dr gillian wood - austin health - microbiology automation

Forward to the Future

Gillian WoodMicrobiologist and Infectious Diseases Physician

Austin Health

Mercy Hospital for Women

Melbourne

Automation in the Microbiology Laboratory

Microbiology Automation

• Component parts to microbiology automation• 3 systems: fundamentally the same

• Kiestra system and what it does

• Reasons for automation

BD Kiestra Work Cell

BD Kiestra Total Laboratory

Automation (TLA)

WASPLab

BioMerieux FMLAFull Microbiology Lab Automation

SpecimenHoly Grail

The Single Colony

ORGANISMIdentification

and Susceptibilities

Report

MICROBIOLOGY (BACTERIOLOGY)

Current Microbiology (Bacteriology)

Specimen: •Registration•Bar code •Setup protocol

Plate:Selection labelling Inoculation streaking

Plate Incubation:Overnight1st plates– 24hLast plates – 10h

Plate Reading+

Colony pick off

Identification:MALDI: Minutes Others: 8-24h

Susceptibility testing:AST: 8-24hDDS/Etest: 18-24h

•1st shift: hours•Plates on bench•Negatives with positives•Colonies of different maturity

Specimens•Registration •Bar coded•Setup protocol

Manual Inoculation

NON-liquids

What is Microbiology Automation?Schematic Diagram

AutomatedSpecimenProcessor

Plate selection, Bar coding

Liquid specimensInoculation + streakingBroths+DDSSlides

Eswabs!

Dacron Gel vs Eswab

READING ROOMReading of Digital ImagesContinuously available!

Standardised incubation timeColonies targeted

Specimens•Registration •Bar coded•Setup protocol

Predetermined Incubation time

RoboticIncubators

CO2, O2

Digital Plate

Imaging

Manual Inoculation

NON-liquids

Work BenchesManualColony Pick Off

Automatedcolony pickerInoculation of

MALDI + broths forAST+ DDS

What is Microbiology Automation?Schematic Diagram

AutomatedSpecimenProcessor

Plate selection, Bar coding

Liquid specimensInoculation + streakingBroths+DDSSlides

MALDI-TOFOther ID systems

Automated

SusceptibilitySystems (AST)

Broth Disc Susceptibility (DDS)

Eswabs!

This is where went!

MAY TO SEPTEMBER 2014

Inoqula

Reading Room/Training Room

InoculA• Automatic specimen processor• Largest capacity

– Loading: 288 tubes– 400 plates/hour– Plate silos: 720+

• Decapping/capping• Broth + slide inoculation• Manual interactive station

• Non-liquid specimens

• Soon - disc dispenser• DDS

• Pipette inoculation– 10uL +

• Magnetic bead streaking• Reusable

Protocol B: Mixed Cultures Suspension C: 80% E. Coli + 10% E. Faecalis + 10% S. Aureus x5 plates

(single colony count + standardization)

InoqulA: Manual

Single Colonies

1 drop BC into Eswab 10uL urine

Wound Eswab

Lawn Suspension

“SMART” INCUBATORSReadA Compact

• 1152 plate capacity

• Each plate has a uniquelocation

• Random access/rapid retrieval

• Controlled temp + CO2 or O2

• Hepa filtered imaging section

Digital Imaging

Software

Vision Tool Box

High resolution digital enhancements

Sophisticated image acquisition

Differential analysis

• Artefact free, accurate digital representation of the culture plate

• Ability to recall and collate the images as desired

• Permanent record

Imaging track

Output track

Input track

Digital Image Reading

Reading Room Digital colony targeting

Digital Images

• All of the plates on a specimen together

• Same plates over time– All scientists working on a culture

see same culture “history”

• Patient centred images– All plates from all specimens on

same patient over time!

– Stops work up of same colony from different specimens

– Very different work flow/training• Patient centred not specimen

centred.

Scan 1

Scan 2

Digital Images

• Separates negative plates from positive – MRSA screening

– Urines

• 12-20 negative plates per screen

• 15 seconds to read and report 20 samples– Automated soon

Digital Images

Other uses• Remote bacteriology

• Telemedicine

• Assist colleagues

• Second opinions– Less experienced

• eLearning– Hugh database of culture

plates

• Collaboration

House

iPhone/ iPad

After Incubation:

Work Benches → Colony Processing

• Manual retrieval of plates from incubators• Take plates to work benches• Pick off targeted colonies:

• Perform appropriate work for ID and Senses etc?Automated?

The Case for Automation It is fun, interesting and exciting!

It is expensive!

Decreased turnaround time to clinically useful results

– Greatest potential of the systems = Faster Microbiology

– Paradigm shift for microbiology FROM• Single daily plate reading

• Leaving plates on benches pre and post incubation

• De-emphasis of “waiting for bugs to grow”

• As soon as culture is ready the instrument will go bing!

Matthews. Clin Microbiol Infect 2011;17:651-654

The Case for Automation

Results available 10-12 hours earlier– Enhanced treatment effectiveness

– Improved antibiotic stewardship • Fewer DDD of antibiotics

– Infection control (MROs)

– Results available to those working extended hours

– Results available earlier in the morning• Ward rounds = decision-makers (consultants) present

– Earlier hospital discharges

• Assists ED with NEAT targets

• Reduced LOS per DRG

• Research needs to be directed at relating this to:Matthews. Clin Microbiol Infect 2011;17:651-654


Increased productivity: 2.5 fold increase

• Staffing issues

– Cope with more specimens!!!

– Possibly fewer and/or lower grades of staff• 25% lab FTE in inoculating plates and broths

– Staff do other things• Freed from repetitive boring work

• Research, development, teaching

Matthews. Clin Microbiol Infect 2011;17:651-654Mischnik. J Clin Micro 2012:50:2732-2736


Inoqula– Plating 60 vs 24 samples per hour

• Plates into incubator ASAP

• No tea breaks

• Not affected by hangovers or influenza

– Aim for all samples to be plated within 20 minutes!

– Fewer mistakes and less rework• Mislabelled plates, wrong plates, contamination

– 5-15% more single colonies• Saves replating

• Saves 24 hours on time-to-results

– 3 fold increase in recovery of bacteria (liquid media)

– Shorter time to commence incubation



Smart Incubators – ReadA Compact

– Controlled internal temperature and atmosphere

– Each plate has a unique location

– Random access/rapid retrieval

– No opening and shutting doors

– No plates sitting on benches for hours!• Out of incubator > 1 minute to be photographed

– Improved plate incubation and reading

• Shorter time to identification and susceptibility results



Digital images– Produced automatically

• Set times

• Different lighting and exposures

• Images available constantly at shortest possible time

– Effective incubation and plate reading through the day • Aim to have all specimens in incubators

• Better with a 24/7 lab - ESSENTIAL

– Reduced incubation times• Digital image resolution

– Superior and earlier growth detection

– Negative cultures

» Automatic and early reporting


Digital image analysis!– Vision Toolbox assisted imaging

– Time course imaging, growth curves and software• Earlier detection and pick off of colonies

• Identification of organisms by growth characteristics and colour

– Earlier reading of the disc zones• Disc susceptibilities go back into incubators

– Optimum incubation

– Image analysis allows detection of result as earliest possible time

– EUCAST DDS: 12 hours incubation

Reduced TAT For preliminary and completed results


Increased accuracy and traceability

• Error rate <0.5%

• Fewer mistakes– Labelling plates

– Plate selection

– Specimen mix-ups

– NO lost plates!

• Consistent and standardised incubation, inoculation, streaking» More single colonies

• Permanent record of plate and susceptibility images

• Complete traceability – Media batches, inoculated plates, digital images, results

– Required now for Lab and hospital accreditation

What We Have


Thank You

Implementation• Head Key User (implementation person)• Key User Group

– 6 staff– 2 and a half days training

• IT Specialists– 3 staff

• 1 IT, 2 lab staff

• Front Line support Staff– 3 staff (good with screw drivers)

• Quality validations– 3 staff

• Staff training– One and a half days training

Automation Evaluation and Changes

Data from Everyone in Micro

Compiled Peter Ward

Eswab Collection and Transport System

Amies Liquid + Nylon Flocked Swab

White Cap

NEW ESWABPathology Department

21st July 2014

Peel apart plastic film layers

Stand tube upright Avoid spills

DO NOT DISCARD LIQUIDRemove swab from package

Collect specimen

Remove lidReturn swab to container

Snap of swab at score line

Replace lidSwab shaft is captured in lid

Complete Patient details

Dacron Gel vs Eswab

Bacterial Survival

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

MRSAGel

swab

MRSAEswab

PsaeGel

swab

PsaeEswab

H.infGel

swab

H.infEswab

N.gonGel

swab

N.gonEswab

P anaGel

swab

P anaEswab

Log10 Survival at 4ºC

4° 0 hrs

4° 4 hrs

4° 24 hrs

4° 48 hrs

at 4ºC after 24 hrs

at RT after 24 hrs

N gonorrhoea SurvivalEswab vs. Gel Swab

Pos BC

Kiestra Manual Manual Kiestra

Aim of Kiestra Users?

Get everything into an Eswab container!

– Either as a Eswab or just using the container!

– Eswabs are better than dacron swabs

– Eswabs can be automatically plated by Kiestra

– Streaking by Kiesta provided more single colonies

Blood Culture Gram Stains

• Compare Manual Gram vs. Kiestra Gram prep

– Similar numbers of organisms (++ vs. ++)

– Often clearer and better quality because of even spread of material

Urines

• >200 urines plated Kiestra vs. manual

– More isolated colonies

– Contamination easier to see

– Very heavy growth isolated colonies on K, confluent on manual

UrinesManual 1uL loopKiestra 10uL spot

UrinesKiestra 10uL spot Manual 1uL loop

Urogenital/Wounds Semi-automated Gel vs manual Gel

• 40 samples from wounds & urogenital swabs• Gel swabs run in parallel (manual vs InoqulA).

• NO significant differences

• Recommendation:

• Split HBA/MAC plates are suitable for urogenital & wound swabs instead of full HBA and full MAC

UrogenitalSemi-auto vs manual Gel

Sputum

• Semi-automated Kiestra vs full manual

– Similar culture results,

– More isolated colonies

– Limited numbers available

– Need to use the SL (sputum lysis) system

Buccal Swabs

• Kiestra/Eswab vs. Gel/Manual systems

• Culture– More isolated colonies

– >>more AnO2 colonies on Kiestra and improved growth

• Gram stains– More even and easier to examine instead of

searching

MRSA

• MRSA Screening • Change to combined swab of 2

sites instead of separate sites as per CDC etc.

• CDC recommend pooling MRSA screening swabs

» http://hicsigwiki.asid.net.au/index.php?title=Screening_and_Clearance_Process-MRSA

• Waiting for swabs

– Survival already validated

– Split chrome to be checked for MSSA/MRSA

http://hicsigwiki.asid.net.au/index.php?title=Screening_and_Clearance_Process-MRSA

Mediastinal Collection Aspiration Gel swab and Eswab saturated with specimen

Gram Stains

Gel Eswab

Mediastinal collection asp @ 24 hrs

Mediastinal collection asp @ 48 hrs

Eswab/Kiestra Eswab/KiestraGel swab/Manual Gel swab/Manual

Mediastinal collection asp Anaerobic @ 48 hrs

Eswab/Kiestra Gel swab/Manual

Future

More and improved automation = Processing• Colony picker

• Biohazard hood

Digital image analysis = Vision Toolbox = Diagnositics!– Reduced incubation times

• Now usually 18-24 hours: < 12 hours

• EUCAST DDS incubation of 12 hours

– Digital image resolution• Negative cultures: Automatic and early reporting

– Time course imaging, growth curves and software• Earlier detection and pick off of colonies

• Identification of organisms by growth characteristics

• Earlier reading of the disc zones

– Reduced TAT For preliminary and completed results

Kiestra Total Laboratory Automation (TLA)

dr gillian wood - austin health - microbiology automation

Health & Medicine

microbiology laboratory

digital imagesall

colony fr

specimen togethersame

culture plateability

wound eswab

dacron gel vs eswab

tubes400 plateshourplate