Phamerator: a bioinformatic tool for comparative bacteriophage genomics

BACKGROUND

Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.

RESULTS

We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.

CONCLUSIONS

Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.

Drowning associated pneumonia: a descriptive cohort

PURPOSE

Pneumonia is the most common infectious complication of drowning. Pneumonia is potentially life threatening and should be treated by effective antibiotic therapy. However the risk factors, microbiological causes, diagnostic approach and appropriate therapy for pneumonia associated with drowning are not well described. The microbiological ecology of the body of water where immersion occurred could be of import. The aim of this study was to report on microorganisms involved in pneumonia associated with drowning and out of hospital cardiac arrest after successful cardiopulmonary resuscitation. Additionally, we retrieved and undertook microbiological analysis on samples of water from our local river.

METHODS

This retrospective study included all patients having suffered an out of hospital cardiac arrest due to drowning and admitted to our tertiary care academic hospital between 2002 and 2010. Data concerning bacteriological lung samples (tracheal aspirate or bronchoalveolar lavage) at admission were reported and compared to bacteriological samples obtained from our local river (the river Seine).

RESULTS

A total of thirty-seven patients were included in the study. Lung samples were obtained for twenty-one of these patients. Lung samples were positive in nineteen cases, with a high frequency of multi-drug resistant bacteria. Samples from the Seine River found microorganisms similar to those found in drowning associated pneumonia.

CONCLUSIONS

Drowning associated pneumonia can be due to multi drug resistant bacteria. When treating drowning associated pneumonia, antibiotics should be effective against bacteria similar to those found in the body of water where immersion occurred.

Do clinicians consider the results of the BinaxNOW Streptococcus pneumoniae urinary antigen test when adapting antibiotic regimens for pneumonia patients?

The BinaxNOW Streptococcus pneumoniae urinary antigen test is a rapid and reliable immunochromatographic test (ICT) for the identification of a pneumococcal aetiology of pneumonia. The aim of this study was to evaluate the attitude of clinicians in their everyday practice towards prescription of the ICT and the impact of its results on the adaptation of the antibiotic therapy when pneumonia is suspected. From October 2007 to March 2008, we prospectively evaluated 541 consecutive inpatients for whom the ICT was performed in our institution. Of the 541 patients evaluated, only 233 (43%) were suspected by the treating physicians to have a pneumonia, 58 of whom had a positive ICT result. Among these 58 patients, four (7%) and 26 (45%), respectively, were treated with amoxycillin monotherapy before and after the ICT result had been obtained (p <10(-4)). Although a positive ICT result led to a rise in the proportion of patients treated with amoxycillin alone, a large number continued to be treated with broader-spectrum antibiotics. These results suggest that prescription monitoring of the ICT should be implemented along with encouragement to adhere more strictly to treatment guidelines.

Corynebacterium jeikeium pacemaker infection associated with antineutrophil cytoplasmic antibodies: a single positive blood culture could be sufficient for diagnosis

Corynebacterium jeikeium, a member of the non-diphtheria corynebacteria, has been rarely reported as being responsible for cardiovascular-device infection. Here, we report what is believed to be the first case of C. jeikeium pacemaker infection associated with the presence of proteinase-3 antineutrophil cytoplasmic antibodies. The diagnosis was established based on the positivity of a single positive blood culture and led to pacemaker extraction. This observation highlights the difficulty in the diagnosis of cardiac-device infection in the presence of a single positive blood culture with a fastidious microorganism that could be considered as a contaminant. It also underscores the need for device extraction to ensure healing.

Trajectories of alcohol consumption following liver transplantation

Any use of alcohol in the years following liver transplantation (LTX) approaches 50% of patients transplanted for alcoholic liver disease (ALD). We collected detailed prospective data on alcohol consumption following LTX for ALD to investigate ongoing patterns of use. Using trajectory modeling we identified four distinct alcohol use trajectories. One group had minimal use over time. Two other groups developed early onset moderate-to-heavy consumption and one group developed late onset moderate use. These trajectories demonstrate that alcohol use varies based on timing of onset, quantity and duration. Using discriminant function analysis, we examine characteristics of recipient's pre-LTX alcohol histories and early post-LTX psychological stressors to identify the profile of those at risk for these specific trajectories. We discuss the relevance of these findings to clinical care and preliminarily to outcomes.

[Bacteriological study of ethmoid specimens from patients with nasal polyposis after ethmoidal surgery]

OBJECTIVE

To compare the bacteriological and clinical findings in ethmoid specimens from patients with nasal polyposis after radical ethmoidal surgery.

PATIENTS AND METHODS

From June to November 2008, 60 patients were prospectively included. For each patient, two samples for each ethmoidal cavity were taken. Aerobic and anaerobic bacterial cultures and fungal cultures were processed and the antibiotic susceptibility was evaluated for each isolated bacterial strain.

RESULTS

Pathogenic bacteria were isolated in 48 patients (80%) including predominantly Staphylococcus aureus (60%) or a Gram-negative bacterium. The microorganisms were nearly all susceptible to antibiotics, including the aminoglycosides. No correlation between the presence of pathogenic bacteria and the clinical status of the patients was found.

CONCLUSION

In this study, a great number of patients was colonized with pathogenic bacteria. However, the presence of pathogenic bacteria was not correlated with the clinical status of the patients.

Complex physiological traits as biomarkers of the sub-lethal toxicological effects of pollutant exposure in fishes

Complex physiological traits, such as routine aerobic metabolic rate or exercise performance, are indicators of the functional integrity of fish that can reveal sub-lethal toxicological effects of aquatic pollutants. These traits have proved valuable in laboratory investigations of the sub-lethal effects of heavy metals, ammonia and various xenobiotics. It is not known, however, whether they can also function as biomarkers of the complex potential range of effects upon overall functional integrity caused by exposure to mixtures of chemicals in polluted natural environments. The current study used portable swimming respirometers to compare exercise performance and respiratory metabolism of fish exposed in cages for three weeks to either clean or polluted sites on three urban European river systems: the river Lambro, Milan, Italy; the rivers Blythe, Cole and Tame, Birmingham, UK; and the river Amstel, Amsterdam, The Netherlands. The UK and Italian rivers were variously polluted with high levels of both bioavailable heavy metals and organics, and the Amstel by mixtures of bioavailable organics at high concentrations. In both the UK and Italy, indigenous chub (Leuciscus cephalus) exposed to clean or polluted sites swam equally well in an initial performance test, but the chub from polluted sites could not repeat this performance after a brief recovery interval. These animals were unable to raise the metabolic rate and allocate oxygen towards exercise in the second trial, an effect confirmed in successive campaigns in Italy. Swimming performance was therefore a biomarker indicator of pollutant exposure in chub exposed at these sites. Exposure to polluted sites on the river Amstel did not affect the repeat swimming performance of cultured cloned carp (Cyprinus carpio), indicating either a species-specific tolerance or relative absence of heavy metals. However, measurements of oxygen uptake during swimming revealed increased rates of routine aerobic metabolism in both chub and carp at polluted sites in all of the rivers studied, indicating a sub-lethal metabolic loading effect. Therefore, the physiological traits of exercise performance and metabolic rate have potential as biomarkers of the overall sub-lethal toxic effects of exposure to complex mixtures of pollutants in rivers, and may also provide insight into why fish do not colonize some polluted environments.

Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus

Four cytokine receptor genes are located on Chr21q22.11, encoding the alpha and beta subunits of the interferon-alpha receptor (IFNAR1 and IFNAR2), the beta subunit of the interleukin 10 receptor (IL10RB) and the second subunit of the interferon-gamma receptor (IFNGR2). We previously reported that two variants in IFNAR1 were associated with susceptibility to malaria in Gambians. We now present an extensive fine-scale mapping of the associated region utilizing 45 additional genetic markers obtained from public databases and by sequencing a 44 kb region in and around the IFNAR1 gene in 24 Gambian children (12 cases/12 controls). Within the IFNAR1 gene, a newly studied C --> G single-nucleotide polymorphism (IFNAR1 272354c-g) at position -576 relative to the transcription start was found to be more strongly associated with susceptibility to severe malaria. Association was observed in three populations: in Gambian (P=0.002), Kenyan (P=0.022) and Vietnamese (P=0.005) case-control studies. When all three studies were combined, using the Mantel-Haenszel test, the presence of IFNAR1 -576G was associated with a substantially elevated risk of severe malaria (N=2444, OR=1.38, 95% CI: 1.17-1.64; P=1.7 x 10(-4)). This study builds on previous work to further highlight the importance of the type-I interferon pathway in malaria susceptibility and illustrates the utility of typing SNPs within regions of high linkage disequilibrium in multiple populations to confirm initial positive associations.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Identification of higher-order functional domains in the human ENCODE regions

It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. We hypothesized that diverse experimental data types generated by The ENCODE Project Consortium could be combined to delineate active and quiescent or repressed functional domains and thereby illuminate the higher-order functional architecture of the genome. To address this, we coupled wavelet analysis with hidden Markov models for unbiased discovery of "domain-level" behavior in high-resolution functional genomic data, including activating and repressive histone modifications, RNA output, and DNA replication timing. We find that higher-order patterns in these data types are largely concordant and may be analyzed collectively in the context of HeLa cells to delineate 53 active and 62 repressed functional domains within the ENCODE regions. Active domains comprise approximately 44% of the ENCODE regions but contain approximately 75%-80% of annotated genes, transcripts, and CpG islands. Repressed domains are enriched in certain classes of repetitive elements and, surprisingly, in evolutionarily conserved nonexonic sequences. The functional domain structure of the ENCODE regions appears to be largely stable across different cell types. Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture.

Unsupervised segmentation of continuous genomic data

The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line utility for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs). Scale specificity is achieved by an optional wavelet-based smoothing operation. HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data.

AVAILABILITY

http://noble.gs.washington.edu/proj/hmmseg

In vitro-clinical correlations for amphotericin B susceptibility in AIDS-associated cryptococcal meningitis

Reliable measures of antifungal drug susceptibility are needed. We tested the susceptibility of Cryptococcus neoformans from patients treated with amphotericin B. In vitro susceptibility employed a modified broth macrodilution method. We demonstrate a strong correlation between the quantitative measures of in vitro amphotericin B susceptibility and the quantitative response observed in patients.

Development and validation of a bioanalytical method using automated solid-phase extraction and LC-UV for the simultaneous determination of lumefantrine and its desbutyl metabolite in plasma

A bioanalytical method for the determination of lumefantrine (LF) and its metabolite desbutyl-lumefantrine (DLF) in plasma by solid-phase extraction (SPE) and liquid chromatography has been developed. Plasma proteins were precipitated with acetonitrile:acetic acid (99:1, v/v) containing a DLF analogue internal standard before being loaded onto a octylsilica (3 M Empore) SPE column. Two different DLF analogues were evaluated as internal standards. The compounds were analysed by liquid chromatography UV detection on a SB-CN (250 mm x 4.6 mm) column with a mobile phase containing acetonitrile-sodium phosphate buffer pH (2.0; 0.1 M) (55:45, v/v) and sodium perchlorate 0.05 M. Different SPE columns were evaluated during method development to optimise reproducibility and recovery for LF, DLF and the two different DLF analogues. The within-day precisions for LF were 6.6 and 2.1% at 0.042 and 8.02 microg/mL, respectively, and for DLF 4.5 and 1.5% at 0.039 and 0.777 microg/mL, respectively. The between-day precisions for LF were 12.0 and 2.9% at 0.042 and 8.02 microg/mL, respectively, while for DLF 0.7 and 1.2% at 0.039 and 0.777 microg/mL, respectively. The limit of quantification was 0.024 and 0.021 microg/mL for LF and DLF, respectively. Different amounts of lipids in plasma did not affect the absolute recovery of LF or DLF.

The effects of acclimation to reversed seasonal temperatures on the swimming performance of adult brown trout Salmo trutta

Adult brown trout (Salmo trutta) were acclimatised to and maintained at seasonal temperatures (5 degrees C in winter; 15 degrees C in summer) and acclimated to reversed seasonal temperatures (15 degrees C in winter; 5 degrees C in summer) while exposed to the natural (i.e. seasonally variable) photoperiod. The mean critical swimming speeds (U(crit)) of animals acclimatised to the seasonal temperatures were similar, but more than 30% greater than those for fish acclimated to the reversed seasonal temperatures. The lower values of U(crit) that accompanied acclimation to reversed seasonal temperatures appeared largely to result from the inability of white muscle to function maximally, since the concentrations of lactate and ammonia in white muscle of fish swum to U(crit) at reversed seasonal temperatures were significantly lower than those in fish swum at seasonal temperatures. These observations, together with biochemical and morphometric attributes of muscle tissue, suggest that swimming ability is influenced, at least in part, by seasonal factors other than temperature. These data have important implications for the design of experiments using fish that experience predictable, usually seasonal, changes in their natural environment (temperature, dissolved oxygen, changes in water levels, etc.).

Minor physical anomalies are not increased in the offspring of mothers with systemic lupus erythematosus

OBJECTIVE

To determine the incidence and type of minor physical anomalies (MPAs) in infants born to mothers with systemic lupus erythematosus (SLE).

METHODS

Each trimester, pregnant women with SLE were assessed for disease activity, prescribed drug use, and exposure to tobacco, alcohol, and illicit drugs through a self reported questionnaire. Infant examinations were performed on 30/39 (77%) live births in women with SLE and the incidence of MPAs determined.

RESULTS

2/30 (7%) patients had three or more MPAs; 4 (13%) had two; 7 (23%) had one; and 17 (57%) had none. One in three women reported alcohol, tobacco, and illicit drug use. Facial anomalies were the most common MPAs. The relative risk and 95% confidence interval for any MPA were 2.05 (0.99 to 4.26) for tobacco use; 1.95 (0.92 to 4.11) for alcohol use; 1.36 (0.165 to 11.23) for maternal disease flare; 0.63 (0.27 to 1.47) for prednisone use; and 0.72 (0.21 to 2.44) for aspirin use.

CONCLUSION

13/30 (43%) infants had minor anomalies-a similar incidence to that of the general population. Counselling for preventable self reported exposure is advisable in addition to counselling specifically for lupus management during pregnancy.

Area deprivation predicts lung function independently of education and social class

The cross-sectional association between socioeconomic status (at both the individual and area-based level) and lung function, as measured by forced expiratory volume in one second, in a large population-based cohort was investigated. The study population consisted of 22,675 males and females aged 39-79 yrs. They were recruited from the general community in Norfolk, UK using general practice age/sex registers, as part of the European Prospective Investigation into Cancer (EPIC-Norfolk). It was found that being in a manual occupational social class, having no educational qualifications and living in a deprived area all independently predicted significantly lower lung function, even after controlling for smoking habit. The influence of area-deprivation on lung function, independent of individual socioeconomic status and of individual smoking habit, suggests that apart from targeting individuals who are at high-risk, such as smokers, environmental determinants also need to be examined when considering measures to improve respiratory health.

Vitamin C and the risk of developing inflammatory polyarthritis: prospective nested case-control study

OBJECTIVE

To investigate whether, there is an association between consumption of fruit and vegetables and dietary antioxidants and the risk of developing inflammatory polyarthritis (IP).

METHODS

In a prospective, population based, nested case-control study of residents of Norfolk, UK, men and women aged 45-74 years were recruited, between 1993 and 1997 through general practice age-sex registers to the Norfolk arm of the European Prospective Investigation of Cancer (EPIC-Norfolk). Dietary intake was assessed at baseline using 7 day diet diaries. Seventy three participants who went on to develop IP between 1993 and 2001 and were registered by the Norfolk Arthritis Register (NOAR) were identified. Incident cases of IP, assessed by general practitioners, fulfilled the criteria of two or more swollen joints, persisting for a minimum of 4 weeks. Each case of IP was matched for age and sex with two controls free of IP.

RESULTS

Lower intakes of fruit and vegetables, and vitamin C were associated with an increased risk of developing IP. Those in the lowest category of vitamin C intake, compared with the highest, increased their risk of developing IP more than threefold, adjusted odds ratio (OR) with 95% confidence intervals (CI) 3.3 (95% CI 1.4 to 7.9). Weak inverse associations between vitamin E and beta-carotene intake and IP risk were found.

CONCLUSION

Patients with IP (cases) consumed less fruit and vitamin C than matched controls, which appeared to increase their risk of developing IP. The mechanism for this effect is uncertain. Thus similar studies are necessary to confirm these results.

Abdominal obesity and respiratory function in men and women in the EPIC-Norfolk Study, United Kingdom

Poor respiratory function and obesity are associated with all-cause and cardiovascular disease mortality. Obese persons may also have impaired lung function, but the mechanism is unclear. The authors investigated the relation between abdominal pattern of obesity and respiratory function in the European Prospective Investigation into Cancer and Nutrition-Norfolk (EPIC-Norfolk) cohort in Norfolk, United Kingdom. This analysis included 9,674 men and 11,876 women aged 45-79 years with no known preexisting serious illness who had complete anthropometric and respiratory function measures obtained at a health visit between 1993 and 1997. Waist:hip ratio was used to assess abdominal obesity, and forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC), obtained by spirometry, were used to assess respiratory function. Both FEV1 and FVC were linearly and inversely related across the entire range of waist:hip ratio in both men and women. This relation persisted after adjustment for age, body mass index, cigarette smoking, social class, physical activity index, prevalent bronchitis/emphysema, and prevalent asthma. The association remained significant among nonobese nonsmokers without preexisting respiratory disease. In the general adult population, abdominal fat deposition may play a role in the impairment of respiratory function among the abdominally obese.