Microbiology of Today and Tomorrow, How Changes in Technology will Impact the Care We Deliver

Transcription

1 We Practice What We Teach Microbiology of Today and Tomorrow, How Changes in Technology will Impact the Care We Deliver Nathan A Ledeboer Associate Professor of Pathology Medical College of Wisconsin Medical Director, Microbiology and Molecular Pathology Dynacare Laboratories and Froedtert Hospital Medical Director, Laboratory Outreach, Logistics, and Reference Services Dynacare Laboratories Milwaukee, WI

2 We Practice What We Teach Financial Disclosures Consultant Nanosphere ThermoFisher Scientific LabCorp icubate Copan Diagnostics BD Diagnostics GeneWeave Board Member Evogen Research Grants Meridian, Quidel, IMDx, Cepheid, BD, biomérieux, Bruker Daltonics, Nanosphere, Seegene, Life Technologies, Prodesse, Great Basin Corp, icubate, Biohelix, BioRad, Alere, Hardy Diagnostics, GenMark Will discuss applications/products that are not FDA approved

3 Objectives Drivers of Change Advances in Microbiology: Culture/Mass Spectrometry Molecular Microbiology Sequencing Panel Testing Outcomes will be King We Practice What We Teach

4 Current pathways of communication for the diagnosis and treatment of infectious diseases We Practice What We Teach

5 The future organization of clinical microbiology services a Paradigm Shift We Practice What We Teach

6 The Future of Bacterial Culture Increased Consolidation Automation Culture will be used less as molecular will replace many applications Continued migration to mass spectrometry for microbial ID based on performance and cost We Practice What We Teach

7 The Process of Mass Spectrometry We Practice What We Teach

8 Time course of the numbers of total isolates misidentified using phenotypic identification (PID*), isolates confirmed by a second PID* and isolates confirmed by molecular identification (ID**) over 11 years of routine identification in our clinical laboratory. Seng P et al. J. Clin. Microbiol. 2013;51: We Practice What We Teach

9 Time course of the numbers of isolates of 128 rare species, 48 of which were identified using phenotypic identification (PID), and 75 of which were identified using molecular identification (ID). Seng P et al. J. Clin. Microbiol. 2013;51: We Practice What We Teach

10 We Practice What We Teach Differentiation of subspecies Fangouos MS, et al. JCM. 2014

11 We Practice What We Teach The Future of Molecular Biology Migration away from singleplex PCR to disease state testing Eg. stool pathogen panels, sepsis panels, pneumonia panels Moving testing closer to patient Increased competition based on price Increased need for clinical data supporting use of molecular tests Movement to FDA approved kits

12 We Practice What We Teach Scope of problem- Definition- Enteritis Enteric illness affects millions yearly in US alone Mortality in infants and elderly 3 unformed stools in 24 hr period Causes- Foodborne Salmonella, Campylobacter, Y. enterocolitica, V. parahaemolyticus, ETEC, EPEC Environmental Cryptosporidium, Giardia, Isospora/Cyclospora, Aeromonas, Plesiomonas Contagious Rotavirus, Norovirus, Shigella, V. cholerae, C. difficile Toxin mediated STEC, EHEC, C. perfringens, B. cereus, S. aureus

13 We Practice What We Teach Molecular Enteric Pathogen Testing Advantages Rapid rule out for common CA pathogens (high NPV/sens) Positive stools may not require further workup Work-up of negative stools can be more focused (O&P, allergic, toxin) Antibiotic stewardship Hold empiric therapy Salmonella, EHEC, noro may not require therapy; Campylobacter, Shigella AST, treat Infection control Identify outbreak or potential outbreak h sooner contain Family members, school/daycare isolate Shigella, Norovirus, possible source EHEC Cost neutral Comparable to manual workup (labor not cheap, FNs etc.) Full-automation walk-away Compliance with CDC for stx1/2 at no added cost.

14 Increased Sensitivity of Molecular Panels? Culture sensitivity compared to ProGastro SSCS TP TN FP FN Total Sens Spec Campylobacter* % 100.0% Salmonella % 99.9% Shigella % 100.0% stx1/2 (EIA) % 100.0% *C. coli or C. jejuni Limited number of pathogens Requires nucleic acid extraction and two different master mix reactions Manual pipetting, setup Buchan et al, JCM, 2013 We Practice What We Teach

15 Next Generation Sequencing Benefits Detection of unculturable organisms Interrogate genomes for novel and known resistance determinants Direct from specimen identification Challenges Need for clinically relevant databases Cost Turnaround We Practice What We Teach

16 We Practice What We Teach Whole chromosomal Optical Maps of the EHEC O104:H4 outbreak and related strains. Mellmann A, Harmsen D, Cummings CA, Zentz EB, et al. (2011) Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. PLoS ONE 6(7): e doi: /journal.pone

17 Heat Map Per Amplicon Coverage Metric as Estimated by Percentage of Uniquely Mapped Reads Dyn #9 D?? Dyn #5 B Bile Dyn #10 E Rectal Dyn #2 A Stool Dyn #6 B Bile Dyn #7 C Bile Dyn #8 C Bile Dyn #11 E Rectal We Practice What We Teach Dyn #12 E Rectal Dyn #3 A Urine Dyn #1 A Stool Dyn #4 B Blood High NDM-bla amplicons High TEM.2 amplicon Significantly different from all other samples No automatic clustering by either tissue or patient type

18 We Practice What We Teach Outcomes, the Example of Sepsis

19 We Practice What We Teach Early Antibiotics Improves Survival in Septic Shock

20 We Practice What We Teach Current Blood Culture Workflow Blood drawn in ER, ICU, hospital floors Culture positive Pathogen group Pathogen ID Pathogen resistance Bottle culture Gram stain Samples plated for sub-culturing Resistance testing t=0 t=8h t=24-36h t=48-72h Workflow with Rapid Tests Blood drawn in ER, ICU, hospital floors Culture positive Pathogen group 1-2 hrs Pathogen ID and resistance Bottle culture Gram stain Rapid - Test t=0 t=8 t=10h

21 Froedtert Health Results Time to Optimal Therapy, IQR (hours) Time to Effective Therapy, IQR (hours) Pre- Intervention n = ( ) Post- Intervention n = ( ) p-value ( ) 4.3 ( ) 0.51 LOS, IQR (days) 8.9 ( ) 7.9 ( ) 0.7 ICU LOS, IQR (days) Never Reached Optimal Therapy (number) 5.3 ( ) 2.8 ( ) IQR = interquartile range, LOS = length of stay, ICU = intensive care unit Revolinski S., ICAAC, 2014

22 We Practice What We Teach Stewardship is Critical Organism Pre-PCR Mean (range) time to optimal antibiotic therapy (h) Post-PCR Mean (range) time to optimal antibiotic therapy (h) Difference (h) (95% CI) P S. aureus 23.8 ( ) 25.0 ( ) +1.2 ( 5.1, 9.8) > 0.1 MRSA 10.7 ( ) 14.4 ( ) +3.7 ( 1.8, 9.1) > 0.1 MSSA 32.8 ( ) 35.1 ( ) +2.3 ( 10.5, 15.2) > 0.1 MSSA isolates initially treated with vancomycin monotherapy All 55.3 ( ) 62.3 ( ) +7.0 ( 20.9, 24.9) > 0.1 No PCR performed 57.3 (55.4,59.3) +2.0 > 0.1 Antibiotics optimized after PCR, before C & S Antibiotics optimized after PCR and C & S 48.4 ( ) 6.9 ( 21.6, 7.7) > ( ) (3.0, 33.7) Frye AM, Baker CA, Rustvold DL et al. J Clin Microbol. 2012;50:

23 ID in the Bottle We Practice What We Teach

24 We Practice What We Teach Conclusions Significant shift away from culture based lab practices to molecular approaches Decrease turnaround, results available when needed Increased Cost Sequencing may be the future of microbiology, considering the amount of data that is produced. Role of sequencing will be determined by bioinformatics and reductions in turnaround. Future laboratory test updates will require justification beyond turnaround and reimbursement, future changes will be based on how clinical care is impacted.

25 Questions? We Practice What We Teach