Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa.

A series of extensively drug-resistant isolates of Pseudomonas aeruginosa from two outbreaks in UK hospitals were characterized by whole genome sequencing (WGS). Although these isolates were resistant to antibiotics other than colistin, we confirmed that they are still sensitive to disinfectants. The sequencing confirmed that isolates in the larger outbreak were serotype O12, and also revealed that they belonged to sequence type ST111, which is a major epidemic strain of P. aeruginosa throughout Europe. As this is the first reported sequence of an ST111 strain, the genome was examined in depth, focusing particularly on antibiotic resistance and potential virulence genes, and on the reported regions of genome plasticity. High degrees of sequence similarity were discovered between outbreak isolates collected from recently infected patients, isolates from sinks, an isolate from the sewer, and a historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years. The ability to translate easily from outbreak investigation to detailed genome biology by use of the same data demonstrates the flexibility of WGS application in a clinical setting.

Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains.

Clostridium difficile is the most frequent cause of nosocomial diarrhea worldwide, and recent reports suggested the emergence of a hypervirulent strain in North America and Europe. In this study, we applied comparative phylogenomics (whole-genome comparisons using DNA microarrays combined with Bayesian phylogenies) to model the phylogeny of C. difficile, including 75 diverse isolates comprising hypervirulent, toxin-variable, and animal strains. The analysis identified four distinct statistically supported clusters comprising a hypervirulent clade, a toxin A(-) B(+) clade, and two clades with human and animal isolates. Genetic differences among clades revealed several genetic islands relating to virulence and niche adaptation, including antibiotic resistance, motility, adhesion, and enteric metabolism. Only 19.7% of genes were shared by all strains, confirming that this enteric species readily undergoes genetic exchange. This study has provided insight into the possible origins of C. difficile and its evolution that may have implications in disease control strategies.

The relationship of medical, demographic and psychosocial factors to direct and indirect health utility instruments in rheumatoid arthritis.

OBJECTIVES: Cost-effectiveness analysis (CEA) is essential for the comparison of treatments for rheumatoid arthritis (RA). CEA centres on accurate measurement of health utility (HU) preferences. Direct measures of HU in RA patients demonstrate weaker correlations with health status (functional disability and pain) than indirect measures. We examined whether demographic and psychosocial factors relate to HU in RA patients. METHODS: HU was measured for 142 RA patients (76% women; mean age 58.75 yr) directly through standard gamble (SG) and time trade-off (TTO), and indirectly on the EuroQol (EQ-5D). Current pain (100 mm visual analogue scale) and recent functional disability (Health Assessment Questionnaire; HAQ) were assessed. A subsample of 48 provided demographic and psychosocial information (education, employment, marital/family status, knowledge about RA, medication beliefs, desirable responding, social support, optimism, and the Hospital Anxiety and Depression Scale; HADS). RESULTS: Direct HU had higher means (SG = 0.88, TTO = 0.86) than indirect HU (EQ-5D = 0.52). HAQ functional disability correlated with SG (r = - 0.28), TTO (r = - 0.31) and EQ-5D (r = - 0.67). Current pain correlated with TTO (r = - 0.19) and EQ-5D (r = - 0.36). HADS depression correlated with TTO (r = - 0.35) and EQ-5D (r = - 0.64); HADS anxiety also correlated with EQ-5D (r = - 0.46). CONCLUSIONS: Demographic and psychosocial factors cannot completely explain either the significant differences between direct and indirect HUs in RA patients or the moderate correlations of direct HUs with health status. Characteristics of the SG and TTO may make them inappropriate for HU assessment and CEA among RA patients.

Use of a corporate needs assessment to define the information requirements of an arthritis resource centre in Birmingham: comparison of patients' and professionals' views.

OBJECTIVES: Education and information are important components of the management of chronic disease, though provision of these in the routine clinic setting may be suboptimal. We carried out a corporate needs assessment, both to evaluate stakeholders' perceived usefulness of potential facilities that could be offered by a community-based arthritis resource centre in Birmingham and to compare the views of patients with rheumatological conditions and health professionals. METHODS: Rheumatology patients (n = 201 responders/309 contacted) and health professionals (n = 232/430) were asked to complete a questionnaire to assess both current rheumatology service provision and perceived needs for further information that could be offered within the proposed resource centre. Views of patients and professionals were compared using odds ratios. Logistic regression analysis determined patient characteristics associated with perceived usefulness of various information types. RESULTS: The overall response rate was 58%. Most patients were currently receiving medication but only 38% received written information on arthritis. Over 80% of responders felt that more information would be useful, particularly information in written leaflets. Compared with professionals, patients gave higher value to certain types of medical, non-medical, support and skills information, particularly individual information from trained volunteers, and specific information on benefits, diet and alternative therapy, and symptom management. Non-Caucasian patients gave higher value to the provision of material in different languages and the availability of multilingual volunteer staff. CONCLUSION: Rheumatology patients and professionals identified a relative lack of information for patients. There was wide interest in the provision of more information, with value placed on the provision of material in different languages, at an educational resource centre. This work has been used to develop the facilities currently offered at the Birmingham Arthritis Resource Centre. Further research is needed to investigate the effectiveness of the provision of good quality information to patients with arthritis.

A two-component system that controls the expression of pneumococcal surface antigen A (PsaA) and regulates virulence and resistance to oxidative stress in Streptococcus pneumoniae.

Recent genomic-based studies have identified 13 two-component signal transduction systems (TCS) in Streptococcus pneumoniae. Bacterial TCSs are important for regulating expression of bacterial genes, including those which are important to the virulence of pathogenic bacteria. We have used virulence assays together with microarray analysis to investigate the importance of pneumococcal TCS04 in the virulence and gene regulation of this pathogen. Deletion mutants of the response regulator of TCS04, rr04, were examined in three independent pneumococcal strains representing three different pneumococcal serotypes. Analysis of the virulence of the three strains enabled us to identify a serotype-specific attenuation of virulence due to deletion of rr04. Microarray comparison of the transcriptional profiles of the wild-type strains with the rr04 mutants allowed us to determine which transcriptional changes were occurring in the rr04 mutants. Virulence-associated changes were demonstrated in the attenuated strain with significant downregulation of a previously determined virulence locus, psaB, psaC and psaA.

Determining liver stage parasite burden by real time quantitative PCR as a method for evaluating pre-erythrocytic malaria vaccine efficacy.

The detection and quantitation of blood stage parasitaemia is typically used as a surrogate endpoint for estimating the efficacy of vaccines targeted against the hepatic stage, as well as the erythrocytic stage, of the parasite. However, this does not provide an adequate means of evaluating the efficacy of vaccines, which may be only partially effective at the liver-stage. This is a particular concern for effective evaluation of immune enhancement strategies for candidate pre-erythrocytic stage vaccines. Here, we have developed and validated a method for detecting and quantitating liver stage parasites, using the TaqMan fluorescent real-time quantitative PCR system (PE Applied Biosystems). This method uses TaqMan primers designed to the Plasmodium yoelii 18S rRNA gene and rodent GAPDH to amplify products from infected mouse liver cDNA. The technique is highly reproducible as demonstrated with plasmid controls and capable of efficiently quantitating liver-stage parasite burden following a range of sporozoite challenge doses in strains of mice, which differ in their susceptibility to sporozoite infection. We have further demonstrated the capacity of this technique to evaluate the efficacy of a range of pre-erythrocytic stage vaccines. Our data establish this quantitative real-time PCR assay to be a fast and reproducible way of accurately assessing liver stage parasite burden and vaccine efficacy in rodent malaria models.

Immunogenicity and protective efficacy of a Plasmodium yoelii Hsp60 DNA vaccine in BALB/c mice.

The gene encoding the 60-kDa heat shock protein of Plasmodium yoelii (PyHsp60) was cloned into the VR1012 and VR1020 mammalian expression vectors. Groups of 10 BALB/c mice were immunized intramuscularly at 0, 3, and 9 weeks with 100 microg of PyHsp60 DNA vaccine alone or in combination with 30 microg of pmurGMCSF. Sera from immunized mice but not from vector control groups recognized P. yoelii sporozoites, liver stages, and infected erythrocytes in an indirect fluorescent antibody test. Two weeks after the last immunization, mice were challenged with 50 P. yoelii sporozoites. In one experiment the vaccine pPyHsp60-VR1012 used in combination with pmurGMCSF gave 40% protection (Fisher's exact test; P = 0.03, vaccinated versus control groups). In a second experiment this vaccine did not protect any of the immunized mice but induced a delay in the onset of parasitemia. In neither experiment was there any evidence of a protective effect against the asexual erythrocytic stage of the life cycle. In a third experiment mice were primed with PyHsp60 DNA, were boosted 2 weeks later with 2 x 10(3) irradiated P. yoelii sporozoites, and were challenged several weeks later. The presence of PyHsp60 in the immunization regimen did not lead to reduced blood-stage infection or development of parasites in hepatocytes. PyHsp60 DNA vaccines were immunogenic in BALB/c mice but did not consistently, completely protect against sporozoite challenge. The observation that in some of the PyHsp60 DNA vaccine-immunized mice there was protection against infection or a delay in the onset of parasitemia after sporozoite challenge deserves further evaluation.

The influence of previous experience on predictive motor control.

Anticipating the consequences of our motor commands is a fundamental component of sensorimotor control. For example, when one hand pulls on an object held in the other, the restraining hand generates an anticipatory increase in grip force thereby preventing the object from slipping. To investigate how such anticipation is learned subjects held an object, whose properties were under computer control, between their hands. This allowed instant changes in the behaviour of the manipulated object on a trial by trial basis. The extent of grip force modulation seen in one hand, when the other pulled on the object was found to depend in a systematic way on the object's properties experienced over at least the previous three trials.

Learning and decay of prediction in object manipulation.

Anticipating the consequences of our own actions is a fundamental component of normal sensorimotor control and is seen, for example, during the manipulation of objects. When one hand pulls on an object held in the other hand, there is an anticipatory increase in grip force in the restraining hand that prevents the object from slipping. This anticipation is thought to rely on a forward internal model of the manipulated object and motor system, enabling the prediction of the consequences of our motor commands. Here we investigate the development of such a predictive response. Each hand held an object that was attached to its own torque motor. On each trial the subject was required to pull on the object held in the left hand and to maintain the position of the object held in the right hand. The torque motors were computer controlled so that the objects could be either "linked" so that the forces on the objects were equal and opposite, acting as though they were a single object, or "unlinked," so that they acted as two independent objects. A predictive response in the restraining hand is only necessary when the objects are linked and is unnecessary in the unlinked condition where there is no risk of the object slipping. To examine the learning and decay of predictive responses, we measured the grip force responses during unlinked trials that followed a linked trial. After a single linked trial, anticipatory grip force was quick to develop, but decayed slowly over the following unlinked trials. Varying the time between trials showed that the rate of decay depended on the number of trials since the last linked trial rather than time. Increasing the frequency of linked trials showed an increased level of subsequent grip force modulation, but did not alter the decay rate. When the torque motors simulated a linked object that did not have normal physical properties, prediction was reduced. These results show that the use of predictive responses has a different time course for learning and decay, and the response depends on experience and the physical properties of the objects.

Guanylyl cyclase activity associated with putative bifunctional integral membrane proteins in Plasmodium falciparum.

We report here that guanylyl cyclase activity is associated with two large integral membrane proteins (PfGCalpha and PfGCbeta) in the human malaria parasite Plasmodium falciparum. Unusually, the proteins appear to be bifunctional; their amino-terminal regions have strong similarity with P-type ATPases, and the sequence and structure of the carboxyl-terminal regions conform to that of G protein-dependent adenylyl cyclases, with two sets of six transmembrane sequences, each followed by a catalytic domain (C1 and C2). However, amino acids that are enzymatically important and present in the C2 domain of mammalian adenylyl cyclases are located in the C1 domain of the P. falciparum proteins and vice versa. In addition, certain key residues in these domains are more characteristic of guanylyl cyclases. Consistent with this, guanylyl cyclase activity was obtained following expression of the catalytic domains of PfGCbeta in Escherichia coli. In P. falciparum, expression of both genes was detectable in the sexual but not the asexual blood stages of the life cycle, and PfGCalpha was localized to the parasite/parasitophorous vacuole membrane region of gametocytes. The profound structural differences identified between mammalian and parasite guanylyl cyclases suggest that aspects of this signaling pathway may be mechanistically distinct.

gammadelta T cells are a component of early immunity against preerythrocytic malaria parasites.

We tested the hypothesis that gammadelta T cells are a component of an early immune response directed against preerythrocytic malaria parasites that are required for the induction of an effector alphabeta T-cell immune response generated by irradiated-sporozoite (irr-spz) immunization. gammadelta T-cell-deficient (TCRdelta(-/-)) mice on a C57BL/6 background were challenged with Plasmodium yoelii (17XNL strain) sporozoites, and then liver parasite burden was measured at 42 h postchallenge. Liver parasite burden was measured by quantification of parasite-specific 18S rRNA in total liver RNA by quantitative-competitive reverse transcription-PCR and by an automated 5' exonuclease PCR. Sporozoite-challenged TCRdelta(-/-) mice showed a significant (P < 0.01) increase in liver parasite burden compared to similarly challenged immunocompetent mice. In support of this result, TCRdelta(-/-) mice were also found to be more susceptible than immunocompetent mice to a sporozoite challenge when blood-stage parasitemia was used as a readout. A greater percentage of TCRdelta(-/-) mice than of immunocompetent mice progressed to a blood-stage infection when challenged with five or fewer sporozoites (odds ratio = 2.35, P = 0.06). TCRdelta(-/-) mice receiving a single irr-spz immunization showed percent inhibition of liver parasites comparable to that of immunized immunocompetent mice following a sporozoite challenge. These data support the hypothesis that gammadelta T cells are a component of early immunity directed against malaria preerythrocytic parasites and suggest that gammadelta T cells are not required for the induction of an effector alphabeta T-cell immune response generated by irr-spz immunization.

Predictive motor learning of temporal delays.

Anticipatory responses can minimize the disturbances that result from the action of one part of the body on another. Such a predictive response is evident in the anticipatory increase in grip force seen when one hand pulls on an object held in the other hand, thereby preventing the object from slipping. It is postulated that such a response depends on predicting the consequences of the descending motor command, as signaled by efference copy, using an internal model of both one's own body and the object. Here we investigate how the internal model learns the temporal consequences of the motor command. We employed two robots to simulate a virtual object held in one hand and acted on by the other. Delays were introduced between the action of one hand on the object and the effects of this action on the other hand. An initial reactive grip force response to the delayed load decayed with the development of appropriate anticipatory grip force modulation. However, no predictive modulation was seen when the object's movement was not generated by the subject, even when the motion was cued by a tone. These results suggest that, when an internal model learns new temporal relationships between actions and their consequences, this learning involves generating a novel response rather than adapting the original predictive response.