Role of the Laboratory in Antimicrobial Stewardship

Daniel Diekema, MD, D(ABMM)Director, Division of Infectious Diseases

Disclosure: Research funding from bioMérieux

Objectives

• Discuss the major roles of the clinical lab in AS

• Identify promising developments in diagnostic testing, including when and how such testing should be incorporated into AS efforts

• Develop and interpret an antibiogram that is consistent with CLSI recommendations

Where does the lab fit in?

What roles does the microbiology lab have

in promoting optimal antimicrobial therapy?

Laboratory workflow

Opportunities for laboratory support of antibiotic stewardship exist at every stage

Pre-analytic

• Ordering

• Collection

• Transport

Analytic

• Processing

• Testing

Post-analytic

• Reporting

• Intervention

Pre-analytic: Focus on test ordering

• Performance characteristics of a test (positive and negative predictive value) depend upon pre-test likelihood of disease

Lowest Highest

False positive False negative

Best performance

Impact of guideline-based intervention to reduce urine culture ordering

• Pre-post study with control arm (2 VA systems)

• Diagnostic algorithm based upon IDSA guidelines

• Audit and feedback

• Case based presentations

Results:

• Reduced urine cultures

• Decrease in overtreatment of asymptomatic bacteriuria

– 1.6 to 0.6/ 1000 bed daysTrautner, et al. JAMA Intern Med 2015;175:1120-27.

Reducing C. difficile test ordering

Madden GR, et al. Infect Control Hosp Epidemiol 2018 (ePub)

• Computer decision

support tool• Stool frequency

• Repeat testing

• Financial incentive

• 41% reduction in

test ordering

• 31% reduction in

HO-CDI rates

Pre-analytic: Sample collection

Tenets of specimen collection and management

• Collect samples prior to antibiotic tx

• Specimen >>>> swab of a specimen

• Adequate volume

• Transport conditions/time

• Proper sampling site

Baron EJ, Miller JM, et al. Clin Infect Dis 2013;57:485-88.

Diagnostic yield of blood cultures:Neutropenic fever patients

Hummel, et al. Scand J Infect Dis 2009;41:650-55.

%

Improve your blood culture collection!

• Poor site preparation/technique– contaminants, costs, antibiotic use

• Low volume– yield, false negative cultures

• Multiple cultures from a single stick– interpretability of contaminated sample

• Drawing through catheters– contaminants, antibiotic use

Kirn TJ, Weinstein MP. Clin Microbiol Infect 2013;19:513-20.

Analytic: sample is now in the lab….Specimen screening/rejection approaches

• Sputum culture screening criteria– Evaluate # squamous epithelials vs. neutrophils

– Reduces workup of oropharyngeal colonizers

• Urine culture screening criteria– “Reflex” protocols: test only when pyuria present

• C. difficile testing only on liquid stool

Impact of “reflex urine culture”• Quasi-experimental study of

reflex protocol in ICU pts

• Cx only if >10 WBC/hpf

• Results:– Fewer cultures

– Lower bacteriuria rates

– Fewer antibiotic starts for index urine culture

• 23% vs. 41%, p=0.002

Sarg, et al. Infect Cont Hosp Epidemiol 2016;37:448-54.

More analytic interventions

• Change testing algorithms to improve utility

– Include toxin EIA in C. difficile testing algorithm

• May help in distinction between infected/colonized

– Do rapid identification or susceptibility tests when possible (e.g. + blood cultures, respiratory panels)

• MALDI-TOF, PCR/NAAT, rapid phenotypic testing

McDonald, et al. Clin Infect Dis 2018;66:e1-e48

Timbrook, et al. Clin Infect Dis 2017;64:15-23.

Culture based diagnostics and turnaround time

Munson E, Diekema D, et al. J Clin Micro 2003;41:495.

“Release of AST data did not appear to have [an] important impact on

antimicrobial management among patients with bloodstream infection.”

All culture basedNGS/metagenomics

Species identification

In silico antibiogram

Sequence type

Emerging diagnostic technologies:Speed, accuracy, sensitivity

• Mass spectrometry (MALDI-TOF)– Matrix-assisted laser desorption/ionization-TOF

• Magnetic resonance– Applied directly to sample after short amplification step

• Automated microscopy + FISH– Rapid phenotypic testing

• Nucleic acid amplification/detection (NAAT)– PNA-FISH, PCR approaches (microarrays, multiplex)

MALDI-TOF• Matrix assisted laser desorption ionization-time of flight

• Produces detailed fingerprint based upon the mass-to-charge ratio of the proteins (primarily ribosomal)

• Accurate, rapid and inexpensive species ID

MALDI-TOF Update

• Highly successful—low cost, accurate IDs

• Main limitation—requires culture growth

– Modifications allow for more rapid testing from + blood cxs

• Precision has unintended consequences

– Clinicians unfamiliar with nomenclature

– HAI definitions affected as well

• Can improve time to appropriate antibiotic tx

Vlek AL, et al. PLoS One 7:e32589

Lockwood AM, et al. Infect Cont Hosp Epidemiol 37:425-32.

Magnetic resonance diagnostics• Magnetic particles coated with capture probes

• Amplified product in sample causes agglomeration

• Detected with MR signal

Neely, et al. Sci Trans Med 2013;5:1.

T2MR diagnostics

• Advantage: Applied directly to blood sample– Other rapid panels applied to + blood cultures

• Published data available for Candida spp.– Sensitivity ~90%, Specificity 98-99%

– PPV 71-84%, NPV ~99% if prevalence 5-10%

– Time to detection and species ID ~4 hours

• Bacterial panel FDA approved this week

Mylonakis E, et al. Clin Infect Dis 2015;60:892.

Automated digital microscopy and FISH technology: Rapid “phenotypic” testing (ID + AST results)

Pancholi, et al. J Clin Microbiol 2018;56:e01329.

RT-PCR, Multiplex, Microarray:Sample-to-answer technology

• MTB + rifampin R

• C. difficile toxin genes

• Bacterial resistance genes– mecA, vanA, carbapenemases

• Microarray/multiplex panels– Respiratory

– CNS infection

– Gastroenteritis

– Bloodstream infection (+ culture)

Gastroenteritis Meningitis/Encephalitis Respiratory tract Bacteremia

Campylobacter spp. Escherichia coli K1 Adenovirus Enterococcus spp

Clostridium difficile Haemophilus influenzae Coronavirus 229E Listeria monocytogenes

Plesiomonas shigelloides Listeria monocytogenes Coronavirus HKU1 Staphylococcus (aureus)

Salmonella spp. Neisseria meningitidis Coronavirus OC43 Streptococcus (4 species)

Yersinia enterocolitica Streptococcus agalactiae Coronavirus NL63 Acinetobacter spp

Vibrio spp. Streptococcus pneumoniae Human metapneumovirus Haemophilus influenzae

Vibrio cholerae Cytomegalovirus Rhinovirus/Enterovirus Neisseria meningitidis

Enteroaggregative E. coli Enterovirus Influenza A Pseudomonas aeruginosa

Enteropathogenic E. coli Herpes simplex virus 1 Influenza A/H1 Enterobacteriaceae

Enterotoxigenic E. coli Herpes simplex virus 2 Influenza A/H1-2009 Enterobacter cloacae

Shiga-like toxin producing Human herpes virus 6 Influenza A/H3 Escherichia coli

Shigella/enteroinvasive EC Human parechovirus Influenza B Klebsiella (oxytoca/pneu)

Adenovirus F 40/41 Varicella zoster virus Parainfluenza 1 Proteus spp.

Astrovirus Cryptococcus neoformans Parainfluenza 2 Serratia marscescens

Norovirus GI/GII Cryptococcus gattii Parainfluenza 3 Candida albicans

Rotavirus A Parainfluenza 4 Candida glabrata

Sapovirus (I-IV) Respiratory syncytial virus Candida krusei

Cryptosporidium, Giardia lamblia Bordatella pertussis Candida parapsilosis

Cyclospora Chlamydophila pneumoniae Candida tropicalis

Entameoba histolytica Mycoplasma pneumoniae mecA vanA KPC

Does rapid testing improve outcomes? Meta-analysis for bacteremia

• Included 31 studies, 5,920 patients

• Defined rapid as: commercially available molecular test with results in <=24 hours

• 20 NAAT, 6 PNA-FISH, 4 MALDI-TOF, 1 combo

• Main outcome: all-cause 30 day mortality

• Most (84%) pre-post, quasi-experimental

• 20 of 31 had ASP facilitating the interventionsTimbrook et al. Clin Infect Dis 2017;64:15-23.

WITH ASP

OR = 0.64

WITHOUT ASP

OR = 0.72

OVERALL

Timbrook, et al.

CID 2017

Rapid testing improves outcomes• Overall OR for 30 day mortality 0.66 (0.54-0.8)

– Statistical significance only with active ASP

– Number needed to treat = 20

• Reduction in time to effective therapy ~ 5 hrs

• Limitations: study designs (most pre-post), hard to know how much of difference due to rapidity of test versus ASP involvement

Timbrook et al. Clin Infect Dis 2017;64:15-23.

When does lab detection = infection?

• C. difficile in the GI tract, bacteria in urine

• Magnified by advances in lab testing

– Increasingly sensitive tests detect gene targets

– Multiple targets in a single test

– Metagenomics: all genetic material in a sample

• Importance of clinical validity & assessment

Limitation of new diagnostic technology

• Most are moderate-to-high complexity tests

• Significant equipment and consumable costs

• Often located in central laboratory

– Increasing # of hospital mergers or acquisitions

– Consolidation of laboratory services is common

– Delivery models and care settings are changing

Sautter and Thomson. J Clin Microbiol 2015;53:1467.

Kozel, et al. JCM 2017;55:2313.

Limitations of LFIA format

• Sensitivity often lower than molecular testing

– Highly dependent upon analyte concentration

– e.g. influenza rapid POC tests 50-70% sensitive• https://www.cdc.gov/flu/professionals/diagnosis/clinician_guidance_ridt.htm

• Limited ability to assess for multiple targets

– Multiplex PCR (“syndromic” testing)

CLIA-waived molecular POC platforms

Influenza A/B, RSV, RV panel, Group A Strep

15-30 minute TAT, on-demand formats

Still require desktop instrument and consumables

Where is POC testing headed?

• Microfluidics– Multiplexing, “lab on the chip”

• Smartphone applications– Test reading and interpretation

– Data sharing and surveillance

• Biomarker detection– CRP, procalcitonin

– Gene expression signatures

Challenges to biomarker development:

1. Distinguish bacterial, viral, other

2. Agree on standard criteria for testing

3. Validate in various clinical settings

4. Develop into affordable POC tests

PLoS One 2016;11(8):e0160278.

Procalcitonin (PCT)• Randomized controlled trials support use of

serial PCT to discontinue antibiotic tx in ICU– 2-4 more antibiotic-free days, no impact on mortality

• Meta-analysis of ICU pts with sepsis/shock:– 7 studies, 1075 patients

– No difference in 28 day mortality

– Median 2 day reduction in antibiotic days

1. Nobre, et al. Crit Care Med 2008;498-505. 2. Hochreiter, et al. Crit Care 2009;13:R83-89. 3.

Bouadma L, et al. Lancet 2010;375:463-74. 5. Prkno, et al. Crit Care 2013;17:R291-301. 6.

Schuetz P, et al. Cochrane Database Syst Rev 2012.

Hot off the presses….14 hospital RCT

• PCT guided vs. usual

• 1656 patients

• ED with ? LRTI

• 4.2 vs 4.3 abx days

• High level of guideline adherence

• Caveats…..

Huang, et al. N Engl J Med 2018;May 20.

• RCT in children 2-59 mo with acute fever

• Smartphone based algorithm

• Clinical information, POC test results

• Compared to existing reference algorithm

• Fewer clinical failures and AEs

• 2.3% (37/1586) vs. 4.1% (65/1583)

• Reduced antibiotic prescribing

• 11.5% vs. 29.7%

PLoS Med 14 (10):e1002411.

Future directions for stewardship:Host gene expression as diagnostic tool

Holcomb, et al. J Clin Microbiol 2017;55:360-68.

Post-analytic interventions• Modify reporting to improve practice

– Combine with active antimicrobial stewardship team

– Selective reporting or cascading of results

• To guide to optimal or preferred therapy

– Clear explanations to reduce inappropriate therapy

• ? skin contaminants, C. difficile carrier, bacteriuria

– Cumulative reports (antibiograms)

Impact of requiring providers to call to request results for non-catheterized patients

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Leis, et al. Infect Cont Hosp Epidemiol 2014;58:980-83.

Daley, et al. Infect Cont Hosp Epidemiol 2018; ePub ahead of print

“This POSITIVE urine culture may represent asymptomatic

bacteriuria or urinary tract infection. If urinary tract infection

is suspected clinically, please call the microbiology

laboratory….for identification and susceptibility results.”

Appropriate therapy 80% in treatment arm vs. 53% in control arm

Selective reporting (“cascading”) of susceptibility test results• Rather than reporting all tested agents, report only a

limited number, algorithm driven:

• Helps to direct prescribers to antibiotic choices preferred in local/national guidelines

• Has been demonstrated to change prescribing behavior (mostly for urinary tract infections)

Tan TY, et al. J Antimicrob Chemother 2003;51:379-84.

McNulty CA, et al. J Antimicrob Chemother 2011;66:1396-1404.

Selective reporting and treatment guidelines:A prospective randomized case-vignette study

Coupat C, et al. Eur J Clin Microbiol Infect Dis 2013;32:627-36.

How to cascade results?• CLSI “Tables 1A” provide a crude framework

– Group A: routine testing and reporting

– Group B: routine testing, selective reporting

– Group C: supplemental testing and reporting

• Local resistance and use issues, treatment guidelines should drive decision making– Collaborative process involving pharmacy, laboratory, infection

prevention, stewardship, and clinical leaders

Clinical and Laboratory Standards Institute. M100-S25. 2015.

CLSI guidelines for antibiograms

• Analyze and present data at least annually

• Include only species with at least 30 isolates

• Include diagnostic, not surveillance, isolates

• Only include drugs routinely tested

• First isolate per patient per period

• Various organism specific and reporting guidance

CLSI. Analysis and presentation of cumulative antimicrobial susceptibility test data. 3rd ed. Wayne, PA: CLSI;2014. Approved guideline M39-A4.

Boehme, et al. Public Health Reports 2010;125(S2):63-72.

Age stratification: Mayo Clinic%

Susceptible

Swami and Banerjee. SpringerPlus 2013;2:63.

Accessibility of antibiogram and local treatment guidance

http://www.microguide.eu/

Summary: Lab support for AS• The lab must be integrated into any ASP:

– Optimal sample ordering, collection and transport

– Specimen rejection, rapid testing, biomarkers (link to AS)

– Antibiotic susceptibility reporting (including antibiograms)

– Bring lab support closer to the point of care

• Novel and future diagnostic approaches may challenge ASPs with “too much information”

• COMMUNICATION and COLLABORATION

Questions?

How much HO-CDI is really HO-CDI?

• Analyzed 490 HO-CDI cases

– NHSN “LabID event” defn

• Excluded if:

– No significant diarrhea

– Laxatives < 48 h prior

– Testing delayed

• 206 (42%) excludedRock C, et al. Am J Infect Cont 2018;Jan 2.

NS diarrhea

Laxatives

Delay

• CRISPR technology to

detect microbial target

• Cas13 activated, then

cleaves tagged RNAs

• Use LFIA to detect

• Can be multiplexed

• Potential for affordable,

robust POC assay

Gootenberg, et al. Science Feb 18, 2018. Caliendo and Hodinka, NEJM 2017;377:1685.

The law of unintended consequences: Malaria RDTs and antibiotic stewardship

Hopkins, et al. BMJ 2017;356:j1054.

Antibiotics prescribed to 69% with negative RDT

(versus 40% with a positive RDT)