Integrated structure-based protein interface prediction.

BACKGROUND: Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents. A variety of computational approaches have been developed for predicting a protein's interfacial residues from its known sequence and structure. Methods using the known three-dimensional structures of proteins can be template-based or template-free. Template-based methods have limited success in predicting interfaces when homologues with known complex structures are not available to use as templates. The prediction performance of template-free methods that only rely only upon proteins' intrinsic properties is limited by the amount of biologically relevant features that can be included in an interface prediction model. RESULTS: We describe the development of an integrated method for protein interface prediction (ISPIP) to explore the hypothesis that the efficacy of a computational prediction method of protein binding sites can be enhanced by using a combination of methods that rely on orthogonal structure-based properties of a query protein, combining and balancing both template-free and template-based features. ISPIP is a method that integrates these approaches through simple linear or logistic regression models and more complex decision tree models. On a diverse test set of 156 query proteins, ISPIP outperforms each of its individual classifiers in identifying protein binding interfaces. CONCLUSIONS: The integrated method captures the best performance of individual classifiers and delivers an improved interface prediction. The method is robust and performs well even when one of the individual classifiers performs poorly on a particular query protein. This work demonstrates that integrating orthogonal methods that depend on different structural properties of proteins performs better at interface prediction than any individual classifier alone.

A head-to-head comparison of hydrogen peroxide vapor and aerosol room decontamination systems.

OBJECTIVE: New technologies have emerged in recent years for the disinfection of hospital rooms and equipment that may not be disinfected adequately using conventional methods. There are several hydrogen peroxide-based area decontamination technologies on the market, but no head-to-head studies have been performed. DESIGN: We conducted a head-to-head in vitro comparison of a hydrogen peroxide vapor (HPV) system (Bioquell) and an aerosolized hydrogen peroxide (aHP) system (Sterinis). SETTING: The tests were conducted in a purpose-built 136-m(3) test room. METHODS: One HPV generator and 2 aHP machines were used, following recommendations of the manufacturers. Three repeated tests were performed for each system. The microbiological efficacy of the 2 systems was tested using 6-log Tyvek-pouched Geobacillus stearothermophilus biological indicators (BIs). The indicators were placed at 20 locations in the first test and 14 locations in the subsequent 2 tests for each system. RESULTS: All BIs were inactivated for the 3 HPV tests, compared with only 10% in the first aHP test and 79% in the other 2 aHP tests. The peak hydrogen peroxide concentration was 338 ppm for HPV and 160 ppm for aHP. The total cycle time (including aeration) was 3 and 3.5 hours for the 3 HPV tests and the 3 aHP tests, respectively. Monitoring around the perimeter of the enclosure with a handheld sensor during tests of both systems did not identify leakage. CONCLUSION: One HPV generator was more effective than 2 aHP machines for the inactivation of G. stearothermophilus BIs, and cycle times were faster for the HPV system.

Prevalence of faecal ESBL carriage in the community and in a hospital setting in a county of Southern Sweden.

The aim of this study was to investigate the prevalence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in patients at various hospital wards and in a group of relatively healthy volunteers, in order to obtain greater knowledge on how common these bacterial strains are in hospital settings and in the general community. Participants (n = 427) were enrolled at a University Hospital and at Primary Health Care Units (PHCUs) in Sweden in 2008 and 2010. The participants provided rectal swabs, which were tested for the occurrence of ESBL-producing bacteria. Positive samples were analysed with polymerase chain reaction (PCR) methods for bacterial strain typing and ESBL phylogroups. In 2008, the prevalence was 2.1% (2/96) in PHCU subjects and 1.8% (2/113) in hospital patients. In 2010, the prevalence was 3.0% (3/100) in PHCU subjects and 6.8% (8/118) in hospital patients. The dominating phylogroups were CTX-M-1 and CTX-M-9. All ESBL-positive isolates were Escherichia coli. We found a higher prevalence of ESBL faecal carriage than expected, both in the hospital setting and in the PHCU group.

Reducing blood culture contamination by a simple informational intervention.

Compared to truly negative cultures, false-positive blood cultures not only increase laboratory work but also prolong lengths of patient stay and use of broad-spectrum antibiotics, both of which are likely to increase antibiotic resistance and patient morbidity. The increased patient suffering and surplus costs caused by blood culture contamination motivate substantial measures to decrease the rate of contamination, including the use of dedicated phlebotomy teams. The present study evaluated the effect of a simple informational intervention aimed at reducing blood culture contamination at Skåne University Hospital (SUS), Malmö, Sweden, during 3.5 months, focusing on departments collecting many blood cultures. The main examined outcomes of the study were pre- and postintervention contamination rates, analyzed with a multivariate logistic regression model adjusting for relevant determinants of contamination. A total of 51,264 blood culture sets were drawn from 14,826 patients during the study period (January 2006 to December 2009). The blood culture contamination rate preintervention was 2.59% and decreased to 2.23% postintervention (odds ratio, 0.86; 95% confidence interval, 0.76 to 0.98). A similar decrease in relevant bacterial isolates was not found postintervention. Contamination rates at three auxiliary hospitals did not decrease during the same period. The effect of the intervention on phlebotomists' knowledge of blood culture routines was also evaluated, with a clear increase in level of knowledge among interviewed phlebotomists postintervention. The present study shows that a relatively simple informational intervention can have significant effects on the level of contaminated blood cultures, even in a setting with low rates of contamination where nurses and auxiliary nurses conduct phlebotomies.

[Systemic sclerosis. Objectives for the treatment]. / Systemische Sklerose. Zielkriterien der Behandlung.

Systemic sclerosis (SSc) is a multi-systemic fibrotic disorder with worldwide distribution and high morbidity and mortality. Characteristic features of this disease are widespread vasculopathy, inflammation, autoimmunity, and fibrosis. The better clinical outcome in recent years is mainly due to better management of organ complications. To date, there is no approved specific therapy to prevent or slow down the overall progression of the disease. So far, conventional disease-modifying antirheumatic drugs (DMARDs) have had no major impact on the disease course and have not prolonged survival. Based on recent studies of molecular pathomechanisms and various animal models, key molecules of fibrogenesis and vasculopathy in SSc could be identified. Therefore, to date, we have to reconsider and redefine the objectives of our treatment strategies. In this article, we discuss current and future therapeutic concepts as well as the objectives of new treatment strategies and of the evaluation of diagnostic tools with respect to pulmonary arterial hypertension, lung fibrosis and skin/systemic fibrosis.

Electroosmotic flow patterning using microfluidic delay loops.

A theoretical and experimental investigation of alternating electroosmotic flow patterns by means of specially designed delay loops is presented. Using elementary methods of compact network modeling and detailed FEM simulations the flow behavior and, in particular, the rearrangement of sample plugs is modeled. The proposed designs rely on flow splitting in combination with electroosmotic delay loops leading to a runtime difference or phase shift between two sub-streams. Due to this phase shift, a new fluid interface is generated at the merging point. The approach is experimentally validated by injection of a Rhodamine 6G solution into an aqueous sodium tetraborate buffer.

Renal pathology and premortem clinical presentation of Caucasian patients with AIDS: an autopsy study from the era prior to antiretroviral therapy.

PRINCIPLES: Renal disease in patients with HIV infection is becoming increasingly frequent. A particular form of HIV-associated nephropathy (HIVAN) has been found in patients of predominantly African-American and Hispanic origin. However, only limited data are available on renal pathology and premortem clinical presentation of kidney disease in Caucasian patients with AIDS. METHODS: To determine the prevalence, clinical presentation and aetiology of renal disease in Caucasian patients with AIDS at the time of death we have performed a prospective autopsy study with 239 patients who died of AIDS between 1981 and 1989. None of these patients had received HIV-specific antiretroviral therapy. Autopsies and histological analyses were performed on the basis of a standardised protocol. Clinical and laboratory data were gathered according to a uniform questionnaire. RESULTS: 95% of patients were of Caucasian race. 75% of all patients had extended AIDS (stage IV). Clinical signs of nephropathy prior to death were found in 36% of patients, including proteinuria (18%), abnormal urinary sediment (19.5%), and renal insufficiency (11%). Histopathological lesions were present in 43% of the autopsies, with two or more distinct structural lesions in 12.5% of patients. Of the pathological findings 28% were glomerular or vascular, 33% were non-glomerular, and 29% were combined lesions. The remaining 10% were renal infiltrations of infectious agents or neoplastic tissue. The most common findings were ischaemic changes and vascular scars (18% of patients), as well as pyelo- and interstitial nephritides (12.2%). Importantly, FSGS was present in only 1.7% of patients, and only a single African patient had classical HIVAN. CONCLUSIONS: Renal involvement in HIV disease is very common at the time of death among patients of Caucasian origin. However, classical HIV-associated nephropathy is absent in this population. These findings suggest that kidney disease affects all races and supports the hypothesis that HIVAN is specifically related to non-Caucasian ethnicity. The results reflect renal disease unaffected by HIV-specific antiretroviral therapy.

Fewer bacterial relapses after oral treatment with norfloxacin than with ceftibuten in acute pyelonephritis initially treated with intravenous cefuroxime.

This double-blind, multicentre study was performed at nine centres on a total of 171 patients who presented with fever (> 38.5 degrees C) and signs of acute pyelonephritis. All were initially treated with intravenous cefuroxime. After 2-3 d, when the fever had subsided and urinary culture had revealed growth of Gram-negative bacteria ( > 10(7) colony-forming units per litre), treatment was changed to oral administration of ceftibuten 200 mg b.i.d. or norfloxacin 400 mg b.i.d. for 10 d. The patients were followed for signs of bacterial or clinical relapse 7-14 d after the end of treatment. The initial clinical and bacteriological cure was excellent in both groups, but there were significantly fewer bacterial relapses after oral treatment with norfloxacin than with ceftibuten in acute febrile pyelonephritis initially treated with intravenous cefuroxime. The causal strain was eradicated in 75% of patients (73% of males, 76% of females) in the ceftibuten group and in 89% of patients (94% of males, 85% of females) in the norfloxacin group. The relative frequency of eradication was 0.84 (p < 0.05; 95%, confidence interval 0.74-0.97). Adverse events were reported by 47% of the patients in the ceftibuten group and by 38% in the norfloxacin group. This difference was not significant, but diarrhoea or loose stools occurred more frequently in the ceftibuten group.

Alpha1-antitrypsin deficiency may be a risk factor for duodenal ulcer in patients with Helicobacter pylori infection.

BACKGROUND: Most individuals with Helicobacter pylori infection in Western countries have no evidence of peptic ulcer disease (PUD). We therefore assessed the PiZ deficiency variant of the major plasma protease inhibitor alpha1-antitrypsin (alpha1AT) as a risk factor for PUD in H. pylori-infected individuals. METHODS: The cohort comprised 100 patients with endoscopically or surgically proven PUD (30 patients with duodenal ulcer (DU) and 70 patients with gastric ulcer (GU)) and 162 age- and sex-matched controls with PUD-negative endoscopic findings and no history of PUD. Plasma samples were screened for alpha1AT deficiency (PiZ) with an enzyme-linked immunosorbent assay (ELISA) and phenotyped by isoelectric focusing. H. pylori infection was evaluated with an IgG ELISA technique. RESULTS: Among the 262 patients 17 (6.5%) were positive for the PiZ alpha1AT deficiency, a frequency of the same magnitude as in the Swedish general population (4.7%). Of the PiZ carriers 76% (13 of 17) had H. pylori antibodies compared with 61% (151 of 245) of the non-PiZ carriers (NS). The prevalence of DU tended to be higher in H. pylori-positive PiZ carriers than in non-PiZ carriers (15.4%, 4 of 26 versus 0 of 4). Furthermore, among patients with DU a high PiZ allele frequency (13.3%, 4 of 30) was found compared with the general population (4.7%) (odds ratio (OR), 3.2; 95% confidence interval (CI), 1.09-8.94; P = 0.02). All DU patients carrying the PiZ allele were positive for H. pylori. In addition, four of five PiZ carriers with H. pylori infection and PUD had DU. CONCLUSIONS: The PiZ allele may be a contributing factor in the development of DU in H. pylori-positive individuals.

Hypofrontal symptoms from olanzapine: a case report.

Olanzapine acutely induced disabling hypofrontal symptoms in a 31-year-old male. This occurred after 13 years of exposure to typical neuroleptics without such symptoms. Presumably, hypofrontal symptoms should limit the dose of atypical neuroleptics in some patients. Milder expressions of hypofrontal symptoms should be more common.

[Antibiotic resistance of Helicobacter pylori in Malmö. Therapeutic success in spite of antibiotic resistance]. / Antibiotikaresistens hos Helicobacter pylori i Malmö, Behandlingsframgång trots antibiotikaresistens.

Triple therapy (omeprazole, clarithromycin and metronidazole) is associated with a sensitive Helicobacter pylori (HP) eradication rate of over 90 per cent. As treatment failure is mainly due to poor patient compliance, satisfactory patient information is vital. Despite the high prevalence (29-40%) of metronidazole-resistant HP in Malmö, the eradication rate is over 90%. Clarithromycin-resistance among HP strains has increased in prevalence from 1 to 7% over the past four years, and always results in treatment failure. In order to avoid unnecessary antibiotic treatment, especially in cases of patients not responding to triple therapy, it is important to follow treatment up with, for example, the urea breath test.

Trovafloxacin susceptibility of aerobic clinical bacterial isolates from Sweden.

Trovafloxacin susceptibility was studied in aerobic clinical isolates of bacterial pathogens from 5 microbiology laboratories in Sweden. Trovafloxacin and ciprofloxacin minimum inhibitory concentration (MIC) determinations were performed on 474 clinical isolates. Disk diffusion tests using trovafloxacin and ciprofloxacin 10 microg disks were performed on a total of 7142 clinical isolates (trovafloxacin). Susceptibility interpretations for trovafloxacin and ciprofloxacin were determined from MIC values and disk diffusion tests using species-related MIC-limits and zone diameter breakpoints. Eight of 12 gram-positive species groups were fully susceptible to trovafloxacin as judged by MIC tests. Trovafloxacin gave MIC50 values of 0.032 mg/l for S. aureus, 1.0 mg/l for MRSA, 0.064 mg/l for coagulase negative staphylococci, 1.0 mg/l for MRSE, 0.064 mg/l for S. saprophyticus, 0.125 mg/l for group A and group B streptococci, 0.064 mg/l for group C and G streptococci and S. pneumoniae, 0.25 mg/l for E. faecalis, and 16.0 mg/l for E. faecium. These MIC values were 4-16-fold lower than those of ciprofloxacin. Both MIC and disk tests showed similar levels of susceptibility among gram-negative isolates for trovafloxacin and ciprofloxacin. For most gram-negative species the trovafloxacin MIC50 values were similar to or slightly higher than those for ciprofloxacin. Trovafloxacin MIC values were much lower for Acinetobacter strains, but higher for P. mirabilis compared with ciprofloxacin. The favourable susceptibility levels of Swedish aerobic pathogens to trovafloxacin emphasize the potential of this drug for the treatment of serious infections.

Calibration of disk diffusion antibiotic susceptibility testing: species-related trovafloxacin interpretive zone breakpoints and selection of disk potency.

International comparisons of antibiotic susceptibility require the use of common minimum inhibitory concentration (MIC) limits. Disk diffusion test results are not directly suitable for such comparisons, since different standards are often used and zone breakpoints issued might reflect different MIC limits. We have used single strain regression analysis (SRA) for the calibration of the disk test, both according to species and individual laboratory, and for quality control of trovafloxacin disk diffusion tests in 5 laboratories in Sweden. Preliminary controls using histogram analysis including subtraction histograms of reference strains revealed marked differences between different laboratories. SRA was performed on 4 reference strains, S. aureus, E. faecalis, E. coli and P. aeruginosa, using disks containing 1, 3, 10, 30 and 100 microg trovafloxacin. The results using SRA showed a difference between laboratories using Biodisk PDM medium, which produced smaller zones, and those using Oxoid IsoSensitest. Species-related regression lines for laboratories using either medium were calculated and corresponding interpretive zone breakpoints determined for MIC limits. Rational criteria for the selection of a suitable disk content of an antibiotic were also defined and applied to trovafloxacin. The 10 microg disk selected by NCCLS (National Committee for Clinical Laboratory Standards) proved optimal.

Antimicrobial susceptibilities and biotypes of Arcanobacterium haemolyticum blood isolates.

Isolates obtained from the blood of ten patients with Arcanobacterium haemolyticum septicaemia were biotyped as smooth or rough using morphological and biochemical criteria, and their susceptibilities to 18 antibacterial agents were determined. Nine of the clinical cases included here have not been reported previously and are discussed in brief. One of the strains was highly resistant to macrolides and clindamycin. With one exception, the strains belonged to the smooth biotype. The data presented here indicates that the treatment of systemic Arcanobacterium haemolyticum infections should be based on the antibacterial susceptibility profiles of individual strains and on the site of the infection.

Quantitative 1H MRS in the evaluation of mesial temporal lobe epilepsy in vivo.

Hippocampal metabolite concentrations were determined by localized in vivo proton magnetic resonance spectroscopy (1H MRS) in eleven patients suffering from refractory mesial temporal lobe epilepsy (MTLE), as well as in eleven age-matched healthy volunteers, and compared with patient history, postoperative outcome and histopathology. Main results are: 1) In patients, the decrease in N-acetylaspartate (NAA) concentrations was highly significant ipsilateral, and less but still significant contralateral to the electroencephalogram-defined focus, as compared to controls. 2) The decrease in ipsilateral NAA measured preoperatively correlates with the degree of hippocampal sclerosis but 3) does not reliably predict postoperative outcome, although there is a trend toward better outcome in patients with a marked decrease of NAA. 4) Hippocampal NAA decrease (ipsi- and contralateral) is highly correlated with early onset age of epileptic seizures. 5) Among patients with similar onset age in early childhood, there is a strong association between duration of the disease and contralateral (and, though less clear-cut, ipsilateral) NAA loss. These results are concordant with the notion of a generally progressive worsening and complicating course of symptoms in poorly controlled MTLE.

Limiting the spread of penicillin-resistant Streptococcus pneumoniae: experiences from the South Swedish Pneumococcal Intervention Project.

In an attempt to limit the spread of penicillin-resistant pneumococci (PRP), an intervention project was initiated in the Malmöhus County, southern Sweden in January 1995. The ongoing project combines traditional communicable disease control measures and actions aiming at reducing antibiotics consumption. All patients in the county with a nasopharyngeal culture positive for PRP with MIC of Penicillin G > or =0.5 mg/L are followed with nasopharyngeal cultures until PRP-negative. Nasopharyngeal cultures are obtained from family members and close contacts of the index cases. Preschool children carrying PRP are denied attendance at group day-care. From January 1995 to March 1997, 1,038 PRP-carriers (429 index cases and 609 contact cases) were identified. Children aged 1-6 years dominated (83%). Antibiotics sales decreased during the study period, and epidemiologic data indicate that the intervention may have limited the dissemination of PRP in the county, but further evaluation is needed.

Bacteriologic evidence of infection caused by coagulase-negative staphylococci in total hip replacement.

Coagulase-negative staphylococci are important agents of infected hip arthroplasties, but sample contamination from the skin flora may confuse the diagnosis. Recovery of multiple identical strains has been regarded as indication of true infection. We have evaluated 29 total hip replacement operations with cultures positive for coagulase-negative staphylococci in a prospective study, 16 with > or = 3 isolates available for strain identity analysis. In 26 episodes, > or = 3 cultures were positive for coagulase-negative staphylococci, but only 19 of them had strong or intermediate clinical evidence of infection. Negative clinical evidence of infection coincided with the absence of a predominating strain according to plasmid profile analysis. A reliable identity analysis may help to rule out infection when multiple cultures are positive in patients who lack clinical evidence of infection.

Antimicrobial susceptibility testing in Sweden. III. Methodology for susceptibility testing.

A subcommittee of the Swedish Reference Group for Antibiotics, SRGA-M, has worked with standardization of methodology for susceptibility testing. In vitro data obtained with the disk diffusion procedure were collected from 5 clinical laboratories, compiled and presented as histograms of inhibition zones, and compared with data [minimum inhibitory concentrations (MICs) and inhibition zones] obtained from the reference laboratory at the Swedish Institute for Infectious Disease Control on a collection of clinically relevant bacterial species. Results from the reference collection of strains were presented as MIC histograms, and their corresponding inhibition zones were inserted in the compiled zone histograms as identifiable bars. These distributions formed the basis for decisions of breakpoints. Special tests were recommended for the detection of certain resistance mechanisms. A beta-lactamase test should be used for Haemophilus influenzae, Moraxella catarrhalis, Neisseria gonorrhoeae and enterococci. Screening for beta-lactam resistance caused by altered penicillin binding proteins should be done by using oxacillin 1 microgram for Streptococcus pneumoniae and Staphylococcus aureus (MRSA), and by phenoxymethylpenicillin 10 micrograms for H, influenzae. The standardized disk diffusion procedure was helpful in detecting enterobacteria carrying beta-lactamases with extended spectra. Registration of inhibition zones will provide a powerful tool for the epidemiological surveillance of antibiotic resistance.

A hospital outbreak of high-level beta-lactam-resistant Enterobacter spp.: association more with ampicillin and cephalosporin therapy than with nosocomial transmission.

We studied an 8 month outbreak of a 7-fold increased isolation rate of high-level beta-lactam-resistant Enterobacter spp. from clinical infections (20 patients, 22 isolates: 20 E. cloacae, 2 E. aerogenes). In a case-control analysis the occurrence of resistant Enterobacter spp. was found to be associated with treatment with multiple antibiotics (p = 0.03), broad-spectrum beta-lactam agents (p = 0.0001) including ampicillin (p = 0.04), and cephalosporins (cefuroxime and cefotaxime, p = 0.004). Biochemical fingerprinting and pulsed-field gel electrophoresis (PFGE) typing showed no identity between the resistant isolates, indicating that neither cross-infection nor nosocomial transmission from a common source was the immediate cause of the problem. The outbreak was not paralleled by the overall Enterobacter spp. isolation rate or the antibiotic usage pattern in the hospital. Thus, the underlying cause of the outbreak remained obscure.

Antimicrobial susceptibility of bacterial isolates in south Sweden including a 13-year follow-up study of some respiratory tract pathogens.

The antibiotic susceptibility of consecutive isolates of the upper respiratory tract pathogens Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Branhamella catarrhalis, and Staphylococcus aureus, (100 strains of each species collected each year during March through April 1985, 1988 and 1992) to penicillin V, amoxycillin, cefaclor, cefuroxime, doxycycline, erythromycin, and cotrimoxazole was investigated by MIC determination on PDM and PDM II agar. The MICs of the upper respiratory isolates from 1992 supplemented with 100 isolates each of Escherichia coli, Klebsiella spp., Enterobacter cloacae, Proteus mirabilis and Staphylococcus saprophyticus collected during 1992 were determined against the above antibiotics plus cefadroxil, cefpodoxime, roxithromycin, ciprofloxacin, ofloxacin, and BAY Y 3118. Beta-lactamase production was found in 10% of H. influenzae and 80-90% of S. aureus and B. catarrhalis in 1992. Among H. influenzae isolates, non-beta-lactamase-induced resistance to all beta-lactam antibiotics was first detected in 1988 and amounted to 3% of isolates in 1992. Decreased susceptibility of S. preumoniae to penicillin (> or = 0.12 mg/l), co-trimoxazole > or = 32 mg/l, doxycycline (> or = 2 ml/l) and erythromycin (> or = 1 mg/l) was detected in 11%, 7%, and 8%, respectively, in 1992, which is significantly higher than in previous years at the same laboratory. Decreased susceptibility of S. pyogenes to doxycycline and erythromycin was detected in 11% and 9% in 1992. The two most recently developed antibiotics, cefpodoxime and BAY Y 3118, showed high antibacterial activity. The study emphasizes the need to screen for resistance mechanisms such as beta-lactamase production and lowered penicillin affinity.