1. Total Laboratory Automation in Clinical Microbiology
@EBabady
Total Laboratory Automation in Clinical Microbiology
Esther Babady, PhD, D (ABMM)
Associate Attending Microbiologist, Department of Laboratory Medicine
Director of Clinical Operations, Microbiology Laboratory Service
Director, Clinical Microbiology Fellowship
Memorial Sloan Kettering Cancer Center
April 11th, 2019

2. Sample
Bacteria
Viruses
Sample
Sample
Parasites
Fungi
Sample

3. Direct Examination by Microscopy
Sample
Direct Examination by Microscopy
Culture
Serology
Molecular Testing

4. Why automation?

6. 1989
2015

7. Microbiology culture is a complex process which made automation a significant challenge
GPCC
S. aureus
MRSA
Sample
T=0
Minutes
Hours
Days

8. Automation of microbiology is challenging
Sample

9. Automation of microbiology is challenging
Sample

10. Automation of microbiology is challenging
Sample

11. Automation of microbiology is challenging
Sample

12. Automation of microbiology is challenging
37°C, CO2
37°C, Non-CO2

13. Automation of microbiology is challenging
Pathogens?
Commensal?

14. Why automation?

15. Why automation?

16. Journal of Clinical Microbiology, v 51, #6, pp 1658-1665. 2013

17. Several new technologies support and drive the need for microbiology automation

18. Several new technologies support and drive the need for microbiology automation

19. Several new technologies support and drive the need for microbiology automation

20. Several new technologies support and drive the need for microbiology automation

21. Perfect storm
Need
Opportunity

22. JCM April 2018 Volume 56 Issue 4 e00176-18

23. Several steps can be automated
Specimens receiving
Specimens sorting
Specimens processing
Specimens
smearing
plating
Plates incubation
Plates monitoring
Culture work-up
Colonies picking
Colony ID
Colony AST
Culture report
End of life
Molecular
Biochem.
MALDI
E-test KB
MIC
Reading
Verifying
Staining

24. Currently, two commercial options exist to automate all or almost all steps
2012
2006

25. BD Kiestra TLA
Journal of Clinical Microbiology, v 51, #6, pp

26. Copan WASP Lab

27. The level of automation varies by systems
Croxatto, A. et al. CMI V (22), # 3, March 2016, Pages

28. Kiestra InoquIA
WASP DT
Liquid samples
Yes
Non-liquid samples
Off line
Broths inoculation
Slide smears
Plates barcoding
Yes, side
Plates streaking
Magnetic beads
Calibrated loops
Inoculation volume µL
1, 10, 30 µL
Modified from: Croxatto, A. et al. CMI V (22), # 3, March 2016, Pages

29. Kiestra InoquIA
WASP DT
Decapping/capping
Yes
Vortex
Centrifuge No
Media
Up to 12 options
Up to 9 options
Throughput
Up to 235 per hour
Up to 130 per hour
HEPA filters
Modified from: Croxatto, A. et al. CMI V (22), # 3, March 2016, Pages

31. Kiestra ReadA WASPLab Incubator
Capacity
~1200/single
900/single
Plate loading/unloading
600/600 per hour
360/250 pe hour
Camera definition
5 Mp
48 Mp
Image size
3 Mb
20-25 Mb
Light source
Front/Back/Side/ No light
Front/Back/Side/No light
Priority settings
Yes
Modified from: Croxatto, A. et al. CMI V (22), # 3, March 2016, Pages

33. Memorial Sloan Kettering Cancer Center
Specialty hospital: Cancer and other immunocompromised patients
Inpatient hospital : 470 beds
Outpatient locations
Manhattan, Brooklyn, Long Island, Westchester County, New Jersey

34. Clinical Microbiology Laboratory
50 FTEs
Receiving/Accessioning
Bacteriology/Mycology/Myco bacteriology/Parasitology
Virology/Serology/Molecular
~300,000 tests/year
170,000 tests inpatients
130,000 tests outpatients

35. Copan WASP Lab

36. The WASP DT Interfaced with LIS Primary containers (IF programmed)
Specimens receiving
Specimens sorting
Specimens processing
Specimens
smearing
plating
Plates incubation
The WASP DT
Interfaced with LIS
Primary containers (IF programmed)
Centrifuge, vortexes samples
Decap tubes (Tarzan)
Makes slides
Use calibrated loops (1, 10 or 30 ul) to streak plates (Jane)
Inoculate broths
Recap tubes (Tarzan)
Moves plates to smart incubators

37. Specimens receiving
Specimens sorting
Specimens processing
Specimens
smearing
plating
Plates incubation

38. The WASP DT Reading Verifying Staining Specimens processing Specimens
smearing
plating

39. The Smart incubators Plates incubation Plates monitoring
Culture work-up
Colonies picking
The Smart incubators
Pre-set times for images captures
Techs read plates when image is available instead of when tech is available.
New tasks workflow
Screener
Reader
Picker

40. Plates incubation
Plates monitoring
Culture work-up
Colonies picking

41. Screener Reader Picker Digital Microbiology
Culture work-up
Colonies picking
Colony ID
Colony AST
Culture report
End of life
Screener
Reader
Picker
Digital Microbiology

42. Colonies picking Colony ID Colony AST Culture report End of life
Molecular
Biochem.
MALDI
Colonies picking
Colony ID
Colony AST
Culture report
End of life
E-test KB
MIC

43. Additional tools for laboratory automation
Molecular
Biochem.
MALDI
Colonies picking
Colony ID
Colony AST
Culture report
End of life
E-test KB
MIC
Additional tools for laboratory automation

44. Interpretation software: PhenoMATRIX

45. Reading Verifying Staining E-test KB MIC Specimens receiving
Specimens sorting
Specimens processing
Specimens
smearing
plating
Plates incubation
Plates monitoring
Culture work-up
Colonies picking
Colony ID
Colony AST
Culture report
End of life
Reading
Verifying
Staining
Molecular
Biochem.
MALDI
E-test KB
MIC

49. Blood Culture
0 hour

50. Blood Culture
0 hour
4 hours
12 hours

51. Blood Culture

52. Hype or Hope?

53. Urine cultures: First read 16 hours vs 18 hours. Final read 24 hours
18 hours: 16,391 cultures vs 16 hours: 53, 113 cultures. Set up 24/7 with reading on day shift only.
Results
Significant decrease in time-to-final-result TAT for positive cultures (~10 h)
Impact highest for Gram-negative organisms (e.g. Escherichia coli )
But reduction in TAT was accompanied by a decrease in sensitivity from 9.01% at 18 hours to 88.06% at 16 hours.
Balance faster with sensitivity

54. Urine cultures: Manual (1st read 24 hours) vs TLA: (1st read 16 hours)
Urine cultures: Manual (1st read 24 hours) vs TLA: (1st read 16 hours). Final read 24 hours
Pre: 40, 597 cultures vs Post: 68, 905 cultures. Set up 24/7 with reading on day shift only.
Lainhart, W. et al. JCM, August 2018 Volume 56 Issue 8 e

55. Blood culture: 1st read 8 hours, work-up (ID/AST) ON vs 1st read and work-up at 8 hours). Final read 24 hours
Pre: 100 cultures vs Post: 100 cultures.

56. Quiblier, C. et al. JCM, March 2016 Volume 54 Number 3, 585-591

57. Summary
Laboratory automation is now a reality for clinical microbiology laboratories
Integration of laboratory automation with current innovative technology has the potential to significantly impact patient care
Questions?
@EBabady