Automated methods in the Microbiology Lab-Issues and Troubleshooting! Presented By: Dr B. Oboudi

Transcription

1 In the name of GOD

2 Automated methods in the Microbiology Lab-Issues and Troubleshooting! Presented By: Dr B. Oboudi

3 Overview Background/history Plate streakers and Gram stainers Blood cultures Automated Susceptibility Testing Automated ID testing Automated Urine Analysers Molecular assays MALDI-TOF

4 Background Manual streaking of plates has not really changed since solid agar plates were first used Microscopy is mostly unchanged Incubators while probably more reliable are essentially the same Plate reading has not really changed over the years

5 Obstacles to automation in Microbiology Microbiology is too complex to automate: blood, sterile body fluids, urine, catheter tips, tissues, prosthetic devices, lower respiratory tract specimens Variations in the processing of specimens: tissue digestion, urine colony count, impression smears preparation Machines are programmable but humans are flexible Costs of automation Microbiology labs are small for automation

6 Pre analytical Specimen separators Media pouring Issues with each are unique

7 Issues and solutions Sterility at every point or risk of contamination Tubings need to be autoclaved UV light needs to be regularly inspected and maintained

8 Conventional blood culture 7 days

9 Blood Cultures Standard in most diagnostic labs, varying sizes. Better detection times More advanced media Reduced total incubation before calling a bottle a final negative Suppliers: BacT/Alert (BioMerieux), BACTEC FX (BD), Versa TREK

10

11 Issues with blood culture systems False positives due to high TLC count Continuous power supply needed Cost

12 Conventional ID and susceptibility testing hours

13 Automated ID and Sens Automated ID testing available since 1977 Biochemical substrates miniaturised and read by colorimetric or fluorometric means Available in many labs Multiple Antibiotics in different dilutions available on Cards or panels to ascertain MIC Suppliers: Microscan Walkaway (Dade Behring) Vitek2 (BioMerieux) BD Phoenix (BD)

14

15 Issues with identification systems Pure culture Simple tests are not covered like oxidase, catalase, motility, pigment production Variability of identification in rarer organisms Only organisms covered in database Inoculum size can affect MIC interpretations MICs of some antibiotics are not actual MICs but extrapolations from related antibiotics

16 Automated Urine Analysers Automated Dip-strip inoculation and reading Cell counts performed automatically either by flow cytometry or (more recently) high resolution optics taking pictures of cells High Negative predictive value for urine cultures

17 Issues with urine analysers Back to basics Appropriate specimen collection Early transport

18 Molecular methods GeneXpert- not just for TB, MRSA, C. difficile, etc.

19 Issues with molecular methods Cannot differentiate live from dead Negative results do not rule out infection

20 MALDI-TOF(Matrix assisted LASER Desorption Ionisation-Time of Flight Mass spectrometry) Protein based spectral identification of bacteria Identifications available in literally minutes not hours Tiny amount of bacterial growth needed not affected by media or incubation conditions Minimal cost per test (in cents not even dollars), virtually no consumables Suppliers : Bruker, BioMerieux

21

22

23 Issues with MALDI-TOF Pure culture In mixed cultures, will pick up the dominant organism Antimicrobial susceptibility not possible Viruses not identified Identifies only organisms in database

24 Plate Streakers Select appropriate media Loads the samples Spreading the inoculum to obtain isolated single colonies following incubation Suppliers: WASP (Copan) Previ-Isola (BioMerieux) Innova (BD) and Inoqula (KIESTRA) Not all systems include Gram stain preparation

25

26

27 DL-96II Microbial ID/AST System Provide bacteria ID and AST tests results at the same time with automated reading and analysis Effective identification of wide range covering vast routine organisms (over 600 in total) including major clinical pathogenic bacteria and fungi Advanced expert system presents testing results with high accuracy and instructive interpretation Identification range: 5 categories of test cards covering Micrococcaceae, Streptococcus, Enterobacteriaceae, Non-fermentative bacteria, Yeast-like fungi Test Principles: Identification: colorimetry / Susceptibility testing: turbidimetry Throughput: sample per hour Optional Configuration : Automated sampling device, sampling plates per hour Printer: External printer Interface: 17 inch display, support LIS/HIS Environmental temperature: Relative humidity: 10%--90%; Atmospheric pressure: 76kPa--106kPa;

28 DL-Bt64 Auto Blood Culture System Auto blood culture system for both blood and sterile body fluid specimens Expendable modular design to meet different size laboratory s capacity needs High sensitivity & specificity: able to detect anaerobic/aerobic and fungi for both adult and child, characterized for its excellent recovery of fungi FAN bottle (Fastidious Antibiotic Neutralization ) with unique resin design enables absorbing most of antibiotics, consequently rises up the sensitivity of detection rate.

29 Test Principles: Colorimetry & CO2 sensor. Sample Type: Blood and various sterile body fluid specimens. Capacity: 64 bottles / 112bottles / 224 bottles Detection Method: Adopt continuous swinging vibration mode, non-stop monitoring. The system automatically reads the color data of the sensor at the bottom of each bottle every 10 minutes by each independent detector Real-time detection and warning, with audio, visual and software alarm of positive samples or negative samples. Interpretation Method: Analyze sustained acceleration, Speed, Initial threshold. Sample Loading: Able to accept samples in random position and at any time in any rack. Able to resume the procedure if a sample is picked up and reinserted within 2 hours. Incubation detection period: to be set by the operator, and at most 7 days. System hardware: Main instrument with 17' internal touch-pad, barcode scanner.

30 DL-Bt 112 Auto Blood Culture System Auto blood culture system for both blood and sterile body fluid specimens Expendable modular design to meet different size laboratory s capacity needs High sensitivity & specificity: able to detect anaerobic/aerobic and fungi for both adult and child, characterized for its excellent recovery of fungi FAN bottle (Fastidious Antibiotic Neutralization ) with unique resin design enables absorbing most of antibiotics, consequently rises up the sensitivity of detection rate

31 Test Principles: Colorimetry & CO2 sensor. Sample Type: Blood and various sterile body fluid specimens. Capacity: 64 bottles / 112bottles / 224 bottles Detection Method: Adopt continuous swinging vibration mode, non-stop monitoring. The system automatically reads the color data of the sensor at the bottom of each bottle every 10 minutes by each independent detector Real-time detection and warning, with audio, visual and software alarm of positive samples or negative samples. Interpretation Method: Analyze sustained acceleration, Speed, Initial threshold. Sample Loading: Able to accept samples in random position and at any time in any rack. Able to resume the procedure if a sample is picked up and reinserted within 2 hours. Incubation detection period: to be set by the operator, and at most 7 days. System hardware: Main instrument with 17' internal touch-pad, barcode scanner

32 Way ahead.. Total lab automation???????

33 Obstacles to automation in Microbiology Microbiology is too complex to automate: blood, sterile body fluids, urine, catheter tips, tissues, prosthetic devices, lower respiratory tract specimens Variations in the processing of specimens: tissue digestion, urine colony count, impression smears preparation..but THE SIMPLER METHODS CAN BE AUTOMATED Machines are programmable but humans are flexible Costs of automation Microbiology labs are small for automation...not all!!!

34 CONCLUSION-TWO QUOTES The first rule of any technology used in a business is that automation applied to an efficient operation will magnify the efficiency. The second is that automation applied to an inefficient operation will magnify the inefficiency. -Bill Gates

35 CONCLUSION-TWO QUOTES

36 THANK YOU

37

38