tricore reference laboratories tricore clinical microbiology … · shiga-toxin producing e. coli...

11/12/2016

1

Karissa Culbreath, PhD D(ABMM)Scientific Director – Infectious Disease, TriCore Reference Laboratories

Assistant Professor – Department of Pathology, University of New Mexico

Impact of Culture-Independent Diagnostics in the Clinical Laboratory

and Public Health

Objectives

• Describe the implementation of culture-independent diagnostics into the microbiology lab.

• Discuss the impact of CIDTs on the workflow in the clinical lab and on patient care.

• Evaluate the challenges to public health raised by the loss of culture isolates

• Hospital Laboratory for 2 major health systems in New Mexico– Presbyterian Health System

• 8 Hospitals

– University of New Mexico Health System

• 2 Hospitals (Level 1 Trauma Center, Cancer Center)

• Commercial Physician and Hospital Clients throughout the state– Samples are delivered by courier

24/7

• Infectious Disease Laboratory Test Volume– 775,000 Infectious Disease tests

per year

TriCore Reference Laboratories

• Infectious Disease Laboratory Test Volume– 775,000 Infectious Disease

tests per year

• Esoteric and routine testing

• 15,000 Urine cultures/month

• Use of portable incubation system for transport of specimens from distance rural facilities

TriCore Clinical Microbiology Laboratory

From There to Here

“An individual who gets used to hard work can thereafter never live without it. Work is the foundation of everything in this world.” ~Louis Pasteur

From There to Here

“An individual who gets used to hard work can thereafter never live without it. Work is the foundation of everything in this world.” ~Louis Pasteur

NAAT NAATA Microbiologist

~ 2016 Microbiologist

11/12/2016

2

Diagnostic Tools for Pathogens

Serology Antigen Detection

Culture MolecularDetection

How does it work?

Detection of antibodiesDeveloped against pathogen

Detection of antigens produced by the pathogen

Isolation of pathogen through growth

Nucleic acidamplification detection of specific genetic target

Advantages Can detect acute and past infection

Rapid, remains positive after treatment

Inexpensive High sensitivity,Usually rapid

Disadvantages Delay due to time to develop antibodies

Lower sensitivity

Time consuming

Expensive,Must know the target of interest

When to use Withpathogens unable or difficult to culture

Specific diseasescenarios

Emergence of new pathogens, susceptibility testing, strain typing

When rapid/accurate diagnosis is necessary

You decide… PCR vs. Culture

• Patient with liver abscess secondary to cirrhosis

• Patient with 3-week history of cough consistent with pertussis

• Patient with diarrhea following chemotherapy

• Identification of patients colonized with MRSA for infection control

• Patient presents to the emergency room with symptoms suspicious for bacterial meningitis

The CIDT Balancing Act

Positive

Negative

Traditional Diagnostics

Organism identification

Susceptibility testing

Strain typing, serotyping

Culture-Independent Diagnostics

Organism identification

Susceptibility testing

Strain typing, serotyping

Antigen-Based Testing

• Urinary Antigen Tests

– Streptococcus pneumoniae

– Legionella pneumophila

• Direct Fluorescent Antigen Testing

– Respiratory viruses

Molecular Testing

• Single or Small Multiplex

– Flu A/B, RSV

• Large Multiplex Tests

Respiratory Pathogen CIDT

11/12/2016

3

Fluorescent Respiratory Viral Panel Results

C D

InfluenzaAdenovirus RSV

Parainfluenza

BA

Seasonality of Respiratory Viruses

http://www.tricore.org/infectious_disease_report

• FilmArray Meningitis/Encephalitis panel

– 84.4% Positive Agreement

– 99.9% negative agreement

• Studies include few prospective cases of bacterial or viral meningitis

• False positive/unconfirmed results

Meningitis/Encephalitis CIDTs

• Implementation of antigen-based CIDT improved detection of pathogens

• Shiga-toxin EIA

• Campylobacter EIA

• Rotavirus EIA

• Giardia-Cryptosporidium EIA, FA

Gastrointestinal Antigen-Based CIDTs

Shiga-Toxin Producing E. coli

October 2009 CDC Recommendation for implementation of EIA for detection of STEC

National Enteric Disease Surveillance: Shiga toxin-producing Escherichia coli (STEC) Annual Report, 2013

Gastrointestinal Molecular (Multiplex) CIDTs

xTAG GPP (Luminex)

FilmArray GI Panel (BioFire)

Verigene EP (Nanosphere)

BD MAX EBP (BD)

NAAT

11/12/2016

4

BD MAX EBP Discrepant Results

What could we miss?

N % of total Species

145 87.6 C. jejuni8 5.5 C. coli7 4.8 C. upsaliensis1 0.7 C. lari1 0.7 “Novel” Campylobacter species per CDC

1 0.7 pending ID

July 2015 – July 2016 Campylobacter isolates sent to State Laboratory for characterization

FilmArray GI xTAG GPP Verigene EP BD Max EBPC. jejuni X X X XC. coli X X X XC. upsaliensis X

C. lari X X


Positive

• Increased detection of targeted common pathogens

• Previously undetected pathogens (eg Sapovirus)• Rapid detection of pathogens

Negative

• Decreased detection of emerging pathogens (egNovel Campylobacter sp)

Mission Minded

Clinical Laboratory

• Address the needs of the specific patient

Public Health

• Health of populations

?

Competing or Collaborating Mission?

• Clinical Microbiology Laboratory

– Identification of bacterial, viral, fungal and parasitic agents that cause human disease

– Providing diagnostic and therapeutic support for the clinical management of patients

– Preventing the transmission of infectious diseases in both the health care system and the community

11/12/2016

5

Competing or Collaborating Mission?

• Public Health Surveillance– Individual case investigation for localized disease

control activities– Assessment of disease burden and trends to prioritize

and assess impact of population-based control measures

– Outbreak detection to protect the population and identify gaps in control measures

– Microbiologic characterization of reported infection to improve understanding of pathogens their virulence mechanisms and their epidemiology

Clinical Perspective

• Rapid diagnostics

• Potential for lower cost

• Potential for easier specimen collection

Public Health Perspective

• Rapid detection of cases

• Potential increased testing leading to increased case ascertainment

Culture-Independent Diagnostics Advantages

Detection of wider range of pathogensBetter sensitivity for some pathogens

Clinical Perspective

• False-positive results impacting clinical judgement

• Loss of susceptibility testing

Public Health Perspective

• Loss of subtyping for outbreak detection

• Loss of ability to detect trends in subtypes

• Increased false positive results leading to unnecessary investigation

Culture-Independent Diagnostics Challenges

No more isolates

Where do the isolates go?

FoodNet

• Collaborative program among state health departments, the CDC, USDA, FDA

• Collects data intended to provide insight into characteristics of outbreak investigations

Emerging Infections Program

• Conducts population- and laboratory-based surveillance for foodborne, health care-associated, respiratory and invasive bacterial pathogens of public health importance

• Data are used for national projections of disease incidence and formulation of national public health policy for prevention and control of disease


• Isolate collection– Serotyping and serogrouping data for evaluation

of vaccines

– Measure the effectiveness of prevention programs

– Identify outbreaks

– Detect emergence of new strains affecting• Vaccine efficacy

• Resistance

• Virulence factors


Active Bacterial Core

surveillance

S.PneumoniaeH.influenzae

N. meningitidisGroup A Strep Group B Strep

MRSA PertusssisLegionella

FoodNet

Campylobacter Salmonella

ShigellaVibrio

YerseniaCryptosporidium

Cyclospora

Shiga-toxin producing E. coli

Health care–associated infections

Gram-negative bacilli

Candida spp.

C. difficile

Influenza associated

hospitalizations

Influenza virus

11/12/2016

6



surveillance




FoodNet


ShigellaVibrio


Cyclospora




Candida spp.

C. difficile


hospitalizations

Influenza virus

Case definition key: Pathogen Isolation Only, Isolation or CIDT, CIDT only



surveillance




FoodNet


ShigellaVibrio


Cyclospora




Candida spp.

C. difficile


hospitalizations

Influenza virus

Case definition key: Pathogen Isolation Only, Isolation or CIDT, CIDT only

• ≥ 1,000 foodborne disease outbreaks are reported to the CDC each year– ≥ 20,000 illnesses

• Foodborne disease outbreak definition

– ≥ 2 cases of a similar illness resulting from the ingestion

of a common food

– Etiologic agent is reported in ~60% of outbreaks

FoodNet

Rendi Murphree et al. Clin Infect Dis. 2012;54:S498-S503

FoodNet Surveillance

Shiferaw B, et al Clin Infect Dis. 2012; 54:S458-S463


Positive

• Detection of targeted common pathogens

• Previously undetected pathogens (egSapovirus)

• Rapid detection of pathogens

Negative

• Decreased detection of emerging pathogens (eg Novel Campylobacter sp)

• Decreased availability of isolates for surveillance

11/12/2016

7

Performance of Culture-Independent Diagnostics

Value of the Test Characteristic

Speed Cost Ease of Use

Clinical Lab ++++ ++ ++++

Public Health ++ +++ ++

Sensitivity and Specificity must be placed in the context of prevalence to understand what we are really asking:

Positive Predictive Value and Negative Predictive Value


• Positive Predictive Value - probability that it is a true positive

• Negative Predictive Value - probability that it is a true negative


Test XX - 95% Sensitivity 97% Specificity

Organism Approximate Prevalence in Diarrheal Stool

Campylobacter 5%

Salmonella 1%

Cholera 0.00001%


PPV False Positive/100

NPV False Negative/100

3% Prevalence 49% 50 99.8% <1

1% Prevalence 24% 75 99.9 <<1

Test XX - 95% Sensitivity 97% Specificity

Organism Approximate Prevalence in Diarrheal Stool

Campylobacter 5%

Salmonella 1%

Cholera 0.00001%

False Positive Results

• Respiratory virus shedding from operator

• Testing performed my non-molecular staff

– Failure to decontaminate work surfaces

– Carry-over from control material

• Detection of dead organism

False Negative Results

• Mutation in target regions

• Specimen adequacy

• Target not included in the panel

Additional Performance Concerns

11/12/2016

8

Clinical Laboratory

• Patients may receive unnecessary therapy

• Clinicians may stop looking for other cause of disease

• Clinicians incorporate the result into clinical presentation, risk factors, etc.

Public Health

• Unnecessary outbreak investigation

• Unnecessary exclusion from work, childcare, food-service

Impact of False Positive Result The CIDT Balancing Act

Positive

• Detection of targeted common pathogens

• Previously undetected pathogens (eg Sapovirus)

• Rapid detection of pathogens

• Rapid detection of true outbreaks

Negatitive

• Decrease detection of emerging pathogens (eg Novel Campylobacter sp)

• Availability of isolates for surveillance• Investigation of pseudooutbreaks

Culture-Independent Diagnostic Tests:

What Can We Do Together?

What does the Clinical Laboratory Do?

• Communicate with public health departments and laboratories changes to your diagnostic protocols

• Develop a protocol to ensure that an isolate is generated for further characterization

• Ensure that the health of the community is maintained through changing diagnostic times

What Does Public Health/Surveillance Do?

• Conduct periodic surveys to monitor changing test practices

• Evaluate criteria for case definitions

• Work with laboratory to generate isolates for further characterization

• Continue to develop surveillance strategies for molecular characterization on direct patient specimens

Our Strategy for Isolate Submission

11/12/2016

9

Population Health Infrastructure

Utilization Measures

PublishedRisk

Factors

National TreatmentGuidelines

PathologySupport

PQRSTriCoreTesting

HEDIS

LISLISs

Billing System

Central Normalized Repositories

Bills

Orders

Albuquerque Metro Area (FLURSV)Zip Positive Tests Rate

87102 26 210 12%

87104 5 64 8%

87105 79 558 14%

87106 17 172 10%

87107 33 250 13%

87108 53 390 14%

87109 34 254 13%

87110 34 230 13%

87111 34 280 12%

87112 43 293 15%

87113 9 82 11%

87114 37 269 12%

87120 41 334 12%

87121 87 713 12%

87122 9 68 13%

87123 49 338 14%

87068 9 30 30%

Suspected

Confirmed

Mission Minded

Clinical Laboratory

• Address the needs of the specific patient

Public Health

• Health of populations

?

tricore reference laboratories tricore clinical microbiology … · shiga-toxin producing e. coli...

Documents