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/

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

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)

Typical High Tech Lab Today

The Molecular Lab – Labs of the Future

Blood Cultures Procedures and Contamination Rates

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.

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

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

Blood Culture Systems

bioMerieux BacT/Alert BD BACTEC Thermo VersaTREK

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

Blood Culture Organism Identification

Challenges with Traditional Methods

Slow Specimen / quality dependent Inexpensive $ (for lab not hospital) May have inferior performance

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

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

Blood Culture Based Diagnostic Technologies

• Molecular

• MALDI-TOF Mass Spectrometry

• Traditional ID/AST

• Emerging Rapid AST

Cepheid GeneXpert

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

Cepheid GeneXpert

Workflow

Test

Differentiation

17 min 1 hour

GeneXpert I, IV, XVI Infinity

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

BIOFIRE TORCH (BIOMERIEUX)

12

Results in 90 min

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

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)

LUMINEX Verigene - Nanosphere

Results in 2.5 hrs

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

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)

T2 Biosystems – for Yeast

T2 Biosystems

Workflow

Technology

Menu

Blood Culture Assay

(1) Build Cassette (2) Remove cap on blood (3) Invert into Cassette

Load onto T2Dx

T2 Biosystems

Workflow

Technology

Menu

Blood Culture

Assay

T2 Biosystems

Workflow

Technology

Menu

Blood Culture Assay

T2Candida • Candida albicans / tropicalis • Candida parapsilosis • Candida krusei / glabrata

$200-250 / test

Maldi-tof

Vitek MS

Biotyper

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

33

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

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

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

http://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+htmlhttp://jcm.asm.org/content/48/2/444.full.pdf+html

Antimicrobial Sensitivity Tests (AST)

Automated ID/AST - Standard of Care

• bioMérieux Vitek

• Beckman Coulter Microscan

• Becton Dickinson Phoenix

Vitek 2 MicroScan

Phoenix

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

Accelerate Diagnostics Pheno Blood Culture System

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

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

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

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

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

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

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

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