The future of our culture in clinical microbiology.

Transcription

1 The future of our culture in clinical microbiology. Susan E. Sharp, Ph.D., ABMM, FAAM Scientific Director Copan Diagnostics, Inc. Murrieta, CA 1

2 The Clinical Microbiology Laboratory Genomics Proteomics Metabolomics Digital imaging Algorithms AI 2

3 Clinical Microbiology is Facing Big Challenges Increasing Workload Hospital-Associated Infections (HAI) Emerging antibiotic resistance bacteria Laboratory consolidations Pressure for shorter patient LOS Need for more rapid results Decreasing Resources Less reimbursement Laboratory consolidations Aging workforce / retirements Lack of personnel entering the profession

4 Current State 4

5 But What Does the Future Hold? 5

6 But What Does the Future Hold? 6

7 77% of 13,000,000 annual test volume are sorted/tested by automation. Autoloaders ~ 30,000 specimens / day 80% are autoverified by the LIS the technologist never looks at the result. Automated Core Lab Line at Kaiser Permanente in Portland, OR Photograph provided by Jeff Smith, IT Director Kaiser Permanente, Portland, OR 7

8 77% of 13,000,000 annual test volume are sorted/tested by automation. Autoloaders ~ 30,000 specimens / day 80% are autoverified by the LIS the technologist never looks at the result. Automated Core Lab Line at Kaiser Permanente in Portland, OR Photograph provided by Jeff Smith, IT Director Kaiser Permanente, Portland, OR 8

9 Microbiology is Unique The Specimen Challenge We receive various sample viscosities, and container types. Difficult to standardize and automate. 9

10 Traditional Swabs 3% of sample is retrieved from the swab 10

11

12

13 Liquid Based Microbiology Swabs Flocked swab + 1mL Liquid Amies Collection and transport device for aerobic, anaerobic, and fastidious bacteria for up to 48 hours. *The exception is Neisseria gonorrhoeae which is stable for up to 24 hours. > 90% of the specimen elutes into the Amies medium Better Gram stains Better growth and recovery Allows for automated processing

14 2017 study evaluating ESwab for use with 20 different yeast and moulds. Their results showed that colony counts equal to or greater than those seen at time zero were obtained for all organisms They concluded that ESwabs effectively maintains these fungi for at least 48 hours. Molecular assays too.

15 1. Liquid-based microbiology allows for specimen collection optimization. 2. Helps reduce cost due to the smaller number of different devices they had to store and use. 3. Reduces the time spent by medical and nursing staff, as there is less confusion regarding collection device selection = one flocked swab type. 4. Fewer samples were being collected from the patient using multiple different devices. 5. This related to time saved for laboratory staff as there are fewer samples to handle per patient. Conclusion: Liquid-Based Microbiology allows for improvement in patient comfort as multiple sample collections can be avoided. They also point out that using a single flocked swab will allow for several assays to be performed from the same collection device which guarantees quality and standardization due to all testing being able to be performed from the sample.

16 Researchers completed 8 tests with one flocked swab collection 1 Rapid Point-of-Care Strep A test 1 Reflex plate culture for Strep A, C/G 4 culture plates for F.necrophorum 1 PCR test for Strep A, C/G 1 PCR for F.necrophorum

17 Flocked Swabs Throats Wounds Genitals

18 Stool Sputum Urine

19 Managing Fecal Samples, Traditionally

20 Liquid Based Microbiology Stool Samples Easy to Use Standardize and Simplify Tube contains Cary-Blair transport media Can be used directly from stool Or as rectal swab

21 2016 study evaluating use of FecalSwabs with molecular testing in the pediatric emergency department. 190 fecal specimens, collected at 3 different hospital sites, were sent on FecalSwabs and in routine Cary-Blair stool preservative for comparison. Conclusions: 1. FecalSwab collections were comparable to the routine Cary-Blair stool preservatives for detection of pathogens using the FilmArray GI panel. 2. When a stool specimen could not be provided, FecalSwabs would allow for sample collection at the time of the patient visit, and the generation of actionable results for the majority of significant infections in their acute care setting.

22 Liquid Based Microbiology Snot Buster This novel collection device offers a DTT liquefying solution in a ready-to-use tube with an effective sputum tool for collecting the most viscous part of the sputum sample. More consistent planting & streaking Does not affect cell morphology or growth of organisms Room temperature stable

23 Deliver within 2 hours

24 Liquid Based Microbiology Uri-Sponge 2 mls urine 48 hour stability

25 Liquid Based Microbiology UriSponge UriSponge maintained significantly more urinary pathogens than the urine culture paddle with fewer mixed or contaminated cultures. UriSponge was comparable to boric acid preservative tubes for maintenance of pathogens, with fewer mixed cultures. No fill line is necessary. Rennie, et al., Diagn Microbiol Infect Dis Aug;85(4):401-4

26

27

28 Flocked Swabs and other novel collection devices Have opened the Door for Liquid Based Microbiology Liquid Based Microbiology Opens the Door for Automated Specimen Processing

29 Comparison of recovery of pathogens from stool cultures before and after introduction of automated specimen processing. Mischnik A., et al. Annals of Laboratory Medicine, pre vs. 64 post

30 2016 Automated streaking by WASP significantly increased the number of single colonies recovered. Automated WASP processing resulted in a higher number of detected morphologies, species, and pathogens.

31 Comparison of Manual/Rayon Swab to Automated Processed/LBM Swab for the recovery of S.agalactiae in pregnancy No. with indicated test result Direct plating True positive False positive True negative False negative Total no. Sensitivity (%) Specificity (%) Manual/ rayon swab Automated/ flocked swab Enrichment culture Manual/ rayon swab Buchan B et al JCM Automated/ flocked swab Buchan BW, Olson WJ, Mackey T-LA, Ledeboer NA. JCM. 2014;52(6):

32 Comparison of Manual/Rayon Swab to Automated Processed/LBM Swab for the recovery of S.agalactiae in pregnancy No. with indicated test result True positive False positive True negative False negative Total no. Sensitivity (%) Specificity (%) Direct plating Manual/ rayon swab Automated/ flocked swab Enrichment culture Manual/ rayon swab Buchan B et al JCM Automated/ flocked swab

33 Comparison of Manual/Rayon Swab to Automated Processed/LBM Swab for the recovery of S.agalactiae in pregnancy No. with indicated test result True positive False positive True negative False negative Total no. Sensitivity (%) Specificity (%) Direct plating Manual/ rayon swab % Automated/ flocked swab Enrichment culture Manual/ rayon swab Buchan B et al JCM Automated/ flocked swab

34 Comparison of Manual/Rayon Swab to Automated Processed/LBM Swab for the recovery of S.agalactiae in pregnancy No. with indicated test result True positive False positive True negative False negative Total no. Sensitivity (%) Specificity (%) Direct plating Manual/ rayon swab % Automated/ flocked swab Enrichment culture Manual/ rayon swab % Buchan B et al JCM Automated/ flocked swab

35 Benefits of Automated Specimen Processing in Microbiology Improved quality/accuracy of specimen inoculation Better detection of pathogens Decreased time to results and Improved Patient Care Specimen traceability Improved ergonomics - decrease repetitive motion injuries Increased efficiency and productivity

36 Liquid Based Microbiology Has made Automated Specimen Processing possible Automated Specimen Processing Opens yet Another Door to Total Laboratory Automation (TLA) in clinical microbiology.

37 BD Kiestra Copan WASP 37

38 Sort specimens 38

39 Streak plates 39

40 Send to incubators on track lines 40

41 Plates on bench not incubating Slower growth of colonies

42 Smart Incubators Unique Location for Each Plate Homogenous atmospheric conditions Excellent thermal conductivity Earlier Plate Reading Results in improved TAT Delivery of actionable results sooner

43 TLA: Plates always incubating More rapid growth of colonies

44 Imaging for Microbiology Imaging times are set by the user Examples: urine = 12, 14, 16 hours sputum = 24 and 48 hours

45 Image plates 45

46 Digital Imaging Plates are displayed on the screen Colonies digitally selected and instructions for each colony entered Plates can be sent for other automated processes Or users get plates at the bench

47 Pick your colonies for ID/AST 47

48 BD Kiestra Study - A total of 16,111 MRSA screening culture reports were issued during the study times: 2015 (pre-automation) 2016 (post-automation) Time to report negative MRSA cultures # of cultures with a Final report of > 3 days PRE POST Difference with Automation 48.5 hours 24 hours 24.5 hours % reduction 48

49 BD Kiestra Study - 49

50 BD Kiestra Study -

51 Measuring the Impact: FTE Impact Reduction 51

52 Microbiology Laboratory Snapshot Annual Volume and FTE WASPLab Implemented Annual Volume FTE

53 Urine Culture Financial Impact Annual Labor Per Culture Labor Pre Automation $90, $0.47 Post Automation $45, $

54 Automated Specimen Processing Has opened the Door to TLA in clinical microbiology. TLA Opens a large door to Digital Microbiology, Artificial Intelligence, and Algorithms to assist with microbiology culture work up

55 PhenoMATRIX software Aids the staff with culture reading/reporting digital microbiology / imaging analysis artificial intelligence segregation algorithms 55

56 PhenoMATRIX software AI Algorithms 1. Chromogenic detection of organisms 2. Urine culture segregation based on colony count 3. Colony recognition on standard media

57 PhenoMATRIX software The Algorithm Is something there compared to time zero picture? If yes, it is green? If yes, what color of green is it? Any chromogenic media 57

58 MRSA Screening 57,690 Specimens, 4-Center Study Automatic detection and segregation of Positive from Negative MRSA screening cultures using 3 different manufacturers chromogenic agar Sensitivity of 100% Specificity of 90-96% Detection of 153 positive specimens that were missed manually by the technologist

59 VRE Screening 104,730 Specimen, 3-Center Study Automatic detection and segregation of Positive from Negative VRE screening cultures using 2 different manufacturers on chromogenic agar Sensitivity of 100% Specificity of 89.5% Detection of 499 positive specimens that were missed manually by the technologist

60 Cost of negative workup for VRE Chromagar (n = 87,973) Manual processing/reading/reporting 9.6 min/negative specimen a Automated processing/reading/batch reporting ~2 min/negative specimen $6.40 in labor/negative specimen Technologist Labor is $40.00/hour (w/benefits) $1.33 in labor/negative specimen $563, in labor Savings = $445, $117, in labor a. Shadel et al. Surveillance for vancomycin-resistant enterococci: type, rates, costs, and implications. 60

61 GAS Detection Digital Detection of Group A Streptococcus using Colorex Strep A CHROMagar and WASPLab Chromogenic Detection Module 250 throat specimens (E-swab) - Colorex Strep A agar (CHROMagar) - Compared to PCR assay - Examined after 24 hours incubation in WASPLab (manually and PhenoM) - All orange colonies had IDs confirmed by MALDI 57 / 250 = Positive cultures - PhenoMATRIX: 100% (57/57) sensitivity/96.4% (186/193) specificity - Manual reading: 96.5% (55/57) sensitivity/100% (193/193) specificity 61

62 GBS Detection Validation of image analysis software for automatic reading of Streptococcus agalactiae (GBS) isolates in prenatal screening specimens. Maria Federica Pedna Michela Fantini, Vittorio Sambri. Unit of Microbiology, The Greated Romagna Area Hub Laboratory, Pievesestina, Italy ChromID Strepto B agar (biomerieux) and WASPLab 1054 cultures were analyzed (35/37 weeks; LIM broth enriched) 556 (52.75%) were negative by PhenoMATRIX 498 (47.25%) were positive by PhenoMATRIX Sensitivity : 100% Specificity: 78.8% (compared to manual reading) Pink to Red 62

63 63

64 PhenoMATRIX Software AI Algorithms 1. Chromogenic detection of organisms 2. Urine culture segregation based on colony count 3. Colony recognition on standard media

65 (CHROMID SPC Elite agar - biom) KEY: M manual A automation P positive > 10 4 N negative < % agreement 1581 Urines cultures examined 85.5%8 65

66 (CHROMID SPC Elite agar - biom) (CHROMID SPC Elite agar - biom) KEY: M manual A automation P positive > 10 4 N negative < Urines cultures examined 96.5% agreement Over 50% of these were the result of microcolonies that were not seen by the technologist or reading errors. 2 MP/AN = GBS screens (2-3 colonies on each agar) 66

67 (CHROMID SPC Elite agar - biom) 6 hr / NEG 8 hr / POS 67

68 PhenoMATRIX Quantitation Segregation Algorithms S. M. Poutanen, MD MPH FRCPC Sinai Health System/University Health Network, University of Toronto, Toronto, Canada 68

69 Brilliance UTI agar (Oxoid) Burgundy Pink (UTI) & NG on CNA= E.coli UTI CNA 69

70 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 70

71 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 71

72 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 72

73 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 73

74 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 74

75 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 75

76 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 76

77 Brilliance UTI agar (Oxoid) E.coli for AST E.coli for AST 77

78 Brilliance UTI agar (Oxoid) No Growth No Significant Growth Mixed Growth E.coli for AST E.coli for AST E.coli for AST ID/AST 78

79 No Growth 79

80 No Significant Growth 80

81 Mixed Growth 81

82 E.coli for AST 82

83 ID/AST 83

84 No Significant Growth (r/o GBS) 84

85 Mixed Growth (r/o GBS) 85

86 PhenoMATRIX URINE OPTIMIZATION No Growth No Significant Growth Mixed Growth BP for AST ID/AST 35% 27% 2% 6% 3% 86

87 PhenoMATRIX URINE OPTIMIZATION No Growth No Significant Growth Mixed Growth BP for AST ID/AST 35% 27% 2% 6% 3% resulted with the push of a button 87

88 PhenoMATRIX URINE OPTIMIZATION No Growth No Significant Growth Mixed Growth BP for AST ID/AST 35% 27% 2% 6% 3% resulted as E. coli and sent directly for AST 88

89 PhenoMATRIX URINE OPTIMIZATION No Growth No Significant Growth Mixed Growth BP for AST ID/AST 35% 27% 2% 6% 3% sent for ID/AST 89

90 PhenoMATRIX URINE OPTIMIZATION No Growth No Significant Growth Mixed Growth BP for AST ID/AST 35% 27% 2% 6% 3% 73% read/routed by PhenoMATRIX 27% manually reviewed 90

91 PhenoMATRIX URINE OPTIMIZATION - SUMMARY Turn-around-time (TAT) PhenoMATRIX reduce TAT Improves workflow PhenoMATRIX facilitate workflow Improves quality Consistency in following SOP Images facilitate review and training Cost savings Reduced need to hire despite retirements/ workload Eliminates mundane tasks for staff 91

92 PhenoMATRIX Software AI Algorithms 1. Chromogenic detection of organisms 2. Urine culture segregation based on colony count 3. Colony recognition on standard media

93 Digital Image Analysis to Interpret Urine Cultures on Blood, CNA and MacConkey agars 5,201 Preliminary Specimen Study: Significant (>10 4 ) vs. insignificant colony counts (<10 4 ) Differentiate colonies on Blood, CNA and MacConkey agars compared to manual analysis AI: Uses shape, color, appearance Agreement of the AI software with manual interpretation of colony counts: 99% for significant cultures 92.6% for insignificant cultures 2 more sites enrolled (15,000 plates for final data)

94 Algorithms in Digital Microbiology The Future of Artificial Intelligence with WASPLab Total Laboratory Automation Assessed the ability of PhenoMatrix using non-chromogenic media to: Perform colony counts Determine clinical cutoff (<10 4 CFU/mL / >10 4 CFU/mL ) and the numbers of isolates present on the culture plate ( 3 morphologies). 94

95 #

96 Algorithms in Digital Microbiology The Future of Artificial Intelligence with WASPLab Total Laboratory Automation Ability to detect polymicrobic cultures. Isolates Detected by Software TOTAL Isolates % Agreement 2 organism polymicrobic mixtures % 3-4 organism polymicrobic mixtures % TOTAL % 96

97 Software Interpretation Algorithms in Digital Microbiology The Future of Artificial Intelligence with WASPLab Total Laboratory Automation Determine clinical cutoff (<10 4 CFU/mL) and the numbers of isolates present on the culture plate ( 3 morphologies). > 5000 specimens Manual Interpretation Analysis No Contaminated Culture Review % Agreement Growth for ID/AST No Growth % Contaminated % Culture Review % for ID/AST 97

98 Software Interpretation Algorithms in Digital Microbiology The Future of Artificial Intelligence with WASPLab Total Laboratory Automation Determine clinical cutoff (<10 4 CFU/mL) and the numbers of isolates present on the culture plate ( 3 morphologies). > 5000 specimens Manual Interpretation Analysis No Contaminated Culture Review % Agreement Growth for ID/AST No Growth % Contaminated % Culture Review % for ID/AST 98

99 Today s Microbiology Testing Challenges / Automation Solutions Employee Satisfaction and Retention Department Quality Turn-Around- Time Cost Vacancies and putting in overtime vacancies take a toll on staff Automation can fill those Manual workload Automation reduces can lead to repetitive motionrelated injuries keystrokes and manual plate handling & reporting Increase in workload these errors + decrease in staffing can impact error-rate and overall department quality Automation decreases Automation provides realtime metrics: process improvement, quality assurance, training, and competency assessment Routine culture is slow compared to molecular and AST results methods Automation significantly decreases TAT for culture Microbiology requires significant hands on time from highly trained technologists Automation allows for redistribution of labor - allowing technologist to focus on more complex tasks 99

100 LBM / TLA / AI Software Shaping the Future of Microbiology 100

101 Organism Identification hours hours hours A few minutes! 6-18 hours 101

102 MALDI-TOF Set up A small amount of colony is smeared onto a small circle on the target slide. After drying, a 1ul of matrix solution (a-cyano-4-hydroxycinnamic acid) is applied to the organisms which are again allowed to dry. The slide is placed into the MALDI-TOF MS for analysis. 102

103 Performing a MALDI run Matrix Assisted Laser Desorption/Ionization Matrix Analyte Target slide 103

104 Performing a MALDI run Matrix Assisted Laser Desorption/Ionization Target slide 104

105 Performing a MALDI run Matrix Assisted Laser Desorption/Ionization

106 The positively charged proteins drift in flight tube; smaller proteins drift faster Detector Drift region 106

107 Intens. [a.u.] Intens. [a.u.] MALDI-TOF profiles 3000 Bacteria, Yeast, Filamentous Fungi, Nocardia, AFB E.coli Escherichia coli DH5alpha Bacillus subtilis Bacillus subtilis Candida albicans ATCC Candida albicans Aspergillus fumigatus Aspergillus fumigatus m/z Hours/Days/Weeks Minutes! 107

108 108

109 45 Rapid AST testing: FDA-Approved 2017 Accelerate PhenoTest BC ID and next gen phenotypic AST 1.5 hour ID using FISH Sensitivity 98% 7 hour AST using time-lapse imaging and analysis of bacterial growth 96% agreement with conventional AST MIC determination with SIR interpretations 109

110 By-passing the blood culture altogether? 56 T2 Candida Requires no blood culture Tested on whole blood FDA approved for 5 most common yeast in sepsis C.albicans C.tropicalis C.parapsilosis C.krusei C.glabrata Hands on time of < 5 minutes Results in 3-5 hours LOD as low as 1 CFU/mL Sensitivity 91.1% Specificity 99.4% 110

111 >80 potential sepsis causing pathogens. Direct from whole blood. 111

112 112

113 113

114 METABOLOMICS 114

115 microfluidics-based AST platform; flow cytometry-based ID platform 115

116 microfluidics-based AST platform; flow cytometry-based ID platform 116

117 Genomics, Proteomics, Metabolomics, TLA: Will they change our culture? They already have. How far will this go? 117

118 118

119 119

120 120

121 121

122 122

123 123

124 124

125 125

126 126

127 The difficulty lies not so much in developing new ideas as in escaping from the old ones. 127

128 128

129 The future of clinical microbiology is here! Susan E. Sharp, Ph.D., ABMM, FAAM Scientific Director Copan Diagnostics, Inc. Murrieta, CA 129