FEDERATION OF
infection societies
CONFERENCE 2018

13th – 15th November 2018 | Sage Gateshead – Newcastle

FEDERATION OF
infection societies
CONFERENCE 2018

13th – 15th November 2018 | Sage Gateshead – Newcastle

FEDERATION OF
infection societies
CONFERENCE 2018

13th – 15th November 2018 | Sage Gateshead – Newcastle

Posters

DIAGNOSTICS – Poster Nos. 161-188

161
Comparison of four commercial rapid tests for the identification of carbapenamase enzyme activity

Abstract - 161

Poster 161

Comparison of four commercial rapid tests for the identification of carbapenamase enzyme activity

Fiona Shaw, Chris Gerrard, James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. Basic microbiology and virology services are provided by the on-site laboratory.

Clinical and surveillance isolates of Enterobacterales and Pseudomonas species are screened for suspected carbapenemase production as below:

  • Isolates with reduced zone size (<25 mm) to ertapenem or meropenem discs are tested for carbapenem MICs by gradient strip
  • Isolates with an MIC >0.12 mg/L are screened as per PHE guidance for carbapenemase production
  • Isolates are screened with the Rosco KPC/MBL confirmation kit plus temocillin
  • Isolates identified with suspected carbapenemase production are referred to PHE for molecular confirmation

The laboratory performed a comparison of four commercial tests in response to the problems identified:

  • PHE confirmation takes several weeks to return
  • In-house phenotypic screening shows multiple false-positives

Methods: Four commercial carbapenemase detection tests were evaluated following the manufacturer’s guidance. These tests were:

  • Rapidec CarbaNP (bioMérieux) (chromogenic, identifies activity)
  • β-CARBA (Bio-Rad) (chromogenic, identifies activity)
  • Resist-4 O.K.N.V. (Coris Bioconcept) (lateral flow, identifies enzyme)
  • NG-Test CARBA 5 (NG Biotech) (lateral flow, identifies enzyme)

The tests were evaluated using:

  • 5 CPE control organisms (purchased from Pro-Lab)
  • 15 clinical isolates previously referred to PHE

The clinical isolates had been reported by PHE with a number of different resistance mechanisms:

  • 2 NDM
  • 4 KPC
  • 3 ESBL with impermeability (ertapenem MIC 1-16 mg/L)
  • 3 AmpC with impermeability (ertapenem MIC 1-4 mg/L)
  • 2 Unknown mechanism, possible ESBL (ertapenem MIC 8-16 mg/L)
  • 1 Impermeability with possible K1 hyperproduction (ertapenem MIC 2 mg/L)

Results

Rapidec CarbNP

  • Correctly identified carbapenemase activity in IMP, VIM, KPC, OXA-48-like and NDM expressing control strains
  • Correctly categorised 15/15 clinical strains on initial incubation, however 4 isolates showed false-positive activity on extended incubation

β-CARBA

  • Correctly identified carbapenemase activity in IMP, KPC, OXA-48-like and NDM expressing control strains, but not VIM
  • Correctly categorised 13/15 clinical strains

Resist-4 O.K.N.V.

  • Correctly identified VIM, KPC, OXA-48-like and NDM activity in control strains, but not IMP (not included in the enzyme panel)
  • Correctly categorised 15/15 clinical strains

NG-Test CARBA 5

  • Correctly identified IMP, VIM, KPC, OXA-48-like and NDM activity in control strain.
  • Correctly categorised 15/15 clinical strains

Discussion: The most appropriate carbapenemase screening test will not be the same for each laboratory. From the cases identified at Alder Hey we have NDM and KPC enzymes only, and so we required a test that confidently identified these enzymes or their activity. If our epidemiology however showed the presence of IMP enzymes for example, this would make the Resist-4 lateral flow assay unsuitable.

The two lateral flow assays were preferred in the laboratory for their ease of use and their clear unambiguous end points. The chromogenic tests were felt to be more difficult to read confidently.

The two lateral flow assays were felt to perform equally well given the local epidemiology, and both tests were considered suitable for in-house use. A small number of Rapidec tests are also held for cases where there is a high clinical concern of possible carbapenemase activity and the lateral flow assay is negative (i.e. to detect carbapenemase activity from other enzymes).

162
Verification of an existing blood culture incubation system when moving to a new laboratory

Abstract - 162

Poster 162

Verification of an existing blood culture incubation system when moving to a new laboratory

Chris Gerrard, James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. Basic microbiology and virology services are provided by the on-site laboratory.

The BacT-ALERT platform has been in use at Alder Hey for blood culture incubation for over ten years. In autumn 2015 the laboratory moved to the new Alder Hey building. The subsequent UKAS inspection in December 2017 identified that there was no formal verification record for the BacT-ALERT following the transfer of the laboratory. We therefore describe the method used to verify the performance of the system after the move.

Methods: The performance of the BacT-ALERT blood culture incubator was assessed for:

  • Limit of Detection: McFarland 0.5 suspensions of EUCAST control strains of Escherichia coli (NCTC 12241), Staphylococcus aureus (NCTC 12973), Pseudomonas aeruginosa (NCTC 12903), Streptococcus pneumoniae (NCTC 12977), Haemophilus influenzae (NCTC 12975) and Candida albicans (CNM-CL F8555) were made in sterile saline and serial dilutions made in Brain-Heart Infusion broth. Isolate cfu counts were estimated by serial Miles and Misra plating starting at a 1:10000 dilution and PF Plus blood culture bottles were inoculated with 1 ml of suspension starting at a 1:100000 dilution.
  • False-negative results: 50 clinical blood cultures submitted to the laboratory were sub-cultured at 5 days to blood agar (BA), chocolate agar (CA), MacConkey agar (MA), Sabouraud agar (SA) and Fastidious Anaerobic Agar (FAA). All plates were read at 48 hours, and SA and FAA plates again after 5 days incubation. Sub culture, agar inoculation and incubation were performed according to the departmental standard operating procedure (based on the national SMIs).

Results

Limit of Detection:

  • Each tested strain was detectable down to a calculated level of <1 organism per millilitre of inoculum.
  • For H. influenzae cultures, higher concentration than shown in the graph failed to grow after 5 days incubation and failed to grow on terminal subculture; this is assumed to be due to the fastidious nature of the organism and that the cultures were inoculated without the nutrients that would be available from blood itself under normal clinical use.

False-negative results:

  • 50 consecutive negative PF Plus blood culture bottles were terminally sub-cultured as described above.
  • Of the sub-cultures where growth was observed, the growth on one BA (1 cfu coagulase-negative Staphylococcus, CoNS) and two CA (1 cfu and 2 cfu CoNS) plates were considered to be laboratory contaminants (the three plates represented three different blood cultures).
  • One clinically negative blood culture grew a Micrococcus species on BA, CA and MA and is considered to represent a true false-negative culture.
  • Negative predictive value of a negative blood culture at 5 days incubation = 49/50, 98%
  • The incubation graph for the false-negative culture was reviewed and showed no evidence of growth (i.e. the curve was flat).

Discussion: Verification records for laboratory equipment forms part of the evidence required for UKAS accreditation. We have therefore presented our verification method in the hope that others may find it useful, especially those who are moving existing and long-standing equipment to new settings as we did.

It was reassuring to confirm that the BacT-ALERT continues provides suitable detection of clinically significant organisms down to the level of single-digit organisms per millilitre of inoculum (using the paediatric bottles as these represent the overwhelming majority of Alder Hey blood cultures).

We did identify a 2% false-negative rate, although no clinically significant organisms were detected.

 

 

163
The AdvanDx Staphylococcus QuickFISH test for the differentiation of Staphylococcus aureus and coagulase-negative staphylococci from positive blood cultures

Abstract - 163

Poster 163

The AdvanDx Staphylococcus QuickFISH test for the differentiation of Staphylococcus aureus and coagulase-negative staphylococci from positive blood cultures

Teresa Barton, Kate Ball, Susie Batley, Pamela Hulme, Jane Johnson, Jessica Jones, Jane McGrane, Norma Thompson, Chris Gerrard, James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. Basic microbiology and virology services are provided by the on-site laboratory.

Staphylococcus aureus bloodstream infection is a significant event requiring prompt antibiotic management, whereas blood cultures yielding coagulase-negative staphylococci (CoNS) are often simply growing skin flora collected at the time of sampling. Rapid differentiation between the different staphylococci helps appropriate antibiotic management.

The Staphylococcus QuickFISH test was evaluated as a possible rapid test for the identification of S. aureus and CoNS directly from positive blood cultures.

Methods: Positive blood cultures showing Gram-positive cocci in clusters were tested using the QuickFISH in accordance with the manufacturer’s instructions, in addition to the routine processing (including direct tube coagulase) according to the local standard operating procedure (based on the national SMIs).

Results

QuickFISH

37 positive blood cultures were evaluated with the QuickFISH test:

  • 7 samples suggested the presence S. aureus and absence of CoNS by QuickFish; all grew S. aureus, none grew CoNS
  • 2 samples suggested mixed S. aureus and CoNS by QuickFISH; both grew mixed S. aureus and CoNS
  • 26 samples suggested the presence of CoNS  and absence of S. aureus by QuickFISH; all grew CoNS, none grew S. aureus
  • 2 samples were negative by QuickFISH; neither grew a Staphylococcus species (1 Micrococcus spp., 1 Kocuria spp.)

The performance of the QuickFISH test in our evaluation was:

  • Sensitivity for S. aureus: 100%
  • Specificity for S. aureus: 100%
  • Positive predictive value for S. aureus: 100%
  • Negative predictive value for S. aureus: 100%

Comparison with direct tube coagulase

32 positive blood cultures had both the QuickFISH test and the result of a tube coagulase test performed directly from the blood culture bottle and reported at 4 hours incubation; 8 of 8 blood cultures which grew a S. aureus were also direct tube coagulase positive, 24 of 24 cultures where S. aureus was not isolated were direct tube coagulase negative.

During the evaluation period the direct tube coagulase test therefore proved as effective at identifying S. aureus from blood culture bottles as the QuickFISH test, but added a delay to the result (<30 minutes for QuickFISH v’s 4 hours for the tube coagulase).

Retrospective review of direct tube coagulase results

39 blood cultures collected between January and July 2018 were identified as growing S. aureus (meticillin-sensitive or resistant, pure or mixed with other isolates). 30 of these cultures had the results of the direct tube coagulase test recorded at 4 hours; 4 cultures containing S. aureus (13.3%) were missed at four hours using the direct tube coagulase and therefore not identified until the following day.

Discussion: The AdvanDx Staphylococcus QuickFISH test was clearly able to differentiate between S. aureus and CoNS from positive blood culture bottles. The test was fairly simple to perform and provided results typically within 30 minutes of the Gram stain result.

The ability to confidently identify or exclude S. aureus in a positive blood culture rapidly was beneficial to the clinical teams in the appropriate management of a positive result and antimicrobial stewardship.

Although cost-per-test is higher than for example the Bruker SepsiTyper, the initial capital outlay is much lower (fluorescent microscope compared to MALDI-TOF). The test could also be used as an initial screen on positive blood cultures, where samples containing S. aureus could then be further characterised by for example Cepheid GeneXpert or BioFire FilmArray PCR tests.

Following this initial evaluation of the QuickFISH test, the performance in our hands was considered satisfactory enough to put forward a business case to request funding to introduce the test into routine clinical use. 

164
Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: preclinical verification testing and unexpected findings

Abstract - 164

Poster 164

Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: preclinical verification testing and unexpected findings

Fiona Shaw, James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. CSF culture is performed on-site, with referred testing to Liverpool Clinical Laboratories (LCL; virology), Public Health England (PHE; meningococcal/pneumococcal PCR), or Great Ormond Street (GOSH; 16S PCR) as required.

The BioFire/bioMérieux FilmArray has been used for respiratory viral PCR since 2013. The CSF PCR test was introduced in 2015 for use on critical care and general paediatrics, and later to neurology. A phased introduction, aiming to establish the effectiveness of the test before full introduction, was made in three stages:

  1. A pre-clinical verification using known stored CSF samples,
  2. An initial clinical phase during which the test was performed on request without any sample restrictions, and
  3. Testing on request provided the sample met specific acceptance criteria

We here present the results of the initial pre-clinical verification exercise.

Methods: Pre-clinical verification was performed using stored CSF samples as described below.

Bacteriology

  • 10 samples which were culture-negative and either PHE meningococcal/pneumococcal PCR-negative (9) or 16S PCR-negative (1).
  • 10 samples either culture positive (3 S. agalactiae, 2 E. coli, 1 L. monocytogenes also VZV positive, 1 N. meningitidis) or PCR positive (3 N. meningitidis).

Virology

  • 10 CSF samples which were culture-negative and viral PCR-negative.
  • 10 samples positive on our standard referred viral PCR (6 Enterovirus, 2 Parechovirus, 2 VZV).

Spiked samples

  • 10 unknown spiked samples were provided by the LCL virology department to include S. pneumoniae and HSV samples (as no positives were available in-house for testing).

Results

Unexpected results are noted below and considered further in the discussion.

Bacteriology

  • Negative controls: all negative for bacterial targets on the FilmArray panel. Unexpected positive results were seen for Enterovirus (1, not previously tested) and HHV-6 (1).
  • Positive control: 8 samples agreed with the expected results. False-negative results were seen with E. coli (1) and N. meningitidis (1, originally PCR positive only).

Virology

  • Negative controls: all negative for viral targets on the FilmArray panel. An unexpected positive result was seen for H. influenzae (1).
  • Positive control: 9 samples agreed with the expected results. A false-negative result was seen with VZV (1).

Spiked samples

The FilmArray gave the expected results for 8 of the unknown spiked samples (1 negative, 1 H. influenzae, 1 N. meningitidis, 1 mixed N. meningitidis and S. pneumonae, 1 VZV, 1 HSV1, 2 HSV2). The two unexpected results detected N. meningitidis in samples spiked with N. subflava (1) or S. pneumoniae (1).

Discussion: False-negative results from stored CSFs (1 culture positive E. coli, 1 PCR-positive N. meningitidis, 1 VZV all FilmArray negative) are thought to be due to the use of small remaining sample volumes, less than that required according to the manufacturer’s instructions. Alternate explanations include the degeneration of genomic material in storage, or in the case of E. coli the presence of a non-K1 strain. There was no remaining sample for any of these in order to investigate further, and serotyping of the E. coli had not been performed

Unexpected viral-positive results were either in samples where viral testing had not been originally requested (Enterovirus) or not included in current testing (HHV6). The H. influenzae PCR detection was unexplained and no sample was left for further investigation.

For the spiked samples, testing at GOSH identified N. meningitidis from the N. subflava sample, and no meningococcal PCR result was available for the original CSF sample spiked with S. pneumoniae.

Overall the FilmArray showed:

  • Sensitivity: 80% bacteriology, 91% virology
  • Specificity: 97% bacteriology, 93% virology
  • Negative predictive value: 94% bacteriology, 96% virology

Following this the laboratory proceeded to a phased clinical introduction of the test.

165
Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: initial clinical introduction and lessons learnt

Abstract - 165

Poster 165

Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: initial clinical introduction and lessons learnt

James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. CSF culture is performed on-site, with referred testing to Liverpool Clinical Laboratories (LCL; virology), Public Health England (PHE; meningococcal/pneumococcal PCR), or Great Ormond Street (GOSH; 16S PCR) as required.

The BioFire/bioMérieux FilmArray has been used for respiratory viral PCR since 2013. The CSF PCR test was introduced in 2015 for use on critical care and general paediatrics, and later to neurology. A phased introduction, aiming to establish the effectiveness of the test before full introduction, was made in three stages:

  1. A pre-clinical verification using known stored CSF samples,
  2. An initial clinical phase during which the test was performed on request without any sample restrictions, and
  3. Testing on request provided the sample met specific acceptance criteria

The results of the first phase of clinical use are presented here.

Methods: The results of the first 50 tests were reviewed.

Results: Over half of the tests were negative (27/50, 54%). Of the remaining 3 identified a single bacterial pathogen (6%), 18 identified a single viral pathogen (36%), and 2 identified both a viral and bacterial pathogen (4%).

Confirmed results

Bacteriology:

  • One bacterial pathogen was confirmed by other samples (N. meningitidis).

Virology:

  • The most single common pathogen detected were Enterovirus (10) or Parechovirus (3). There were 2 HHV6, 2 HSV1, and 1 VZV.
  • 6 Enterovirus-positive samples were confirmed by PHE (the remaining had no sample left for referral).
  • 1 Parechovirus was confirmed by LCL (the remaining had no sample left for referral).
  • HHV6 results would not have been detected previously by routine CSF testing.
  • The VZ positive was confirmed by LCL.

Problem samples

Bacteriology:

  • Two bacterial pathogens were unable to be confirmed (1 S. pneumoniae, 1 H. influenzae).

Virology:

  • The HSV1 results were unconfirmed (1 sample tested negative on routine viral PCR, 1 sample was insufficient for referral but a repeat CSF was negative both on FilmArray and referred PCR).

Mixed results:

  • H. influenzae and HSV2 both unconfirmed (negative 16S PCR and viral PCR).
  • S. pneumoniae and Enterovirus both unconfirmed (insufficient sample for further investigation).

Discussion: The results of the initial 50 tests showed a number of unconfirmed potential false-positive results:

  • The FDA validation study showed the presence of unconfirmed S. pneumoniae results in keeping with our potential false-positive result.
  • The H. influenzae detection was from a heavily bloodstained sample; PHE report the presence of incidental S. pneumoniae in blood PCR in our young patients and it was thought that this result may have been similar as it did not fit the clinical picture.
  • The FDA validation study was only able to confirm 12 of 16 HSV-positive results. No false-positive HSV results were detected in pre-clinical evaluation in-house. The referred sample was only small volume and therefore may have diluted below the level of detection. In neither case was the clinical picture in keeping with HSV infection.
  • The mixed S. pneumoniae / Enterovirus samples was heavily bloodstained and therefore the result may reflect the presence in blood rather than CSF

Following this review it became apparent that patients were being treated on the basis of the PCR results (regardless of sample quality) rather than on clinical grounds. Conditions were therefore introduced to restrict testing:

  • Samples must not be bloodstained (based on macroscopic appearance rather than cell count).
  • Samples must be of sufficient volume to allow for a fully-sensitive confirmatory test (i.e. a minimum volume of 200 microlitres for FilmArray plus 400 microlitres minimum for referred tests plus ~100 microlitres for routine laboratory processing in bottle 3).

Estimated sample volumes are now reported with the microscopy results.

166
Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: sensitivity and specificity in the diagnosis or exclusion of paediatric meningitis and encephalitis

Abstract - 166

Poster 166

Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: sensitivity and specificity in the diagnosis or exclusion of paediatric meningitis and encephalitis

James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. CSF culture is performed on-site, with referred testing to Liverpool Clinical Laboratories (LCL; routine viral PCR, Enterovirus/Parechovirus/VZV/HSV/CMV), Public Health England (PHE; meningococcal/pneumococcal PCR), or Great Ormond Street (GOSH; 16S PCR) as required.

The BioFire/bioMérieux FilmArray has been used for respiratory viral PCR since 2013. The CSF PCR test was introduced in 2015 for use on critical care and general paediatrics, and later to neurology. A phased introduction, aiming to establish the effectiveness of the test before full introduction, was made in three stages:

  1. A pre-clinical verification using known stored CSF samples,
  2. An initial clinical phase during which the test was performed on request without any sample restrictions, and
  3. Testing on request provided the sample met specific acceptance criteria

The results of the second phase of clinical use are presented here.

Methods: FilmArray PCR was available from lumbar puncture samples that were not bloodstained and had sufficient sample volume to be subsequently referred for confirmatory testing (this included referral for viral PCR when the FilmArray was negative).

The laboratory records were reviewed for all samples tested by FilmArray following the introduction of these restrictions.

Results: Between 1st October 2016 and 30th April 2018 154 FilmArray PCRs were performed (including 4 non-lumbar puncture samples, all acutely inserted external ventricular drains)

Negative results

114 FilmArray tests were negative for all pathogens

  • All bacterial culture negative.
  • 86 referred to LCL for viral confirmation, 84 confirmed viral PCR negative, 1 insufficient sample, 1 Enterovirus detection.

Bacteriology

(2 samples also referred for viral PCR, both negative)

  1. meningitidis:
  • Two detections.
  • Both confirmed by PHE meningococcal PCR.
  1. agalactiae:
  • Three detections.
  • All confirmed (1 cultured from CSF, 1 cultured from blood, 1 confirmed by 16S PCR).
  1. pneumoniae:
  • Three detections.
  • 1 cultured from CSF, the remaining 2 not confirmed and clinical false positive.
  • 154 samples, 8 positive by FilmArray, 6 confirmed by culture or PCR. No false negative FilmArray results.

Overall bacteriology:

  • Sensitivity 100.0%
  • Specificity 98.6%
  • Positive predictive value 75.0%
  • Negative predictive value 100%

Virology

(All bacterial culture negative)

Enterovirus:

  • Twenty detections.
  • Nineteen samples referred for confirmation (LCL or PHE virus reference department), all confirmed. (1 untypable Enterovirus confirmed by PHE reported as undetected by LCL).

HHV6:

  • Five detections.
  • Not referred for HHV6 confirmation, all negative by routine viral PCR at LCL.

Parechovirus:

  • Three detections.
  • Samples did not receive additional testing.

VZV:

  • Two detections.
  • Both reported negative by LCL.

Mixed detection:

  • One mixed HSV1 and Enterovirus.
  • Both viruses confirmed by LCL.

Overall virology: 114 samples with both in-house and referral results (HHV6-positives considered negative for sensitivity analysis)

  • Sensitivity 95.0%
  • Specificity 97.9%
  • Positive predictive value 90.5%
  • Negative predictive value 98.9%

Discussion: The FilmArray Meningitis/Encephalitis PCR panel has shown very good results in our hands, particularly in the exclusion of infection. From the results above a test provides a high degree of confidence in excluding many common infections, including meningococcus, pneumococcus, enterovirus and herpes simplex virus. (It should be noted that during the period reviewed there were no cases of E. coli or H. influenzae infection, and so the negative predictive value against these infections cannot be established. We have also never evaluated the test against CMV or Cryptococcus infection.)

False positive results for S. pneumoniae were reported in the original FDA approval study, and two thirds of our detections do not appear to have been clinically relevant. The false-positive VZV results have also not been adequately explained at this time.

Overall, the FilmArray appears effective at excluding common causes of meningitis and encephalitis in children.

167
Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: does the introduction of a rapid test affect the length of stay or sample quality?

Abstract - 167

Poster 167

Introducing the FilmArray Meningitis/Encephalitis panel to a specialist paediatric hospital: does the introduction of a rapid test affect the length of stay or sample quality?

James Cargill
Alder Hey Children’s Hospital, Liverpool

Introduction: Alder Hey is a specialist paediatric hospital in Liverpool, providing clinical services across north-west England and north Wales. CSF culture is performed on-site, and the BioFire/bioMérieux FilmArray Meningitis/Encephalitis panel was introduced in 2015 with the aim to speed testing and reduce the number of referred samples. A phased introduction, aiming to establish the effectiveness of the test before full introduction, was made in three stages:

  1. A pre-clinical verification using known stored CSF samples,
  2. An initial clinical phase during which the test was performed on request without any sample restrictions, and
  3. Testing on request provided the sample met specific acceptance criteria

The effect of the introduction of the test on the length of stay (LoS) for patients and on the quality of CSF samples submitted is presented here.

Methods: The admission and discharge dates for all patients from whom a lumbar puncture sample was submitted to microbiology were requested from the hospital. These were then filtered to exclude routine cases (e.g. neurology and oncology planned day-case admissions). The LoS pre-introduction and post-introduction (tested and not tested) were then compared.

Sample quality was evaluated by the sample description (bloodstained or not) and by the recorded sample volume (categorised for analysis as ≤500 microlitres or >500 microlitres)

Results

Length of stay

The LoS was evaluated over two time frames, 20/06/15 to 17/05/16 (from the introduction of the new laboratory computer system until the day before the first FilmArray test) and 4/10/16 to 24/06/17 (after the introduction of sample criteria for testing).

Pre-FilmArray

427 patient episodes (350 excluding critical care admissions)

  • Mean LoS 13.75 +/- 35.52 days (9.56 +/- 23.55 days excluding critical care admissions)
  • Median LoS 4 days, interquartile range 2-9 days (3 days, interquartile range 2-7 days, excluding critical care admissions)

After FilmArray introduction

72 episodes with FilmArray test (37 excluding critical care admissions)

  • Mean LoS 8.08 +/- 8.97 days (5.29 +/- 5.38 days excluding critical care admissions)
  • Median LoS 5 days, interquartile range 2-10 days (3 days, interquartile range 2-6 days, excluding critical care admissions)

337 episodes without FilmArray test (298 excluding critical care admissions)

  • Mean LoS 8.88 +/- 17.91 days (5.99 +/- 9.99 days excluding critical care admissions)
  • Median LoS 3 days, interquartile range 2-7 days (3 days, interquartile range 2-5 days, excluding critical care admissions)

Sample quality

Recording of sample volumes was introduced in October 2016.

  • For the six month October 2016 to March 2017, 208 of 313 samples had a recorded volume greater than 500 microlitres.
  • During the same period 85 of 313 samples were recorded as bloodstained (slightly, heavily, or clotted)
  • For the first six months of 2018, 189 of 300 samples had a recorded volume greater than 500 microlitres.
  • During the same period 81 of 300 samples were recorded as bloodstained.

Discussion:The LoS is a non-normally distributed variable, as can be seen from the standard deviation compared to the mean value, and is influenced by small numbers of long-stay patients. The better measure of the LoS is therefore the median and interquartile distribution. There is no evidence from the length of stay of a significant change in the LoS following the introduction of the FilmArray test; the median LoS for patients not admitted to critical care has remained at 3 days throughout.

The percentage of samples received that are bloodstained or have a small volume less than 500 microlitres is also unchanged following the introduction of the rapid test and associated sample requirements (sample volume greater than 500 microlitres, must not be bloodstained).

There is no evidence that the availability of rapid testing of CSF has affected either the quality of samples sent or the LoS.

168
A prospective evaluation of the clinical impact of Unyvero multiplex PCR in blood stream infections

Abstract - 168

Poster 168

A prospective evaluation of the clinical impact of Unyvero multiplex PCR in blood stream infections

Thomas Smith, Gosia Poznalska, Aiden Plant, Stephanie Murdoch, Cressida Auckland
Royal Devon & Exeter NHS Foundation Trust, Exeter

Introduction: Blood culture (BC) remains the gold standard for guiding antimicrobial treatment in blood stream infections (BSI). Although BC has a reported high specificity, results are limited by a considerable time delay and often slow-growing or fastidious organisms are not identified.

PCR has been proposed to offer early identification of pathogens (most studies report results available within 4-6 hours) and detection of certain antimicrobial resistance genes. To help assess the clinical benefit of this at our institution we conducted a small, prospective, laboratory verification trial, comparing routine practice with the added diagnostic step of Unyvero multiplex PCR.

Methods: A single centre, prospective, verification trial, comparing routine practice with an added initial diagnostic step (Unyvero multiplex PCR) will be conducted at the Royal Devon and Exeter Hospital.

Inclusion criteria: ‘positive’ BC samples will be submitted for Unyvero multiplex PCR, if, as determined by attending clinical microbiology consultant:

  1. Initial gram stain suggests GNR or yeast and there is a high index of suspicion of a resistant organism, or
  2. Initial gram stain is suggestive of Streptococci and there is a high index of clinical suspicion of a pathogenic organism

Exclusion criteria: patient death before completion of PCR analysis or laboratory errors that leads to disruption of standard methods.

Primary outcome will be the concordance of Unyvero multiplex PCR with standard methods. Further secondary outcomes will include: antimicrobial stewardship, infection control precautions (initiated or stopped), and effect on length of hospital stay, retrospectively collected and interpreted by a medical microbiologist.

The study protocol will be followed for the first 22 blood cultures received that meet the inclusion criteria, commencing February 2018.

Results: The 20 tests included (2 tests excluded as per criteria) yielded 33 PCR results.

There were 22 true positive results- 16 where Unyvero matched routine methods and provided both the genus and species and 4 where Unyvero matched genus but there was no identification of species. For 2 results ‘Universal bacterium’ was detected; in these cases the Unyvero P50 PCR panel did not include the bacteria identified by culture.

There were 5 false negative results. There were 6 false positive results. PPV was 79% and Sensitivity 81%.

Average time to Unyvero result was 5 hours. Standard methods produced organism identification in a mean of 18 hours 17 minutes and sensitivities within 48 hours.

In 2 cases resistance markers were detected: aac(6′)/alph(2″), an aminoglycosides resistance marker, was identified. In neither case did it impact upon secondary outcomes.

Interpretation of PCR result did not affect measured clinical outcome with regard to: infection control measures or time to discharge in any case. In 5 cases antibiotic stewardship would have been affected- a net sum of 1 dose of restricted antibiotic would have been saved.

Discussion: Use of PCR result would have had no effect on the clinical outcome, with regard to time to discharge or infection control procedures. And further only a small effect on antimicrobial stewardship- in sum saving a dose of restricted antibiotic. This owed primarily to lack of information regarding resistance. The information gleaned from the initial gram stain and clinical history was usually sufficient to formulate an initial plan, including antibiotic choice, and PCR results did little to change this.

A substantial reduction in time to positive result was noted, as expected. However, whilst PCR offers the potential for early identification of organism and resistance markers, this small study shows this does not necessarily significantly impact clinical outcome. Further evaluation, with greater number of samples, and broader inclusion criteria is required to further elucidate its true value.

169
A retrospective audit of the blood culture contamination rate at Southend University Hospital NHS Foundation Trust

Abstract - 169

Poster 169

A retrospective audit of the blood culture contamination rate at Southend University Hospital NHS Foundation Trust

Rachel Davies-Foote, John Day, Josephine Elfick
Southend University Hospital NHS Foundation Trust

Introduction: Current national guidelines advocate that blood culture contamination rates of less than 3% are desirable; higher rates should be investigated and corrected with educational efforts.i

Contaminant blood cultures complicate patient care and lead to unnecessary use of antimicrobials driving antimicrobial resistance. Furthermore contaminants place an avoidable burden on medical staff and resources.

We aimed to determine the contamination rate of positive blood cultures at Southend University Hospital NHS Foundation Trust (SUH).

Methods: Data was obtained for all 8542 blood cultures taken at SUH from February 2017 to December 2017. The blood culture data was grouped on a monthly basis using the date on which the blood culture was taken. The clinical significance of positive isolates was determined by discussion with consultant microbiologist about all pathogens isolated enabling grouping of isolates into three categories: significant, contaminant and an indeterminate ‘overlap’ group. The overlap group monthly total was halved and this figure was added to the monthly significant total and the monthly contaminant total. Monthly contamination rate was calculated. (Total monthly contaminants / Total number of blood cultures taken x 100).

Results: Of 8542 blood cultures taken over the 11-month period, 399.5 (4.67%) grew contaminants. The monthly contamination rate ranged from 3.40% in April 2017 to 6.33% in November 2017. The contamination rate peaked in the months of July 2017 and November 2017 (6.12% and 6.33% respectively). Contamination rates were lowest in the months of March and April 2017 (3.55% and 3.40% respectively).

Discussion: Results reveal blood culture contamination at SUH to be above the desired rate.

It was proposed that training in blood culture collection using an aseptic technique is indicated. We made the recommendation to the medical education department at SUH that a compulsory e-learning module should be introduced as part of the mandatory training for all healthcare providers whose role includes blood culture collection. For example junior doctors within the trust must complete a list of mandatory modules and upload evidence of completion to their ePortfolios; the blood culture e-learning module, which is not currently mandatory, should be included in this list for the next cohort of junior doctors.

Additional educational efforts to ensure that blood cultures are only taken when there is an appropriate clinical need to do so could also help to reduce the number of contaminants. Hospital guidelines are in place for when blood cultures are indicated. We therefore made the recommendation that this should be included in the junior doctor induction alongside the mandatory blood culture e-learning module in the form of a short antimicrobial teaching session.

The 89 isolates in the overlap category exposes a level of uncertainty for the true incidence of blood culture contamination.

References
Taking Blood Cultures A summary of Best Practice. [updated 2010 July 2010; cited 2011 7 Apr]. Department of Health (United Kingdom) http://webarchive.nationalarchives.gov.uk/20120118171812/http://hcai.dh.gov.uk/files/2011/03/Document_Blood_culture_FINAL_100826.pdf

170
Predictive value of urinary interleukins (IL-6 and IL-8) for differentiating between asymptomatic and symptomatic bacteriuria in elderly patients

Abstract - 170

Poster 170

Predictive value of urinary interleukins (IL-6 and IL-8) for differentiating between asymptomatic and symptomatic bacteriuria in elderly patients

Fenella Halstead1,2, Claire Williams3, Helena Ogbonna1, Emily Rousham4, Jon Hazeldine1,5, Beryl Oppenheim1
1NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham. 2University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital. 3Birmingham Community Healthcare Trust. 4School of Sport, Exercise and Health Sciences, Loughborough University. 5Institute of Inflammation and Ageing (IIA), University of Birmingham Research Laboratories, Queen Elizabeth Hospital

Introduction: Urinary tract infections (UTIs) are the most common cause for Abx prescriptions in the elderly. Subtle symptoms, poor memory recall and the complexity of interpreting microbiological test results however make accurate diagnosis challenging.  Asymptomatic carriage of bacteria in the urine (ASB) is common in elderly patients, and leads to further diagnostic confusion.

This study was undertaken to investigate whether urinary interleukins (IL6 and IL8) were useful biomarkers for differentiating between ASB and UTI in elderly patients for whom accurate diagnosis based on clinical symptoms may be difficult.

Methods: Serial urine samples (n=88) were collected from 23 asymptomatic elderly patients in a geriatric ward of a large hospital. Following qualitative culture and urinalysis, samples were tested for IL6 and IL8 biomarkers using a Bio-Plex Pro™ Human Cytokine 2-plex Assay (designed for serum). 

Results: Biomarker testing on an initial subset of 14 patients revealed that IL6 and IL8 could be detected in urine samples using this kit, and that there was some association between high IL6/8 levels and the high WBC and bacterial counts. There were four patients with substantially higher values, potentially indicating a different biomarker profile. Two of these subsequently (and independent to our findings) received treatment for UTI. 

Discussion: Although only a small number of urines have been tested to date, there is some evidence that urinary interleukins (IL-6 and IL-8) may be useful for differentiating between asymptomatic and symptomatic bacteriuria in elderly patients when symptoms are difficult to identify, and reduce the overconsumption of antibiotics by this patient group.

171
A review of the use of 16S rDNA PCR results as a diagnostic and stewardship tool at Severn Pathology services

Abstract - 171

Poster 171

A review of the use of 16S rDNA PCR results as a diagnostic and stewardship tool at Severn Pathology services

Georgina Beckley, Ian Head, Alasdair Macgowan
Southmead Hospital, Bristol

Introduction: 16S rDNA PCR (16SPCR) is used widely as a tool to aide in the investigation of a broad range of clinical syndromes, usually requiring long term antimicrobials, where no bacteria have been found using standard culture (bone and joint infection, meningoencephalitis and infective endocarditis).

Severn Pathology provides microbiology services to University Hospitals Bristol NHS Foundation Trust (UHB) and North Bristol NHS Trust (NBT).

The main objective of this study was to review of the usefulness of this test as both a diagnostic and stewardship tool at Severn Pathology. 

Methods: Data was collected retrospectively by searching the Laboratory Information System (LIMS) for all samples sent from UHB and NBT for 16SPCR between July 2017-July 2018. Patient notes, microbiology notes, and electronic patient record (where available) were examined to assess whether changes were made based on the result of 16S PCR testing.  A useful 16SPCR positive test was defined as a result that identified the infective organism or changed a patients antimicrobial therapy (agent, duration).  A useful negative 16SPCR test was defined as a result that excluded infection, and/or stopped antimicrobials.

Samples were excluded if they were sent incorrectly, or represented multiple samples from the same patient taken on the same day.  

Results: In total 70 samples were reviewed. 25 were positive. 15/25 (60%) were useful, 5/25 (20%) were deemed not useful . 5/25 (20%)samples could not be categorised due to a lack of patient records.

There were 45 negative samples.  12/45 (26.7%) were useful.  23/45 (51%) were not useful.  6/45 (13.3%) could not be categorised. In four patients, further examination of the notes provided another positive significant result not available prior to the 16SPCR being requested (Mycobacterial Tuberculosis 3/4, Leishmanial PCR positive in 1/4).

The most common clinical syndromes for which 16SPCR was sent were Prosthetic joint infection, Prosthetic valve infective endocarditis, Meningoencephalitis and Pyrexia of unknown origin.

The most common positive result was a “Mixed” signal, with a broad range of other organisms representing the remaining positive results (Corynebaterium sp, Kingella Kingae, Streptobacillus monoliformis, and Neisseria meningitis).

Discussion: Almost two thirds of the positive results affected management of the patient, not only by directing antimicrobial therapy, but also preventing unnecessary investigations (repeated joint aspiration in suspected prosthetic joint infections or repeated imaging in the case of pyrexia of unknown origin).  The 20% of positive 16SPCR results that were not useful were mainly considered by the microbiology and clinical teams to be contaminants e.g. Microbacterium, Fusobacterium or a mixed signal.

In around 25% of the samples, both the Medical Microbiology and clinical teams would use a negative result as a reason to stop antimicrobials in those with a low clinical suspicion of bacterial infection.  Thus providing evidence of its use as a stewardship tool or as an indicator to look for a non-bacterial diagnosis (mycobacterial and parasitic infection, or a non-infective diagnosis)

The turnaround time of 16SPCR is currently 14 days by which time a significant number of patients had been discharged. This meant we had to rely on outpatient records. The review was limited by: The unavailability of a number of outpatient records.  No clear documentation that the clinical team had seen, or acted on the result.  Different practices across the two trusts.  This lead to a high degree of “unknown outcomes” which could affect the validity of our results.

This review confirms 16SPCR continues to be useful in the confirmation/exclusion of bacterial infection. It has also highlighted that better communication of a negative result may aide its use as a stewardship tool, or as a prompt to investigate for non-bacterial causes of a patients symptoms.  

172
Analysis of blood culture sampling practice and detection rates within Brighton and Sussex University Hospitals Trust

Abstract - 172

Poster 172

Analysis of blood culture sampling practice and detection rates within Brighton and Sussex University Hospitals Trust

Simon Stoneham1,2, William Schilling1, Alberto San Francisco Ramos1, Matthew Longbone1, Martin Llewelyn1,2
1Microbiology and Infection, Royal Sussex County Hospital, Brighton. 2Global Health and Infection, Brighton and Sussex Medical School

Introduction: Blood cultures provide vital information for patient management but sample handling impacts on both sensitivity and specificity. Current UK standards are that two sets of paired aerobic and anaerobic samples be sent for culture in most situations with a volume of 20-30 mL per set. Low volume cultures have both reduced sensitivity and a higher contamination rate. In reality, most blood cultures sent have inadequate volumes and are sent as single sets. The value of routine anaerobic cultures has been questioned and in our Trust a decision was made around 10 years ago to switch to routine aerobic only blood cultures at the main acute hospital site. The aim of the current study was to establish the impact of this policy on blood culture sampling and yield.

Methods: Brighton and Sussex University Hospitals NHS Trust includes two acute sites: RSCH in Brighton (approx. 600 beds) and PRH in Haywards Heath (approx. 293 beds)

Records of all blood cultures were obtained from Winpath on 31/05/2018, from 15/10/2006 to 30/04/2018. Records contained patient identifiers, date received, laboratory number, culture results and, where available, time to positivity. Samples from patients under 18 or without a recorded date of birth were excluded.

Samples from a patient were considered as having been performed for the same episode if they were received in the lab on the same calendar day.

To assess volumes of blood being taken for culture, all blood culture bottles were weighed for a 10 day period (7th-17th July) at the end of incubation (n=678).

Results: Data from a total of 151,278 blood cultures were available with 122,939 (81%) from the RSCH site [32,870 (27% pairs)] and 28,339 (19%) from the PRH site [24,402 (86% pairs)]. The overall positivity rate for blood cultures was significantly higher at PRH than RSCH (3867/28,339, (13.6%) vs 13,117/122,939 (10.7%) p<0.001). This was true for both paired and unpaired cultures (14.1% vs 9.9% and 11.5% vs 11.3% at PRH and RSCH respectively). Positivity rates for paired samples from PRH and single samples from RSCH were substantially different 3,448/24,402 (14.1%) and 8,645/85,398 (11.3%) respectively (odds ratio 1.62 (1.56-1.70)) reflecting higher detection rates of key pathogens. However, when data from both sites were pooled, differences were smaller with 6,715 / 57,272 (11.7%) paired samples being positive compared to 10,025 / 88,701 (11.3%) single aerobic bottles (p=0.02).

Comparing anaerobic and aerobic cultures taken at PRH, we find significantly higher detection rates for Staphylococcus aureus in anaerobic bottles (91.4% vs 82.8% p=0.006) and equivalent detection of Escherichia coli (84.8% vs 84.4% p=0.37) which comprise 25.7% of all positive cultures.

Only a small minority of cultures performed at either hospital involved more than one set being taken: 9.8% at PRH and 10.8% at RSCH (p=0.17).   

Analysis of blood culture weights demonstrated no difference between aerobic bottle filling at the two sites 152.5g [95%CI 151.6 – 153.4] vs 152.7g [95%CI 152.2 – 153.2] (p=0.719).

Discussion: The lower rates of overall positivity among even paired cultures taken at the RSCH site may reflect differences in patient mix or threshold for taking cultures. Nevertheless, we find use of anaerobic blood culture identifies a small but significant number of bacteraemias which are missed by culturing aerobic bottles only. This is likely to represent predominantly reduced volume sent for culture from each episode because withdrawal of routine anaerobic bottles has not been accompanied by more patients having two samples sent for culture. Returning to routine use of paired cultures would be expected to identify an additional 75-100 clinically significant bacteremias per year at our acute hospital trust at the cost of taking and processing an additional 10,000 blood culture bottles.

173
Comparison between the Vitek2 yeast identification and antifungal susceptibility testing with the reference laboratory methods

Abstract - 173

Poster 173

Comparison between the Vitek2 yeast identification and antifungal susceptibility testing with the reference laboratory methods

Sahar Eldirdiri1, William Olver2
1Microbiology, Ninewells Hospital, Dundee. 2Ninewells Hospital, Dundee

Introduction: The decision to identify a yeast to species level is based on a combination of clinical and microbiological factors. Rapid identification of yeast provides timely information to physicians for patient management. Yeast identification and antifungal susceptibility testing was previously performed using commercial Vitek2 (bioMérieux, France) in Ninewells hospital, Dundee. In this study, the Vitek2 system was evaluated by comparing it’s results with those obtained by the Mycology reference laboratory in Glasgow (Southern General Hospital).

Methods: Data was collected retrospectively from the microbiology computer system(CliniSys LabCentre® 1.7) from April- September 2015. The data covered a sample of 56 specimens.

MALDI from bioMérieux was used for identification of all yeast in the Mycology reference laboratory. Sensititre (Thermo Scientific) was used to test only samples from sterile sites for antifungal susceptibility while all other samples were tested by disc diffusion methods.

Results: The types of specimens investigated in the study were blood cultures, sputum, high vaginal swab, endotracheal aspirate, mouth swab, wound swab, throat swab, line tip and bronchoalveolar lavage(BAL). Samples were received from different clinical specialties including sexual health clinics, GP, paediatrics, haematology, renal, oncology and cystic fibrosis clinics.

Among the 56 specimens included in the study, 57 isolates were identified as Candida. albicans (n=23), C. glabrata (n=10), C. krusei (n=2), Saccharomyces cerevisiae (n=2), C. parapsilosis (n=2), C. dubliniensis (n=3), C. guilliermondii (n=3),  C. famata (n=4), C.sphaerica  (n=1), Rhodotorula mucilaginosa (n=1) and unidenetified fungus( n=6). One specimen contained 2 isolates (C. albicans & C. glabrata )

There was 79% agreement between the vitek2 results and the reference lab results for identification of isolates. A total of 26 (46%) species had the same identification and sensitivity results as the reference laboratory. 6(10.5%) species were misidentified by Vitek2. Additionally, another 6 species (10.5%) were unidentified fungus by Vitek2.

Nineteen (33%) species had different sensitivity pattern compared with the reference lab results. Fluconazole resistant rate was higher by Vitek2 than reference lab results, the rate was calculated as 17.5%.

In this study all the clinical bloodstream yeast isolates had the same identification by both the vitek2 system and the reference lab methods apart from one C.guilliermondii misidentified as C.famata.

Discussion: We have noticed discrepancy in fluconazole sensitivity testing between the Ninewells lab and the reference lab. This overestimated resistant rate may have a major clinical implications as fluconazole considered to be the first recommended antifungal for many infections. Four isolates of C.glabrata (n=10) were found to have  intermediate sensitivity by both vitek2 and the reference lab methods. The clinical breakpoints have been revised to categorise the entire wild-type population of C. glabrata as intermediate, thereby facilitating discrimination between wild-type and isolates with elevated MICs and acquired resistance mechanisms (MIC 0.002-32) (EUCAST technical note 2013). All C.famata (n=4) were misidentified, one sample identified by the reference lab as C.albicans and others as C.guilliermondii. These disappointing results are due to the fact that C. guilliermondii and C. famata show similar biopatterns, which could not be sufficiently discriminated by the YST card. Unfortunately we do not have explanation to C.albicans misidentified as C.dublinesis from high vaginal swab. The results of 79% agreement between the vitek2 results and reference lab results for identification of yeast in this study confirmed the result of previous project done in Ninewells lab in 2010 with a rate of 80% agreement.

As a result of this study we have changed our practice in Ninewells laboratory. We have started using the MALDI-TOF( Bruker- Germany) for identification of yeasts from all clinical samples. Furthermore, antifungal susceptibility testing are currently all done by Mycology reference laboratory in Bristol.

174
How can fast identification & antimicrobial susceptibility testing improve patient care and antibiotics stewardship in critically ill patients?

Abstract - 174

Poster 174

How can fast identification & antimicrobial susceptibility testing improve patient care and antibiotics stewardship in critically ill patients?

Houdini H.T. Wu, Steve Wilson, Li Xu-McCrae, Paul Connor, Ahmed Hussain, Karen Reynolds, Abid Hussain
PHE Public Health Laboratory Birmingham

Introduction: Conventional culture-based (CCB) methods are the current standard of care (SOC) methodology prior to routine microbial identification (ID) and antimicrobial susceptibility testing (AST). In contrast to this time-consuming method, the Accelerate Pheno™ system is a new fully automated compact platform capable of performing both ID and AST directly from positive blood cultures in approximately 7 hours, bypassing the need of CCB that can take upto 24 hours. Under the emerging pressure of antimicrobial resistance (AMR), the World Health Organization (WHO) implemented the Global Action Plan to optimise the use of antibiotics (i.e. antibiotics stewardship). Here, we aim to compare the performance of both methods and evaluate the potential clinical benefits from a quick ID & AST in hospital settings that commonly require heavy use of broad-spectrum antimicrobial agents (i.e. the critically-ill setting).

Methods: In total, 53 episodes of blood stream infections (BSI) were selected in real-time from three hospital settings: intensive care units (16 samples), neonatal units (12 samples) and a haematology ward (16 samples). The 16-weeks study compared both ID & AST performance by the SOC CCB and Pheno™ methods. This was followed by a retrospective observational study to investigate the potential impact of these early results on patient care (e.g. clinical outcome including changes to antibiotic therapy, length of stay, patient safety etc.) and antibiotic stewardship (e.g. cost saved, AMR in the long run).

Results: There were 43 blood cultures eligible for this study. Of these, 58.1% were gram positive organisms, 41.9% were gram negative organisms and 2.3% were yeast. The Pheno™ system provided a definitive and correct result for 38/43 runs, along with an overall sensitivity of 88.4% and specificity of 99.5%. An AST result was available for analysis in 31 instances (96.9%). The overall category agreement between the Pheno™ system and CCB AST was 100% for gram positive organisms and 92.7% for gram negatives organisms with 5 minor errors (4.1%), 3 major errors (3.8%) and 1 very major error (2.6%). On average, the Pheno™ system provided an ID result in 1.5 hours and AST in 6.9 hours. The utilisation of the Pheno™ system reduced the time-to-result for ID by 12.3 hours (ranging between 1.8 – 18.4 hours) and AST by 27.8 hours (ranging between 16.7 – 31.2 hours), when compared SOC CCB methods in our laboratory setting. Ongoing effort are being made to collect the clinical data to evaluate potential impact of these early results to patient care and antibiotic stewardship at the time of writing.

Discussion: This study demonstrated the use of the Pheno™ system is able to provide a fast organism ID & AST data, while significantly improving the turn-around time in blood culture diagnostics. We believe that through the provision of a quick ID & AST results, it will lead to a better clinical outcome for the patient in those critically ill.

 

175
Thermonuclease test accuracy is significantly reduced in methicillin-resistant Staphylococcus aureus isolates

Abstract - 175

Poster 175

Thermonuclease test accuracy is significantly reduced in methicillin-resistant Staphylococcus aureus isolates

Benjamin Canning1, Iskandar Mohamed1, Nimal Wickramasinghe2, Jonathan Swindells1, Matthew O’Shea3
1Sandwell and West Birmingham Hospitals NHS Trust. 2University Hospitals Birmingham NHS Foundation Trust. 3University of Birmingham

Introduction: Staphylococcus aureus (S. aureus) can cause devastating infections and delays in diagnosis and management deleteriously effect outcomes. Thermostable TNase, encoded for by the nucgene, is a specific heat-stable deoxyribonuclease that degrades DNA. The Thermonuclease or TNase test is a rapid test used to presumptively distinguish S. aureuspresent in blood cultures from coagulase-negative staphylococci (CoNS), which are negative by TNase test. TNase tests have a reported sensitivity of 96.7% and specificity of 100%.

PCR-based testing offers rapid identification of S. aureusdirectly from patient samples, with a sensitivity and specificity of over 95%. The nucgene is often the specific target. Variations in this gene can lead to misidentification of methicillin-resistant S. aureus (MRSA) via false-negative PCR results.

We examined the sensitivity and specificity of the TNase test performed as part of a clinical microbiology laboratory’s routine evaluation of positive blood cultures, with particular assessment of the effect of MRSA on test performance.

Methods: We performed a retrospective audit of the performance of consecutive TNase tests in a UK clinical microbiology laboratory. Every positive adult blood culture (BacT/ALERT 3D Microbial Identification System, bioMérieux) that showed Gram-positive cocci in clusters on Gram-stain underwent a TNase test according to the manufacturer’s instructions (Thermonuclease Agar, Southern Group Laboratory Ltd.). 1mL of positive blood culture fluid was centrifuged, incubated at 112oC for 20 minutes, placed in a 5mm well cut into the TNase media and incubated at 37oC for 2 hours. Negative (S. epidermidis ATCC 12228) and positive (S. aureus NCTC 571) controls were used, and the presence of a zone of clearing recorded at 30 minutes, 1 hour and 2 hours. Results were recorded as positive or negative, along with the volume of the blood in the initial samples (normal or low). Workup of samples followed standard operating protocols. Final bacterial identification and sensitivities were confirmed using the VITEK MS and VITEK 2 platforms (bioMérieux).

Results: Of 1331 blood culture results with adequate blood volumes, 189 were TNase positive. Of these, 176 (93.1%) were subsequently confirmed as S. aureus. Of the 1142 TNase negative results, 13 (1.1%) were identified as being S. aureus. The TNase test sensitivity was 93.1% (95% CI 88.5-96.3%) and specificity was 98.9% (95% CI 98.1-99.4%) for all S. aureus isolates, irrespective of methicillin sensitivity. 

Of the 189 S. aureus isolates, 9 were MRSA (4.8%). Among these, 8 isolates (88.9%) were TNase positive. In the context of MRSA, the sensitivity and specificity of the TNase test was 88.9% (95% CI 51.8-99.7%) and 86.3% (95% CI 84.3-88.1%). There was a significant difference in the accuracy of the TNase test between non-MRSA and MRSA isolates (p = 0.026).

Discussion: Our data show that with adequate volumes of blood, the TNase test remains a generally reliable method for the presumptive discrimination between S. aureus and CoNS in blood cultures. However, the sensitivity and specificity of the TNase test is significantly reduced when applied to MRSA isolates, which may lead to false-negative results and the potential misidentification of MRSA as CoNS. This is the first report of reduced TNase functionality in MRSA and our findings support previously raised concerns about molecular tests using the nucgene as the sole target to identify S. aureus. 

The TNase test has a role in rapid identification, however caution must be applied in the context of MRSA and TNase results should be interpreted with caution. 

176
Quality improvement project: reducing the inappropriate use of urine dipsticks in the management of suspected urinary tract infection

Abstract - 176

Poster 176

Quality improvement project: reducing the inappropriate use of urine dipsticks in the management of suspected urinary tract infection

Maurice Madeo1, Bethan Stoddart2, Linda Barker3, Jayne Girdham3, Joanne Jones3, Marion Hewis3, Noelle Williams3
1Deputy Director Infection Prevention and Control, North Lincolnshire and Goole NHS Foundation Trust. 2Lead Consultant Microbiologist, Path Links, North Lincolnshire and Goole NHS Foundation Trust. 3Infection Prevention and Control, North Lincolnshire and Goole NHS Foundation Trust

Introduction: Urinary tract infections (UTI) are the second most common clinical indication for empirical antimicrobial treatment in primary and secondary care, and urine samples constitute the largest single category of specimens examined in many medical bacteriology laboratories.

The diagnosis and management of patients with suspected or confirmed UTI varies greatly often resulting in the inappropriate use of antimicrobials. However, the increasing incidence of Gram-negative bloodstream infection is of national concern. Effective treatment and prevention of urinary tract infection is a key driver to improve the current position.

Diagnosing UTI is particularly difficult in elderly patients. They are more likely to have asymptomatic bacteriuria, and may present with non-classical signs and symptoms, such as acute confusion and falls. It is a common practice for clinicians to request or use a urine dipstick test to help assist in the diagnosis of a UTI. Although this is a useful tool if used in the right context this is often not the case and treatment may be commenced based on an inappropriately obtained dipstick result. NICE cautioned their use especially in adults aged over 65 years, and state it is important that factors other than the results of dipstick testing are taken into consideration when diagnosing urinary tract infections in older people to ensure appropriate management and avoid unnecessary use of antibiotics.

Methods: The project has two strands

1) Assessing and improving the knowledge base regarding diagnosis and management of UTI, through an audit and education process, including a staff survey based on the Michie behaviour change model piloted on the admissions areas, which is where it was perceived that the greatest influence could be demonstrated.

2) Restricting use of urine dipsticks to specific clinical areas (which included the admissions units, children’s wards and urology) and indications (excluding catheter urines and patients >65yrs), and restricting the breadth of testing so that the leucocyte and nitrite components of the dipstick are not part of the routine screen on most medical and surgical wards.

A decision tool has been provided to clinical areas to aid diagnosis and management of UTI based on NICE guidelines.

Results: 27 medical staff (25%), 46 registered nurses (44%), and 34 other healthcare staff including HCA and student nurses completed surveys, demonstrating several areas for targeting behaviour change interventions. These included practice surrounding when urine should be sent for culture, when urine dips including leucocytes and nitrites should be used and lead to further action, and closing the gap between knowledge about appropriate prescribing and real-life practice.

Results of urine microbiology testing will be presented on the poster, but indicate an improvement in sampling through a reduction in proportion of apparently non-significant results following implentation of these measures. 

Discussion: This quality improvement initiative succeeded in improving the knowledge base of staff, used nudge theory to improve appropriate urine dipstick use, and changed the nature of urine microbiological sampling. The next step will be to investigate whether improvements in antimicrobial use and patient outcomes follow.

 

177
The impact of improving Influenza testing turnaround times on hospital flows and length of stay

Abstract - 177

Poster 177

The impact of improving Influenza testing turnaround times on hospital flows and length of stay

Maurice Madeo1, Lyn Clare2, Bethan Stoddart3
1Deputy Director Infection Prevention and Control, North Lincolnshire and Goole NHS Foundation Trust. 2Infection Prevention and Control Data Analyst, North Lincolnshire and Goole NHS Foundation Trust. 3Lead Consultant Microbiologist, Path Links, North Lincolnshire and Goole NHS Foundation Trust

Introduction: Testing for influenza using PCR is no longer the preserve of specialist virology laboratories. Commercially available CE marked assays allow local laboratories to offer a PCR service reducing the transport times associated with sending samples to reference centres. Moreover, batch analysis is being replaced by random access platforms with further improvement of turnaround times. This observational study investigated whether these potential improvements in turnaround times were realised by the Path Links laboratory service in Lincolnshire, and how this improvement translated into a positive impact on patient care.

Previously all respiratory virus PCR had been referred to Addenbrooke’s virology laboratory in Cambridge. In January 2017, the Werfen Arrow extraction / Cepheid Smartcycler system was introduced allowing batch PCR analysis. Later, from January 2018, the GeneXpert, a random access cartridge-based system was implemented.

The intention was that by optimising laboratory processes, the turnaround time for influenza samples would be improved, alongside an advantage in releasing BMS staff time which had been a challenge using the Werfen system. The anticipated benefits in confirming or refuting an influenza diagnosis rapidly were both treating individual patients more effectively and helping to prevent the spread of influenza in the hospital. Antibiotic stewardship benefits were envisaged, but were not measured during this study. Furthermore it could enable patients to be discharged quicker to recover at home thus reducing their length of stay and freeing up hospital beds. 

Methods: Data from the periods January to March 2017 and 2018 from the laboratory, patient administration, and infection prevention department database were collated and compared. Parameters examined included laboratory turnaround time, final result, and patient length of stay. During times of particular laboratory pressure or analyser down-time, samples were referred for testing, so some data for reference testing during the same period are available. Those patients with length of stay of over 30 days duration were excluded from the analysis, as it was felt that there were other causes of increased duration of hospital admission.

Results

From January to March 2017 samples number = 249, influenza detected = 24

From January to March 2018 samples number = 787, influenza detected = 163.

Impact of testing method on turnaround times:

            Batch analysis Mean turnaround time 2.8 days

            Random access cartridge based system 1.1 days

            (Reference laboratory 5.2-6.0 days)

The mean length of stay for patients with suspected influenza: January to March 2017 was 10.0 days and in the same period in 2018 this had reduced to 8.2 days.

Further results including graphical statistical analysis, data distributions and impact on infection prevention and control interventions will be presented on the poster.

Discussion: We acknowledge that there are many reasons why length of stay may reduce over time, and also note that the influenza epidemic during the winter season 2017-18 had a particularly high impact. However, unlike the previous year during that period, there were no full ward closures because of influenza despite the challenge of isolation facilities of <15% in some areas. 

This observational study demonstrated that improving laboratory turnaround times for influenza testing can have a real life benefit for both individual patients and the hospital system as a whole, including reduced length of stay and improved use of isolation facilities.

178
The clinical impact of early MALDI-TOF identification of bacteria from positive blood cultures

Abstract - 178

Poster 178

The clinical impact of early MALDI-TOF identification of bacteria from positive blood cultures

Philip House, Gemma Winzor
Heartlands Hospital, Birmingham

Introduction: Identification of bacteria causing bacteraemia aids the making of clinical decisions on bacteraemia significance, likely source of infection and antimicrobial choice. Earlier microbiological diagnosis should therefore have a positive impact on patient outcomes and antimicrobial stewardship.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) is an established method for the identification of cultured bacterial isolates. We examined the clinical impact of a change in standard operating procedure in which positive blood culture broths were spread and cultured for 4 hours before undergoing MALDI-TOF. For eligible blood cultures, this essentially allows bacterial identification one day earlier than previously. Comparing the clinical utility of this standard operating procedure for Gram positive versus Gram negative organisms was of particular interest.

Methods: Blood culture bottle broths underwent ‘4-hour MALDI-TOF’ if they flagged positive overnight or before 11am on a weekday; all blood cultures flagging positive outside of this time period underwent MALDI-TOF the next day.

We collected data on all positive blood cultures from a three hospital-site NHS trust over a 30 day period, including the clinical impact of early microbiological diagnosis.

Results: Over 30 days there were 280 positive blood cultures from 250 different patients. 109 (38.9%) cultures were eligible to undergo ‘4-hour MALDI-TOF’, which proceeded successfully on 88 (80.7%) of cultures.

Early bacterial identification was clinically useful in 35 (39.8%) cases. The most common reason early identification was deemed useful was the earlier determination of positive cultures being of doubtful clinical significance (24 out of 88 cases [27%]). There were 12 (13.6%) cases in which early identification led to a change in antibiotic; 6 cases (6.8%) in which an investigation was recommended earlier based on bacterial identification; 4 cases (4.5%) in which bacterial identification changed the working diagnosis with regards to source of infection and 1 case (1.1%) in which earlier identification had significant infection control implications.

The clinical utility of early MALDI-TOF identification was highest in Gram positive organisms with the appearance of Staphylococci on microscopy (27 out of 35 [75%] clinically useful) and least useful in Gram negative bacilli (2 out of 34 [5.9%] clinically useful).

Discussion: This analysis shows that early MALDI-TOF identification of bacteria is clinically useful in real-world practice. The highest clinical utility came with Staphylococci, generally by allowing the earlier initiation of appropriate antibiotics in Staphylococcus aureus bacteraemia and the earlier determination of positive cultures being of doubtful clinical significance in the case of most coagulase-negative Staphylococci.

There was far lower clinical utility with Gram negative bacilli, as most changes in treatment required results of antimicrobial susceptibility testing, rather than just microbiological diagnosis. However there were cases in which early identification did lead to a change in antimicrobials (e.g. early identification of Pseudomonas aeruginosa bacteraemia).

These results justify the continued use of this standard operating procedure and also allow prioritisation of workflow (i.e. towards Gram positive cocci rather than Gram negative bacilli) for days when resources are limited.

 

179
Review of the clinical significance of the aerobic blood culture bottle since its addition to the blood culture service in Newcastle Hospitals

Abstract - 179

Poster 179

Review of the clinical significance of the aerobic blood culture bottle since its addition to the blood culture service in Newcastle Hospitals

Richard Capstick, Angela Geering, Jennifer Collins, Ali Robb
Newcastle upon Tyne

Introduction: Newcastle Laboratories has recently implemented the use of the aerobic blood culture bottle within the BacT/Alert automated system. This is in addition to the anaerobic bottle system that was already in place, validated and had passed CPD accreditation. We carried out a retrospective review of adult blood culture results over a 2 month period to establish what additional benefit the second bottle has added to the blood culture service.

Methods: A Cognos search was performed for all blood cultures booked into the lab within the designated period. The data downloaded included patient demographics and the culture results including which organisms were isolated and in which bottles. The aerobic positive results were pulled out and the patient electronic record and the specimen lab record were reviewed to establish whether the result was significant and whether the result lead to a change in patient management.

Results: The rate of positive blood culture sets, either aerobic, anaerobic or both, was 9.2% over the 2 months. Of the positive results, 29.5% were aerobic only. By reviewing the clinical details of each patient we established that 60.8% of the positive aerobic cultures were considered a significant pathogen. To further establish the significance we looked to see if the result lead to a change in management following discussion with the clinical team. In order to do this we reviewed patient episodes, defined as 48 hours from the first positive result, rather than individual blood culture results. Using this method, we found that there was a change in management following the culture result in 45 patient episodes, which prior to the service being implemented would have been delayed or would not have occurred.

Discussion: This data suggests that, in our hospital, the use of aerobic bottles has an important role to play in the management of patients with bacteraemia or candidaemia.

180
Poor sensitivity of the qSOFA assessment when deployed as a standalone screening tool for sepsis in adult inpatients at a large District General Hospital

Abstract - 180

Poster 180

Poor sensitivity of the qSOFA assessment when deployed as a standalone screening tool for sepsis in adult inpatients at a large District General Hospital

Robert Gray, Hala Kandil, Moira Surridge, Tejal Vaghela
West Hertfordshire Hospitals NHS Trust, Watford

Introduction: Sepsis, defined as a life-threatening organ dysfunction due to a dysregulated host response to infection, has a case mortality rate in the UK of around 30%. Despite this, it has been long considered that recognising the early signs of sepsis is challenging. Multiple initiatives have targeted improving the early recognition of sepsis. The quick Sequential Organ Failure Assessment or qSOFA has gained prominence as a bedside test for detecting sepsis. It requires three parameters to be measured: blood pressure, respiratory rate and acute alteration in mental state. Presence of two positive parameters out of three was shown from datasets of over 700,000 patients to predict higher mortality if treated in the non-ICU setting. Its ease of use and strong predictive value of poor clinical outcome has led many to propose its use as a bedside prompt to screen for sepsis. Here we report the results of an audit evaluating the use of qSOFA as an early prompt for sepsis in the assessment of adult inpatients at Watford General, a large district general hospital.

Methods: From April 2017 The qSOFA score was added to the clerking proforma for adult admissions at Watford General under the banner “Think Sepsis”. As qSOFA is not recommended as a screening tool, an audit was carried out to assess its effectiveness. During a six month period in 2018, a sepsis  nurse and lead antimicrobial pharmacist identified 279 patients on 16 inpatient wards with clear evidence of sepsis (using NEWS score; sepsis red flags; new rise in inflammatory markers; clinical concern and clinician commencement of intravenous antibiotics). The data was analysed retrospectively to see whether the patient had triggered a qSOFA score of 2 or more at the time that sepsis was suspected.

Results: 26.5% (74 out of 279) of patients triggered a qSOFA score of 2 or more, indicating probable sepsis with risk of an adverse outcome. Inpatient mortality among all patients studied was 19.3%. Positive qSOFA score was found to increase the likelihood of inpatient mortality: 22% vs 18.5% (Odds Ratio of death = 1.2) but the difference in mortality was not statistically significant (95% Confidence Interval 0.63 to 2.33, p=0.57).

Discussion: This retrospective study determined the sensitivity of a qSOFA value of 2 or more as only 27% sensitive when used at a single point of assessment for the recognition of sepsis. It did however associate with a higher rate of mortality, although this association was not statistically significant in this limited-sized study. Nevertheless these results support the conclusion of the qSOFA score developers that the assessment tool should not be used in isolation as a standalone sepsis screen. Further it highlights that qSOFA may perform better when measured serially, with an increase in score indicating the development of sepsis, rather than when used as a one off indicator.

In conclusion, qSOFA has been extensively validated as a measure which can identify which patients with infection are at higher risk of dying, but further investigation is required as to how the score can be applied usefully to clinical practice. Practitioners must be advised that one-off assessment with qSOFA is not a sufficient screen for sepsis.

181
Point of care influenza testing has not led to a increase in discharge within 24 hours of Influenza positive patients

Abstract - 181

Poster 181

Point of care influenza testing has not led to a increase in discharge within 24 hours of Influenza positive patients

Milo Cullinan, Yusri Taha, Shirelle Burton-Fanning
Newcastle-upon-Tyne Hospital Trusts

Introduction: Point of care (POC) testing for Influenza in the Assessment Suite (AS) of the Royal Victoria Infirmary, Newcastle-upon-Tyne Hospital Trust (NUTH) has previously been demonstrated to have reduced time to availability of result, reduced time to isolation of the individual and reduced time to prescription of antiviral medication. With two further years of data since its introduction, we look to see if POC influenza testing in an acute medical unit has increased the proportion of patients, with laboratory confirmed influenza, discharged within 24 hours of admission.

Methods:  A Cepheid GeneExpertTM analyser was introduced to the AS in the autumn of 2015 to be used as a point of care test for influenza. Junior medical staff in the unit were trained to perform the test.

Electronic records were interrogated to identify all throat swabs taken between 1st October and the 30th April of each of the winter seasons for 2014-15, 2015-16, 2016-17 and 2017-18, from patients who attended the Emergency Department (ED) or the Ambulatory Care Unit (ACU) or were admitted to the AS, and which were tested for influenza . This identified 5605 samples.  

A query was then run on the Cerner Powerchart eRecord system to identify those patients which were admitted either while or within 24 hours of the sample being taken. This identified 4345 admissions and provided the length of admission.

264 patients were excluded as the sample was taken at greater than 24 hours into their admission and a further 52 were excluded as they were under 18, leaving 4062 patients of which 936 tested positive for Influenza.

Results: During the 2014 season, 345 swabs were tested for influenza of which 54 tested positive. 15 (27.8%) of these patients were discharged within 24 hours. Over the combined 2015, 2016 and 2017 seasons 3717 samples were taken, of which 882 tested positive. 309 (35.0%) of these patients were discharged within 24 hours. This shows a slight increase but was not statistically significant (Χ2= 0.20).

The 2015 season saw increase in the number discharged within 24 hours to 61 out of 127 influenza positive patients (48%, X2=0.01) but this was not sustained to the 2016 season where 91(34%, Χ2 = 0.34) patients out of 263 who tested positive were discharged within 24 hours.

This was the case despite testing for influenza increasing from 345 tests in the 2014 season to 1911 tests in the 2017 season. Patients who were influenza positive were also more likely to be discharged within 24 hours of admission than patients who tested negative, both before (OR= 1.74, 95% CI 1.29 to 2.36) and after (OR=1.75, 95% CI 1.49 to 2.06) the introduction of POC.

Discussion: It is difficult to compare the cohorts of patients from before and after the introduction of point of care testing as testing for influenza increased greatly year on year subsequently. This suggests that the pre-test suspicion of influenza is likely different between the cohorts and the severity of their symptoms may also differ. The virulence and prevalence of the influenza each season may also have changed. It is not clear that these factors would mask any potential for earlier discharge that a POC might provide. The initial introduction did appear to increase early discharge and so may suggest further opportunity to research what factors lead to this and why it wasn’t sustained.

Furthermore, showing that more patients were tested for influenza and that those who test positive were more likely to be discharged within 24 hours encourages us to investigate if this led to a greater proportion of patients who present with respiratory tract symptoms being discharged earlier.

182
Diagnostic stewardship in practice – optimising urine testing

Abstract - 182

Poster 182

Diagnostic stewardship in practice – optimising urine testing

Ila Aggarwal, John Shone, Anne Serman
NHS Tayside, Dundee

Introduction: The increasing spread of antimicrobial resistance is a global concern. Reducing unnecessary testing of microbiology samples can lead to a reduction in inappropriate prescribing of antibiotics. The presence of bacteria in the urine may indicate urinary tract infection (UTI); however many patients with asymptomatic bacteriuria (ASB) do not require antibiotics.

Methods: In 2015, we introduced a urinary testing algorithm via our electronic test requesting system throughout the regions of Tayside and Angus (catchment population approx. 400,000). The algorithm was for individuals > 16 years old, and was based on confirmation of the presence of symptoms. Other indications for testing included sepsis and acute confusion; for ASB testing was indicated in pregnancy, post renal transplant and pre urological surgery (1) and for screening for resistant organisms. We introduced further interventions after assessing the initial response which included visiting general practitioners and their teams, and arranging meetings with consultants and specialist nurses in urology, renal medicine and biochemistry. All changes to test requesting and interventions were communicated to service users via email bulletins. We continuously evaluated the effect of the algorithm and subsequent interventions.

Results: The number of urines processed by our laboratory per year in the target population fell from a mean of 85819 for the 5 years prior to introduction of the algorithm to 73567 in 2017 (absolute reduction 12252,14.3%). In the whole population, the percentage decrease was similar at 14.4%. 5639 (9.67%) less urines were received from general practice.  A comparison of the number of urines received per month by chi-squared test showed a statistically significant reduction. Overall, there was an increase in the number of urines reported with significant growth (29.9 % vs 24.4%) which may be due to better patient selection or changes in labarotory procedures.

Discussion: We adopted a multi-disciplinary approach to urine testing in Tayside. By consulting with other specialities we were able to produce recommendations for haematuria testing and management, and for the testing of proteinuria while minimising unnecessary urine culture. We were able to address the concerns of primary care providers by looking into apparent conflicting guidance provided by different specialities and providing advice on catheter management. By adopting this approach we found it is possible to achieve a sustained reduction in microbiology testing of urine samples.

183
Evaluation of the Alere BinaxNOW® pneumococcoal urinary antigen test in community acquired pneumonia with S. pneumoniae bacteraemia. Time for a change?

Abstract - 183

Poster 183

Evaluation of the Alere BinaxNOW® pneumococcoal urinary antigen test in community acquired pneumonia with S. pneumoniae bacteraemia. Time for a change?

Stephen Hughes1, Scott Pallett1, Nabeela Mughal1,2, Luke Moore1,2
1Chelsea & Westminster NHS Hospitals, London. 2National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London

Introduction: Streptococcus pneumoniae is a common cause of community acquired pneumonia and hospital admission, with potential for life-threatening complications. The Alere BinaxNOW® urinary antigen test (UAT) is widely used as a rapid diagnostic test for S. pneumoniae serotypes that are responsible for over 90% of disease burden in North America and worldwide with the aim of assisting in early diagnosis and guiding treatment choices.

Whilst marked differences have been reported in detection of different serotypes, a recent meta-analysis of the BinaxNOW test shows a pooled sensitivity and specificity of 74.0% and 97.2%. Following the introduction of the 23 and 13-valent vaccines, serotype prevalence causing invasive disease and the utility of current rapid diagnostics to detect invasive serotypes need review. This tests utility and reproductivity are analysed here in our Trust.

Methods: A retrospective single-centre cohort study was completed at an acute NHS Trust reviewing all patients who had a measured pneumococcal UAT from December 2015 to June 2018. UAT was assayed using the Alere BinaxNOW®.  All patients with a blood culture tested within 48 hours of the urinary antigen testing were included in the final analysis. Institutional databases were used to collect data on patient admission data, time of blood culture taken, time of UAT collection, and test results. All S. pneumoniae blood cultures were sent to the Bacteriology Reference Department at Collindale for serotype analysis. Blood culture and pneumococcal antigen test results were matched at a patient level for each admission and analysed in excel. Any duplicate tests were analysed in a sub-group to measure reproducibility of the test and impact of timing on results.

Results: A total of 739 patient episodes were included in the study with matched UAT and blood culture result. Positive UAT was identified in only 4 of 13 identified S. pneumoniae blood culture results with a calculated sensitivity of 28.6% (specificity 94.9%). Five patients had multiple UAT with at least one positive result; however, reproducibility of positive results was identified in only 2/5 (40%) with negative results after 24 hours. The time of UAT to time of blood culture was 9 hour and 3 hours in UAT positive and negative results respectively. 11/13 serotype results available. 2 duplicate isolates were recorded: 1, 3, 3, 7F, 8, 10A, 16F, 22F, 33F, 35B, 35F. Only 22F, 35B and 35F are not covered in the 23-valent polysaccharide pneumococcal vaccine.

Discussion: Positive urinary antigen tests in patients with S. pneumoniae bacteraemia in our patient population was lower than expected. Whilst the Alere BinaxNOW® appears to be useful for detecting serotypes responsible for pneumococcal bacteraemia in community acquired pneumonias, it is notable that 2/13 patients had non-23 valent isolates. The prevalence of non-vaccine isolates in our population needs to be better evaluated in order to assess the utility of current rapid diagnostics available for S. pneumoniae.

The sensitivity of the UAT is recognised as being higher in severe pneumonia where CURB-65>2 has an increase in odds ratio of 18.7 for positive tests. It is likely that patients with severe co-morbidities present early in the disease process and that timing of the sample is an important element, affecting result positivity.

Our study is limited by a small number of paired samples, however the results suggest caution is required in interpreting negative UAT results in the Emergency Department if there is a high index of suspicion for severe community acquired pneumonia and invasive disease with Streptococcus pneumonia.

184
Fungal biomarker turn-around-time (TAT) and antifungal stewardship: how long is too long?

Abstract - 184

Poster 184

Fungal biomarker turn-around-time (TAT) and antifungal stewardship: how long is too long?

Clare Logan1, Jonathan Youngs1, Hassan Al-Ghusein1, Silke Schelenz2, Tihana Bicanic1
1St George’s Hospital, London. 2Royal Brompton Hospital, London

Introduction: Fungal biomarkers are an important tool for antifungal stewardship. Optimising antifungal drug use is essential to limit exposure to toxic drugs, curtail the emergence of fungal resistance and minimise unnecessary drug expenditure. Additionally, fungal biomarkers are important adjuncts to radiological and microbiological investigation in the diagnosis of invasive fungal infection (IFI), where, given the high mortality, timely diagnosis is essential.

The aim of this study was to look at the turn-around-time of fungal biomarkers at two large London teaching hospitals, St George’s Hospital (SGH)  and the Royal Brompton hospitals (RBH), to assess whether in a real-world setting, results are available to clinicians within a meaningful timeframe to assist diagnosis and impact on antifungal stewardship.

Methods: Samples sent for galactomannan (GM) and Beta-D-glucan (BDG) at SGH (01/2010-07/2018) and RBH (01/2014-07/2018) were identified from the respective microbiology databases. The turn-around time (TAT) was defined as the number of days between the date of receipt of specimen in the laboratory to the date of result authorisation. Specimen type, source (ICU, non ICU inpatient, outpatient clinic) and result (positive, indeterminate or negative) were also analysed.   Analyses were conducted in Microscoft Excel 2013 and GraphPad Prism v7.

Results: In total, 3199 samples were sent for GM testing (2229 at RBH, 970 at SGH). All SGH GM samples are sent to the Bristol Mycology Reference Laboratory (MRL) with a median (Interquartile range (IQR)) TAT of 13 days (11-17) days. RBH GM samples prior to August 2015 were also sent to the MRL, with a median (IQR) TAT of 8 (5-14) days (Mann Witney p<0.0001, comparison with SGH TAT). After August 2015, RBH performed the assay in-house, halving the median TAT to 4 (2-5) days (Mann Witney p<0.0001 pre- and post- in house testing comparison for RBH).

For BDG testing, a total of 635 samples were sent with TAT data (RBH=610, SGH=25).  Prior to June 2017 at RBH, samples were sent to the MRL and median (IQR) TAT was 6 (3-7) days. From June 2017, RBH samples were sent to Kings College Hospital, London (KCH) and the median (IQR) TAT reduced to 3 (2-6) days (Mann Witney p<0.0001 pre- and post- KCH send-away comparison for RBH). SGH sent away all samples to the MRL with median (IQR) TAT of 12 days (9-14) days.

Data on specimen type, source and result will also be presented.

Discussion: A median turn-around time of 1-2 weeks significantly devalues the use of fungal biomarkers for both diagnosis of IFI and antifungal stewardship, hindering clinical decision-making. Our results confirm that sending away biomarkers to a geographically distant reference lab prolongs TAT in comparison to having the tests done locally or in-house, with RBH, halving the TAT for GM and BDG by performing it in-house and at a local laboratory respectively.

However it is also apparent that not all TAT prolongation issues are secondary to samples being sent away to Bristol, as shown by the comparison between SGH and RBH TAT for the same tests done at MRL, suggestive of internal logistical issues at SGH laboratory.

With antifungal stewardship high up on the agenda of the NHS England Improving Value Project and a planned rollout of an antifungal CQUIN, guidance and incentives are needed not only around antifungal prescribing but also the performance of fungal diagnostics and recommended minimum TAT. We propose that a TAT of 3-5 days would maximise the diagnostic and antifungal stewardship benefits of fungal biomarkers.  Greater harmonisation and the creation of regional diagnostic hubs will be required to achieve this goal.

185
The impact of routine molecular point-of-care testing for gastrointestinal pathogens in adults hospitalised with suspected gastroenteritis: results of a pragmatic randomised controlled trial (GastroPOC)

Abstract - 185

Poster 185

The impact of routine molecular point-of-care testing for gastrointestinal pathogens in adults hospitalised with suspected gastroenteritis: results of a pragmatic randomised controlled trial (GastroPOC)

Kate Beard1, Ahalya Malachira2, Nathan Brendish1,2, Fraser Cummings3, Marcus Gwiggner 3, Tristan Clark4,2,5
1University of Southampton. 2Infection, University Hospital Southampton NHS Foundation Trust. 3Gastroenterology, University Hospital Southampton NHS Foundation Trust. 4Academic Unit of Clinical and Experimental Sciences, University of Southampton. 5NIHR Post-Doctoral Fellowship Programme, Southampton

Introduction: Patients presenting to hospital with diarrhoea are routinely isolated as an infection control measure, but many have non-infectious aetiology. Side room facilities are a limited resource in hospitals. Routine laboratory testing takes several days to generate results but novel rapid molecular platforms can test comprehensively for GI pathogens and generate a result in 1 hour, making them deployable as point-of-care tests (POCT). Routine use of a POCT could reduce unnecessary isolation facility use in addition to other benefits such as reduction in length of stay and improved appropriate antibiotic use. 

Methods: In this pragmatic, pilot randomised controlled trial, adults presenting to hospital with acute diarrhoea (<14 days) were recruited and randomised 1:1 to receive either POCT (FilmArray GI panel) or routine clinical care. Results of POCT were communicated immediately to clinical and infection control teams. The primary outcome was duration of time in a side room and secondary outcomes included turnaround time, proportion of patients with a pathogen detected, proportion of patients correctly de-isolated, time to de-isolation, length of stay and antibiotic use.

Results: 140 patients were recruited. The groups (n=70) were well matched in terms of baseline characteristics. The median [IQR] turnaround time for results was 1.7 [1.6-2.3] hours in the POCT group and 61 [49-84] hours in the control group, p<0.0001. Pathogens were detected in 44% of patients in the POCT group and 23% in the control group; p=0.012.63% of pathogen-negative patients were correctly de-isolated in the POCT group (after a median of 23 hours) versus 28% in the control group (after a median of 56 hours), p=0.0012.The median duration of side room isolation was 1.9 [1.0-2.9] days in the POCT group compared to 2.7 [1.8-5.1] days in the control group; p=0.001. For those testing negative for pathogens this was 1.3 [0.8-2.5] days in the POCT group versus 2.7 [1.8-5.0] days in the control group, p<0.0001. There was a change of antibiotics in 39% of the patients in the POCT group. 88% of patients in the POCT group received appropriate antibiotic management overall versus 60% in the control group, p=0.0001. Duration of inappropriate antibiotics was 0.5 days in the POCT group and 3.0 in the control group, p=0.0096. Length of stay was 2.9 days in the POCT group and 3.7 in the control group, p=0.15. 

Discussion: POCT using the FilmArray GI panel resulted in faster turnaround time for results and an increase in the proportion of patients with pathogens detected. POCT was associated with an improvement in appropriate and timely de-isolation decisions and a reduction in the duration of unnecessary side room use. POCT was also associated with a higher proportion of patients recieving appropriate anitiboitcs and a trend towards a reduced length of hospital stay . If these benefits are confirmed in larger studies and cost effectiveness is demonstrated, molecular POCT for GI pathogens should replace laboratory-based diagnostic pathways.  

186
Clinical utility of the beta-D-glucan assay in general medical and surgical patients

Abstract - 186

Poster 186

Clinical utility of the beta-D-glucan assay in general medical and surgical patients

Shivani Singh1, Nabeela Mughal2,3, Luke Moore 2,3,4
1Imperial College School of Medicine, London. 2Chelsea & Westminster NHS Foundation Trust, London. 3North West London Pathology at Imperial College Healthcare NHS Trust, London. 4National Institute for Health Research Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London

Introduction: Invasive fungal disease (IFD) is associated with significant mortality, but can be difficult to diagnose in a timely fashion with culture based methods. Antifungal treatment of potential IFD can be associated with considerable toxicity, cost, and development of antifungal resistance. Therefore, accurate methods of diagnosing IFD in certain populations are required.  An assay for detection of (1,3) beta D-glucan (BDG) in serum is now available, and potentially offers a timely means to achieve this. To investigate the clinical utility of this test, we conducted a retrospective single centre observational study in a central London teaching hospital.

Methods: All BDG assays sent between 01/04/2017 and 31/03/2018 were identified from the laboratory information management system. HIV positive, intensive care unit (ICU) and paediatric patients were excluded. Demographic, clinical, laboratory, and treatment information were extracted from electronic health records and pseudoanonymised. BDG turnaround time (TAT) and antifungal initiation and cessation in relation to BDG result dates were assessed. Sensitivity and specificity of the BDG assay, against both fungal culture results and against ‘clinical decision to treat’, were also assessed. The culture result closest to the BDG request date was used, within the time frame of 1 week before to 1 week after BDG request date. The study site currently performs fungal culture in a centralised (off-site) laboratory, but BDG assays are sent to the national mycology reference laboratory.

Results: 83 BDG assays from 72 patients were identified with a mean patient age of 57 years [range 21-81]; 53% were female. There were 15 oncology patients, 26 respiratory patients (17 chronic respiratory disease) and 13 gastroenterology patients (9 gastrointestinal surgery, 4 chronic liver disease); patients deemed at risk from IFD. The mean TAT was 13 days [range 1-37], with 24/83 positive results (BDG cut-off 80 pg/mL). The galactomannan (GM) assay was performed alongside 75 of the 83 BDG assays, with only 1 positive GM result (GM cut-off 0.5 ODI). 

Of the 72 patients for whom BDG was requested, 22 patients were started on antifungals empirically whilst awaiting assay results. 14/22 subsequently returned a negative BDG result, with 9/14 stopping antifungal treatment before, 2/14 stopping on the day of, and 3/14 stopping after the result was received. 6/9 patients who stopped treatment before the BDG result date were discharged before the result was received. In only 5 patients was antifungal treatment initiated after return of the BDG result, suggesting that it was generally not used in the decision to initiate treatment.

The sensitivity of the BDG assay against fungi cultured from invasive samples was 44%, with a specificity of 73%. When comparing BDG results with ‘clinical decision to treat’, BDG sensitivity was 37% and specificity 82%. 

Discussion: Delays in obtaining BDG results mean cessation of antifungals is largely reliant upon clinical parameters. The notable number of patients empirically started on antifungals for whom BDG subsequently returned negative suggests toxic antifungals are being suboptimally used. Improving turnaround times for BDG may significantly improve antifungal stewardship. 

Fungal culture is not an optimal gold standard, but against this current standard of care, the BDG sensitivity was poorer than expected, but with a reasonable specificity. This may be due to many of the fungi cultured representing colonisers rather than IFD. When the BDG results were compared against a composite clinical judgement of the likelihood of IFD, sensitivity decreased, but specificity improved. The clinical utility of the BDG assay most likely lies in its ability to aid an early stop of antifungal therapy rather than to initiate treatment. However, to have any use in the diagnostic process, turnaround times must be improved.

187
Evaluation of acute phase reactants (white blood cell count, procalcitonin and C-reactive protein) in medical admissions – a tertiary hospital experience

Abstract - 187

Poster 187

Evaluation of acute phase reactants (white blood cell count, procalcitonin and C-reactive protein) in medical admissions – a tertiary hospital experience

Pete Dayananda, Nickh Uppal, Joanna Allen, Graham Sutton
Leeds Teaching Hospitals NHS Trust

Introduction: While patients with bacterial blood stream infection classically present with severe illness and sepsis, some patients are less unwell with no evidence of sepsis, presenting a diagnostic challenge, particularly in the early stages of illness. To aid clinical decision making, acute phase reactants such as C reactive protein (CRP) and white blood cell count (WCC) are commonly used. However, these markers may also be elevated in viral infections or non-infectious systemic inflammation, necessitating the need for a test with greater diagnostic accuracy for predicting bacterial infections.

Procalcitonin is one of the emerging biomarkers for bacterial infection and has been shown to facilitate reduction of antimicrobial use in an acute medical unit without resulting in increased mortality/clinical failure.

Procalcitonin was introduced to aid diagnosis of bacterial infections in new medical admissions in a 997-bed hospital in Leeds, United Kingdom in patients without signs of sepsis or evidence of bacterial infection at presentation.

Methods: Two-hundred and eighteen procalcitonin results between February-June 2017 were examined. Laboratory results and patient outcomes were obtained from scanned/electronic notes and the pathology database. Positive cultures from sterile sites (blood and pleural fluid) were considered significant isolates.

Procalcitonin results were interpreted using local cut-off values:

  •  <0.25ug/L – antibiotics discouraged (n=134)
  •  >0.25ug/L – antibiotics encouraged (n=70)

Fourteen procalcitonin results were excluded due to missing information.

Results

Procalcitonin <0.25ug/L group (n=134)

  • There was only 1(0.74%) significant isolate from this patient group.  S. epidermidis was cultured from both peripheral and Hickman line blood cultures in a patient whose procalcitonin was 0.2ug/L. His CRP was 33mg/dL and WCC was 3.35*109/L
  • One hundred and eleven(82.8%) patients had other raised inflammatory markers:
    • CRP >10mg/dL only [n=72(64.9%) mean 69.8; median 44; interquartile range (IQR) 91.8]
    • WCC >11*109/L only [n=8 (7.21%) mean 5.42; median 5; IQR 1.2]
    • Both raised CRP and WCC [n=31 (27.9%)]

Procalcitonin >0.25ug/L group (n=70)

  • Ten patients(14.3%) had positive cultures from a sterile site [blood (n=8) or pleural fluid (n=2)]
    • All 10 patients had CRP >10 (mean 139; median 72; IQR 186), 6 patients also had a WCC >11
  • Sixty six (94.3%) had raised CRP (mean 134; median 95.5; IQR 165) or WCC (mean 10.4; median 9.55; IQR 6.86).

Sensitivity of procalcitonin for blood stream or pleural infection was 90.9% and specificity was 68.9%.

Sensitivity of any raised inflammatory markers (CRP, WCC or procalcitonin) in both groups was 100%. However, the specificity of any raised inflammatory marker was only 12.0%.

Discussion: Procalcitonin in isolation has good negative predictive value (NPV) of 99.3% but a low positive predictive value (PPV) (14.3%) for pleural/blood stream infection. This is however, superior to the PPV of WCC and CRP (14.3 vs 6.21%). The negative predictive value is comparable (99.3 vs 100%). Procalcitonin level of >0.25 coupled with either a raised CRP or WCC, the positive predictive value improved to 15.2%. This reaffirms that procalcitonin is a more accurate marker of bacterial infections compared with WCC and CRP. The low PPV of these biomarkers is likely to be affected by inadequate sample collection prior to antibiotics.

Interestingly, low levels of procalcitonin was seen in one patient with S. epidermidis line infection. This is in keeping with previous studies that procalcitonin level is affected by pathogen and site of infection likely due to activation of different toll-like receptors. This requires further investigation and emphasises that levels must be interpreted with clinical assessment and not in isolation. Further education with users is underway to improve the utility of procalcitonin as a clinical adjunct for diagnosing bacterial infections.

188
5 years of MERS-CoV testing experience in a regional virology centre

Abstract - 188

Poster 188

5 years of MERS-CoV testing experience in a regional virology centre

Bozena Poller1, Anne Tunbridge2, Cariad Evans1
1Virology, Sheffield Teaching Hospitals NHS Foundation Trust. 2Infectious Diseases, Sheffield Teaching Hospitals NHS Foundation Trust

Introduction: Sustained emergence and reporting of MERS coronavirus (CoV) cases in the Kingdom of Saudi Arabia (KSA) and the Arabian Peninsula requires continued surveillance and vigilance for cases in returning travellers. In August 2018 a case of MERS-CoV was identified in the UK, bringing the total laboratory confirmed UK cases to 5 (3 imported and 2 onward transmissions). However, many thousands of people travel to the UK from the Arabian Peninsula every year, including approximately 25,000 British pilgrims who visit KSA to participate in the Hajj. [1]

Experience in the risk assessment, clinical presentation and outcomes of cases fulfilling the MERS-CoV Public Health England (PHE) testing algorithm is imperative to ensure future cases are accurately identified and managed. Sheffield Teaching Hospitals (STH) NHS Foundation Trust provides infectious disease and medical virology referral services across South Yorkshire and Derbyshire, and has a local Sheffield Muslim population greater than the UK average. [2] We retrospectively reviewed 5 years of MERS-CoV testing experience to help inform our clinical practice, systems of surveillance and infection control practice.

Methods: Laboratory data were interrogated to identify all patients where MERS-CoV PCR testing had been arranged via STH Virology & Infectious Diseases between August 2013-August 2018. Relevant clinical information and results of chest radiographs (CXR), blood science tests, and microbiology/ virology tests were then gathered from laboratory systems, electronic records and discharge letters.

Results: Twenty one patients were identified. Most had returned from KSA (13, 62%) with the remainder from UAE (4), Iraq (2), Bahrain (1) and Iran (1). High risk exposures were identified in 4 patients: 3 had camel exposure (close contact or consumption of unpasteurised milk), and 1 patient was hospitalised in KSA. Two of these cases and a further five had been exposed to unwell contacts (not known to be MERS cases) or were returning pilgrims.

Of the 17 available CXR reports, 10 (59%) had evidence of acute infection: consolidation (8), perihilar changes (1), effusion (1).

Blood results from admission were available for 17 cases: the majority had raised C-reactive protein (16, with range of 120-339 in 8 cases), 11 had neutrophilia, 2 had lymphocytosis and 7 lymphopaenia.

All 21 patients were negative for MERS-CoV on sputum or throat swab (PHE laboratory or STH). In addition, 17/21 had a positive result on a respiratory virus PCR panel: 2 influenza A H1, 7 influenza A H3 (3 co-infected with adenovirus, parainfluenza 3, standard coronavirus), 1 influenza A (type unknown), 3 influenza B, 2 rhinovirus, 1 adenovirus and 1 RSV.

Only 3 positive bacterial pathogens were detected despite frequent testing: Chlamydia pneumoniae (PCR on sputum), Haemophilus influenzae (sputum) and Group A Streptococcus (throat swab), the latter 2 on patients co-infected with influenza. No positive blood cultures were observed.

Discussion: Previous data in the UK and Bangladesh demonstrated detection of a viral pathogen in 50-30% of patients tested. [3,4] Our data demonstrated a significantly higher rate of 81%, highlighting the need for rapid local respiratory viral testing to allow pathogen identification and treatment. In our data, influenza predominated despite the Hajj not coinciding with the KSA influenza season (September to March, similar to the UK). [5] The UK annual influenza vaccine production aims to deliver in September each year, making availability difficult for those travelling out of season. Although vaccine failures are well recognised, when high rates of Pilgrim vaccination have been achieved (100%, China), subsequent screening on return has shown mostly asymptomatic or mild presentations, [6] potentially reducing burden of illness, hospital admission and onward transmission to others. Finally, our data emphasise the ongoing need to counsel patients pre-travel in respiratory hygiene measures and avoidance of high-risk exposures.

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