colonisation was detected in 10 LRTI patients and 8 controls (p=0.5). Antibiotic usage prior to sampling was significantly higher in the LRTI than control group 19 v. 3 (p8000 copies/ml on qPCR pneumococcal colonisation was found in 3 LRTI patients and 4 controls (p > 0.05). CONCLUSIONS We conclude that neither prevalence nor density of nasal pneumococcal colonisation (by culture and qPCR) can be used as a method of microbiological diagnosis in hospitalised adults with LRTI in the UK. A community based study recruiting patients prior to antibiotic therapy may be a useful future step

The properties of extragalactic radio sources selected at 20 GHz

We present some first results on the variability, polarization and general properties of radio sources selected in a blind survey at 20 GHz, the highest frequency at which a sensitive radio survey has been carried out over a large area of sky. Sources with flux densities above 100 mJy in the AT20G Pilot Survey at declination -60 to -70 were observed at up to three epochs during 2002-4, including near-simultaneous measurements at 5, 8 and 18 GHz in 2003. Of the 173 sources detected, 65% are candidate QSOs, BL Lac objects or blazars, 20% galaxies and 15% faint (b > 22 mag) optical objects or blank fields. On a 1-2 year timescale, the general level of variability at 20 GHz appears to be low. For the 108 sources with good-quality measurements in both 2003 and 2004, the median variability index at 20 GHz was 6.9% and only five sources varied by more than 30% in flux density. Most sources in our sample show low levels of linear polarization (typically 1-5%), with a median fractional polarization of 2.3% at 20 GHz. There is a trend for fainter sources to show higher fractional polarization. At least 40% of sources selected at 20GHz have strong spectral curvature over the frequency range 1-20 GHz. We use a radio `two-colour diagram' to characterize the radio spectra of our sample, and confirm that the radio-source population at 20 GHz (which is also the foreground point-source population for CMB anisotropy experiments like WMAP and Planck) cannot be reliably predicted by extrapolating the results of surveys at lower frequencies. As a result, direct selection at 20 GHz appears to be a more efficient way of identifying 90 GHz phase calibrators for ALMA than the currently-proposed technique of extrapolation from all-sky surveys at 1-5 GHz.Comment: 14-page paper plus 5-page data table. Replaced with published versio

Pneumococcal colonisation is an asymptomatic event in healthy adults using an experimental human colonisation model

Introduction Pneumococcal colonisation is regarded as a pre-requisite for developing pneumococcal disease. In children previous studies have reported pneumococcal colonisation to be a symptomatic event and described a relationship between symptom severity/frequency and colonisation density. The evidence for this in adults is lacking in the literature. This study uses the experimental human pneumococcal challenge (EHPC) model to explore whether pneumococcal colonisation is a symptomatic event in healthy adults. Methods Healthy participants aged 18–50 were recruited and inoculated intra-nasally with either Streptococcus pneumoniae (serotypes 6B, 23F) or saline as a control. Respiratory viral swabs were obtained prior to inoculation. Nasal and non-nasal symptoms were then assessed using a modified Likert score between 1 (no symptoms) to 7 (cannot function). The rate of symptoms reported between the two groups was compared and a correlation analysis performed. Results Data from 54 participants were analysed. 46 were inoculated with S. pneumoniae (29 with serotype 6B, 17 with serotype 23F) and 8 received saline (control). In total, 14 became experimentally colonised (30.4%), all of which were inoculated with serotype 6B. There was no statistically significant difference in nasal (p = 0.45) or non-nasal symptoms (p = 0.28) between the inoculation group and the control group. In those who were colonised there was no direct correlation between colonisation density and symptom severity. In the 22% (12/52) who were co-colonised, with pneumococcus and respiratory viruses, there was no statistical difference in either nasal or non-nasal symptoms (virus positive p = 0.74 and virus negative p = 1.0). Conclusion Pneumococcal colonisation using the EHPC model is asymptomatic in healthy adults, regardless of pneumococcal density or viral co-colonisation

The Australia Telescope 20GHz (AT20G) Survey: analysis of the extragalactic source sample

The Australia Telescope 20 GHz (AT20G) survey is a blind survey of the whole Southern sky at 20 GHz with follow-up observations at 4.8, 8.6, and 20 GHz carried out with the Australia Telescope Compact Array (ATCA). In this paper we present an analysis of radio spectral properties in total intensity and polarisation, sizes, optical identifications, and redshifts of the sample of the 5808 extragalactic sources in the survey catalogue of confirmed sources over the whole Southern sky excluding the strip at Galactic latitude |b|<1.5deg. The sample has a flux density limit of 40 mJy. Completeness has been measured as a function of scan region and flux density. Averaging over the whole survey area the follow-up survey is 78% complete above 50mJy and 93% complete above 100mJy. 3332 sources with declination <-15deg have good quality almost simultaneous observations at 4.8, 8.6, and 20GHz. The spectral analysis shows that the sample is dominated by flat-spectrum sources. The fraction of flat-spectrum sources decreases from 81% for 20GHz flux densities S>500mJy, to 60% for S<100mJy. There is also a clear spectral steepening at higher frequencies with the median spectral index decreasing from -0.16 between 4.8 and 8.6GHz to -0.28 between 8.6 and 20GHz. Simultaneous observations in polarisation are available for all the sources at all the frequencies. 768 sources have a good quality detection of polarised flux density at 20GHz; 467 of them were also detected in polarisation at 4.8 and/or at 8.6GHz so that it has been possible to compare the spectral behaviour in total intensity and polarisation. We have found that the polarised fraction increases slightly with frequency and decreases with flux density. Cross matches and comparisons have been made with other catalogues at lower radio frequencies, and in the optical, X-ray and gamma-ray bands. Redshift estimates are available for 825 sources.Comment: 15 pages, 16 figures, accepted for publication in MNRA

The Australia Telescope 20 GHz (AT20G) Survey: The Bright Source Sample

The Australia Telescope 20 GHz (AT20G) Survey is a blind survey of the whole Southern sky at 20 GHz (with follow-up observations at 4.8 and 8.6 GHz) carried out with the Australia Telescope Compact Array (ATCA) from 2004 to 2007. The Bright Source Sample (BSS) is a complete flux-limited subsample of the AT20G Survey catalogue comprising 320 extragalactic (|b|>1.5 deg) radio sources south of dec = -15 deg with S(20 GHz) > 0.50 Jy. Of these, 218 have near simultaneous observations at 8 and 5 GHz. In this paper we present an analysis of radio spectral properties in total intensity and polarisation, size, optical identifications and redshift distribution of the BSS sources. The analysis of the spectral behaviour shows spectral curvature in most sources with spectral steepening that increases at higher frequencies (the median spectral index \alpha, assuming S\propto \nu^\alpha, decreases from \alpha_{4.8}^{8.6}=0.11 between 4.8 and 8.6 GHz to \alpha_{8.6}^{20}=-0.16 between 8.6 and 20 GHz), even if the sample is dominated by flat spectra sources (85 per cent of the sample has \alpha_{8.6}^{20}>-0.5). The almost simultaneous spectra in total intensity and polarisation allowed us a comparison of the polarised and total intensity spectra: polarised fraction slightly increases with frequency, but the shapes of the spectra have little correlation. Optical identifications provided an estimation of redshift for 186 sources with a median value of 1.20 and 0.13 respectively for QSO and galaxies.Comment: 34 pages, 19 figures, tables of data included, replaced with version published in MNRA

The Australia Telescope 20 GHz Survey: The Source Catalogue

We present the full source catalogue from the Australia Telescope 20 GHz (AT20G) Survey. The AT20G is a blind radio survey carried out at 20 GHz with the Australia Telescope Compact Array (ATCA) from 2004 to 2008, and covers the whole sky south of declination 0 deg. The AT20G source catalogue presented here is an order of magnitude larger than any previous catalogue of high-frequency radio sources, and includes 5890 sources above a 20 GHz flux-density limit of 40 mJy. All AT20G sources have total intensity and polarisation measured at 20 GHz, and most sources south of declination -15 deg also have near-simultaneous flux-density measurements at 5 and 8 GHz. A total of 1559 sources were detected in polarised total intensity at one or more of the three frequencies. We detect a small but significant population of non-thermal sources that are either undetected or have only weak detections in low-frequency catalogues. We introduce the term Ultra-Inverted Spectrum (UIS) to describe these radio sources, which have a spectral index alpha(5, 20) > +0.7 and which constitute roughly 1.2 per cent of the AT20G sample. The 20 GHz flux densities measured for the strongest AT20G sources are in excellent agreement with the WMAP 5-year source catalogue of Wright et al. (2009), and we find that the WMAP source catalogue is close to complete for sources stronger than 1.5 Jy at 23 GHz.Comment: 21 pages, accepted for publication in MNRA

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.

Asthma is a common disease with a complex risk architecture including both genetic and environmental factors. We performed a meta-analysis of North American genome-wide association studies of asthma in 5,416 individuals with asthma (cases) including individuals of European American, African American or African Caribbean, and Latino ancestry, with replication in an additional 12,649 individuals from the same ethnic groups. We identified five susceptibility loci. Four were at previously reported loci on 17q21, near IL1RL1, TSLP and IL33, but we report for the first time, to our knowledge, that these loci are associated with asthma risk in three ethnic groups. In addition, we identified a new asthma susceptibility locus at PYHIN1, with the association being specific to individuals of African descent (P = 3.9 × 10(-9)). These results suggest that some asthma susceptibility loci are robust to differences in ancestry when sufficiently large samples sizes are investigated, and that ancestry-specific associations also contribute to the complex genetic architecture of asthma