A set of novel multiplex Taqman real-time PCRs for the detection of diarrhoeagenic Escherichia coli and its use in determining the prevalence of EPEC and EAEC in a university hospital

<p>Abstract</p> <p>Background</p> <p>Accurate measurement of the incidence of diarrhoeagenic <it>E. coli </it>in patients with diarrhoea is hindered by the current methods of detection and varies from country to country. In order to improve the diagnosis of diarrhoeagenic <it>E. coli </it>(DEC), we developed a set of multiplex TaqMan real-time PCRs designed to detect the respective pathogens from an overnight stool culture.</p> <p>Methods</p> <p>Over the period Jan. 2006 to Dec. 2006 all stool specimens (n = 1981) received were investigated for EPEC and EAEC.</p> <p>Results</p> <p>Of these, 371 specimens had no growth of <it>Enterobacteriaceae</it>. Of the remaining 1610 specimens 144 (8,9%) were positive for EPEC and 78 (4,8%) positive for EAEC. Among the EPEC positive stool specimens 28 (19,4%) were received from the tropical diseases unit, 49 (34%) from the paediatric dept. and 67 (46,5%) from the remainder of the wards. The EAEC were distributed as follows: 39 (50%) - tropical diseases, 19 (24,4%) -paediatrics and 20 (25,6%) other wards. Proportionately more EAEC and EPEC were found in children less than 3 years of age than other age groups. In only 22,2% of the detected EPEC and 23% of EAEC was the investigation requested by hospital staff.</p> <p>Conclusions</p> <p>This is, to our knowledge, the first study using a multiplex TaqMan PCR for the successful detection of diarrhoeagenic <it>E. coli</it>. In conclusion, due to the high prevalence of DEC detected, investigation of EPEC and EAEC should be recommended as a routine diagnostic test for patients with infectious diarrhoea.</p

Impact of COVID-19 on accident and emergency attendances and emergency and planned hospital admissions in Scotland:an interrupted timeseries analysis

Funding: This analysis is part of the Early Assessment of COVID-19 epidemiology and Vaccine/anti-viral Effectiveness (EAVE II) study. EAVE II is funded by the Medical Research Council (MR/R008345/1) with the support of BREATHE -The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Additional support has been provided through the Scottish Government DGHealth and Social Care. HRS is supported by the Medical Research Council [MR/R008345/1].Objectives: Following the outbreak of SARS-CoV-2, health systems and the populations who use them have faced unprecedented challenges. We aimed to measure the impact of COVID-19 on the uptake of hospital-based care at a national level. Design: The study period (weeks ending 05 January to 28 June 2020) encompassed the pandemic announcement by the World Health Organization (WHO) and the initiation of the UK lockdown. We undertook an interrupted time-series analysis to evaluate the impact of these events on hospital services at a national level and across demographics, clinical specialties and NHS Health Boards. Setting: Scotland, UK. Participants: Patients receiving hospital care from NHS Scotland.Main outcome measures: A&E attendances, and emergency and planned hospital admissions measured using the relative change of weekly counts in 2020 to the averaged counts for equivalent weeks in 2018 and 2019. Results: Before the pandemic announcement, the uptake of hospital care was largely consistent with historical levels. This was followed by sharp drops in all outcomes until UK lockdown, where activity began to steadily increase. This time-period saw an average reduction of -40.7% (95% CI: -47.7 to -33.7) in A&E attendances, -25.8% (95% CI: -31.1 to -20.4) in emergency hospital admissions and -60.9% (95% CI: -66.1 to -55.7) in planned hospital admissions, in comparison to the 2018-2019 averages. All subgroup trends were broadly consistent within outcomes, but with notable variations across age groups, specialties and geography. Conclusions: COVID-19 has had a profoundly disruptive impact on hospital-based care across NHS Scotland. This has likely led to an adverse effect on non-COVID-19 related illnesses, increasing the possibility of potentially avoidable morbidity and mortality. Further research is required to elucidate these impacts.PostprintPeer reviewe

Early (Days 1–4) post-treatment serum hCG level changes predict single-dose methotrexate treatment success in tubal ectopic pregnancy

Acknowledgements S.C.M. was supported by the South-East Scotland Academic Foundation Programme. Medical Research Council (MRC) Centre grants to the Centre for Reproductive Health (CRH) (G1002033 and MR/N022556/1) are also gratefully acknowledged. Funding This project was supported by funding from the Efficacy and Mechanism Evaluation programme, a Medical Research Council and National Institute for Health Research partnership (grant reference number 14/150/03).Peer reviewedPublisher PD

Winners and losers as mangrove, coral and seagrass ecosystems respond to sea-level rise in Solomon Islands

A 2007 earthquake in the western Solomon Islands resulted in a localised subsidence event in which sea level (relative to the previous coastal settings) rose approximately 30-70 cm, providing insight into impacts of future rapid changes to sea level on coastal ecosystems. Here, we show that increasing sea level by 30-70 cm can have contrasting impacts on mangrove, seagrass and coral reef ecosystems. Coral reef habitats were the clear winners with a steady lateral growth from 2006-2014, yielding a 157% increase in areal coverage over seven years. Mangrove ecosystems, on the other hand, suffered the largest impact through a rapid dieback of 35% (130 ha) of mangrove forest in the study area after subsidence. These forests, however, had partially recovered seven years after the earthquake albeit with a different community structure. The shallow seagrass ecosystems demonstrated the most dynamic response to relative shifts in sea level with both losses and gains in areal extent at small scales of 10-100 m. The results of this study emphasize the importance of considering the impacts of sea-level rise within a complex landscape in which winners and losers may vary over time and space

Prevalence and characterization of antimicrobial resistance among gram-negative bacteria isolated from febrile hospitalized patients in central Ethiopia

BACKGROUND: Infectious diseases are among the leading causes of death in many low-income countries, such as Ethiopia. Without reliable local data concerning causative pathogens and antimicrobial resistance, empiric treatment is suboptimal. The objective of this study was to characterize gram-negative bacteria (GNB) as pathogens and their resistance pattern in hospitalized patients with infections in central Ethiopia. METHODS: Patients ≥ 1 year of age with fever admitted to the Asella Referral and Teaching Hospital from April 2016 to June 2018 were included. Blood and other appropriate clinical specimens were collected and cultured on appropriate media. Antibiotic susceptibility testing (AST) was performed using the Kirby–Bauer method and VITEK® 2. Species identification and detection of resistance genes were conducted using MALDI-ToF MS (VITEK® MS) and PCR, respectively. RESULTS: Among the 684 study participants, 54.2% were male, and the median age was 22.0 (IQR: 14–35) years. Blood cultures were positive in 5.4% (n = 37) of cases. Among other clinical samples, 60.6% (20/33), 20.8% (5/24), and 37.5% (3/8) of swabs/pus, urine and other body fluid cultures, respectively, were positive. Among 66 pathogenic isolates, 57.6% (n = 38) were GNB, 39.4% (n = 26) were gram-positive, and 3.0% (n = 2) were Candida species. Among the isolated GNB, 42.1% (16/38) were Escherichia coli, 23.7% (9/38) Klebsiella pneumoniae and 10.5% (4/38) Pseudomonas aeruginosa. In total, 27/38 gram-negative isolates were available for further analysis. Resistance rates were as follows: ampicillin/sulbactam, 92.6% (n = 25); cefotaxime, 88.9% (n = 24); ceftazidime, 74.1% (n = 20); cefepime, 74.1% (n = 20); gentamicin, 55.6% (n = 15); piperacillin/tazobactam, 48.1% (n = 13); meropenem, 7.4% (n = 2); and amikacin, 3.7% (n = 1). The bla(NDM-1) gene was detected in one K. pneumoniae and one Acinetobacter baumannii isolate, which carried an additional bla(OXA-51) gene. The ESBL enzymes were detected in 81.5% (n = 22) of isolates as follows: TEM, 77.2% (n = 17); CTX-M-1 group, 68.2% (n = 15); SHV group, 27.3% (n = 6); and CTX-M-9 group, 9.1% (n = 2). Based on the in vitro antimicrobial susceptibility results, empiric treatment initiated in 13 of 18 (72.2%) patients was likely ineffective. CONCLUSION: We report a high prevalence of ESBL-producing bacteria (81.5%) and carbapenem resistance (7.4%), with more than half of GNB carrying two or more ESBL enzymes resulting in suboptimal empiric antibiotic therapy. These findings indicate a need for local and national antimicrobial resistance surveillance and the strengthening of antimicrobial stewardship programs

Scaling of the B and D meson spectrum in lattice QCD

We give results for the $B$ and the $D$ meson spectrum using NRQCD on the lattice in the quenched approximation. The masses of radially and orbitally excited states are calculated as well as $S$-wave hyperfine and $P$-wave fine structure. Radially excited $P$-states are observed for the first time. Radial and orbital excitation energies match well to experiment, as does the strange-non-strange $S$-wave splitting. We compare the light and heavy quark mass dependence of various splittings to experiment. Our $B$-results cover a range in lattice spacings of more than a factor of two. Our $D$-results are from a single lattice spacing and we compare them to numbers in the literature from finer lattices using other methods. We see no significant dependence of physical results on the lattice spacing. PACS: 11.15.Ha 12.38.Gc 14.40.Lb 14.40.NdComment: 78 pages, 29 tables, 30 figures Revised version. Minor corrections to spelling and wordin

Genetic characterization and emergence of the Metallo-β-Lactamase GIM-1 in Pseudomonas spp. and Enterobacteriaceae during a long-term outbreak

Since the first isolation in 2002, the metallo-β-lactamase GIM-1 has not been detected outside Germany. The data presented here, for 50 clinical blaGIM-1-positive isolates, including Pseudomonas spp. and Enterobacteriaceae (Enterobacter cloacae, Klebsiella oxytoca, Serratia marcescens, Escherichia coli, and Citrobacter freundii), collected between 2007 and 2012 at the original site in an ongoing outbreak, demonstrate a diverse genetic background and dissemination of the gene conferring resistance to enteric bacteria

The translation research in a dental setting (TRiaDS) programme protocol

Background: It is well documented that the translation of knowledge into clinical practice is a slow and haphazard process. This is no less true for dental healthcare than other types of healthcare. One common policy strategy to help promote knowledge translation is the production of clinical guidance, but it has been demonstrated that the simple publication of guidance is unlikely to optimise practice. Additional knowledge translation interventions have been shown to be effective, but effectiveness varies and much of this variation is unexplained. The need for researchers to move beyond single studies to develop a generalisable, theory based, knowledge translation framework has been identified.For dentistry in Scotland, the production of clinical guidance is the responsibility of the Scottish Dental Clinical Effectiveness Programme (SDCEP). TRiaDS (Translation Research in a Dental Setting) is a multidisciplinary research collaboration, embedded within the SDCEP guidance development process, which aims to establish a practical evaluative framework for the translation of guidance and to conduct and evaluate a programme of integrated, multi-disciplinary research to enhance the science of knowledge translation.Methods: Set in General Dental Practice the TRiaDS programmatic evaluation employs a standardised process using optimal methods and theory. For each SDCEP guidance document a diagnostic analysis is undertaken alongside the guidance development process. Information is gathered about current dental care activities. Key recommendations and their required behaviours are identified and prioritised. Stakeholder questionnaires and interviews are used to identify and elicit salient beliefs regarding potential barriers and enablers towards the key recommendations and behaviours. Where possible routinely collected data are used to measure compliance with the guidance and to inform decisions about whether a knowledge translation intervention is required. Interventions are theory based and informed by evidence gathered during the diagnostic phase and by prior published evidence. They are evaluated using a range of experimental and quasi-experimental study designs, and data collection continues beyond the end of the intervention to investigate the sustainability of an intervention effect.Discussion: The TRiaDS programmatic approach is a significant step forward towards the development of a practical, generalisable framework for knowledge translation research. The multidisciplinary composition of the TRiaDS team enables consideration of the individual, organisational and system determinants of professional behaviour change. In addition the embedding of TRiaDS within a national programme of guidance development offers a unique opportunity to inform and influence the guidance development process, and enables TRiaDS to inform dental services practitioners, policy makers and patients on how best to translate national recommendations into routine clinical activities