1

Practical application of laboratory results in infection prevention and

healthcare epidemiology

Richard A. Van Enk, Ph.D., CICDirector, Infection Prevention and Epidemiology,

Bronson Methodist Hospitalvanenkr@bronsonhg.org

2

ObjectivesYou will be able to:

• Describe the roles of microorganisms in health and disease

• Give examples of and distinguish between the main types of infectious disease laboratory tests

• Analyze and apply the results of typical infectious disease laboratory tests to infection prevention and hospital epidemiology

3

Introduction

• Your relationship with your hospital’s laboratory is probably the most important relationship in your daily work

• Almost all the surveillance and outbreak investigation data you need come from the laboratory

• Your microbiologist is your most important friend• The more you know about microbiology, the

more effective you will be in infection prevention

4

The laboratory/infection prevention relationship

• How can you work with the laboratory productively?– Take a microbiology class– Do a rotation in the microbiology laboratory and vice

versa– Hire a Medical Technologist microbiologist as an infection

preventionist– Visit your laboratory every day, or at least regularly– If you don’t know or understand something, ask them;

they will be happy to talk about what they do• Your laboratory friends will gain as much from this

relationship as you will

5

Microorganisms in health and disease

• Many people (including doctors and nurses) think that all microorganisms are bad

• Nothing is farther from the truth; bacteria are our friends, they are essential to our health, and we need to own, love, and protect them

• Our bodies are filled and covered with bacteria that protect us from infection; we are colonized with normal flora bacteria

• The bacteria that live in and on us are called our microbiome, and we are learning a lot about it from the Human Microbiome Project

6

Why study the human microbiome?

• The human body consists of 90% bacteria (1014 versus 1013 human cells)– 1-3% of our mass, but 360 times

more DNA than human– 10,000 unique species, most

have never been cultured

• Our microbiome has evolved with us, is in constant interaction with us and contributes to health and disease

• Understanding our microbiome will open up a new world of medicine

7

What do we know about the human microbiome?

• It is like another organ• We have core and transient

flora• Can change over time• Differences within the

population• Similarities with race and

family• There is a relationship to

health and disease• Microbiome is unstable up to

age 2-3, then stabilizes• Protects us from infection

8

What about infectious diseases?

• Normally we live in a symbiotic relationship with the microorganisms in, on and around (colonizing) us

• An infection is an ecological accident; the microorganisms damage us– A normal flora organism in the wrong place– An exogenous organism that our microbiome could not

keep out• Most cultures grow normal flora– Respiratory, urine, stool, wounds– No normal flora; blood, spinal and synovial fluid

9

What about infectious diseases?• It is very important as an infection preventionist to be

able to distinguish between normal bacteria that should be in the specimen and pathogens that are causing damage– Strict pathogens almost always cause infections in any

patient– Opportunistic pathogens are normal flora that cause

infections only sometimes when they have an advantage• You need to know what should be in each specimen so

you can tell what shouldn’t be there; an infection– Often the laboratory report will help– Good laboratories do not do identification and susceptibility

tests on non-pathogens

10

What about infectious diseases?

• The difference between infection and colonization in the patient is that typically infection causes inflammation– Heat, swelling, redness, pain– Typically white blood cells

get involved and increase at the site of the infection; leukocytosis or presence in lung or urine

– Typically the patient has a fever

11

The clinical laboratory

• Laboratories are organized into departments– The big five: chemistry, hematology, blood bank,

microbiology, anatomic pathology– As the laboratory gets bigger, these are subdivided

• No laboratory does all possible tests; some are sent to reference laboratories

• Laboratory testing is done by Medical Technologists and headed by pathologists as medical directors

• Laboratorians are experts in their area; use them

12

Non-microbiology infectious disease tests

• Tests and departments outside of microbiology that can give clues to infectious diseases– Histology/cytology– Serology– Body fluids– Urinalysis– C-reactive protein, procalcitonin, sedimentation rate– Complete blood count (the WBC numbers)– Fecal leukocytes (stool lactoferrin test)

• None of these are diagnostic, but some are good clues that something infectious might be going on

13

The microbiology laboratory

• The job of the microbiology laboratory is to perform testing to diagnose and treat infectious diseases

• There are several kinds of tests included in infectious diseases; cultures, antigen tests, serology, molecular

• Microbiology is different from other laboratory testing because it is largely (but getting less) manual, requires more technical skill by the people doing the testing, takes longer, and results are more subjective

• More than any other department, the quality of the microbiology culture result depends on the quality of the specimen you send

14

Types of laboratory tests for infectious disease

• Direct microscopic examination of the specimen with differential stains– Gram, Acid-fast, fluorescent– Gram stain is finished in less

than one hour (same day result)

– Automatically included in some cultures, not others

– Almost diagnostic in some situations

15

Types of laboratory tests for infectious disease

• Traditional culture for bacteria and fungi– Specimen is streaked on media,

incubated for 16-24 hours (next day result), pathogens are quantitated and selected, identified, tested for antibiotic susceptibility

– A semi-quantitative result (rare, few, moderate, many)

– The predominant pathogen is presumed to cause the infection

– Typically limited to 3 pathogens

16

Types of laboratory tests for infectious disease; quantitative cultures

• Urine cultures– All urine contains some normal

bacteria– Urine cultures are quantitative;

>10,000 pathogens per ml defines a UTI

• Bronchoalveolar lavage cultures– Included in the NHSN definition

• Wound cultures– Done for burns to assess for

skin transplant

17

Types of laboratory tests for infectious disease

• Antibiotic susceptibility testing– Test the pathogens against a

panel of antibiotics relevant to that organism and infection (not all antibiotics)

– Heavily regulated by CLSI– Takes 4-24 hours– Can be automated or manual– Relevant results are

susceptible, intermediate and resistant

18

Types of laboratory tests for infectious disease

• Rapid antigen tests– Group A streptococcus test

for pharyngitis is the most popular; others

– Often done at the point of care, sometimes in the laboratory

– Very fast; 15 minutes– Somewhat specific but

generally not sensitive (misses a lot of cases)

– Being replaced by molecular tests

19

Types of laboratory tests for infectious disease

• Serology testing for infectious disease– Patients make antibody

after they have an infection• IgM first, IgG later

– You can see if a patient has ever had an infection with a single IgG serology (an immune status test)

– You can see if a patient currently has an infection by looking for IgM or rising IgG

20

Types of laboratory tests for infectious disease

• Molecular tests– New tests look directly for

pathogen-specific sequences of nucleic acid

– Typically use the PCR method– Replacing many traditional

tests– Good: fast and accurate– Bad: expensive, finds only the

target, can’t tell dead pathogens from alive, no susceptibility test, few are FDA-approved

21

The life of a culture (from the patient to the incinerator)

• Day 1– 10:00; specimen (sputum) collected from the patient– 10:30; specimen arrives in laboratory, is accessioned– 11:00; specimen is plated, plates incubated, Gram

smear prepared– 11:30; Gram stain is read and reported

• Day 2– 9:00; plates are read, semi-quantitative results reported,

rapid identification tests completed, complete identification and susceptibility tests set up

– 20:00; all final results completed and reported

22

Laboratory results for routine surveillance

• The beginning of all infection surveillance is the positive culture report from the laboratory– IPs often program a report to

print all final culture results – Remember that results are being

generated all day

• Some results require immediate action by the IP and require a phone call or page– Tell the laboratory what you need

23

Laboratory results for special action

• Special precautions– Droplet and airborne special

precautions are started based on the patient’s clinical presentation

– Often contact precautions are based on a culture that grows a Multi-Drug Resistant Organism (MDRO)

• Reportable diseases– Most reportable diseases in

Michigan require a definitive laboratory test

24

Laboratory results for routine surveillance

• You will often be expected to know how to collect and transport specimens, how to interpret results, and which results require special precautions

• You will be expected to know your antibiotics, what they are used for, the types of antibiotic resistance, and how to interpret susceptibility results

• You may be asked to help pharmacy with antibiotic stewardship

• You may be asked to be the liaison between the laboratory and nursing/physicians; embrace that role

25

Special laboratory testing for epidemiology

• Normal microorganism identification gives you a genus and species (or just one name for viruses)

• Microorganisms with the same name can be quite different; different strains within the species

• For outbreak investigation; to see if two infections were related to each other, you want to see if organisms with the same name are really the same, sometimes called “ fingerprinting”

• You can do this by strain typing in several ways

26

Special laboratory testing for epidemiology

• Strain information your laboratory already has– Colony morphology• Some strain differences are

obvious by the colony appearance on plates; look at the cultures

– The biochemical profile from the identification system• Example: Vitek does 32

tests; print this profile and compare, usually the same for same strains

27

Special laboratory testing for epidemiology

• The antibiotic susceptibility panel– Same strains should

give identical antibiotic profiles (to category if not MIC); print and compare

– Example: Vitek tests about 18 drugs; not all are displayed, so get this from the laboratory

28

Special laboratory testing for epidemiology

• Strain information your laboratory can get by sending the strains to a reference laboratory– MDCH does strain typing by DNA analysis– Some laboratories do ribosomal RNA analysis

(ribotyping)– This may be expensive and takes several days– You have to tell the laboratory exactly which organisms

from which cultures to save• Remember that the laboratory saves cultures for about one

week, so if you wait too long, they are gone

– Typically requires an investigation plan by the infection control officer; don’t do this for fun

29

Special laboratory testing for epidemiology

30

Sources of information

• Buy and read this book1. Specimen collection2. Culture and Gram stains3. Blood cultures4. Immunology5. Antimicrobial testing6. Urinalysis, fluids7. Mycobacteriology8. Mycology9. Parasitology10. Virology11. Other topics

31

References: text

• Moore, V. L. Microbiology basics, pp. 16-1 to 16-17. In: APIC Text of Infection Control and Epidemiology, 3rd edition. 2009. Association for Professionals in Infection Control and Epidemiology, Washington, DC.

• Moore, V. L. Laboratory testing and diagnostics, pp. 17-1 to 17.7. In: APIC Text of Infection Control and Epidemiology, 3rd edition. 2009. Association for Professionals in Infection Control and Epidemiology, Washington, DC.

32

References: text

• APIC. The Infection Preventionist’s Guide to the lab. 2012. Association for Professionals in Infection Control and Epidemiology, Washington, DC.

• Stratton, C. W. and J. N. Green. Role of the microbiology laboratory and molecular epidemiology in healthcare epidemiology and infection control, pp. 1418-1431. In: Mayhall, C. G., Hospital Epidemiology and Infection Control, fourth edition. 2012. Lippincott Williams and Wilkins, Philadelphia, PA.

33

References: links

• http://cid.oxfordjournals.org/content/early/2013/06/24/cid.cit278.full

• http://www.biomerieux-usa.com/upload/VITEK-Bus-Module-1-Antibiotic-Classification-and-Modes-of-Action-1.pdf