bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida auris real-time PCR for surveillance of patients and environment
Authors: Taori Surabhi , Khonyongwa Kirstin , Kumarage Jeevani , Smith Melvyn 
Published: March 2020

Background– Candida aurisis an emerging fungus which has caused nosocomial outbreaks worldwide. Screening for surveillance is challenging as it’s a slow grower, samples may have multiple candida spp and many commercial assays have limited accuracy. Following an outbreak in 2016, a real-time PCR was developed for rapid patient and environmental screening. Laboratory parameters, results and pitfalls from Jan 2018 to March 2019 are described.
Methods– Evaluation was performed using EQA panels and validated on clinical swabs and urine samples. Patient screening was performed in high risk clinical areas from nose, throat, axilla and groin swabs and catheter urine. Environmental screening was done in areas where transmission was detected. Positive or indeterminate samples were cultured and colonies identified on the Vitek 2 and confirmed by PHE reference laboratory.
Results–The Limit of detection was 100 organisms/ml. Sensitivity, specificity, PPV and NPV were 100.00%, 99.35%, 85.71%, and 100.00%. 4,792 urines and 10,819pooled swabs were tested. 21 colonised patients were identified in two outbreaks and two isolated transmission events. Median turn-around time for positive results was 24h30min (range 04:22-96:46h) and 143h14min (range 75-406h) for PCR and culture respectively. Urine samples did not add to the overall sensitivity of screening.C. aurisDNA was detected in 30/84 (35%) environmental swabs but C. auris isolated in only 2/84. Drawbacks of the PCR include reagent contamination seen on two occasions.
Conclusion – C. auris screening by PCR is a rapid means of detection in both patients and environment but prudent use of culture is required to help determine infectivity.
Metabolite X is a novel biomarker for sepsis diagnosis and treatment
Authors: Fitzpatrick Susan , Lambden Simon , Macias David , Puthucheary Zudin , Pietsch Sandra , Mendil Lee , McPhil Mark , Johnson Randall 
Published: March 2020

Background: Sepsis develops when the initial, appropriate host response to an infection becomes amplified and subsequently dysregulated. Recent research has shown that the pathogenesis of sepsis can only partially be explained by an aberrant inflammatory response, metabolic deregulation also plays a vital role. Here we have investigated the role of a novel metabolite in sepsis pathophysiology.
Methods: Urine was obtained from an LPS mouse model of sepsis and human septic patients. A colorimetric assay and mass-spectroscopy were performed to determine the expression levels of metabolite X (mX). Furthermore, mice were implanted with radiotelemetry probes and the effect of supplementation with mX on clinical symptomology was determined. Following co-administration of LPS and mX real-time measurements of temperature, heart-rate and blood pressure were obtained.
Results: The urinary excretion of mX is significantly reduced in both a mouse model of LPS-induced sepsis, and in samples taken from human septic patients. Subsequent data showed that this is due to enhanced activation of the enzyme responsible for mX degradation. Moreover, co-administration of LPS and mX in mice modulates a number of aspects of physiological responses to sepsis, and in particular, protects against sepsis-induced hypothermia. The mechanism underlying this protective effect is due to suppressed nitric-oxide signalling.
Conclusion: Our results identify a novel role for mX in sepsis pathophysiology and suggest that this metabolite is a critical diagnostic and therapeutic target for sepsis. Future studies will fully elucidate the mechanisms underlying our observations.
mX not disclosed due to IP application but will be disclosed for presentation.
Safe, sustained reduction in meropenem and piperacillin/tazobactam use in a medical high dependency unit
Authors: Robertson Paul , Altmeyer Ursula , Hamilton Kayleigh , Rennie Natalie , Cottrell Richard , Williams Gethin 
Published: March 2020

There is widespread overuse of ultra-broad spectrum antibiotics (UBSA) such as meropenem and piperacillin/tazobactam (PTZ). Reductions in their use are needed to preserve their effectiveness.
Using electronic prescribing data we recorded administrations of meropenem and PTZ per month in a 12-bed medical high dependency unit (HDU) from April 2016 to March 2019. During this time there were three interventions (an antimicrobial stewardship round began in March 2017, PTZ was removed from empirical prescribing guidelines in May 2017, and a restricted antimicrobial audit began in June 2017). The latter two interventions were prompted by a national PTZ shortage.
In 2016/17 meropenem and PTZ use was 56 and 113 daily defined doses/100 acute occupied bed days (AOBD) respectively, falling to 32 and 60 in 2017/18, and to 25 and 38 in 2018/19. This represented a 55% reduction in meropenem use and a 77% reduction in PTZ use over 2 years. The drop in use was due to both fewer patients being started on UBSA and shorter durations of treatment. The use of 4C antibiotics (clindamycin, cephalosporins, co-amoxiclav and ciprofloxacin/levofloxacin) did not increase. There was no increase in unit mortality, or change in the prevalence of ESBL-producing organisms.
We describe a multi-modal intervention that, coupled with strong clinical engagement, resulted in a safe, sustained reduction in both meropenem and PTZ use in a medical HDU, without using more 4C antibiotics. We hypothesize that “top down” policies helped reduce UBSA initiation, whereas a “bottom-up” ward-based initiative helped review and stop unnecessary use.
Utilisation of Antimicrobial Stewardship (AMS) Electronic Interventions (i-Vents) as a metric of pharmacy AMS at Cambridge University Hospitals (CUH) NHS Foundation Trust
Authors: Brown Claudia , Enoch David , Micallef Christianne 
Published: March 2020

Background: The aim of the project was to identify the contribution clinical pharmacists make to antimicrobial stewardship (AMS) at CUH. The EPIC e-hospital system in place allows pharmacists to record interventions (i-Vents) electronically; these can be used as a metric of pharmacist AMS.
Method:A bespoke electronic report of all AMS i-Vents which occurred in April 2018 was generated using EPIC.Each i-Vent was categorised by type, clinical speciality, grade of pharmacist making the i-Vent and whether the i-Vent was following on from a previous one. The antimicrobials(s) mentioned in each i-Vent were also recorded.
Results:During April 2018 554 pharmacist i-Vents were recorded. I-Vent types included therapeutic drug monitoring (31%), dose optimisation (22%), course length optimisation (12%), interaction and contraindication management (2%) and patient counselling (0.2%). AMS i-Vents were recorded for patients under the care of 42 clinical specialties including neonatology (12%), diabetes and endocrinology (11%) and respiratory (8%). I-vent numbers increased with seniority of pharmacist with band 8 pharmacists making the most interventions (44%) and band 6 pharmacists making the fewest (16%). There were 645 separate references to a total of 53 individual antimicrobial agents. The top three drugs mentioned in i-Vents were vancomycin (30%), gentamicin (12%), and ciprofloxacin (8%). Follow-up i-Vents constituted 111 (20%) of all recorded i-Vents.
Conclusion:Our findings demonstrate that pharmacists contribute significantly to AMS at CUH, especially on therapeutic drug monitoring and dose-optimisation issues.We suggest that AMS i-Vents are a reliable metric for monitoring AMS pharmacist activities, related directly to patient care.
From bedside to bench – optimising the local blood culture pathway
Authors: Popoola Pelumi , Stoneham Simon , Davies Bethany 
Published: March 2020

Background
Optimising the blood culture (BC) pathway is essential to ensure maximal benefits for patients. There are national standards for expected turnaround times. At our acute teaching hospital, there was limited data on this. We aimed to map the local BC pathway to identify obstacles and areas for improvement in the process.
Methods
In this prospective study, all BCs taken from adult patients in the Emergency Department (ED) on allocated days over three months were included. Study days were chosen to reflect the whole working week, including out of hours. Information was gathered from multiple stakeholders, including ED clinical staff, porters, microbiology laboratory staff and clinicians. BCs were trailed from when the sample was taken until results were reported. The time taken for each stage was compared against national standards (SMIB37).

Results
107 BCs were included in the study. Only 23% achieved the 4hr target between collection and incubation; times ranged from 50 mins–27hrs8mins. None of 43 samples taken at the weekend achieved the target. Process mapping allowed the following problems to be identified: fixed, infrequent transport by porters; delays between the general laboratory and the microbiology receptions; and delay in loading the analyser. BC bottles could not be transported via the vacuum system and the analyser was only accessible when the microbiology laboratory was open, which is not 24/7.

Conclusion
The BC pathway at the hospital fails to ensure that national standards are met. Identifying key bottlenecks impeding flow will help enable the trust to make essential changes.
Evaluation of Microbiological Sampling Practice in Community Acquired Pneumonia at a South London Trust: The Cheaper, the Better?
Authors: Owusu-Agyei Andrew , Kundu Shantanu , Goodman Anna 
Published: March 2020

NICE guidelines suggest cases of community acquired pneumonia (CAP) in hospital have blood and sputum cultures and legionella and pneumococcal antigen tests be considered in specific cases. Local guidelines advise respiratory viral swabs, sputum and blood culture in specific cases and urinary antigen tests only in severe cases. We assessed the frequency and appropriateness of microbiological testing in CAP.

Methods:
The electronic records of admissions to St Thomas’ Hospital, London in January 2019 were scrutinised to identify cases of CAP. The severity of each case was categorized using CRB65 scoring. Microbiological tests and their results were analysed.

Results:
64 cases of CAP were identified. Severe disease (CRB>/= 2) was present in 31%. Respiratory viral/flu swabs were sent in 76% of cases and were positive in 39% of these cases [12 (63%) were influenza]. Sputum culture was collected in 39% of cases and revealed pathogens in 24% of these. Urinary pneumococcal antigen was sent in 7 cases of non-severe disease and 1 case of severe disease and was positive in 25% of those tested. Legionella urinary antigen tests were sent in 6 cases, only 2 of whom had reasons documented for sending the test; all were negative. Blood cultures were sent in 69% of cases (44 patients) and none revealed pathogens.
Discussion:
During the influenza season the most useful microbiological test was the respiratory viral swab. Sputum culture is a cheap test that could be used more often. Expensive legionella antigen tests were performed inappropriately.
Knowledge, Attitude, Practice and Implementation of community pharmacists role in treating tuberculosis patients in south India Region
Authors: Ganachari Madiwalayya Shivakantayya , Rangaswamy Uday Kumar 
Published: March 2020

Background: Knowledge, attitude, practice and implementation of community pharmacist role in treating tuberculosis patients. Community Pharmacy education in India faces many challenges. An assessment of the challenges and opportunities of community pharmacist role in eradication of Tuberculosis in India has not been conducted.
Methods: This was a cross sectional study A one-day training was conducted in 6th may 2019 in Belagavi , Karnataka state, India. A selected sample of stake holders was invited experts Like Medical education expert in the field of tuberculosis, District Tuberculosis controller officer, Deputy Drugs controller, Assistant Drugs controller. The training Program was conducted by Dept. of Pharmacy Practice, KLE college of Pharmacy, Belagavi in association with District Tuberculosis center Belagavi and Regional office of Deputy Drugs Controller, Belagavi, India.
Results: A total of 60 community pharmacists are responded. The lowest number of correct answers were to the questions were Patients with active TB disease can infect people by talking (56.7%), TB is often spread from person to person through sex (53.3%), aware of Public Private mix (PPM) for Tuberculosis control and care (35%), Anti-TB drugs which are contraindicated in pregnancy (35%).
Conclusion: There are significant gap in knowledge, Attitude and practice on TB infection and control among community pharmacist. Proper training is essential to overcome the gap between community pharmacist and Government sector to eradicate TB by 2025 from India.
Validation and Implementation of the Roche FLOW System in a Large Routine Molecular Diagnostic Laboratory
Authors: Wilson Steve , Kirk-Granger Helen , Tanner Hannah , Lewis Clare Overton , Ratcliffe Daina , Workman Judith 
Published: March 2020

Background - The PHE Public Health Laboratory, Birmingham at Heartlands hospital has an annual turn-over in excess of 750,000 specimens, 41,000 of which are processed using real-time PCR in the molecular section. In 2017, due to the age of existing instrumentation, the laboratory began a programme of replacement.
Methods - During 2017-19 the entire molecular service was replaced with a new high-throughput automated Roche FLOW system, consisting of a primary sample handler (PSU), two MagNA Pure 96 instruments, a PCR set-up unit (PSU), three 384-well LightCycler 480 II instruments and overarching FLOW software responsible for automated data handling, specimen tracking and workflow between the instruments.
Results - The bulk of the in-house developed assay repertoire, representing 34 viral, bacterial and fungal targets was re-optimised in 19 multiplexes. These were fully validated against existing molecular tests and were introduced into routine diagnostic service in June 2018. The FLOW software was successfully interfaced with the LIMS system, allowing rapid two-way communication of test requests and results. Over the following ten months, the service was expanded with an additional seven targets. The new system and assays were audited by UKAS in April 2019 and achieved accreditation to ISO:15189:2012 in August 2019.
Conclusion – The Roche FLOW system was successfully validated and introduced into routine diagnostic service and now offers significant improvements in assay performance, sample throughput and turnaround time. Details of the validation process, post-implementation modifications, trouble-shooting and lessons learnt will be of value to other diagnostic laboratories considering the introduction of this technology.
Review of antibiotic prophylaxis for the prevention of surgical site infection in low and middle income countries (LMICs)
Authors: Cooper Lesley , Sneddon Jacqueline 
Published: March 2020

Background
The Scottish Antimicrobial Prescribing Group (SAPG) is supporting two hospitals in Ghana via a Fleming Fund healthcare partnership to develop antimicrobial stewardship. Initial intelligence gathering suggests that antibiotic prophylaxis to prevent surgical site infection (SSI) is suboptimal. To inform a quality improvement programme we have reviewed the evidence for use of surgical prophylaxis in LMICs including staff behaviours and attitudes.

Methods
MEDLINE, Embase, Cochrane, CINHAL and Google Scholar were searched from inception to 22 July 2019 for trials, audits, guidelines and systematic review in English. Grey literature, websites and reference lists of included studies were searched. The following data were extracted; study characteristics, interventions, outcomes and recommendations. In view of heterogeneity between studies descriptive analysis was conducted.

Results
Of 185 records screened, 26 studies related to SSI and timing of antibiotic prophylaxis in LMICs were included. The incidence of SSI is significantly higher in LMICs compared with high income countries, recording of infection surveillance data is poor and a lack of local guidelines for antibiotic prophylaxis. Several projects in Africa have reported reduction in SSI with single dose preoperative antibiotic use compared with post-operative prophylaxis and a reduction in cost and nurse time. Despite evidence to the contrary, many surgeons continue to use post-operative antibiotic prophylaxis.

Conclusion
Education to improve incidence of SSI in LMICs through appropriate antibiotic prophylaxis can be successful. Interventions must include local context and address strongly held beliefs. The establishment of local multidisciplinary teams will promote ownership and sustainability of change.
Impact of the Scottish Reduction in Antimicrobial Prescribing (ScRAP) Programme on primary care prescribing for urinary tract infection (UTI)
Authors: Sneddon Jacqueline , Thomson Anne , Malcolm William , Baxter Linsey 
Published: March 2020

Introduction
The ScRAP programme was developed as a national initiative to support improvements in managing patients presenting with symptoms of UTI. The programme comprises educational content plus improvement ideas. It was implemented in one large, mainly urban, NHS board region covering 21% of the Scottish population via Prescribing Support Pharmacists working with individual GP Practices. A key aim was to reduce unnecessary antibiotic use.

Method
A facilitated learning session was delivered and all clinical and non-clinical GP Practice staff, were invited to attend. Evidence supporting best practice in managing UTI, local prescribing data and local practice was considered and discussed. The session concluded with action planning to reflect on current practice and identify areas for improvement.
National data held by NHS National Services Scotland was used to evaluate prescribing across all NHS board regions in Scotland focusing on total use of antibiotics and use of trimethoprim and nitrofurantoin which are used solely for UTI.

Results
Analysis of national prescribing data comparing the implementation region with the rest of Scotland suggests the intervention has been successful. Comparing data from prior to and for one year after the intervention period reductions for the intervention board versus the rest of Scotland were as follows: all antibiotics 7.29% vs 6.11%; trimethoprim 6.14% vs 3.73%; nitrofurantoin 3.92% vs 0.56%.

Conclusion
Quantitative evaluation provides evidence of the impact of ScRAP on prescribing rates. This suggests that improved practice has led to reduction in unnecessary use of antibiotics for acute and recurrent UTI.
Incidence of Group B Streptococcus bacteraemia in mum and newborn following antimicrobial prophylaxis- To screen or not to screen?
Authors: Hughes Stephen , Davidson Alex , Moore Luke , Mughal Nabeela 
Published: March 2020

Introduction
There is no routine screening for antenatal Group B Streptococcus (GBS) carriage in the UK. However invasive GBS in newborns, whilst rare (0.57/1000 births), is associated with mortality (5%) and long-term disability (9%). Antimicrobialsperi-partum can reduce the risk of invasive infection.

Method
We undertook a retrospective observational study at a London teaching hospital to investigate the incidence of invasive GBS peri-partum in both mother and child between 1/4/16 and 31/3/19.

Results
There were 16,869 live births recorded at Chelsea & Westminster Hospital during the study period. Operative, caesarean and spontaneous delivery accounted for 16.7%, 34.9% and 48.2%; with incidence of neonatal GBS bacteraemia being 0.18%, 0.08% and 0.11%, respectively. 20 (0.12%) neonates had invasive GBS infections, with 7/20 neonates having concurrent maternal GBS bacteraemia. 34(0.22%) ladies had GBS bacteraemia peri-partum; none had GBS isolated prior to delivery. 543 women had a positive GBS clinical isolate prior to labour;69.1% received GBS prophylaxis peri-partum with no invasive GBS transmission. Despite no prophylaxis in 168/543 GBS colonised women, no invasive GBS neonatal cases were identified.
Conclusions
Our local data identifies a low prevalence (0.12%) of invasive GBS infection in newborns. Maternal GBS bacteraemia is more frequently observed and associated with concurrent newborn GBS bacteraemia. Antimicrobial prophylaxis adherence peripartum although recommended is suboptimal, even though no invasive GBS transmission was identified. All invasive GBS infections were not known to be colonised pre-delivery. The current recommendations for targeting recent GBS culture do not appear to be a sensitive predictor of invasive peri-partum GBS infection.
Modernising respiratory diagnostics: the impact of biofire FilmArray pneumonia panel plus and respiratory panel on the detection of viruses and atypical bacteria
Authors: Wearmouth Debbie , Burns Phillipa 
Published: March 2020

BACKGROUND
The incidence of pneumonia is high within our local patient population and it is a significant cause of morbidity and mortality. The adoption of rapid molecular technology enables targeted clinical interventions and the initiation of appropriate antimicrobial and antiviral therapy.
METHOD
From February 2019, all lower respiratory samples submitted for microbiological analysis were examined to assess if a Pneumonia FilmArray would be a suitable investigation; indications for testing included radiological evidence of pneumonia or relevant clinical information suggesting atypical infection. Nasal pharyngeal swabs could be requested by clinicians across the hospital based on presenting signs and symptoms.
RESULTS
In total 883 nasal pharyngeal swabs and 175 lower respiratory tract samples from 927 patients were tested, 514 positive results were obtained; 450 from nasal pharyngeal swabs and 64 from lower respiratory tract samples.
Notably, two Bordetella pertussis and two Legionella pneumophiliaand five Mycoplasma pneumoniae were detected. One of the Bordetella pertussis was confirmed by culture, 9 days after the molecular result and the other case was detected in a neutropenic adult within an oncology, enabling rapif infection control intervention. Both Legionella cases were confirmed with urinary antigen testing, however neither grew on culture.
CONCLUSION
FilmArray technology enables the rapid identification of the causative agents of viral and atypical pneumonia, it is a useful adjunct to traditional testing and it enables rapid clinical and infection control intervention.