Attendees will understand the early experience and clinical impact of GI multiplex PCR diagnostics in children

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2 Participants will understand the role of a comprehensive business case in considering the introduction of novel technology affecting multiple areas of the laboratory Attendees will learn about the impact on the laboratory of the introduction of a multiplex assay that will replace various components of conventional GI pathogen diagnostics Attendees will understand the early experience and clinical impact of GI multiplex PCR diagnostics in children

3 Pfizer Unrestricted educational grant for study of neonatal candidiasis Astellas Site PI clinical trial of micafungin in neonatal candidiasis Luminex Molecular Diagnostics In kind support for xtag GPP assay evaluation

4 370 bed pediatric hospital affiliated with University of Toronto General pediatrics Emergency Surgery General, cardiac, neurosurgery, orthopedics Critical care unit Neonatal intensive care unit Oncology / Bone marrow transplantation Solid organ transplantation Kidney, heart, liver, lung, small bowel Dialysis Burn Unit Trauma Center Cystic Fibrosis Center (n=300)

5 Bacterial culture and susceptibility Salmonella, Shigella, Yersinia enterocolitica, Campylobacter jejuni/coli, E. coli 0157:H7, (Aeromonas/Plesiomonas) Ova and parasites Refer to public health laboratory Virus detection by electron microscopy Rotavirus, adenovirus, torovirus, calicivirus, astrovirus, norovirus Clostridium difficile toxin detection Tissue culture cytotoxin assay until late 2011 C. difficile PCR subsequently

6 Bacterial C&S Stool in Carey-Blair transport medium O&P EM Stool in preservative Stool in empty sterile container C. difficile PCR Stool in empty sterile container

7 Bacteriology C. difficile PCR O&P 0.5 FTE send-out and results return Virology 0.5 FTE

8 Bacterial culture Electron microscopy Ova and parasites C. difficile cytotoxin assay C. difficile PCR 6.6% 7.1% 1.7% 8.0% 13.5%

9 Advantages Inexpensive reagents Modifiable detection conditions Susceptibility testing Clinical suspicion directs investigation May include organisms not on molecular panels (e.g. some viruses parasites) Gold standard Disadvantages Labour-intensive Widely varying technical expertise required EM purchase and maintenance expense Clinical suspicion directs investigation Unusual, uncultivable or difficult to detect organisms may not be diagnosed

10 Improved sensitivity of detection, with good specificity Single test for GI pathogens across organism boundaries Resource rationalization Rapid diagnosis Diagnosis of clinically unsuspected pathogens Ability to detect co-infections Infection control of nosocomial diarrhea (viruses and C. difficile) Public health outbreak pathogen identification

11 May lack certain targets of interest Viruses Torovirus (33% of SickKids) Calicivirus Astrovirus Sapovirus Parasites Dientamoeba fragilis (77% SickKids) Lack susceptibility data Require fully developed and experienced molecular lab Cost

12 Bacteria Salmonella spp. Shigella spp. Campylobacter jejuni/coli Yersinia enterocolitica E. coli 0157:H7 Non-0157 shiga-toxin producing E. coli (STEC, EHEC) Clostridium difficile toxin A/B Enterotoxigenic E. coli Vibrio cholerae Viruses Rotavirus A Adenovirus 40/41 Norovirus GI/II Parasites Giardia lamblia Entamoeba histolytica Cryptosporidium

13 Bacteria Salmonella spp. Shigella spp. Campylobacter spp. Vibrio spp. C. difficile toxin B C. perfringens Y. enterocolitica Aeromonas spp. E. coli 0157:H7 VT-producing E. coli Viruses Rotavirus Norovirus GI/GII Adenovirus 40/41 Astrovirus Not on panel Parasites ETEC

14 Gastrofinder Smart 17 Fast (Pathofinder, Netherlands) Similar to Seegene assay plus parasites (including D. fragilis) Prodesse ProGastro SSCS (Hologic MDx) (FDA approved) Salmonella, Shigella, Campylobacter, Shiga Toxin 1 (stx1) and Shiga Toxin 2 (stx2) genes

15 48 reference isolates, 254 clinical specimens (stool Carey- Blair, raw) Culture, EIA/IC, microscopy and single-plex PCR as comparator Discrepant analysis: comparator method Overall sensitivity 94.5%, specificity 99% 100% sens: adenovirus, norvirus, rotavirus, V. cholerae, Y. enterocolitica, E. histolytica, Cryptosporidium spp., E. coli O157:H7 94-5% sens: G. lamblia, ETEC, STEC 92-3% sens: Shigella, Salmonella 90-1% sens: C. difficile, C. jejuni 12.2% co-infections ETEC/STEC, Salmonella, G. lamblia, C. difficile, C. jejuni, rotavirus Inhibition 8% Discrepant 13.4%, without E. histolytica 4%

16 440 stools (1/2 children) Comparator conventional assays Culture Salmonella, Shigella, Campylobacter, Y. enterocolitica, V. cholerae, pathogenic E. coli serovars (children), toxigenic C. difficile (children) EIA/IC Rotavirus, adenovirus, norovirus, CD toxin PCR (EHEC) Microscopy (parasites) More sensitive than conventional (p 0.01) Rotavirus, norovirus, Salmonella, Campylobacter, C. difficile toxin 176 positive (40%) Viruses (23%) Bacteria (14%) Parasites (2.9%) 7% co-infections Discrepants not analyzed

17 450 stools (2012) Comparator conventional assays Culture Salmonella, Shigella, Campylobacter, E. coli O157:H7 (not Yersinia) EIA/IC: CD (GDH and toxin), norovirus, adenovirus, rotavirus Virus discrepants (single-plex PCR) Microscopy (parasites) CD PCR Prevalence 8% conventional 26% GPP Norovirus 4-fold increase, confirmed by single-plex PCR Rotavirus and adenovirus confirmed by single-plex PCR Co-infections 10% 2200 stools (2013) 48% of diagnosed infections were not suspected by clinician primarily viral and parasitic, i.e. test not requested Decreased TAT (bacteria and parasites) Predicted decreased isolation days

18 167 frozen selected stools (65 pos) 20 bacterial culture pos Salmonella (8), C. jejuni (5), E. coli O157 (3), Y. enterocolitica (1), Shigella sonnei (1) 14 EM virus pos Adenovirus (5), rotavirus (6), norovirus (3) 25 CD PCR pos 6 O&P pos (PHL) Giardia (1), E. histolytica (5) 102 negative stools 40 cult neg, 37 EM neg, 25 CD neg Easymag extraction GPP panel on Luminex 100 instrument

19 65 positive stools 6/65 false negative 3/6 repeated positive 3/65 false negative (4.6%) 95.4% sensitivity vs. conventional tests

20 GPP negative for all targets tested Adenovirus 7 (1) Aeromonas hydrophila (1) torovirus (3) astrovirus (3) calicivirus (2) E. dispar (4)

21 Stool C&S pos (21) CD (7) norovirus (9) rotavirus (1) Stool C&S neg (40) norovirus (9) CD (5) rotavirus (1) Stool EM pos (25) CD (3) Stool EM neg (37) CD (3) norovirus (5) rotavirus (1) Campylobacter (1) Stool CD pos (25) norovirus (7) Giardia (1) Stool CD neg (25) norovirus (2) CD (2) Campylobacter (1) Stool O&P pos (10) norovirus (1) Giardia (1) CD (1) Total 57 unsuspected GI pathogens

22 Target Strain SickKids LoD Luminex LoD STEC E. coli O84:HNM, O101:HNM, O111:HNM, O103:H2 9 x x10 5 CFU/ml 9 x10 5 CFU/ml V. cholerae non-o1 non-o139, O139 [O1 El Tor (Inaba)] 1 x x10 7 plasmid copy/ml 1.3 x10 3 plasmid copy/ml ETEC E. coli O49:HNM 1 x10 4 CFU/ml 1.5 x10 7 CFU/ml Y. enterocolitica biogrp 3 serotype 3, biogrp 5 Campylobacter spp. 1.7 x x10 7 CFU/ml 1.4 x10 8 CFU/ml Campylobacter coli 3 x10 2 CFU/ml 6 x10 4 CFU/ml Shigella spp. S. dysenteriae type 1, S. boydii type x10 3 CFU/ml 3.3 x10 4 CFU/ml

23 Elucidate clinical and microbiological rationale Advantages for patient care Advances and efficiencies for the laboratory Estimate test # Single multiplex test predicted to reduce testing volume by ~50% if used exclusively GPP vs. C&S + EM + CD + O&P Define testing algorithm Outpatients and inpatients 4 days: GPP Inpatients >4 days: CD PCR single-plex + EM Determine conventional testing required Bacterial culture, EM, CD single-plex PCR, (norovirus singleplex PCR?) Determine equipment (incl. service contracts) and reagent costs Conventional low GPP high

24 Determine human resource requirements Conventional 1.0 FTE GPP 0.5 FTE Identify risks and dependencies Obtain stakeholder input and support Pediatrics Infectious Diseases Infection Prevention and Control Perform financial analysis and implications Develop formal business plan Negotiate contract

25 Stool should be tested for infectious pathogens when 3 loose stools in 24 hours Should take the shape of the container Difficult to assess in laboratory due to receipt in Carey-Blair transport medium Stool should not be sent after a single loose stool Drugs Osmotic diarrhea Diet Stool should be sent in Carey-Blair transport medium so that culture can be attempted if GPP positive

26 Gl multiplex PCR (GPP) Performed 4 times per week Negative or positive results not repeated except after approval by the Microbiologist C. difficile PCR results not reported on children 1year Stool positive by GPP for Y. enterocolitica, Salmonella and Shigella will be cultured to enable susceptibility testing Ova and parasite microscopic examination If GPP negative and a high index of suspicion for parasitic infection Conventional microscopy (need O&P container with preservative)

27 C. difficile toxin PCR Performed 3 times per week Not performed until one week after negative GPP Repeat accepted weekly if previous CD PCR negative C. difficile PCR results not reported on children 1year of age Electron microscopy for viruses GPP rejected unless approved by microbiologist

28 182 stools tested 47 stools pos (25.8%) 53 targets pos (29.1%) Bacteria Salmonella (3) Yersinia enterocolitica (3) Camplybacter spp. (5) E. coli O157:H7 (1) ETEC (2) C. difficile toxin A/B (23) Viruses Adenovirus (5) Norovirus (9) Parasites Giardia lamblia (1) Cryptosporidium spp. (1) 32 (26%) cancelled, outside of protocol 2/3 confirmed by culture 3/3 confirmed by culture Co-infections 10.6% stools (5/47) Adeno + CD + Campy Campy + Giardia CD + noro CD + Campy Noro + Campy Inhibition 2.2% stools (4/182) ¾ repeat no inhibition

29 Bacterial culture Electron microscopy Ova and parasites C. difficile cytotoxin assay C. difficile PCR Luminex xtag GPP (1 st 6 weeks) C. difficile (GPP or single-plex) Co-infections (5) 6.6% 7.1% 1.7% 8.0% 13.5% 29.1% (25.8% pts) 11.8% 10.6%

30 Training all technologists on new assay Excellent support from LMD Requirement for all steps to proceed without interruption and for use of cold blocks for manipulation of reagents, to avoid false positives Determination of threshold to repeat testing if multiple targets identified Interpretation of low MFI results for certain targets Norovirus and Salmonella Education of clinicians regarding new testing algorithm and implications of testing

31 Introduction of GPP has increased the rate of detection of all classes of enteric pathogens in children, over conventional methods, with excellent sensitivity and specificity Different algorithms for community-acquired and nosocomial diarrhea have focused GPP testing on the population at greatest need of very broad testing Enabled by in-house EM and CD PCR Replacement of conventional diagnostic methods with GPP can be achieved without increased cost, but probably requires efficiencies attained by reducing human resources

32 Farhad Gharabaghi Karan Greenock Fern Parisian Nursrin Dewsi John Nishikawa Microbiology technologists Astrid Petrich Yvonne Yau David Polchert