SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

<p>Abstract</p> <p>Background</p> <p>SHV β-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (<url>http://www.lahey.org/Studies/</url>). Besides, information about SHV β-lactamases can be found in the rapidly growing NCBI protein database. The SHV β-Lactamase Engineering Database (SHVED) has been developed to collect the SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions.</p> <p>Description</p> <p>The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.</p> <p>The SHVED is accessible at <url>http://www.LacED.uni-stuttgart.de/classA/SHVED/</url>. It provides sequences, structures, and a multisequence alignment of SHV β-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download.</p> <p>Conclusions</p> <p>The SHV β-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV β-lactamases.</p

SN 2005hj: Evidence for Two Classes of Normal-Bright SNe Ia and Implications for Cosmology

HET Optical spectra covering the evolution from about 6 days before to about 5 weeks after maximum light and the ROTSE-IIIb unfiltered light curve of the "Branch-normal" Type Ia Supernova SN 2005hj are presented. The host galaxy shows HII region lines at redshift of z=0.0574, which puts the peak unfiltered absolute magnitude at a somewhat over-luminous -19.6. The spectra show weak and narrow SiII lines, and for a period of at least 10 days beginning around maximum light these profiles do not change in width or depth and they indicate a constant expansion velocity of ~10,600 km/s. We analyzed the observations based on detailed radiation dynamical models in the literature. Whereas delayed detonation and deflagration models have been used to explain the majority of SNe Ia, they do not predict a long velocity plateau in the SiII minimum with an unvarying line profile. Pulsating delayed detonations and merger scenarios form shell-like density structures with properties mostly related to the mass of the shell, M_shell, and we discuss how these models may explain the observed SiII line evolution; however, these models are based on spherical calculations and other possibilities may exist. SN 2005hj is consistent with respect to the onset, duration, and velocity of the plateau, the peak luminosity and, within the uncertainties, with the intrinsic colors for models with M_shell=0.2 M_sun. Our analysis suggests a distinct class of events hidden within the Branch-normal SNe Ia. If the predicted relations between observables are confirmed, they may provide a way to separate these two groups. We discuss the implications of two distinct progenitor classes on cosmological studies employing SNe Ia, including possible differences in the peak luminosity to light curve width relation.Comment: ApJ accepted, 31 page

A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry

<p>Abstract</p> <p>Background</p> <p>Relatively recently, the software KB™ Basecaller has replaced <it>phred </it>for identifying the bases from raw sequence data in DNA sequencing employing dideoxy chemistry. We have measured quantitatively the consequences of that change.</p> <p>Results</p> <p>The high quality sequence segment of reads derived from the KB™ Basecaller were, on average, 30-to-50 bases longer than reads derived from <it>phred</it>. However, microbe identification appeared to have been unaffected by the change in software.</p> <p>Conclusions</p> <p>We have demonstrated a modest, but statistically significant, superiority in high quality read length of the KB™ Basecaller compared to <it>phred</it>. We found no statistically significant difference between the numbers of microbial species identified from the sequence data.</p

Comparison of oral and vaginal metronidazole for treatment of bacterial vaginosis in pregnancy: impact on fastidious bacteria

<p>Abstract</p> <p>Background</p> <p>Bacterial vaginosis (BV) is a common condition that is associated with preterm birth and acquisition of complex communities of vaginal bacteria that include several fastidious species. Treatment of BV in pregnancy has mixed effects on the risk of preterm delivery, which some hypothesize is due to variable antibiotic efficacy for the fastidious bacteria. Both oral and intravaginal metronidazole can be used to treat bacterial vaginosis in pregnancy, but little is known about the impact of different routes of antibiotic administration on concentrations of fastidious vaginal bacteria.</p> <p>Methods</p> <p>This was a sub-study of a larger randomized trial of oral versus vaginal metronidazole for treatment of BV in pregnancy. Fifty-three women were evaluated, including 30 women who received oral metronidazole and 23 who received intravaginal metronidazole. Bacterial taxon-specific quantitative PCR assays were used to measure concentrations of bacterial vaginosis associated bacterium (BVAB) 1, 2, and 3, <it>Gardnerella vaginalis, Atopobium </it>species, <it>Leptotrichia/Sneathia </it>species, <it>Megasphaera </it>species, and <it>Lactobacillus crispatus </it>before and after antibiotic treatment.</p> <p>Results</p> <p>Concentrations of <it>Leptotrichia </it>and <it>Sneathia </it>spp. and the fastidious Clostridia-like bacterium designated BVAB1 decreased significantly with oral (p = .002, p = .02) but not vaginal therapy (p = .141, p = .126). The fastidious bacterium BVAB3 did not significantly decrease with either treatment. Concentrations of <it>Atopobium </it>spp., reportedly resistant to metronidazole <it>in vitro</it>, dropped significantly with oral (p = .002) and vaginal (p = .001) treatment. There was no significant difference in the magnitude of change in bacterial concentrations between oral and vaginal treatment arms for any of the bacterial species. <it>Lactobacillus crispatus </it>concentrations did not change.</p> <p>Conclusion</p> <p>Both oral and vaginal metronidazole therapy in pregnant women result in a significant decrease in concentrations of most BV-associated anaerobic bacteria, with the exception that <it>Leptotrichia, Sneathia </it>and BVAB1 do not significantly decrease with vaginal metronidazole therapy. These data suggest that the route of antibiotic administration has a minor impact on bacterial eradication in pregnant women with BV.</p> <p>Trail Registration</p> <p>This trial is registered with ClinicalTrials.gov, number NCT00153517</p

Bacterial morphotype grading for periodontal disease assessment

BACKGROUND: Listgarten and Hellden (1978) used darkfield microscopy of wet mounts to differentiate between healthy and periodontally diseased sites in the mouth by expressing the different bacterial morphotypes observed as a percentage of the total number of bacteria counted. This method of periodontal disease assessment gained favour as a diagnostic tool but presented with the limitation of immediate examination to determine the number of motile rods present and an inability to distinguish between gingivitis and periodontitis. Grading of bacterial morphotypes into several distinct categories of health or disease (Ison and Hay, 2002), simplified the scoring system of Gram-stained smears for the diagnosis of bacterial vaginosis (Nugent et al. 1991). The application of a similar grading system using stained smears rather than wet mounts could be advantageous to the diagnosis of periodontal disease. OBJECTIVES/AIMS: This study tested the hypothesis that stained smears of dental plaque collected from the gingival crevice of individuals with varying probing pocket depths (PD) may provide a grading system for periodontal disease assessment. MATERIALS AND METHODS: Subgingival plaque samples were collected from 49 patients, stained with a silver stain and the proportions of each bacterial morphotype graded relative to their respective PD measurements. RESULTS: This technique allowed for a grading system of I–IV, with grade I indicating health and grade IV indicating severe periodontal disease. DISCUSSION: Stained smear examination eliminates the time restriction for motile rod enumeration and allows for storage of smears for future reference. CONCLUSION: Standardization of the microscopic areas to be evaluated or examined will facilitate the agreement of cut-off values for the diagnosis of periodontal disease.This material is based on work partially supported financially by the National Research Foundation (NRF) of South Africa

Human lactobacilli as supplementation of clindamycin to patients with bacterial vaginosis reduce the recurrence rate; a 6-month, double-blind, randomized, placebo-controlled study

<p>Abstract</p> <p>Background</p> <p>The primary objective of this study was to investigate if supplementary lactobacilli treatment could improve the initial cure rate after vaginal clindamycin therapy, and secondly, if lactobacilli as repeated adjunct treatment during 3 menstrual cycles could lengthen the time to relapse after initial cure.</p> <p>Methods</p> <p>Women (n = 100) with bacterial vaginosis diagnosed by Amsel criteria were after informed consent offered vaginal clindamycin therapy followed by vaginal gelatine capsules containing either 10⁹freeze-dried lactobacilli or identical placebo capsules for 10 days during 3 menstrual cycles in a double-blind, randomized, placebo-controlled trial.</p> <p>Results</p> <p>The initial intent to treat (ITT) analysis for the one-month cure rate was 64% in the lactobacilli group and 78% in the placebo group (p > 0.05). However, any patient with missing or unclassified smears at the initial visit who continued the study and whose next smear indicated a cure was included in the cured group; the study also excluded two of the patients in the lactobacilli group who reported that they did not take any vaginal capsules. With consideration to these population changes, the initial cure rate would be 77% in the lactobacilli group. The 76 cured women were followed for 6 menstrual cycles or until relapse within that time span. At the end of the study, 64.9% (24/37) of the lactobacilli treated women were still BV-free compared to 46.2% (18/39) of the placebo treated women. Comparison of the two groups regarding "Time from cure to relapse" was statistically significant (p = 0.027) in favour of the lactobacilli treatment. Adjuvant therapy with lactobacilli contributed significantly to avoidance of relapse with a proportional Hazard Risk ratio (HR) of 0.73 (0.54–0.98) (p < 0.05)</p> <p>Conclusion</p> <p>The study shows that supplementary treatment combining two different strains of probiotic lactobacilli does not improve the efficacy of BV therapy during the first month of treatment, but for women initially cured, adjunct treatment of lactobacilli during 3 menstrual cycles lengthens the time to relapse significantly in that more women remained BV free at the end of the 6-month follow up.</p> <p>Trial registration number</p> <p>ISRCTN62879834</p

A hot and fast ultra-stripped supernova that likely formed a compact neutron star binary.

Compact neutron star binary systems are produced from binary massive stars through stellar evolution involving up to two supernova explosions. The final stages in the formation of these systems have not been directly observed. We report the discovery of iPTF 14gqr (SN 2014ft), a type Ic supernova with a fast-evolving light curve indicating an extremely low ejecta mass (≈0.2 solar masses) and low kinetic energy (≈2 × 1050 ergs). Early photometry and spectroscopy reveal evidence of shock cooling of an extended helium-rich envelope, likely ejected in an intense pre-explosion mass-loss episode of the progenitor. Taken together, we interpret iPTF 14gqr as evidence for ultra-stripped supernovae that form neutron stars in compact binary systems

Antiseptics and disinfectants for the treatment of bacterial vaginosis: a systematic review

Background: The study objective was to assess the available data on efficacy and tolerability of antiseptics and disinfectants in treating bacterial vaginosis (BV). Methods: A systematic search was conducted by consulting PubMed (1966-2010), CINAHL (1982-2010), IPA (1970-2010), and the Cochrane CENTRAL databases. Clinical trials were searched for by the generic names of all antiseptics and disinfectants listed in the Anatomical Therapeutic Chemical (ATC) Classification System under the code D08A. Clinical trials were considered eligible if the efficacy of antiseptics and disinfectants in the treatment of BV was assessed in comparison to placebo or standard antibiotic treatment with metronidazole or clindamycin and if diagnosis of BV relied on standard criteria such as Amsel\u27s and Nugent\u27s criteria. Results: A total of 262 articles were found, of which 15 reports on clinical trials were assessed. Of these, four randomised controlled trials (RCTs) were withheld from analysis. Reasons for exclusion were primarily the lack of standard criteria to diagnose BV or to assess cure, and control treatment not involving placebo or standard antibiotic treatment. Risk of bias for the included studies was assessed with the Cochrane Collaboration\u27s tool for assessing risk of bias. Three studies showed non-inferiority of chlorhexidine and polyhexamethylene biguanide compared to metronidazole or clindamycin. One RCT found that a single vaginal douche with hydrogen peroxide was slightly, though significantly less effective than a single oral dose of metronidazole. Conclusion: The use of antiseptics and disinfectants for the treatment of BV has been poorly studied and most studies are somehow methodologically flawed. There is insufficient evidence at present to advocate the use of these agents, although some studies suggest that some antiseptics may have equal efficacy compared to clindamycin or metronidazole. Further study is warranted with special regard to the long-term efficacy and safety of antiseptics and disinfectants for vaginal use

Predisposing factors for bacterial vaginosis, treatment efficacy and pregnancy outcome among term deliveries; results from a preterm delivery study

<p>Abstract</p> <p>Background</p> <p>Bacterial vaginosis (BV) during pregnancy is associated with an increased risk of preterm delivery but little is known about factors that could predict BV. We have analyzed if it is possible to identify a category of pregnant women that should be screened for BV, and if BV would alter the pregnancy outcome at term; we have also studied the treatment efficacy of clindamycin.</p> <p>Methods</p> <p>Prospective BV screening and treatment study of 9025 women in a geographically defined region in southeast Sweden. BV was defined as a modified Nugent score of 6 and above. Data was collected from the Swedish Medical Birth Register. Women allocated to treatment were supplied with vaginal clindamycin cream. The main outcome goals were to identify factors that could predict BV.</p> <p>Results</p> <p>Vaginal smears were consistent with BV criteria in 9.3%. Logistic regression indicates a significant correlation between smoking and BV (p < 0.001) and a greater prevalence of BV in the lower age groups (p < 0.001). We found no correlation between BV and history of preterm deliveries, previous miscarriages, extra-uterine pregnancies, infertility problems or reported history of urinary tract infections–factors that earlier have been associated with BV. Treatment with clindamycin cream showed a cure rate of 77%. Less than 1% of women with a normal vaginal smear in early pregnancy will develop BV during the pregnancy. There was no association between BV and the obstetric outcome among women who delivered at term. Women with BV, both treated patients and nontreated, had the same obstetric outcome at term as women with normal vaginal flora.</p> <p>Conclusion</p> <p>BV is more than twice as common among smokers, and there is a higher prevalence in the younger age group. However these two markers for BV do not suffice as a tool for screening, and considering the lack of other risk factors associated with BV, screening of all pregnant women might be a strategy to follow in a program intended to reduce the number of preterm births.</p