bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory lessons in identifying Pasteurella bettyae
Authors: Lee Marco , Justin Winston , Bishop William 
Published: March 2020

Introduction:
We discuss the phenotypic features of a clinically significant blood culture isolate that was ultimately identified as Pasteurella bettyae, with important laboratory learning points.

Laboratory diagnosis:
The blood culture from a female patient with septic shock from an unknown source grew a Gram-negative, oxidase-positive, coccobacillus that was initially identified by API® NH as Haemophilus influenzae (%ID=99.8; T=0.75). A respiratory source was therefore investigated for. The MALDI-TOF result, which was returned to the laboratory 4 weeks after blood culture became positive, revealed the isolate to be Pasteurella bettyae (score=2.305). P. bettyae is an unusual organism associated with gynaecological infections, such as Bartholin’s abscess. Local source control, such as incision and drainage of a Bartholin’s abscess, may accelerate resolution of sepsis. The laboratory misclassification of P. bettyae as H. influenzae using API® NH may lead to misidentification of the source of infection.

Learning points:
1. Correctly identifying P. bettyae as the cause of a Gram-negative coccobacillus bacteremia can prompt suspicion of a gynaecological source of sepsis.
2. P. bettyae and H. influenzae, as members of the same family Pasteurellaceae, have overlapping morphological and biochemical features that can lead to laboratory misclassification. A catalase test and x+v plates can clearly differentiate the isolates (discussed further in poster). It is recommended that laboratories perform both tests, with MALDI-TOF confirmation if possible, rather than rely solely on the result of an API® NH.
A review of the utility of PET imaging in Staphylococcus aureus bacteraemia (SAB) using electronic data
Authors: Cavaliere Chiara , Klein John , Goodman Anna 
Published: March 2020

Introduction:
If the infectious focus is not identified, there is an associated higher mortality in Staphylococcus aureus bacteraemia (SAB) [1]. A retrospective observational study found patients with high-risk SAB who had a PET scan had a 67% reduction in mortality compared to those who did not [2]. We used electronic data to determine the range of infectious foci in SAB and the use of PET in our trust.

Methods:
From 1/1/13 to 31/12/18 all patients with SAB at St Thomas’ Hospital, London, were reviewed by the infectious diseases team and data collected prospectively using an Access database. A retrospective analysis of this database, electronic records, radiology and nuclear imaging was conducted.

Results:
355 episodes of SAB affected 296 patients. 28 (8%) episodes were MRSA in 24 (8%) of patients. Infectious sources found included bone and joint (23%), IV access (15%), vascular infection (15%), no infective focus (13%), SSTI (12%) and endocarditis (9%). Imaging used to determine the focus of infection included MRI (18%), CT (26%) and PET scan (10%). In-hospital mortality was significantly lower in those who had a PET scan than in those who did not (1/31, 3% v. 50/265 patients (last episode), 19%, P=0.03).
Conclusions:
Mortality was lower in those who had PET at our trust. This is consistent with data published from other centres and requires further investigation. A prospective trial of PET in SAB is urgently needed.
References:
[1] PMID: 30179645
[2] PMID: 28336786
Evaluation of Xpert® Xpress Strep A Test for detection of Group A streptococcus in throat swabs
Authors: Eldirdiri Sahar , Omojola James , MacDonald Shona , Carmichael Ian , Parcell Ben 
Published: March 2020

Background

Streptococcus pyogenes (Group A β -hemolytic Streptococcus) infections in humans range from mild pharyngitis to life-threatening infections such as septicaemia and necrotizing fasciitis. We assessed the diagnostic accuracy of the Xpert® Xpress Strep A Assay, a new automated real-time polymerase chain reaction (PCR) that can detect this pathogen.
Methods
We evaluated the diagnostic accuracy (sensitivity, specificity PPV and NPV) of Xpert® Xpress Strep A Test (Cepheid, Maurens-Scopont, France) for the detection of Group A Streptococcus in throat swabs using Copan virus transport medium at Ninewells Hospital & Medical School (Dundee, Scotland, UK). The performance of Xpert t® Xpress Strep A Assay was compared with routine culture (gold standard method).

Results
A total of 323 clinical throat swab samples were tested. The sensitivity of Xpert ® Xpress Strep A Assay was found to be 95% (95% CI, 75.13% -99.87); specificity 96.5% (95% CI 93.83% -98.36%);PPV 65.5% (95% CI 50.61% -77.89%); and NPV 99%(95% CI 97.68% -99.95%). Overall, there were eleven discrepant results, of these 10 were positive by PCR and not confirmed by culture and one sample was recorded positive by culture and negative by PCR. The turnaround time (TAT) was 24 minutes for negative samples and 18 minutes for positive samples.

Conclusion
The Xpert® Xpress Strep A Assay for detection of Streptococcus pyogenes in throat swabs had high sensitivity, specificity and rapid TAT. Use of this technology as a point-of-care test could be explored further to assess its impact on antimicrobial prescribing and infection prevention and control measures.
The public health task force in the management of the Mycobacterium chimaera case in the Vicenza hospital, Italy
Authors: mondino Sara , Manfrin Vinicio , Rassu Mario , Fallico Loredana , Mantoan Paola , Zanon Maria Paola , Cazzaro Romina , Barra Salvatore 
Published: March 2020

BACKGROUND
Since 2013, an ongoing global outbreak of Mycobacterium chimaera among patients who underwent open-chest surgery has been recognized with all cases linked to contamination of a specific brand of heater-cooler device (HCD). Nine cases were diagnosed with disseminated M. chimaera infectionin our hospital. Following the first cases HCD was changed with different technology assuring no release of contaminated particles. The potentially at-risk population was managed throughout a multidisciplinary task force.
METHODS
In November 2018, following an infected patient’ death, a huge impact on public opinion was registered following mass media publicity of the case. A task force was built up to face the concern of the population: apress release [https://context.reverso.net/traduzione/inglese-italiano/press+release]and an official note were publicly released addressing risk factors and critical symptoms and a call center was activated. The notice was transmitted to general practitioners too. People complaining symptoms suggestive for infection, primarily screened by an expert group through telephone interview, were addressed to an infectious consultation.
RESULTS
The official note was delivered to 2181 potentially at risk patients chosen by cardio surgery registry and 567 of them called back the call center and were interviewed. 66 patients were judged to need infectious specialist consultation: 12 were submitted to further microbiological analysis and 4 required hospitalization. No new cases of infectious were detected.
CONCLUSION
The public health task force promptly activated granted safety measures for the population; furthermore HCD will soon be settled in separated place out from operating room.
Application of the Bruker IR Biotyper for Strain Typing During An Outbreak
Authors: Alhasabi Jenan , Balakrishnan Indran , Wey Emmanuel 
Published: March 2020

Background
Molecular typing methods such as whole genome sequencing are relatively time-consuming and expensive. Here we demonstrate the effectiveness of the Bruker IR biotyper in strain typing.
Methods
Isolates of multi-resistant Enterobacteriacae from clinical samples were typed using the Bruker IR Biotyper. The relationships between isolates were analysed using the Bruker IR biotyper software (version 2.1.0.195).

Results
On dendrogram analysis, the 13 E. coli isolates mostly clustered independently with all 5 replicates. Two isolates (RFH035 and RFH007) clustered together, their replicates spanning across 3 clusters, indicating that they are the same isolate. This was confirmed on Principle Component Analysis (PCA).
EightK. pneumoniaeisolates segregated into 7 clusters. Two isolates (RFH033 and RFH006) clustered together initially but separated on the PCA plot.
Discussion
RFH035 and RFH007 both came from patients infected with NDM-producing E. coli. Their PFGE profiles are indistinguishable. Both patients were admitted to hospital and were on the same ward simultaneously, reflecting the co-clustering seen with the Bruker IR biotyper.
Both RFH033 and 006 were NDM producers, but RFH033 co-produced OXA48. They had almost indistinguishable VNTR profiles with only one difference. This relatedness but difference in resistance profile is reflected in the close relationship seen on dendrogram but separation by PCA seen with the Bruker IR biotyper.
The Bruker IR biotyper is therefore able to reliably demonstrate relatedness and discrimination between strains of E. coli and K. pneumoniae. This methodology has much faster turnaround times than conventional methodology, and therefore has the potential to inform outbreak management in a more timely manner.
Towards a harmonised approach to Carbapenemase-producing Enterobacteriaceae (CPE) screening and patient management in North East and Cumbria hospitals
Authors: Love Nicola , Darke Joanne , Howard Simon , Davison Paul , Denton Miles , Samuel Julie , Manley Petra 
Published: March 2020

In mid-2018, a Carbapenemase-producing Enterobacteriaceae (CPE) cluster was investigated in the North East of England, in which transmission had occurred across several hospital trusts. We undertook a survey of current CPE detection and management practices in North East and Cumbria (NEC) trusts to inform a harmonised approach that could be adopted across the region.
A semi-structured survey was carried out with one consultant microbiologist per trust by telephone interview (n=6) or electronic questionnaire (n=3) to determine CPE screening procedures, laboratory techniques and patient management practices.
Screening policies were in place in all trusts, including screening protocols for patients previously admitted outside of the UK or those known to be CPE positive, in accordance with PHE guidelines. Policies for screening patients who had been admitted to other UK hospitals varied across trusts, as did laboratory methods used. Over 80% of trusts communicated CPE status to patients and contacts by information leaflet. However, there was no uniform way of communicating CPE status to social care settings, GPs and other hospital trusts in the event of discharge or inter-hospital transfer.
The results of the survey suggest improvements could be made to the way information on patient CPE status is shared to ensure that the risk of transmission is reduced. This includes improved communication with residential settings, primary care and other hospital trusts in the event of a discharge or inter-hospital transfer. In addition, this work will inform further discussions across NEC towards developing a single regional Infection Prevention and control strategy for CPE.
Real-world experience with Isavuconazole therapy in a large tertiary hospital in Cambridge, UK
Authors: Enoch David , Tyler Netta , Micallef Christianne , Wong Vanessa 
Published: March 2020

Background: Isavuconazole (ISV) is a second-generation triazole antifungal used for invasive fungal infections (IFIs). Here, we describe our experiences of ISV.
Methods: This single-centre retrospective study included all patients who commenced a course of ISV over a 3-year period (1/7/16-30/6/19). ISV was used for the treatment of IFIs when no alternative was suitable. Demographics, clinical details and antimicrobial history were obtained from our integrated electronic health record and laboratory system (EPIC).
Results: Twenty-four patients, aged between 17–78 years (median 54), received ISV in the study period. Sixteen (67%) were haematology patients. Using EORTC criteria, six had possible invasive aspergillosis (IA), 1 had a possible yeast infection, 13 had probable IA, 3 had proven IA and one had a proven yeast infection. Four were neutropenic (neutrophil count <0.5x109/L) and 7 had renal impairment. Half of the patients (12/24; 50%) had received a transplant prior to commencing (nine allografts, one kidney, one lung, one multi-visceral) and a further two underwent an allograft whilst receiving ISV. ISV pre-dose levels ranged from 1.29–7.7mg/L (median 2.73mg/L; IQR 2.1 – 3.13mg/L). ISV was given for 1–733 days (median 42 days). In patients who were still alive during therapy, the treatment duration ranged from 3–342 days (median 97 days). Ten were dead within 42-84 days of commencing therapy; 6 had died by the end of therapy.
Conclusion: Our findings suggest that ISV is used infrequently, predominantly in haematology. More data is needed to determine optimal treatment course and the role of therapeutic drug monitoring.
In-Vitro Antibacterial Therapy of Ficus exasperata, Securinega virosa and Tamarindus indica Leaf Extract on Bacterial Isolate from Otitis Media effusion
Authors: Ojo Abidemi , Ojo Olugbenga , Adebajo Seun , Oladotun Biola , Sodunke Ganiyat , Ejilude Oluwaseun 
Published: March 2020

Background:
Antibiotics resistance which is a global health challenge is no longer a future threat but a present challenge to all facet of clinical settings. Thus, treatment of Otitis media effusion in this regards is a major concern.

Objectives:
The aim of this study was to determine the efficacy of three medicinal plant extract in the treatment of Otitis media as an alternative therapy.

Methods:
The antibacterial effect of absolute methanol leaf extract of Ficus exasperate, Securinega virosa,and Tamarindus indica on organisms isolated from otitis media effusion was determined using agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) was also determined using the double fold dilution technique. Treatment means were compared with Duncan’s New Multiple Range Test at 5% level of significance using Statistical Analysis System

Results:
Bacteria isolated include Staphylococcus aureus 19(39.58%), Klebsiella pneumonia 15(31.25%), Pseudomonas aeruginosa 10(20.83%), Proteus mirabilis3(6.25%) and Streptococcus pneumoniae 1(2.08%). At 1.0mg/ml concentration, At 1.0 mg/ml concentration, Tamarindus indicainhibited all the isolates; For Ficus exasperate,the MIC was 0.39 mg/ml and MBC was 0.78 mg/ml against Pseudomonas aeruginosa; Securinega virosa MIC was 0.78mg/ml and MCB 1.56mg/ml against Staphylococcus aureus, Pseudomonas aeruginosaand Klebsiella pneumoniae. Tamrindus indica lowest MIC was 0.39 mg/ml and MBC of 1.56 mg/ml against streptococcus pneumoniae. The antimicrobial activity of the three extracts shows significant (P<0.05) inhibition for the organisms.

Conclusion:
This study showed the potentials of the aforementioned extracts as treatment options for cases of OME.
Pharmacodynamic evaluation of intermittent versus prolonged infusion dosing regimens of piperacillin/tazobactam in a hollow-fiber infection model against two susceptible Klebsiella pneumoniae clinical isolates
Authors: Sumi Chandra Datta , B.Sime Fekade , Heffernan Aaron J. , Naicker Saiyuri , Islam Kamrul , Cottrell Kyra , Harris Patrick N.A. , Roberts Jason A. 
Published: March 2020

Background - This study aims to compare the bacterial killing and suppression of resistance emergence of intermittent and prolonged infusions of piperacillin/tazobactam (PTZ) against clinical K. pneumoniae isolates.
Methods - Two clinical isolates, CTX-M-14 producing #69 (MIC 1 mg/L), and DHA-1, SHV-106 producing #68 (MIC 8 mg/L), were studied in a dynamic hollow-fiber infection model over 7 days (initial inoculum 107 CFU/mL). Three piperacillin doses (4/0.5g over 0.5h, and 4h infusion 8 hourly; 12/1.5g continuous infusion 24h) against #69, and six dosages of piperacillin (4/0.5g over 0.5h, and 4h infusion 8 hourly, and 12/1.5g continuous infusion 24h; 4/0.5g over 0.5h, and 3h infusion 6 hourly, and 16/2g continuous infusion 24h) against #68 were tested. The total and less-susceptible bacterial populations were determined.
Results - For all PTZ dosing regimens against #69, there were ∼4 logs of bacterial killing over 8h. The amplification of less-susceptible subpopulation were associated with intermittent infusion (T>MIC 90%, Cmin/MIC = 0.4) after 24h, and with extended infusion (T>MIC 100%, Cmin/MIC = 2.76) after 72h. However, continuous infusion (Cmin/MIC = 35) prevented drug resistance amplification and sterilized the model system. For #68, there was a similar initial bacterial killing profile; however, all regimens were associated with the emergence of a resistant subpopulation after 8h. The MIC of resistant subpopulations exceeded 256 mg/L.
Conclusions – To maximize bacterial killing and suppress the emergence of resistance of multiple-beta-lactamases producing K. pneumoniae isolates with higher MIC alternative therapeutic strategies are required.
Positive Serum (1,3)-β-D-Glucan Testing in Surgical Patients across the Bristol Area
Authors: Hodgson Sam , Hamilton Fergus , Jacobson Kim 
Published: March 2020

Background:
An evidence gap exists in anti-fungal diagnostic practice following abdominal surgery, especially when compared to haem-oncology counterparts. In light of the recent Anti-fungal Stewardship CQUIN, our study addresses the utility of serum (1,3)-β-D-Glucan (BDG) testing post-gastrointestinal surgery.

Method:
We identified positive BDG results (>/=80pg/mL) on ITU and surgical wards in 3 major institutions in the Bristol area. Those with a ‘history of abdominal surgery </=30 days previous’ were identified using electronic health records. Other variables included number of days from surgery to testing, value of the result, and past medical history.

Results:
110 patients with positive results were identified. 19 (17.3%) of these had a history of abdominal surgery. By surgical type, 6 (31.6%) had major abdominal surgery. 6 (31.6%) had pancreatic surgery and 5 (26.3%) small bowel resection. 2 had other types of surgery. The mean BDG score was 286pg/mL. 1 patient had risk factors other than gastrointestinal surgery for a positive BDG result.
Only 1 patient died within 28 days. Patients tested between 0-9, 10-19 or 20-30 days of surgery had mean BDG scores of 329pg/mL, 302pg/mL and 390pg/mL respectively. 40% were tested within 9 days of surgery. There was no clear evidence of invasive fungal infections.

Conclusion:
Positive BDG testing is common after surgery, but does not appear to be associated with a significant mortality burden. Ensuring appropriate anti-fungal therapy is essential for treatment, risk reduction and cost containment. More research is needed to identify appropriate testing strategies in patients with abdominal surgery.
Anti-biofilm potential of peptides against foodborne pathogens
Authors: Shen Cunkuan , Kubo Rinka , Masuda Yoshimitsu , Honjoh Ken-ichi , Miyamoto Takahisa 
Published: March 2020

Background:
Biofilm is defined as a community where bacterial cells encased in a matrix of extracellular polymeric substances adhere to each other and/or to a surface. In food industry, foodborne pathogens like Salmonella are capable of forming biofilms on open surfaces. We have shown anti-biofilm effects of ε-poly-lysine (PL) and milk serum protein (MSP) against various bacteria. In this study, peptides derived from egg was investigated for anti-biofilm effects on foodborne pathogens.

Methods:
Effects of several kinds of peptides, including 3 kinds of hydrolysates derived from egg, together with PL and MSP, on biofilm formation of 4 kinds of foodborne pathogens (Escherichia coli O157:H7, S. Typhimurium, Staphylococcus aureus and Listeria monocytogenes) were investigated on microtiter plates through biomass quantification with crystal violet staining.

Results:
Both 0.01% PL and 0.25% MSP significantly decrease biofilm formation of all the pathogens, while PL was more effective than MSP against gram-negative bacteria. All the hydrolysates showed considerable effect under high concentration (1%), among them hydrolysate 2 was more effective than the others since it inhibited biofilm formation of S.Typhimurium, even under concentration of 0.1%.

Conclusion:
The egg white hydrolysate contains some antibacterial peptides that could modulate biofilm formation of S.Typhimurium and other pathogens, which could be beneficial to develop new strategies to combat biofilm infections.
An Assessment of Point-of-Care PCR Testing for the Diagnosis and Management of Meningo-Encephalitis
Authors: Gamio-Izasmendi Diana , Cooke Benjamin 
Published: March 2020

BACKGROUND
Meningitis and Encephalitis are potentially fatal infections. When suspected, empirical treatment is started, and only safely discontinued once excluded. The impact of current CSF investigations is prolonged inpatient stay, and exposure to broad-spectrum antimicrobials. Biofire Filmarray is a point-of-care PCR system. Our aim was to assess time to BioFire result, and its impact on clinical management.
METHOD
BioFire was implemented, in addition to current practice, on CSF samples with WCC ≥10 and all neonatal samples processed between November 2018 and February 2019. Data was collected prospectively for: patient demographics, sampling time, time to result of BioFire and current PCR, antimicrobial regime, and early discharge. Percentage agreement between BioFire and current PCR, mean time to result, percentage cases with reduction in antimicrobials, and mean length of stay for those discharged based on BioFire, were calculated.
RESULTS
There were 22 samples analysed. There was an 86.4% agreement between BioFire and current PCR. In cases of disagreement, BioFire identified pathogens where standard PCR had not. One sample was insufficient for virology PCR however, a full array was obtained from BioFire. Mean time to BioFire result authorization was 17.8 hours, compared to 316 for virology PCR and 331.2 for bacteriology PCR. BioFire allowed narrowing of antimicrobial therapy in 22.7% of patients, discontinuation in 41.0%, and early discharge in 27.3%.
CONCLUSION
BioFire provides comparable diagnosis of meningo-encephalitis faster than current practice. With the current focus on rising bed pressures and antimicrobial stewardship, BioFire allows targeted therapy and safe early discharge where infection is excluded.