new opportunities for microbiology labs to add value to … · 2017-04-28 · threats in the us....

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Patrick R. Murray, PhD Senior Director, WW Scientific Affairs

New Opportunities for Microbiology Labs to Add Value to Antimicrobial Stewardship Programs

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Microbiologists and physicians were asked in a recent survey to name the most significant changes in microbiology in the last 10 years. The most common answers were:

– Evolution and global spread of multidrug-resistant bacteria, mycobacteria, and fungi

– Rapid adoption of molecular tests in infectious disease diagnostics – Use of MALDI mass spectrometry for identification of bacteria,

mycobacteria, yeasts, and molds – Introduction of whole lab automation in clinical microbiology – Rapid development of the field of the human microbiome

For the purposes of this discussion, we will not address the topic of the human microbiome although it is likely to impact future diagnostics and therapeutics.

Introduction

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Deaths attributable to AMR every year Compared to other major causes of death

“Global deaths due to AMR are projected to rise from 700,000 to 10,000,000 per year by 2050 if immediate action is not taken”

“Deaths due to AMR will be disproportionately weighted towards Developing countries due to healthcare infrastructure and resource availability”

Antimicrobial Resistance (AMR)

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In 2013, the CDC published a list of 18 drug-resistant threats in the US. • Urgent threat –

– Carbapenem-resistant Enterobacteriaceae (CRE)

• Serious threat – – Multidrug-resistant Acinetobacter baumannii (MDR) – Multidrug-resistant Pseudomonas aeruginosa (MDR) – ESBL-producing Enterobacteriaceae (ESBL) – Methicillin-resistant Staphylococcus aureus (MRSA) – Vancomycin-resistant Enterococcus (VRE)

In February 2017 WHO announced a list of 12 antibiotic-resistant “priority pathogens”: • Critical threats –

– Acinetobacter baumannii: carbapenem-resistant (CRAB) – Pseudomonas aeruginosa: carbapenem-resistant – Enterobacteriaceae: carbapenem-resistant, ESBL

Antimicrobial Resistance

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Antibiotic Resistance

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Global Prevalence ESBL CTX-M Strains

Resistant to all penicillins and cephalosporins

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Carbapenem Resistance NDM KPC

VIM OXA

Resistant to all beta-lactam antibiotics (penicillins, cephalosporins, carbapenems)

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Dates of Antibiotic Discovery: 30 Years with No New Classes of Antibacterials

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Future of Diagnostic Microbiology

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MALDI-TOF Mass Spectrometry Vitek MS BD Bruker Biotyper

0

1000

2000

3000

4000

5000

4000 4500 5000 5500 6000 6500 7000 7500 8000 m/z

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• MALDI is less expensive - replaces all identification tests with decreased consumable supplies, QC tests, repeat testing and supplemental tests

• MALDI is more accurate - analytical sensitivity equivalent to sequencing 100s of genes so accuracy nearly 100%

• MALDI improves workflow - anaerobes identified as easily as aerobic bacteria with no special procedures such as subcultures, spot biochemical tests, chromatography

• MALDI is rapid - definitive identification of yeasts, molds and mycobacteria the same day growth is detected

• MALDI offers clinical value - blood culture isolates identified within 1 hour of detection

MALDI: Workflow Impact

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Molecular Carbapenemase Assays for Screening for Carriers

Check-Direct CPE assay for BD MAX: • KPC – 17 variants • NDM – 10 variants • VIM – 37 variants • OXA – 9 variants

Cepheid Carba-R for GeneXpert: (number of variants detected not specified) • KPC • NDM • VIM • OXA • IMP

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Molecular Identification/ Resistance Markers

Assay Number of Analytes

ID AST

>90 mecA, vanA, vanB

24 mecA, vanA/B, KPC

22 mecA, vanA, vanB, IMP, KPC, NDM, OXA, VIM

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Genotypic Tests Phenotypic Tests

Molecular Diagnostics (Rule Out)

HOSPITAL FORMULARY

Antibiotic 1

Antibiotic 2

Antibiotic 3

Antibiotic 4

Antibiotic 5

Antibiotic 6

Antibiotic 7

Phenotypic Susceptibility

Tests (Rule In)

Genotypic Tests – Predicts what Antibiotics Can’t Be Used (Resistance)

Phenotypic Tests – Predicts which Antibiotics Can Be Used (Susceptibility)

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Phenotypic Antimicrobial Susceptibility Tests

BD Phoenix bMX Vitek 2 Beckman Coulter MicroScan

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Total Lab Automation

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• Why would you want to automate historical inefficiencies?

• Think of lab automation as not automating what we do today but allowing us to do things we cannot do today!!

• Lab automation requires a cultural change for the benefits to be realized.

The Future is Defined by Innovative Thinking

Think Differently!

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Optimized Image Acquisition Poor SNR

Optimized SNR

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A change is needed if microbiology is going to be clinically relevant for patient care: we need to be patient focused!!

Microbiology Laboratory

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Thank you!

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