Practical application of laboratory
results in infection prevention and
healthcare epidemiology
Richard A. Van Enk, Ph.D., CIC
Director, Infection Prevention and Epidemiology,
Bronson Methodist Hospital
vanenkr@bronsonhg.org
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Objectives
You 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
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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
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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
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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
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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
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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
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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
– Lots of normal flora; respiratory, urine, stool, wounds
– No normal flora; blood, spinal and synovial fluid
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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
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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
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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 often headed by pathologists
as medical directors
• Laboratorians are experts in their area; use them
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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
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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
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Types of laboratory tests for infectious
disease
• Direct microscopic
examination of the specimen
with differential stains
– Gram, acid-fast, fluorescent
– Gram stains are done 24/7 and
finished in less than one hour
(same day result)
• Automatically included in some
cultures, not others
• Almost diagnostic in some
situations
– Acid-fast and fluorescent stains
are usually done once a day
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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
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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
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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
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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
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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
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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 culture and
antigen tests
– Plusses: fast and accurate
– Minuses: expensive, finds only
the target, can’t tell dead
pathogens from alive, no
susceptibility test
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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
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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
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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
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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
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Special laboratory testing for
epidemiology
• Routine microorganism identification gives you a
genus and species (or just one name for viruses)
• Microorganisms with the same name can be
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
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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
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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
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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
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Special laboratory testing for
epidemiology
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Sources of information
• Buy and read this book
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Specimen collection
Culture and Gram stains
Blood cultures
Immunology
Antimicrobial testing
Urinalysis, fluids
Mycobacteriology
Mycology
Parasitology
Virology
Other topics
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References: text
• Moore, V. L. Microbiology basics, pp. 16-1 to 1617. 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.
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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.
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References: links
• http://cid.oxfordjournals.org/content/early/20
13/06/24/cid.cit278.full
• http://www.biomerieuxusa.com/upload/VITEK-Bus-Module-1Antibiotic-Classification-and-Modes-of-Action1.pdf
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