Presentation on theme: "Closer to the front door: clinical aspects of Microbiology automation"— Presentation transcript:
1 Closer to the front door: clinical aspects of Microbiology automation Dr David GarnerBM MSc MRCPCH FRCPathFrimley Health NHS Foundation Trust& Surrey Pathology Services
2 BiographyBackground in paediatrics before training in Microbiology in Nottingham, UKNHS Consultant for 8 years in Nottingham and then Surrey, UKFrimley Health NHS Foundation TrustFrimley Park Hospital & Heatherwood and Wexham Park HospitalsSurrey Pathology ServicesFrimley Park Hospital, Royal Surrey County Hospital, Ashford & St Peters Hospitals
3 BiographyNo specific affiliation to any private company or organisationWill not talk specifically about any product and presentation is not an endorsement of any specific product over another – make your own mind up…Except this one…
4 Aims & Objectives What is automation? What are the potential benefits of automation?Why does this matter?Automation in practiceMy model for the future infection diagnostics service
5 What is automation?Automation - “The use or introduction of automatic equipment in a manufacturing or other process or facility”Automatic – “(of a device or process) working by itself with little or no direct human control”My definition – “anything that a device can do which makes delivery of service easier or more effective”Let humans do what humans need to do and let machines and computers do the rest!
6 Potential benefitsCorrect test done, on the correct sample, from the correct patientImprove accuracy of result (identification, antimicrobial sensitivities & clinical relevance)Reduce laboratory turnaround timeReduce mortality & morbidityReduce length of stayImprove infection controlImprove antimicrobial stewardshipImprove user satisfaction – Patients & Clinicians
7 Why do these matter?Correct test done, on the correct sample, from the correct patientCommon problemsIncorrect specimen typeIncorrect test requested for clinical scenarioInsufficient clinical information with requestInadequate patient identifying informationSolutionPre-analytical automation of test requesting procedure
8 Why do these matter?Improve accuracy of result (identification, antimicrobial sensitivities & clinical relevance)Specific names of bacteria allow prediction of antimicrobial resistance patternsTraditional laboratory methods can miss inducible antimicrobial resistanceJust because you find a microorganism doesn’t mean you have to try and kill it!SolutionIdentification (MaldiTOF, 16sRNA)Sensitivities (reading of EUCAST, MIC methods)Quantification & mixtures: Colonisation vs. Infection
9 Why do these matter? Reduce laboratory turnaround time Solutions Slow results damage reputation and reduce willingness of users to send samplesImpact on mortality & morbidityImpact on length of staySolutionsScreen for negative results as fast as possibleReduce time taken to culture bacteriaReduce time to detect non-culturable microorganisms
10 Why do these matter? Reduce mortality & morbidity Solutions For every hour delay in starting appropriate antimicrobials in sepsis mortality increases by 7.6%Prolonged IV antimicrobial courses increase the risk of complications due to IV therapy e.g. CVC infectionsSolutionsMove the “laboratory” as close to the front door of the hospital as possiblePoint of care diagnosticsRapid identification of antimicrobial resistance
11 Why do these matter? Reduce length of stay Solution Hospital capacity & winter pressures on bed stockIncreased patient turnover = increased financial return for hospitalReduced risk of complications e.g. nosocomial infectionsPatient satisfactionSolutionReduce time to results which diagnose self-limiting infections or allow patients to convert to oral therapy or Outpatient Antimicrobial Therapy (OPAT)
12 Why do these matter? Improve infection control Solution Delays in diagnosing communicable diseases or target organisms delays source isolation leading to increased risk of cross infection and outbreaksSolutionPoint of care tests for communicable diseases or target organisms e.g. MRSA, C. difficile, Norovirus, Influenza etc.Improve accuracy and reduce turnaround time of laboratory screening tests, particularly negative resultsDetection of novel or specific resistance mechanisms e.g. carbapenemases
13 Why do these matter? Improve antimicrobial stewardship Solution Right antibiotic at the right dose, route and duration, for the right infection at the right time to improve patient care whilst reducing antibiotic resistanceSolutionImproved accuracy of sensitivity resultsFaster sensitivity results allowing de-escalation or conversion to targeted antimicrobial therapyDetection of inducible resistanceExpert rules
14 Fundamental aspect of the modern diagnostic laboratory Why do these matter?Improve user satisfaction – Patients & CliniciansCommon complaints pre-automation about turnaround timesUnnecessary antibiotics because unable to get results quickly enoughImproved patient outcomesSolutionResults that are fast, accurate and clinically relevantFundamental aspect of the modern diagnostic laboratory
15 Value What to automate? Volume of work Low High Individual patient impactX√√√√√√
16 √ Low volume, high impact Sample types Blood culturesCerebrospinal fluidsFaeces – hospital onset diarrhoea (C. difficile)Predictive sensitivities by earlier identificationReduced mortality and length of stayIncreased capture of communicable infectionsReduced antibiotic burden by earlier change to targeted treatment
17 √ Blood cultures Pre-automation: 3-6 days Post-automation: 1-2 days Automated incubator 1-2 daysPure culture & identification 1-2 days (predicted sensitivity)Sensitivities 1-2 daysPost-automation: 1-2 daysPure culture & identification 4 hours (predicted sensitivity)Sensitivities 1 day (possible 5-8 hours?)Future: < 1 dayPOC incubator placementPre-incubation + identification direct from blood cultureTargeted multiplex PCR by clinical information
18 √ Cerebrospinal fluids Pre-automation: 2-10 days Culture & sensitivity 2 daysMolecular detection 3-10 daysPost-automation: 1-2 daysMolecular detection 1-2 daysFuture: < 1 dayTargeted multiplex PCR by clinical information
20 √ High volume, low impact Sample types FaecesSputumSerologyIncreased capture of communicable infectionsPredictive sensitivities by earlier identificationReduced antibiotic burden by earlier change to targeted treatmentReduced length of stay
21 √ Faeces Pre-automation: 2-4 days Post-automation: <1 day (+ 1 day) Culture 2 daysSensitivities 2 daysPost-automation: <1 day (+ 1 day)Multiplex PCRTargeted culture and sensitivityFuture: POCImproved “card” techniquesMolecular “plug & play” technologies
22 √ Sputum Pre-automation: 2-4 days Post-automation: 1-3 days Future: Culture 1-2 daysIdentification and sensitivities 1-2 daysPost-automation: 1-3 daysPOC antigen testing for S. pneumoniae and L. pneumophilaIdentification 1 day (predicted sensitivity)Sensitivity 1 dayFuture:Targeted multiplex PCR by clinical information
23 √ Serology Pre-automation: 1-7 days depending on arrival in lab ELISACFTsPost-automation: 1-3 daysTwice weekly or more testingMulti-test platformsSyndromic testing by clinical informationFuture:Limited value?Targeted multiplex PCR by clinical information
24 High volume, high impact √√High volume, high impactSample typesUrinesFaeces – community onset diarrhoeaReduce use of antibiotics by allowing delayed treatmentIncreased capture of communicable infectionsPredictive sensitivities by earlier identificationUser satisfaction in primary care!
25 √√ Urines Pre-automation: 2-4 days Post-automation: ≤1 day Future: Culture 1-2 daysIdentification and sensitivities 1-2 daysPost-automation: ≤1 daySame day screening of negativesCulture 1 daysIdentification 1 day (predicted sensitivity)Sensitivity 1 dayFuture:Improved negative and positive predictive values
26 √√ Faeces Pre-automation: 2-4 days Post-automation: 1-3 days Future: Culture 1-2 daysIdentification and sensitivities 1-2 daysPost-automation: 1-3 daysPOC testing for Norovirus and Rotavirus?Identification 1 day (predicted sensitivity)Sensitivity 1 dayFuture:Multiplex PCR plus selective culture
27 Pan-laboratory automation Kiestra24/7 activityRemote reading – laboratory, off-site, bedside?Visual toolbox – automated reading and reporting of negative culturesTotal lab automationCombine platforms for various tests and use Kiestra to move cultures between them on an automated basisLaboratory Information Management SystemsRules based testing and auto-comments on reportsExpert rules to reduce time for reporting and authorising
28 Ideal network laboratory…? Dear Santa, this year I’d really like…
30 Ideal network laboratory…? BenefitsFast turnaround time of negative resultsSepsis pathwayOnly move samples that require culture or where transport is not the rate limiting factor for turnaroundPOC blood cultures allows true negative turnaround e.g. 36 hours for neonatal unitsMulti-discipline pathology MLAs run screening service on hospital site2 Central labs give emergency back-up if lab failure
31 Target treatment & source control Septic patientSepticaemiaBlood cultureDiarrhoeaFaecesPneumoniaSputumNasopharyngeal SwabUrosepsisUrineMeningoencephalitisCSFPCRC&S16-24 hoursPCRMicroscopyMaldiTOF/PCRAntigens2-4 hoursTarget treatment & source control
33 Teenager with meningism 1 hourBlood cultures taken started on IV CeftriaxoneChest X-ray normal, no diarrhoea, urine dipstick negative2 hoursLumbar puncture performed4 hoursConfirmed Meningococcal meningitisChanged to IV Benzylpenicillin for 7 daysBenefits: reduced complications, duration of antibiotics & length of stay
34 Elderly lady with sepsis 1 hourBlood cultures taken started on IV PiptazobactamChest X-ray no consolidation, no diarrhoea, urine dipstick positive2 hoursUrine microscopy positive, ESBL positive E. coli detected by MaldiTOF or PCRAntibiotics escalated to IV Meropenem16 hoursConfirmed ESBL positive sepsisBenefits: reduced mortality
35 Neonatal sepsis 1 hour 2 hours 4 hours Blood cultures taken started on IV Benzylpenicillin plus GentamicinChest X-ray no consolidation2 hoursLumbar puncture performed raised WBC4 hoursConfirmed L. monocytogenes meningitisChanged to Ampicillin and Gentamicin for 3 weeksBenefits: reduced mortality & complications, public health follow-up
36 The elephants in the room ExpensiveJustify cost to lab against savings by users, reduced mortality, reduced length of stay or increased reputation?Dependent on IT systemUltimately it doesn’t matter how good your lab is if you can’t receive and give out informationMultiple IT platforms in labs, wards and GP practicesHave to be able to recognise sepsis in order to use a sepsis pathway!
37 Recognising sepsis…The problem with managing septic patients is failing to recognise sepsisSurviving Sepsis CampaignThe UK Sepsis TrustShould diagnostic companies be working with these organisations and promoting the recognition of sepsis?
38 ConclusionsGet closer to the front door, the faster the result the better the outcome…?Potential benefits of automation include:Correct test, correct sample, correct patientImprove accuracy of result (identification, antimicrobial sensitivities & clinical relevance)Reduce laboratory turnaround timeReduce mortality, morbidity &length of stayImprove infection control & antimicrobial stewardshipImprove user satisfaction – Patients & CliniciansAutomation is expensive: cost needs to be offset against savings outside of the laboratory (not just financial!)
39 Microbiology Nuts & Bolts Further reading:Microbiology Nuts & Bolts by Dr David GarnerFacebook page for Microbiology Nuts & BoltsAvailable to buy on
41 Royal College of Pathologists A well-written book...concise, well set out and easy to use. It contains a wealth of useful information and is a valuable resourceRoyal College of Physicians This book delivers a uniquely relevant and accessible take on microbiology and does an excellent job of bridging the gap between the dry lists of pathogens learnt at medical school and the clinical reality of infectionBritish Society for Antimicrobial Chemotherapy This book provides an impressively broad coverage of microbiology in theory and practice and I can see uses for it for students, junior doctors and general practitionersRoyal Pharmaceutical SocietyPocket guide to all things infection related packs a vast amount of information into a small space, and would be a useful back-up or portable revision aid for any pharmacist dealing with infectionInstitute of Biomedical Science A comprehensive yet concise book that would be useful to any healthcare professional managing patients with infectionsHospital Infection SocietyA very good pocket guide covering the basics of microbiology… it forms a good base of knowledge for specialist trainees
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