Fred C. Tenover, Ph.D., D(ABMM)Vice President, Scientific Affairs

Cepheid, Sunnyvale, CA, USA

Consulting Professor of PathologyStanford University School of Medicine

Adjunct Professor of EpidemiologyRollins School of Public Heath

Emory University

Molecular Diagnostics for Infection Control and

Antimicrobial Stewardship: Controversies and

Conundrums

Disclosures

*My salary and benefits are paid by Cepheid, a

molecular diagnostics company

*Member, IDSA Rapid Diagnostics Working Group

*Member, CDC Culture Independent Diagnostics

Taskforce

Resistance Among Bacterial Pathogens Impacts Many Aspects of

Our Lives

HealthcareMRSA, VRE, ESBLs, Carbapenem-resistant

Klebsiella pneumoniae,

Pseudomonas aeruginosa, Escherichia coli,

and Acinetobacter baumannii

Sexual health

Ceftriaxone-resistant

Neisseria gonorrhoeae

Food

Ceftiofur-resistant Salmonella

Colistin-resistant Escherichia coli

Next Generation Molecular Detection Methods

BDMAXCepheid

GeneXpert

GenMarkDxRoche Cobas 4800

Nanosphere

Verigene

Biofire/bioMérieux

film array

Alere i

Antimicrobial Stewardship Programs

*These programs help: *reduce inappropriate antimicrobial use

*improve the quality of patient care

*reduce treatment failure rates

*reduce selective pressures that promote resistant

organisms

*reduce hospital Clostridium difficile infection rates

*save hospital money

https://www.cms.gov/Newsroom/MediaReleaseDatabase/Fact-sheets/2016-Fact-sheets-items/2016-06-13.html

How do these three things fit together?

Molecular

Diagnostics

Antimicrobial

Resistance

Antimicrobial

Stewardship

Three Critical Issues for Diagnostics

*Multiple rapid technologies available that provide accurate

diagnosis of infectious diseases often in <1 hour, but uptake by

laboratories has been slow, impeding both therapy and infection

control.

*Rapid diagnostics can improve antimicrobial stewardship but

often need an intermediary, such as a PharmD (pharmacist), to

ensure results are used in a timely manner

*Rapid diagnostics for infection control in some cases are deemed

“too sensitive.” When it comes to preventing spread of MDROs or

C. difficile, is there such a thing as too sensitive for infection

control?

Why Use Molecular Methods for Infectious

Disease Diagnosis?

*Conventional detection methods are too slow*Improve diagnosis of tuberculosis (2 hours vs 3-4 weeks)

*Conventional methods lack sensitivity*Replace inaccurate rapid antigen tests for influenza

*Adequate conventional tests did not exist*Detection of Noroviruses

*Improve antimicrobial stewardship*Rapid results can guide use of antibacterials, antifungals, and antivirals

Examples of Molecular Diagnostics for Blood

Cultures: S. aureus, MRSA, CoNSGPC in clusters

MALDI-TOF ID

PCR/Array with nanoprobes:

Nanosphere (3 hours)

Filmarray (BioFire): S. aureus,

mecA resistance genes (1 hour)

PCR testing Xpert MRSA/SA

(~1 hour)

PCR test Culture/AST

(Hours to appropriate Rx)

(Hours on wrong Rx)

Getting patients on the right drug 10 times faster or

off the wrong drugs 4 times faster using PCR

Cercenado E, Marín M, Burillo A, Marín-Rabadán P, Rivera M, Bouza E

JCM, 2012

Results in ~ 1 hour

NOTE : Off-label use

Detection of Staphylococcus aureus in Lower Respiratory Tact Secretions from

Patients with Suspicion of Ventilator-Associated Pneumonia

To be effective, antibiotic stewardship requires coordinated action:

Laboratory, pharmacy, infectious diseases, infection prevention, and nursing

Change in MRSA Prevalence in Europe:

2005-2014

Infection prevention activities work

MRSA infections in ICUs ↓ 62%

Non-ICU MRSA infections ↓ 45%

(After implementing universal

MRSA screening)

1 negative PCR test = 3 negative cultures

Gets MRSA-negative patients out of costly isolation rooms

(CID 2013)

Estimated Effect on Unnecessary Contact Precaution

Days Avoided and Costs Saved

Strategy Passive

cultures

Active surveillance

cultures

PCR screening

(1 Xpert MRSA)

Discontinuation rates of

contact precautions

6.6% 26.2% 63.8%

Fewer contact precaution days 104 418 1841

Cost savings $86,950 $349,472 $1,539,180

Pulia et al

*Use PCR to screen wounds for MRSA and do PCR nasal screen for MRSA

if patient was going to be admitted to the hospital

*Results available prior to ED discharge in 100% of cases. Turnaround

times: nasal 73 min. and wounds 79 min.

*Ideal antibiotic selection rates improved by 45% in the PCR group

* Conclusion: Using a rapid PCR MRSA assay is an opportunity to

improve antibiotic selection for abscesses and improve infection

control by indicating which patients are colonized prior to admission

SUMMARYPre-operative screening using culture-or molecular-based

methods and subsequent decolonization of patients who are

positive for meticillin-susceptible S. aureus and meticillin-

resistant S. aureus (MRSA) reduces SSIs and hospital stay.

Universal decolonization pre-operatively without screening

for S. aureus may compromise the capacity to monitor for the

emergence of new clones of S. aureus, contribute to

mupirocin resistance, and prevent the adjustment of surgical

prophylaxis for MRSA.

“In five of six strains tested, adaptation to chlorhexidine also led

to resistance to the last resort antibiotic colistin”

CONCLUSION: The potential risk of colistin

resistance emerging in K. pneumoniae as a consequence of exposure to chlorhexidine has

important clinical implications in infection prevention procedures.

Will universal decolonization promote resistance to antibiotic of last resort?

Is PCR too sensitive for infection control

when detecting C. difficile, especially in

patients with diarrhea?

CDC Recommendations (National Antibiotic

Resistance Report 2013)

i.e., infection control is important

FOR Clostridium difficile

On-demand

PCR No additional

costs for missed

cases

GDH+PCR

algorithm

more expensive

overall

n=1034 patient episodes

Sens Spec PPV NPV(%) (%) (%) (%)

99.1 98.9 91.9 99.9

51.0 99.4 91.9 94.3

83.8 94.5 64.7 97.9

J Hosp Infect 87:109-14, 2014

Real-time polymerase chain reaction correlates well with clinical diagnosis of Clostridium difficile infection

• “This study addresses an important question for physicians, hospitals, and policy makers: do toxin-negative patients with a positive C difficile PCR test result require treatment?”

• This was not a study to assess the role of isolation in preventing transmission, but this issue cannot be dismissed or ignored

• 1416 hospitalized adults were evaluated, including

‒131 Tox+/PCR+ patients (9.3%)

‒162 Tox−/PCR+ patients (11.4%)

‒1123 Tox−/PCR− patients (79.3%).

20.7% are PCR +

these have similar

outcomes

• Direct cytotoxin testing detected 30% more cases than antigen testing

• 66 of 162 (41%) PCR+/Toxin- patients were treated for CDI

(physicians not aware of PCR+ results, only toxin-negative)

21%

were

positive

Methods: GDH screen suspected CDI patients with diarrhea, confirm with PCR;

if positive test for toxin A/B

*Compared results from 169 CDI cases [≥3 stools, cytotoxin, toxigenic culture (TC) +] 115 cases positive by both assays; 54 positive by TC only (same result as PCR)

*31.9% of true CDI cases would have been missed if only cytotoxin assays had been used for diagnosis

*This included 10% of severe cases and 1 pseudomembranous colitis case

*149 stools positive by Quik-check complete algorithm, Xpert Cdiff on GDH+/toxin- samples

*56 were GDH+/toxin negative/PCR+

*Conclusion: Diarrhea positive only by TC (PCR) should not be ruled out as colonization without further review

*45% of positive cases would have been missed if PCR not used as part of Quik-Check complete algorithm

“The presence of a binary toxin gene was the single virulence factor independently

associated with recurrence (p <0.02).”

“Binary toxin either is a marker for more virulent C. difficile strains or contributes

directly to strain virulence. Efforts to control C. difficile infection should target all

virulent strains irrespective of PCR ribotype.”

Xpert C diff BT identifies strains producing Binary toxin, even in Toxin A-/Toxin B- strains

Study Conclusions: “This study supports the hypothesis

that carriers of C. difficile contribute to transmission within

hospitals. Approximately a quarter of isolates from

Healthcare Associated -CDI cases were highly related to

isolates from asymptomatic patients identified from

screening tests. This finding suggests that screening and

isolating patients with carriage could potentially lead to

further reductions in CDI incidence.”

3 Key Infection Prevention Questions

*Can patients with diarrhea who are infected

with toxigenic Clostridium difficile transmit

infection to other patients?

*YES

*Should they be in contact precautions?

*YES

3 Key Infection Prevention Questions

*Can patients with diarrhea who are colonized

with toxigenic Clostridium difficile transmit

infection to other patients?

*YES

*Should they be in contact precautions?

*YES

3 Key Infection Prevention Questions

*Can asymptomatic patients who are colonizedwith toxigenic Clostridium difficile transmit infection to other patients?

*YES

*Should they be identified and placed in contact precautions?

*According to SHEA guidelines, no. Reason –lack of data to support this. Data are needed.

KPC OXA-48

NDM VIM

Conclusions.” We observed extensive

transfer of KPC-positive patients

throughout the exposure network of

14 acute care hospitals, 2 LTACHs,

and 10 nursing homes. Although few

cases were identified at most

institutions, many facilities were

affected. Successful control of

KPC-producing Enterobacteriaceae

will require a coordinated,

regional effort among acute

and long-term health care facilities

and public health departments. “

Chicago area hospital and long-term care facilities

Even with a coordinated approach,

prevalence of CREs still

continues to rise every year;

CREs will be a challenge for

years to come

CRE: Infection versus Colonization

Lungs

Infection sites:

Virtually any

body site

Colonization

Sites

WoundsSkin

Detected through routine clinical cultures Only detected through surveillance testing

CDC Recommendations When Enterobacteriaceae isolated

Resistant to a

Carbapenem?Yes (CRE) No

Can the lab

Perform carbapenemase

Testing?

No

Yes Not CPE

CPE Detected

Comprehensive interventions:

Contact precautions, screening contacts

Chlorhexidine bathing

Contact precautions

only

Review susceptibility

to other antibioticsTesting for carbapenemase production is critical

Carbapenemase Gene AssaysCheck-Direct CPE

on ABI 7500

Check-Direct CPE

on BD MAX™

eazyplex SuperBug

CompleteXpert® Carba-R

Assay coverageKPC, OXA-48-like,

NDM/VIM

KPC, OXA-48-like, NDM,

VIMKPC, OXA-48, NDM, VIM

KPC, OXA-48, NDM,

VIM, IMP

‘Big 5’ carbapenemases

NOT detectedIMP family IMP family IMP family

Some OXA-48-like;

some IMP subgroups

Hands on time per

sample<5 min <5 min <5 min <5 min

Assay run time ~1.75 h ~2.5 h 20 min ~50 min

Sample throughput Up to 94 tests in a batch Up to 22 tests in a batch 1 or 2 independent tests1 to 80

independent tests

Findlay J, et al. J Antimicrob Chemother. 2015 May;70(5):1338-42

Xpert Carba-R Assay to Detect Carbapenem-

Resistant Bacteria

Assay detects 5 classes of carbapenem

resistance genes (>90) including those

encoding:

– KPC

– NDM

– VIM

– OXA-48

– IMP

• Sample: carbapenem-non-susceptible

isolates; rectal swab (CE-IVD)

Time to result:48 minutes

CE-IVD marked

US-IVD cleared

Xpert Carba-R Spectrum of Detection

KPC

IMP 7

IMP 13

ALL KPCs

1-19

ALL VIMS

1-40

ALL NDMs

1-12

OXA-48

like

IMPs

1-3, 4, 6, 8, 9, 10, 11, 19, 20-22, 24, 25, 27, 28, 30, 31, 33, 37, 40,

42

OXA-163

OXA-181 OXA-204

OXA-232

OXA-245 OXA-247

OXA-162

OXA-244

OXA-370

Limitations

IMP 14

Check Points Microarray Assay for Beta-

lactamase Genes

40

52 beta-lactamase genes

TEM, SHV, ESBLs,

carbapenemases

6 hours, high complexity,

requires purification of

DNA, multiple instruments

Most effective when used with culture and acid fast smears.

From: Boehme, et.al. NEJM 363:1005. Sept. 9, 2010

CONCLUSIONS

*Many patient populations are already benefiting from rapid

molecular test results, especially for sepsis, tuberculosis, and

C. difficile infection

*Rapid results are only effective if they are communicated

rapidly to physicians and infection preventionists.

*When it comes to stopping the spread of “urgent threat” MDROs

in healthcare settings, including C. difficile, there is no such

thing as a test that is “too sensitive”.

THANK YOU

FOR YOUR

ATTENTION