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Molecular Diagnostics for Blood Cultures – Fast ID/AST Results
Maureen Spencer, M.Ed, BSN, RN, CIC, FAPIC
Director, Clinical Implementation
Accelerate Diagnostics
www.maureenspencer.com
http://www.maureenspencer.com/
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Laboratory Results are Vital to Healthcare
• While laboratory costs are a small part of a hospital operating budget, it has an
substantial influence over the entire budget
Accurate
and Timely
Results
from the
Lab
• Improve patient outcome
• No wasted medical/labor costs
• Increase patient satisfaction
Correct
patient
treatment
executed
quickly
• Higher patient
throughput drive
revenue
• Better resource
utilization
• Improved hospital
financials
70% of Medical
Decisions are Based
Upon a Laboratory’s Results
70% of Medical Decisions are Based Upon a Laboratory’s
Results
Laboratory
Represents only 5%
of Healthcare Costs
2
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Modern and rapid diagnostics are crucial to individual patient care
• Benefits • rapid identification of the causative agent
• initiating optimal therapy
• preventing the spread of highly infectious and pathogenic micro-organisms
• Appropriate and timely diagnostics need to be initiated before starting therapy
• improve infection management on patient level
• avoids inadequate therapy
• prevents collateral damage such as toxicity, antimicrobial resistance and spread of (MDR)
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Typical High Tech Lab Today
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The Molecular Lab – Labs of the Future
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Blood Cultures Procedures and Contamination Rates
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Blood Culture Contamination
• BC contamination - clinically significant problem that results in extra expense and patient harm
• Case-control study in the UK found BC contamination was associated with 5.4 extra hospital days at a cost of approximately $7500 USD
• Similarly, in the US, Gander and colleagues observed excess charges of $8720 per contamination event
• Blood culture contamination is associated with unneeded antibiotic treatment in approximately 30%–40% of patients
• Gander RM, Byrd L, DeCrescenzo M, Hirany S, Bowen M, Baughman J. Impact of blood cultures drawn by phlebotomy on contamination rates and health care costs in a hospital emergency department. J Clin Microbiol 2009; 47:1021–4.
• Alahmadi YM, Aldeyab MA, McElnay JC, et al. Clinical and economic impact of contaminated blood cultures within the hospital setting. J Hosp Infect 2011; 77:233–6.
• Lee CC, Lin WJ, Shih HI, et al. Clinical significance of potential contaminants in blood cultures among patients in a medical center. J Microbiol Immunol Infect 2007; 40:438–44.
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Cost of BC Contamination
• Treatment with broad-spectrum IV antibiotics requiring hospital stay
• Delay in hospital discharge and longer Length of Stays (LOS)
• Additional bed, pharmacy and laboratory (micro, chemistry, radiology) costs
• Contaminated BC may meet the CLABSI surveillance definition and not be a true case - $$ CMS Penalties
• Est. >$8000 per case
Gander et al. J Clin Microbiol. 2009 Apr;47(4):1021-4
Δ $8,720
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New Blood Culture Diversion Technology to Prevent Contamination
Rupp M, et al. Reduction in Blood Culture Contamination Through Use of Initial Specimen Diversion Device. Clin Infec Dis Mar 2017 Change D, et al. Reduction in false positives by 92% and reduction in Vancomycin DOT of 37% (P=0.007 San Antonio Military Medical Center, SHEA, 2017
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Blood Culture Systems
bioMerieux BacT/Alert BD BACTEC Thermo VersaTREK
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Blood Culture Media
Resin (Absorb Antibiotics)
BACTEC™ PEDS PLUS™/F Medium
BACTEC™ Plus Aerobic/F Medium
BACTEC™ Plus Anaerobic/F Medium
BacT/ALERT FA PLUS Aerobic (Resin)
BacT/ALERT FN PLUS Anaerobic (Resin)
BacT/ALERT PF PLUS (Resin)
Charcoal Resin
BacT/ALERT FA Aerobic (Charcoal)
BacT/ALERT FN Anaerobic (Charcoal)
BacT/ALERT PF (Charcoal)
Non-Resin BACTEC™ Lytic/10 Anaerobic/F Medium
BACTEC™ Standard Anaerobic/F Medium
BACTEC™ Standard/10 Aerobic/F Medium
BacT/ALERT SA Standard Aerobic
BacT/ALERT SN Standard Anaerobic
VersaTREK REDOX 1 (aerobic) medium
VersaTREK REDOX 2 (anaerobic) medium
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Blood Culture Organism Identification
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Challenges with Traditional Methods
Slow Specimen / quality dependent Inexpensive $ (for lab not hospital) May have inferior performance
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6 overnight incubation 7 colony selection 8 OPTIONAL: MALDI-TOF ID
.5 McFarland 9 ID & susceptibility 10 optimized therapy 11
ID only and resistance marker technologies are incremental to AST workflow.
1 patient blood draw 2 blood bottle incubation & screening 3 perform gram stain 4 initial plate streaking 5 OPTIONAL: ID and resistance markers
TYPICAL ID & AST WORKFLOW
Incubation depends on the organism’s growth – typically from 6-18 hours
8-12 hrs incubation
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Patient impact – Traditional Methods Antibiotic therapy workflow:
• If bacteremia or sepsis is suspected, empiric therapy started
• Wait on BC bottle positivity
• Next change of therapy at Gram stain results (16-24hrs after BC drawn)
• Gram stain informs on ID of organism only, no antibiotic susceptibilities
• Change to targeted therapy after antibiotic susceptibility results
• VITEK2, BD Phoenix, Microscan results take 12-18hrs
• Targeted therapy begins >50 hours after bacteremia/sepsis is suspected
0 10 20 30 40 50 60
Admission
Blood Draw
Blood Culture
Gram Stain
Isolate Culture
ID
AST
Broad spectrum
ABX started Targeted
ABX started ABX change ABX change
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Blood Culture Based Diagnostic Technologies
• Molecular
• MALDI-TOF Mass Spectrometry
• Traditional ID/AST
• Emerging Rapid AST
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Cepheid GeneXpert
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What does PCR offer?
A single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence
• Offers accuracy & specificity
• Offers speed
• Offers detection at even very small amounts of organisms
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Cepheid GeneXpert
Workflow
Test
Differentiation
17 min 1 hour
GeneXpert I, IV, XVI Infinity
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Cepheid GeneXpert Type of
Infection
Test
Healthcare
Associated
Xpert MRSA
Xpert SA Nasal
Complete
Xpert MRSA/SA
SSTI
Xpert
MRSA/SA BC
Xpert C. difficile
Xpert C.
difficile/Epi
Xpert vanA
Xpert Norovirus
Xpert Carba-R
Type of
Infection
Test
Critical
Infectious
Disease
Xpert
MTB/RIF
Xpert Flu
Xpert
Flu/RSV XC
Xpert EV
Xpert Ebola
Type of
Infection
Test
Sexual
Health/Woma
n’s Health
Xpert CT/NG
Xpert GBS
LB
Xpert GBS
Xpert TV
$50-65 / test
Workflow
Test
Differentiation
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BIOFIRE TORCH (BIOMERIEUX)
12
Results in 90 min
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Biofire Filmarray ID
Workflow Menu Differentiation
FilmArray Pouch Load pouch into loading block
Inject hydration solution
Add patient sample to buffer
Inject sample Load pouch
5 min+ Hands-On 1.25h TAT
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Biofire Filmarray
Workflow Menu Differentiation
Gram Pos. Bacteria ID & Resistance Markers
• Bacterial ID
• Enterococcus
• Listeria monocytogenes
• Staphlococcus
• Staph. aureus
• Streptococcus
• Strep agalactiae
• Strep pyogenes
• Strep pneumoniae
• Resistance markers
• vanA (vancomycin)
• vanB (vancomycin)
• mecA (MRSA indicator)
Gram Neg. Bacteria ID & Resistance Markers
• Bacterial ID
• Acinetobacter baumannii
• Haemophilus influenzae
• Neisseria meningitidis
• Pseudomonas aeruginosa
• Enterobacteriaceae
• Enterobacter cloacae complex
• Escherichia coli
• Klebsiella oxytoca
• Klebsiella pneumoniae
• Proteus
• Serratia marcenscens
• Resistance markers
• KPC (carbapenemase)
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LUMINEX Verigene - Nanosphere
Results in 2.5 hrs
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Nanosphere - Verigene
Workflow
Menu
Differentiation
Load each consumable
into the Processor SP
Remove the cartridge
Disassemble test cartridge
Scan barcode on slide, then place in
Reader
10 min+ Hands-On 2.5 hr TAT
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Nanosphere Verigene
Workflow
Menu
Differentiation
Gram Pos. Bacteria ID & Resistance Markers
• Bacterial ID
• Enterococcus faecalis
• Enterococcus faecium
• Listeria spp.
• Staphylococcus spp.
• Staph. aureus
• Staph. epidermis
• Staph. lugdunensis
• Streptococcus spp.
• Strep. anginosus Group
• Strep. agalactiae
• Strep. pyogenes
• Strep. Pneumoniae
• Micrococcus spp.
• Not FDA-cleared
• Resistance markers
• vanA (vancomycin)
• vanB (vancomycin)
• mecA (MRSA indicator)
Gram Neg. Bacteria ID & Resistance Markers
• Bacterial ID
• Acinetobacter spp.
• Citrobacter spp.
• Proteus spp.
• Enterobacter spp.
• Pseudomonas aeruginosa
• Escherichia coli
• Klebsiella oxytoca
• Klebsiella pneumoniae
• Serratia marcescens
• Resistance markers
• KPC (carbapenemase)
• CTX-M (ESBL)
• NDM (carbapenemase)
• IMP (carbapenemase)
• OXA (carbapenemase)
• VIM (carbapenemase)
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T2 Biosystems – for Yeast
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T2 Biosystems
Workflow
Technology
Menu
Blood Culture Assay
(1) Build Cassette (2) Remove cap on blood (3) Invert into Cassette
Load onto T2Dx
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T2 Biosystems
Workflow
Technology
Menu
Blood Culture
Assay
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T2 Biosystems
Workflow
Technology
Menu
Blood Culture Assay
T2Candida • Candida albicans / tropicalis • Candida parapsilosis • Candida krusei / glabrata
$200-250 / test
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Maldi-tof
Vitek MS
Biotyper
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MALDI-TOF MS
• Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
• Identification by signature high-abundance proteins (primarily ribosomal proteins)
• Signature protein patterns are compared / matched to an extensive open database
• ID of bacteria, yeast and fungi in 40 seconds
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Maldi-TOF Mass Spectrometry
• Isolate-Based Workflow • The most comprehensive coverage of organism ID
• Highly-cost effective approach when capital purchase is amortized out
• Integrated AST results (bM Myla, Bruker + 3P Middleware)
• Examples: Bruker Biotyper, bioMérieux MS
• Direct from +BC Workflow • Same benefits as above, plus…
• Eliminate sub-culturing, and save 24-36 hours in time to ID
• Examples: Bruker Biotyper, bioMérieux MS
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MALDI-TOF benefits and Cons Shared Direct from +BC MS
Little Hands-on-Time
(when batched)
Broad Coverage
1000’s IDs in database
Cumbersome and lengthy (35-
60min) sample prep required
Time to ID is long, and dependent
upon growth
Fast (1-2 hours) and Low Cost-per-
Test
Requires a highly skilled, dedicated
technician
Variable levels of accuracy Reaffirms (not replace) the value of
the Microbiologist
Variable levels of accuracy1
(GN – 90%, GP – 76%, Y – 66%
correct ID)
Integrates with AST results Additional expense (+ $5) from
conventional MS
Lengthy Verification process
Batched workflow (not random
access)
High initial capital cost Subculture MS
Challenges to ID viridans
streptococci group, pneumococci,
anaerobic bacteria, and
polymicrobial samples
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Wash/Centrifuge 5x for 2min @ 8500 rpm
+BC
Load 2x Vacuettes
Carefully remove liquid, and suspend pellets
Combine Suspensions Pellet RBCs
1min @ 1000rpm
Transfer New Tube & Pellet Supernatant 1min @ 13000rpm
Resuspend in RBC lysis solution
Inc. 10min @ 35C
Pellet Supernatant 1min @ 13000rpm
Wash and Re-Pellet 1min @ 13000rpm
Resuspend in 70% EtOH
Stevenson, et al. Rapid Identification of Bacteria in Positive Blood Culture Broths by MALDI-TOF MS. JCM, Feb. 2010, p. 444–447.
Pellet Supernatant 2min @ 13000rpm
Remove liquid Respin 2min
Remove liquid again…
Then, follow standard MS work-up…
“RAPID” MALDI-TOF WORKFLOW – DIRECT FROM + BC
35-60min workup / sample Requires a highly skilled tech
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Antimicrobial Sensitivity Tests (AST)
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Automated ID/AST - Standard of Care
• bioMérieux Vitek
• Beckman Coulter Microscan
• Becton Dickinson Phoenix
Vitek 2 MicroScan
Phoenix
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6 overnight incubation 7 colony selection 8 OPTIONAL: MALDI-TOF ID
.5 McFarland 9 ID & susceptibility 10 optimized therapy 11
ID only and resistance marker technologies are incremental to AST workflow.
1 patient blood draw 2 blood bottle incubation & screening 3 perform gram stain 4 initial plate streaking 5 OPTIONAL: ID and resistance markers
TYPICAL ID & AST WORKFLOW
Incubation depends on the organism’s growth – typically from 6-18 hours
Plate incubates for 6-12 hrs
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Accelerate Diagnostics Pheno Blood Culture System
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3 ID & susceptibility in < 7hrs optimized therapy: de-escalate or escalate
4 1 patient blood draw 2 blood bottle incubation & screening
ACCELERATE PHENO™ SYSTEM WORKFLOW –
DIRECT FROM POSITIVE BLOOD CULTURE
Blood cultures incubate from 6-18 hrs depending on the organism’s growth
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Accelerate Pheno™
Rapid phenotypic AST with MIC • ID coverage of GP, GN, Yeast • Monomicrobial meta call in ~75-80% of samples prevents the need for
further work • ID alone is not sufficient to move to effective therapy in many cases • MIC is necessary for escalation/de-escalation and dosing decisions in
many cases • Covers 80-90% of the causative pathogens direct from +BC - any
technician can run system • Specialized technician can follow up on the remaining 10-20% of
unidentified ID calls • Consolidate ID and AST testing using a LEAN laboratory approach
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Accelerate Blood Culture Organisms and Abx
Accelerate ID:
Acinetobacter baumannii
Candida albicans
Candida glabrata
Citrobacter freundii + C. koseri
Coagulase-Negative staphylococcus
Enterobacter aerogenes + E. cloacae
Enterococcus faecalis
Enterococcus faecium + OE
Escherichia coli
Klebsiella oxytoca + K. pneumoniae
Proteus mirabilis + P. vulgaris
Pseudomonas aeruginosa
Serratia marcescens
Staphylococcus aureus
Staphylococcus lugdunensis
Streptococcus agalactiae
Streptococcus genus
Streptococcus pneumoniae
Streptococcus pyogenes
Amikacin Ampicillin Aztreonam Cefazolin Cefepime Ceftaroline Ceftazidime Ceftriaxone Ciprofloxacin Colistin Daptomycin Doxycycline Ertapenem Erythromycin Gentamicin High-Level Gentamicin High-Level Streptomycin Imipenem Levofloxacin Linezolid Meropenem Minocycline MRSA (Cefoxitin) Penicillin Pipercillin/tazobactam Streptomycin Sulbactam Tobramycin
Trimethoprim/Sulfamethoxazole Vancomycin
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Patient Impact
0 10 20 30 40 50 60
Admission Blood Draw
Blood Culture ID
AST
Antibiotic therapy workflow:
• If sepsis is suspected, empiric therapy started
• Change of therapy after antibiotic susceptibility results
– Accelerate Pheno™ System results take ~7 hours after BC+
• Targeted therapy begins ~20 hours after sepsis is suspected
ACCELERATE WORKFLOW
ID/AST RESULTS
40+ HOURS FASTER!
Broad spectrum
ABX started Targeted
ABX started
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Diagnostic Technology
• Despite advances in diagnostic technology, there is an urgent need for tests that are:
• easy to use • identify the microbe causing the infection • determine whether it is drug resistant • provide results faster than current tests
• Faster, more accurate tests would help ensure that patients are receiving:
• the best treatment for a variety of infectious diseases • guide more effective infection control practices • improve the tracking of outbreaks.
• Better tests would also help protect our dwindling supply of effective antibiotics by reducing their misuse
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IDSA Better Tests, Better Care – Improved Diagnostics
• Stimulate Diagnostics Research and Development
• Expedite Integration of Improved Diagnostic Tests Into Patient Care
• Address Regulatory Challenges and reimbursement
• Encourage Adoption of New Tests
• Educate Healthcare Providers on the Use of Diagnostics
• Diagnosis and Patient Management
• Increased Use of Point-of-Care and Near-Patient Tests
• Future of Infectious Diseases Diagnostics: Use in Outpatient Clinic, Emergency Department, ICU
• Biodefense and Emerging Infectious Diseases
• Communication and Utilization of Results, Test Services and Methods
• Shift From Single-Analyte Testing to Multiplex Testing
• Address Clinical Challenges to Adoption
Improved Infectious Diseases Diagnostics • CID 2013:57 (Suppl 3) • S139
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Micro Lab
Infection Prevention
Pharmacy and ASP
Nursing and Medical Staff
Infectious Disease
Physicians
Improved bench
workflow
Standardized Blood culture procedures
Reduction in BC
contamination rates
Reduction in MDROs, less
isolation
Reduction in outbreaks,
(MDRO,CDI)
Improved sensitivity and
MIC results
Efficient response to sepsis alerts
Escalation or de-
escalation
Rapid transition
to targeted therapy
Reduced
morbidity/mortality
Reduced
morbidity/
mortality,
reduced cost of care
Eliminates
broad-
spectrum abx use
Improved
turnaround
time to ID/AST /MIC
Reduced abx cost:
prep, delivery
Reduced Lab draws and drug admin by
RNs
Less use of restricted antibiotics
Reduction in cases reported to NHSN and CMS
Penalties
Reduction isolation
beds, PPE. Improved
bed utilization
More efficient Abx Stewardship
Program
More efficient use of ICU beds
and staff
Improved Drug/bug
orders and standardized
order sets
Save lives improved services and staff
utilization
Sepsis Alerts in
EMR CEO, CFO, COO,
CNO, CMO Administration
Information Technology
Expedited transfers of +BC patients back to
LTACs
Rapid molecular
diagnostics
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0.152.221
0.72.118
84.88.90
187.188.188
255.135.0
255.49.0
0.229.93
Hospital Benefits with Rapid ID/AST Blood Cultures
# 1 Priority =
Save Lives
• Cost
Avoidance
• Return on
Investment
• Reduced
CMS
Penalties
• Efficient
hospital
processes
Reduced sepsis and severe sepsis cases
Reduced morbidity and mortality
Enhanced patient and family satisfaction
Branding – reputation of the facility – reduced potential for lawsuits
Enhanced bed utilization in ED, ICU, Nursing Units, Diagnostic areas
Reduced MDROs and cross-infection
Reduced C difficile rates
Reduced isolation costs and isolation room utilization
Reduced pharmacy costs
More efficient lab processes and standardization
Reduced hospital supplies (fluids, drugs, less “codes”, reduced blood supplies,
lab supplies, pharmacy supplies, isolation PPE and other supplies)
Reduced CMS penalties (sepsis, readmission with sepsis, C difficile, MDROs, HAIs)
Reduced secondary HAIs from early targeted therapy
More efficient use of staff:
• Microbiologists
• Nurses, Physicians
• Pharmacists
• Infection Preventionists
• Coders, Ancillary staff