Comparative diagnostic accuracy study of three multiplex molecular assays for bacterial gastroenteritis

Transcription

1 Comparative diagnostic accuracy study of three multiplex molecular assays for bacterial gastroenteritis Simon Goldenberg Consultant Microbiologist and Infection Control Doctor Guy s & St Thomas NHS Foundation Trust Honorary Senior Lecturer King s College London

2 Number of emergency admissions Top 10 most frequent reasons for emergency admission, Guy s & St Thomas Hospital, 2014/ Primary diagnosis code

3 Clinical features are not helpful for predicting the etiology of diarrhoea Duration of diarrhoea Abdominal pain Vomiting Blood stools Number of bowel movements Fever Requirement for IV hydration This emphasizes the need for more rapid, sensitive, and simple methods to improve the diagnostic yield Chan et al. Hong Kong J Emerg Med. 2003;10: Svenungusson et al. Clin Infect Dis (5): Munk Petersen et al. Scand J Gastroenterol 1996;31: Svanteson et al. Scand J Infect Dis 1988;20:303-14

4 aripiprazole, acarbose, acamprosate, acebutolol, aceclofenac, acemetacin, acetazolamide, acyclovir, acitretin, activated charcoal, agalsidase beta, alendronate, alfuzosin, allopurinol, almotriptan, amphotericin, amiloride, aminophylline, amitriptyline, amlodipine, amoxicillin, anastrozole, anidulafungin, allantoin, aspirin, atenolol, atorvastatin, aztreonam, azathioprine, azithromycin, barium sulphate, brinzolamide, baclofen, bendroflumethiazide, belimumab, betaxolol, bezafibrate, bisoprolol, bleomycin, bisacodyl, bosutinib, bromocriptine, buprenorphine, bumetanide, busulfan, buspirone, calcium carbonate, calcium folinate, calcium glubionate, calcium lactobionate, caffeine, colestilan, caspofungin, capecitabine, captopril, carglumic acid, carbamazepine, carboplatin, cetirizine, carvedilol, cefadroxil, cephalexin, cefotaxime, cefradine, ceftazidime, ceftriaxone, cefuroxime, celecoxib, celiprolol, chlorambucil, chlorphenamine, colesevelam, ciprofloxacin, cimetidine, citalopram, cisplatin, clarithromycin, clindamycin, clofarabine, clopidogrel, clozapine, codeine phosphate, colchicine, colestipol, colistimethate, corifollitropin alfa, crisantaspase, cytarabine, dacarbazine, daptomycin, darifenacin, decitabine, dantrolene, daunorubicin, deferasirox, deferiprone, desferrioxamine, desloratadine, dihydrocodeine, diazepam, diclofenac, digoxin, diltiazem, docusate sodium, dipyridamole, disodium pamidronate, docetaxel, domperidone, donepezil, dorzolamide hydrochloride, doxazosin, doxorubicin, doxycycline, ethosuximide, esomeprazole, emtricitabine, enalapril, etanercept, entacapone, epirubicin, epoprostenol, etoposide, epoetin alfa, erdosteine, erythromycin, estradiol, ethambutol, ethosuximide, etodolac, ethinylestradiol, exemestane, fentanyl, fenofibrate, ferrous sulphate, ferrous fumarate, flecainide Electronic Medicines Compendium

5 aripiprazole, acarbose, acamprosate, acebutolol, aceclofenac, acemetacin, acetazolamide, acyclovir, acitretin, activated charcoal, agalsidase beta, alendronate, alfuzosin, allopurinol, almotriptan, amphotericin, amiloride, aminophylline, amitriptyline, amlodipine, amoxicillin, anastrozole, anidulafungin, allantoin, aspirin, atenolol, atorvastatin, aztreonam, azathioprine, azithromycin, barium sulphate, brinzolamide, baclofen, bendroflumethiazide, belimumab, betaxolol, bezafibrate, bisoprolol, bleomycin, bisacodyl, bosutinib, bromocriptine, buprenorphine, 3141 bumetanide, drug busulfan, preparations buspirone, calcium carbonate, calcium folinate, calcium glubionate, calcium lactobionate, caffeine, colestilan, caspofungin, capecitabine, captopril, carglumic acid, carbamazepine, carboplatin, cetirizine, carvedilol, cefadroxil, cephalexin, cefotaxime, cefradine, ceftazidime, ceftriaxone, with cefuroxime, celecoxib, diarrhoea celiprolol, chlorambucil, as chlorphenamine, a colesevelam, ciprofloxacin, cimetidine, citalopram, cisplatin, clarithromycin, clindamycin, clofarabine, clopidogrel, clozapine, codeine phosphate, colchicine, colestipol, colistimethate, corifollitropin alfa, crisantaspase, cytarabine, dacarbazine, known daptomycin, unwanted darifenacin, decitabine, dantrolene, effect daunorubicin, deferasirox, deferiprone, desferrioxamine, desloratadine, dihydrocodeine, diazepam, diclofenac, digoxin, diltiazem, docusate sodium, dipyridamole, disodium pamidronate, docetaxel, domperidone, donepezil, dorzolamide hydrochloride, doxazosin, doxorubicin, doxycycline, ethosuximide, esomeprazole, emtricitabine, enalapril, etanercept, entacapone, epirubicin, epoprostenol, etoposide, epoetin alfa, erdosteine, erythromycin, estradiol, ethambutol, ethosuximide, etodolac, ethinylestradiol, exemestane, fentanyl, fenofibrate, ferrous sulphate, ferrous fumarate, flecainide Electronic Medicines Compendium

6 Managing diarrhoea in hospital is time consuming and inefficient 20% of infection control team time is taken is spent on management of diarrhoea Almost all patients (99%) with suspected infectious diarrhoea are isolated in a side room Mean number of wards closed annually due to infectious diarrhoea = 12 per hospital 25% of the time causative pathogens are identified after patient discharge Buchanan et al J Hosp Infect 2015 doi: /j.hin

7 CCDA h CCDA 1 24h ID 2 Antimicrobial susceptibility testing 2-10h 3 3.7h Selenite-F h ABC h ID 2 Biochemical ID and agglutination tests 6 Antimicrobial susceptibility testing 2-10h 3 CT-SMAC h ID 2 Biochemical ID and agglutination tests Antimicrobial susceptibility testing 2-10h XLD h ID 2 Biochemical ID and agglutination tests Antimicrobial susceptibility testing 2-10h Sample transportation Selective culture +/- enrichment Gram stain, basic biochemistry (Oxidase etc) Species level identification using MALDI-TOF MS and biochemical identification (API 20E) Antimicrobial susceptibility testing Total time = 66.5 hours, range - 64 hours (negative) to 118 hours (positive) Conventional culture based detection of bacterial enteric pathogens

8 Poor sensitivity of conventional and culture based tests compared with molecular assays Study Method n % positive conventional Amar. Eur J Clin Microbiol Infect Dis % positive molecular In house de Boer. J Clin Microbiol In house 13, Wessels. Clin Microbiol Infect Luminex xtag GPP Mengelle. Clin Microbiol Infect Luminex xtag GPP McAuliffe. J Infect Fast Track Diagnostics Onori. Diagn Microbiol Infect Dis SeeGene Seeplex ACE Cunningham. J Clin Microbiol In house Biswas. Eur J Clin Microbiol Infect Dis BD Max Enteric Panel

9 Problems with current culture dependent diagnostic methods: Inability to differentiate clinically between different cause of IG Fragmented test request procedure Inefficient laboratory workflow Laborious workflow slow, long TAT Poor sensitivity lack of clinical confidence

10 Enterics panel evaluation: RBioPharm RIDA Gene Bacterial Stool Panel and EHEC/EPEC Manual two-tube real time PCR on ABI7500 Separate automated extraction using Promega Maxwell instrument (magnetic beads) Salmonella, Camylobacter, Y. enterocolitica *, Shigella, E. coli Fast Track Diagnostics Bacterial Gastroenteritis panel Manual two-tube real time PCR on ABI7500 Separate automated extraction using same extract as above Salmonella, Campylobacter, Y. enterocolitica *, Shigella, E. coli, C. difficile * BD Max Gastroenteritis panel Fully automated reat time PCR with built in extraction Salmonella, Campylobacter, Shigella, E. coli

11 Conventional selective culture methods: CCDA Campylobacter, XLD Salmonella/Shigella CT-SMAC EC0157 Selenite F broth & ABC Harlequin Salmonella * C. difficile and Y. enterocolitia not assessed in this evaluation

12 Enterics panel evaluation: 434 non-duplicate samples tested by all 4 methods: 116 retrospective samples selected on the basis of culture positivity Remaining 318 consecutive samples tested semiprospectively

13 Gold standard / True positive: Either culture positive OR 2/3 positive molecular tests

14 Results

15 Campylobacter Shigella Culture Fast Track Diagnostics RIDA-Gene BD Max Salmonella

16 Relative performance characteristics of molecular panels and conventional culture combined samples (n=434) RIDA GENE Bacterial Stool Panel and EHEC/EPEC FTD Bacterial Gastroenteritis Panel BD MAX Enteric Bacterial Panel Conventional culture Sensitivity Specificity Sensitivity Specificity Sensitivity Specificity Sensitivity Specificity Campylobacter 91.1 ( ) 98.8 ( ) 80.2 ( ) 99.4 ( ) 92.1 ( ) (98.9 ) 91.1 ( ) (98.9 ) Shigella 94.4 (81.3 ) 99.7 (98.6 ) 88.9 ( ) (99.1 ) 94.4 ( ) (99.1 ) 86.1 ( ) (99.1 ) Salmonella 55 ( ) 99 ( ) 45 ( ) 99.8 (98.7 ) 75 ( ) (99.1 ) 85 ( ) (98.9 ) Shiga-toxin producing E. coli 0 (0 97.5) 99.5 ( ) (25 ) 99.8 (98.7 ) 25 ) 99.5 ( ) (25 ) (99.2 )

17 Sensitivity Specificity PPV NPV Sensitivity Specificity PPV NPV Sensitivity Specificity PPV NPV RIDA GENE bacterial stool panel and EHEC/EPEC (80.5 ) 99.7 (98.2 ) 94.4 ( ) (98.8 ) ) (98.8 ) (73.5 ) 99.3 ( ) 25 ( ) 99.7 (98.2 ) 50 ( ) 99.1 ( ) Fast Track Diagnostics bacterial gastroenteritis panel BD Max Enteric bacterial panel Campylobacter, prevalence = 5.3% 88.2 ( ) (80.5 ) (98.8 ) (78.2 ) 99.3 ( ) (98.8 ) (80.5 ) (98.8 ) Shigella, prevalence = 4.4% 92.9 ( ) (76.8 ) (98.8 ) (75.3 ) 99.7 (98.2 ) (98.8 ) (76.8 ) (98.8 ) Salmonella, prevalence = 1.3% 50 ( ) (39.8 ) 99.7 (98.2 ) 66.7 ( ) 99.4 ( ) 99.7 (98.2 ) 80 ( ) (98.8 ) Conventional culture 52.9 ( ) (98.8 ) (66.4 ) 97.4 ( ) 71.4 ( ) (98.8 ) (69.2 ) 98.7 ( ) (39.8 ) (98.8 ) (39.8 ) (98.8 ) Relative performance characteristics of molecular panels and conventional culture for the prospective sample only (n=318).

18 Targets detected Total hands on time (based on 24 samples) Total laboratory turnaround time (based on 24 samples) RIDA Gene Bacterial and EHEC/EPEC panels 16s-rDNA (Campylobacter) ipah (Shigella, Enteroinvasive E. coli) eae (EHEC/EPEC) ttr (Salmonella) stx 1 and stx 2 (Shiga toxin producing E. coli and Shigella dysenteriae) ail (Yersinia enterocolitica) 50 mins (including separate extraction) 176 mins 40 mins Maxwell, 86 mins PCR FTD Bacterial Gastroenteritis panel glya and mapa (Campylobacter jejuni and Campylobacter coli) ipah (Shigella) ttr (Salmonella) vtx 1A, 1B, 2A and 2B (Enterohaemorrhagic E. coli) ail (Yersinia enterocolitica) tcdb (Clostridium difficile) 50 mins (including separate extraction) 171 mins 40 mins Maxwell, 81 mins PCR Minimum run size 1 (plus 2 controls) 4, 6 or 12 depending on kit (plus 2 controls) BD MAX Enteric Bacterial Panel tuf (Campylobacter) ipah (Shigella, Enteroinvasive E. coli) spao (Salmonella) stx 1a and stx 2a (Shiga toxin producing E. coli and Shigella dysenteriae) 20 mins 163 mins 1 (controls built in) Maximum run size 47 (plus 2 controls) 1 47 (plus 2 controls) 1 24 (controls built in) Fully automated? No No Yes Reagent storage -20 C -20 C Room temperature Result interpretation Requires interpretation of PCR curves Requires interpretation of PCR curves Consumables cost per sample No interpretation required (detected/not detected) 1 Based on testing with ABI 7500 real-time PCR thermocycler 2 Includes all additional consumables (including extraction) based on a reagent rental contract for 3000 samples per year over x years, excludes tax. Cost for RIDA Gene and FTD panels does not include cost of purchase / rental or maintenance of ABI7500 instrument.

19 Most positives from community patients 28 / 36 (78%) (prospective) 88 / 116 (76%) (retrospective) 33 samples from hospitalised patients: all except one sample sent within D3 of admission One sample had Campylobacter and was submitted on D4

20 Despite advising clinicians of the limited usefulness ~25% of requests for stool culture are from patients with onset of diarrhoea within 3 days of admission

21 Testing strategy at GSTT: Continue current testing methods for Norovirus (in house PCR) and C. difficile (GDH plus Toxin EIA/PCR) Adopt BD Max Bacterial Stool Panel, culture positive Salmonella, Shigella and E. coli O:157 for AST and typing. Campylobacter positives will not be routinely cultured (recommend treatment with macrolide) Demand management savings of ~25% partially offsets the additional cost of PCR Culture: x 8300 = 159,194 BD Max with demand management: 30 x 6800 = 204,000

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23 What proportion of your hospitals beds are in single rooms? Vote Now 1. < 10% % % % % 0.0% % 0.0% 7. > 60% 0.0% 3.2% 3.2% 8. Don't know 19.4% 29.0% 45.2%

24 What proportion of patients with clinically significant diarrhoea are presumptively isolated? Vote Now 1. > 20% % 3.0% % 0.0% 6.1% % 5. > 80 % 6. Don't know 21.2% 24.2% 45.5%

25 Vote Now What method(s) does your laboratory use for the detection of Campylobacter, Salmonella, Shigella and E. coli O:157? 1. Culture with identification based on biochemical methods 2. Culture with identification based on MALDI-TOF MS 3. Molecular panel 4. Combination of 1 and 2 6% 5. Combination of 1, 2 and 3 6. Other 0% 15% 21% 29% 29%

26 Vote Now What is the average turnaround time for detection (and AST if done) of Campylobacter, Salmonella, Shigella and E. coli O:157? 1. < 10 hours hours hours hours 5. > 72 hours 6. Don't know 0.0% 8.8% 8.8% 17.6% 20.6% 44.1%