The Future of Microbiology

Transcription

1 The Future of Microbiology Christine C. Ginocchio, Ph. D., M. T. (A.S.C.P.) Professor of Medicine, Department of Pathology and Laboratory Medicine, Hofstra Northwell School of Medicine, NY VP, Global Microbiology Affairs, biomerieux VP, Scientific and Medical Affairs, BioFire Diagnostics 1 st Coast Infectious Disease Conference Palm Coast, Florida Feb 2, 2018

2 Goals Understand what necessitates change in our approach to Clinical Microbiology List opportunities for the modernization of Clinical Microbiology Describe current and future diagnostics tools Conflict of Interest: Employee of biomerieux and BioFire Diagnostics

3 Drivers of Change Clinical Technological Practical

4 Re-Emerging and Emerging Pathogens Virology Old viruses with new importance: HRV, EV-D68, EV-71, coronaviruses, PIV-4 New viruses: SARS CoV, MERS CoV, pandemic influenza (H1N1), avian influenza, Heartland virus Microbiology MDROs Rapidly growing Mycobacteria Candida auris Invasive fungal disease Borrelia mayonii (new species)

5 Global Spread of Disease West Nile Virus Dengue Chickungunya Zika Yellow Fever Source: ArboNET, Arboviral Diseases Branch, CDC

6 Global Travel: SARS CoV

7 Shift in Pathogen Populations Global Trends in the Distribution of Candida spp. causing Candidemia FIG. 1. Proportion of the most relevant Candida species from population-based studies reporting on candidemia in different countries. FIG. 2. Data compiled from the ARTEMIS DISK registry on the temporal change in species distribution among invasive Candida isolates from 1997 to Guinea J et al. Global trends in the distribution of Candida species causing candidemia. Clinical Microbiology and Infection, Volume 20, Supplement 6, 2014, 5 10

8 Changing Patient Populations Premature infants Aging population with chronic illnesses Greater use of invasive procedures Mechanical ventilation Indwelling catheters, central lines Immunosuppressive drugs Chemotherapy and transplantation Longer length of stay in medical units (ICU)

9 More Patients at Risk for Drug Resistance Infections Extrinsic Factors (Acquisition of DRP) Prior Hospitalization Long Term Care Poor Functional Status Indwelling Catheter Infusion Therapy Hemodialysis Tube Feeding Wound Care MRSA Colonization Prior h/o DRP Cumulative DRP Risk Intrinsic Factors (Host Susceptibility) Chronic Lung Disease Immunosuppression Poor Functional Status Cerebrovascular disease Gastric Acid Suppression Cognitive impairment Tobacco Use Diabetes Aspiration Recent Antibiotic Use (Selective Pressure) Patients with no risk factors!

10 Growing Antibiotic Resistance Threat: US Perspective Additional $21-34 billion cost annually to US healthcare system Additional 8 million hospital days Antibiotic resistance currently accounts for an estimated additional 25,000+ deaths Europe

11 Growing Antibiotic Resistance Threat: Global Perspective

12 Global Carbapenem Resistance 1% 3% 11% 1% 8% 14% 24% 26% 57% 26% 14%

13 Sepsis: Time is Critical Kumar A, Roberts D, Wood KE, et al.: Crit Care Med, 34: , 2006.

14 Empiric Antimicrobial Therapy Initiate broad spectrum antibiotic therapy Diagnostic results and antimicrobial stewardship to ensure appropriate targeted antimicrobial usage once pathogen identified Avoid Antibiotic Resistance Improve Outcome Antibiotic Associated Complications

15 Quiz 1: Who Predicted the Need for Antimicrobial Stewardship in 1945? The microbes are educated to resist penicillin and a host of penicillin-fast organisms is bred out. In such cases, the thoughtless person playing with penicillin is morally responsible for the death of the man who finally succumbs to infection with the penicillin-resistant organism. I hope this evil can be averted. Fleming A. New York Times. 26 June 1945:21

16 Overuse and Misuse of Antimicrobials The most common reason antibiotic prescription (41% of all antibiotic prescriptions ) (ACP, 2016) 24% of all antibiotics prescribed worldwide (Goossens, 2012) 50% of antibiotics prescribed in the US are inappropriate 34.3 Million Antibiotic prescriptions unnecessary 34.6 Million Antibiotic prescriptions appropriate Fleming-Dutra et al. JAMA 2016; 315:

17 Need for Tools that Guide Antimicrobial Selection and Stewardship The Pew Charitable Trusts, FDA

18 Practical Considerations: WorkForce Micro Lab Meeting 2030

19 How can Clinical Microbiology meet these Challenges Today and in the Future? Where we have been, where we are now and where we need to be.

20 Microbiology of the Past

21 Quiz 2: Who really invented the agar plate? Angelina Hesse Cooked both the family's meals and the beef stock that the bacteria ate in her kitchen, suggested that Walter Hesse (who worked for Robert Koch) use agar-agar, which is more heat-stable than gelatin and used to make soups, desserts, and jellies, particularly in Asia. (She had learned about it from Dutch friends who had lived in Indonesia, which was a colony of the Netherlands at the time.) Agar is a sugar polymer derived from algae that most bacteria can't digest. Once it's boiled and cooled, it forms a tough matrix that stays solid at much higher temperatures than gelatin.

22 Culture: The Basics

23 Quiz 3: KIA: Name the Pathogen?

24 Organism ID: Who remembers charts on your desk top?

25 Identification and Antimicrobial Susceptibility Testing

26 Quiz 4: Can you Identify the Pathogens by the AST pattern? Gram negative rods (Circa 1975) Pan susceptible Resistant to ampicillin and carbenicillin Resistant to ampicillin and cefazolin Resistant to tetracycline Resistant to ampicillin and tetracycline

27 Identification and Antimicrobial Susceptibility Testing FDA cleared for: Gram positive, Gram negative bacteria yeast, molds, Nocardia, Mycobacteria FDA cleared for: Gram positive, Gram negative bacteria, yeast

28 Direct from Positive Blood Culture: ID and Phenotypic Susceptibility FISH Morphokinetic cellular analysis

29 Automation: Copan WASP System 18

30 Automation: Becton Dickinson/Kiestra 6

31 Culture Independent Diagnostics PCR was awarded the 1993 Nobel Prize in Chemistry. In 1983, Kary Mullis, PhD, a scientist at the Cetus Corporation, conceived of PCR as a method to copy DNA and synthesize large amounts of a specific target DNA Baby Blue', a prototype automated thermocycler built around 1986 Perkin Elmer 9600 Roche Lightcycler Abbott LCX Thermo Fisher Naica Digital PCR

32 Many Amplification Techniques Inclusive, Bigger and Better PCR, RT-PCR, LCX, NASBA, TMA, LAMP etc Roche GenProbe Abbott

33 Single to Low Multiplex: Targeted Medium to High Multiplex: Syndromic Limitation: Preselected targets and resistance markers BD Max Luminex Aires Cepheid GeneXpert Luminex Verigene GenMark esensor BioFire FilmArray

34 Future: Decentralized Rapid CLIA Waived Point of Care Diagnostics Alere Roche GenePOC Cepheid BioFire

35 Meeting the POC Clinical Need The CLIA waived Alere i Strep A test provides molecular results in 8 minutes or less. Some positive in 3 minutes.

36 Hand Held PCR Technology Accula System (Dock and Test cassette) Paratus Diagnostics: hand-held Paratus PreparedNow System compatible with of a portfolio of tests driven by the technology in the ParatusSDS Cartridge.

37 Future: Extreme PCR: sec Detection Courtesy of Dr Carl Wittwer

38 Past: Sequencing

39 Future: Next Generation Sequencing Targeted or Universal Detection Nanopore Thermo Fisher Ion PGM Illumina MiniSeq Illumina MySeq Illumina FireFly: from purified DNA to answers: stackable two module system for both library preparation and sequencing. Sequencing data will seamlessly move to BaseSpace for analysis.

40 The 1st Key: Information Technology The history of computers starts out about 2000 years ago in Babylonia (Mesopotamia), at the birth of the abacus, a wooden rack holding two horizontal wires with beads strung on them

41 The 2 nd Key: Communication Alexander Graham Bell was awarded the first U.S. patent for the invention of the telephone in 1876.

42 Future: Next Generation Sequencing Needs to be the next Mass Spec-like Black Box Fast, simple, inexpensive Out of the box bioinformatics Growing uses: Organism identification Direct specimen detection Unknown Unculturable Epidemiology, surveillance (culture independent diagnostics)

43 Quiz 4: Name the bottle and the pathogen?

44 Automated Blood Cultures BD biomerieux Trek

45 Specific Technologies Colorimetric Sensor Array: ID/AST Colorimetric sensor array technology for earlier detection and identification of bacterial pathogens in blood culture through sampling of the headspace volatile organic compounds Initial, t 0 After, t 5h Difference Map The fingerprint of E. coli 25922

46 Gram Stain Microscopy

47 Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network Automated image acquisition and convolutional neural network (CNN)-based approach for automated Gram stain classification. Kenneth P. Smith KP et al JCM Accepted Manuscript Posted Online 29 November 2017 J. Clin. Microbiol. doi: /jcm

48 Direct from Positive Blood Culture: AdvanDx PNA FISH Technology Fluorescence tagged peptide nucleic acid probes detects 16S rrna directly from positive blood cultures (G): S. aureus (G): S. aureus (R): CoNS (G) E. faecalis (R) other Enterococcus spp. (G): C. albicans (G): C. albicans (R): C. glabrata (G): C. albicans/c. parapsilosis (R): C. glabrata/c. krusei (Y): C. tropicalis

49 Direct from Positive Blood Culture: ID and Genotypic Susceptibility BD Collected Specimen Specimen Preparation Lysis - DNA Extraction Reconstitution Of Reagents Real-time PCR Analysis on the SmartCycler Definitive On-screen Results Cepheid Luminex Verigene BioFire FilmArray

50 Faster Sepsis Testing: How do we decide? Pull positive blood cultures prior to positivity: Can we reduce TAT? Algorithms for predicting a positive blood culture: clinical assessment, clinical and laboratory parameters Goal a 90% PPV 50,000 blood cultures: 15-20% (10,000) positive minus 3-5 % 3,000 = contamination: 7,000 + Clinical assessment + laboratory parameters = score Reflex to direct detection Wasted effort: 700 tests/yr

51 The Holy Grail : Direct From Blood Sample Roche LightCycler SeptiFast Test Not available in the US

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53 Qvella: Direct Sample Testing

54 Biomarkers: Bacterial versus Viral Infection and Stewardship Sepsis Example PCT LRTI Example: PCT

55 Host Gene Expression: Bacterial versus Viral Infection Robust classification of bacterial and viral infections via integrated host gene expression diagnostics Bacterial infection sensitivity, 94.0%; specificity, 59.8%; viral infection sensitivity, 53.0%; specificity, 90.6%. Sweeney, TE et al Sci Transl Med July 06; 8(346): 346ra91. doi: /scitranslmed.aaf7165.

56 Quiz 5: What Tom Cruise Movie in 1986 Predicted Microbiology s Future?

57 Sample Transport From: Drone Transport of Chemistry and Hematology Samples Over Long Distances Am J Clin Pathol. 2017;148(5): doi: /ajcp/aqx090

58 Role of Rapid Diagnostics

59 Approach for Improved Clinical Care: Rapid Diagnostics Point of Impact 43

60 Microbiology of the Future Rapid to really impact patient care POC testing will be the first line Microbiology will be closely partnered with biomarkers Direct sample testing for ID/AST AST will be a combination of rapid molecular and rapid phenotypic testing Mass Spec will be better and smaller Sequencing will be the next Black Box Full Lab automation with smart incubators and image intelligence

61 Microbiology of the Future The Clinical Microbiology Laboratory will continue to play a pivotal role in optimizing the diagnosis and treatment of Infectious Diseases We will remain the cornerstone of successful antimicrobial stewardship practices We are the essential gate keepers of surveillance, epidemiology and public health However we must embrace CHANGE Think out side the box Not be afraid to approach problems in a new way

62 Microbiologist of the Future