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Understanding the
Basics of Clinical
Microbiology.
RYAN W. STEVENS, PHARM.D., BCPS
INFECTIOUS DISEASES CLINICAL PHARMACY SPECIALIST
PROVIDENCE ALASKA MEDICAL CENTER
Disclosures:

 None
Objectives:

1. Describe the utility of laboratory

testing/chemistries in the workup of infection.
2. Describe general microbiologic culture and
susceptibility methods and their associated time
courses.
3. Describe some forms of rapid diagnostic testing
(RDTs)
Learning Assessment:
1. T/F – Elevations in inflammatory biomarkers including (ESR, CRP, PCT,
and WBC) indicate the presence of an infectious condition.
2. Which of the following is a catalase positive, coagulase positive, latex
positive GPC?
 Staphylococcus aureus
 Streptotoccus pyogenes
 Staphylococcus epidermidis
 Streptococcus pneumoniae
3. Which susceptibility testing method provides a formal MIC? (circle all that
apply)
 Broth microdilution (BMD)
 Epsilometer test (E-test)
 Kirby-Bauer disk diffusion
Non-specific Lab Tests:1,2
 There is NO single definitive test for identification of infection!
 i.e. All have limitations
 Always should be paired with clinical presentation.
 Examples:
 White Blood Cell (WBC) Count:
 Elevate in response to infection
 Also elevate in response to: Drugs (i.e. steroids), stress, inflammation,
etc.
 Bands = immature neutrophils
 “Left Shift”: >9% bands
 Lactate:
 Demonstrates shift to anaerobic metabolism / illustrates tissue
hypoperfusion
 Elevates in response to shock, tissue ischemia, severe liver disease, and
some medication (metformin)
Non-specific Lab Tests:1-3
 CRP and ESR:
 C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR:
 Non-specific acute phase reactant (i.e. non-specific inflammatory marker)
 Elevate vaguely in response to inflammation
 Generally CRP reacts faster than ESR
 Better for trending chronic infections vs. determining if infection present.
 Erythrocyte sedimentation rate (ESR)
 Non-specific inflammatory marker
 Generally reacts slower than CRP
 Procalcitonin:
 116 amino acid precursor of calcitonin
 More sensitive than CRP at detecting bacterial infection
 Detectable in 2-4 hours / Peak = 8-24 hours / Half-life = 24 hours
 Rises not impaired by neutropenia or immunosuppression
 Most useful in community-acquired lower respiratory tract and sepsis
Non-specific Lab Tests:4,5
 Urinalysis:
 Color and Clarity: Non-specific
 Nitrites:
 Reductase: Nitrates  Nitrities
 Weakly sensitive/highly specific for the PRESENCE of
bacteria.
 Leukocyte Esterase:
 Produced by neutrophils
 Indicates pyuria
 WBC: Grades the pyuria
 Bacteria: May signal contamination, ASB, or infection
 Squamous Epithelial Cells: May help determine quality
of specimen.
Asymptomatic Bacteriuria
(ASB):5
 No mater what Bear Grylls tells
you…
…urine is not a sterile body
fluid.

 A “dirty” UA or “pyuria” in the

absence of symptoms is NOT an
indication for antimicrobial
therapy.
 Caveats:
 Pregnancy
 ASB during procedures which
will compromise of urinary
mucosa.
Cultures…the basics:1,6-9
1. Only culture something…if you plan to use the culture to guide therapy.
 May NOT always be necessary (i.e. uncomplicated CAP or perforated
appendicitis)
2. Always culture PRIOR TO administration of antibiotics if possible.
 Sepsis is the obvious exception
 7.6% increase in mortality for every hour antimicrobial therapy is delayed.

3. Take care to avoid contamination with patient’s usual flora.

4. Interpret cultures with a critical eye:
 What source/type of culture was obtained?
 What was the culture method?
 What did the gram-stain/grouping show?
 What grew?
 Does what grew match the clinical suspicions?
 What did susceptibilities show?
Culture Source/Type:1
 Source:
 Blood
 Wound, bone, tissue, abscess
 CSF
 Respiratory
 Stool
 Urine
 Body fluid (pleural, ascites, etc.)
 Type:
 Aerobic
 Anaerobic
 Fungal
 Acid fast bacilli
Culture Source/Type:1
 Some variance in microbiology processing:
 BACTEC alert device
 Blood
 Gram-stain negative Body Fluids
 Required additional processing:
 Tissue
 Bone
 Straight to plate
 Wound
 Respiratory
 Urine
 Gram-stain positive
 CSF
Culture Source/Type:1,8-11
 Anticipate pathogen based on location of infection.
 Skin and Soft Tissue Source:
Skin flora (Staphylococcus/Streptococcus)
 Respiratory Source: S. pneumoniae, M. catarrhalis, L.
pneumophila, M. Pneumoniae, C. pneumoniae, H. influenzae.
Hospital-acquired: MDRO gram-negative rods (including
P. aeruginosa) and S. aureus
 GI Source: E. coli, Klebsiella spp., B. fragilis, S.
anginosus, Enterococcus spp.
Culture Method:10-14
 How was it  Respiratory:
collected?  Sputum (expectorated) vs. sputum
 Is it a good (suction)
specimen?  Endotracheal aspirate vs. Bronchoalveolar
 lavage (BAL) vs. mini-BAL
Could it be
contaminated?  Wounds:
 Purulent vs. Non-purulent
 Superficial swab vs. tissue/biopsy
 General features:
 Chronic ulcer vs. acute wound
 Look for presence of
WBC  Blood:
 Look for absence of  ? Contaminant
squamous epithelial
 How many bottles of how many draws?
cells
 How long did it take to grow?
 Culture Method:15
 Semi-quantitative:  Quantitative:
 Attempts to  Provides more
ESTIMATE the robust estimate
quantity of of number of
organisms in a organisms in a
given culture. given culture.
 Requires fluid
specimen.
 Cultures plated
in one quadrant
on plate  One mL of
 Growth in specimen is
primary plate in plated
quadrant = 1+ and depending
on growth on
 Extension streak estimate
characterized as made.
2+, 3+, and 4+ http://intranet.tdmu.edu.ua/data/cd/disk2/
ch010.htm  i.e. >100,000
cfu/mL
Gram Stains:1
• Specimen applied to slide

• Crystal violet stain applied followed by iodine.

• Alcohol decolorizing solution applied

• Counterstain with safranin

• Gram-negative: Red/Pink
• Gram-positive: Purple in appearance
 Gram Stains:16
 Grouping:
 More relevant in gram
positive cocci (GPC):
 Staphylococcus spp. 
GPC pairs, tetrads, and
clusters
 Streptococcus spp. /
Enterococcus spp. :
 Generally: GPC in chains
 LONG chains  Beta-
hemolytic strep or S.
viridans
 Diplococci and chains
 S. pneumonia

 What about… GPC pairs?

Gram Stains/Grouping:1
Gram Stains:16
Gram Stains x 2:
• Specimen received

• Initial gram stain (1-6 hours)

• Plated and grown (24-48 hours)

• Growth gram stain

• Organism identification (0-24 hours)

• Susceptibilities (18-24 hours)

Gram Stains  Plate Growth:
 Plate Growth:

 Identification…
…what is taking
so long?

 Pure plates vs. mixed plates

 “re-isolating for more
information”
 Poor vs. no plate growth
plates
 Oddly behaving organisms
Plate Growth (GNR):1
Plate Growth (GNR):17
 Gram Negatives:
 Lactose fermentation:
 Helps
to distinguish between
GNRs prior to formal ID.
 Pseudomonas vs. other
 MacConkey agar:
 Inhibits gram-positive growth
 Lactose Fermenting:
 Lowers pH  red agar
 Non-lactose fermenting:
https://en.wikipedia.org/wiki/MacConkey_agar#/media/
 File:MacConkey_agar_with_LF_and_LF_colonies.jpg
Ammonia production
raises pH  Clear/opaque
agar
Plate Growth (GNR):17

 Oxidase:
 Assesses for presence of
cytochrome oxidase
 Not produced by
Enterobacteriaceae
 Produced by pseudomonas
 Positive test = Purple stain
 i.e. agent is oxidized
 Negative test = Colorless
http://www.medical-labs.net/oxidase-test-1291/
 i.e. agent remains reduced
Plate Growth (GPC):1
Plate Growth (GPC):17

 Catalase:
 2H2O2  O2 + H2O
 O2 released as gas = bubbles
 Differentiatesstaphylococcus
from streptococcus
 Staphylococcus = catalase
positive
 Streptococcus = catalase http://4.bp.blogspot.com/-pGWy_YzoaD4/UZXnPopWsUI/
AAAAAAAAAH0/nrnpu-kKutg/s1600/
negative slide+catalase+test+results.jpg
Plate Growth (GPC):17
 Catalase positive:  Catalase negative:
 Latex agglutination:  Hemolysis:
 Antibody for S. aureus  Does it growth cause hemolysis of
on latex beads blood agar
 Latex positive = S.  Alpha = green = partial hemolysis
aureus  S. viridans
 Latex negative =  S. pneumonia
CoNS
 Maybe S. anginosus
 Coagulase:  Beta = clear = full hemolysis
 Converts fibrinogen to  “Typeable” streptococcus
fibrin clot with help of
 Group A, B, C, G
plasma factors
  Gamma = red = no hemolysis
S. aureus = positive
  Enterococcus spp. (PYR)
S. epidermidis and other
CoNS = negative  Maybe S. anginosus
Organism Identification:
• Specimen received

• Initial gram stain (1-6 hours)

• Plated and grown (24-48 hours)

• Growth gram stain

• Organism identification (0-24 hours)

• Susceptibilities (18-24 hours)

Organism Identification:

 VITEK vs. Microscan vs.

Phoenix

 PAMC = VITEK2
 Performs both:
 Organism identification
 Susceptibilities
 Automated broth microdilution
(BMD)
 We will come back to
this!
Organism ID vs. Clinical
Suspicion:
• Culture Source
• Method of Collection
• Suspicion for Contamination
• Gram stains
• Growth
• Organism ID

 Presence of Usual flora?

 Odd organism for culture source?
 Growth that doesn’t match the initial gram stain?
 Initial gram stain that doesn’t match the growth?
Susceptibilities:
• Specimen received

• Initial gram stain (1-6 hours)

• Plated and grown (24-48 hours)

• Growth gram stain

• Organism identification (0-24 hours)

• Susceptibilities (18-24 hours)

 Susceptibilities:1

Qualitative Results:
• Driven by MIC Quantitative
• Actual determinant behind Results:
quantitative results • Susceptible
• Multiple methods (BMD vs. KB vs. • Intermediate
E-test) • Resistant

Valuable…but sometimes hard to User friendly…

interpret. but perhaps
oversimplified.
“Semi” -Qualitative
Susceptibilities:1
 Disk diffusion test (i.e. Kirby Bauer)
 Grow bug  Drop Disk  Measure zone of
inhibition
 Susceptibility of organism is determined by “zone
of inhibition”
 Determined by CLSI standards
 Varies depending on organism
 Varies depending on drug
 Generally:
 Bigger zone of inhibition = more susceptible bug
 Can perform multiple tests (up to 12) on same plate
 Able to choose specific agents to test
 Pros: Reliable, flexible, cheap, and simple
 Cons: May be impacted by incubation temp or bacterial
inoculum
 Qualitative Susceptibilities:1
 Minimum Inhibitory Concentration:
 “The lowest antimicrobial concentration that prevents
visible growth of an organism after ~24 hours of
incubation in a specified growth medium”
 Susceptibility breakpoints determined by CLSI
 Traditionally
 Macrotube dilution method vs. Solid agar
 Labor intensive!
 Present day:
 Automated
 VITEK2 vs. Microscan (turbidity) vs. Phoenix
 Epsilometer Test (I.e. E-test)
 Tells us the level of susceptibility of an organism rather
than just the interpretation of that level.
 E. coli: Piperacillin/tazobactam </= 4 vs. 32 mcg/mL
 MRSA: Vancomycin <0.5 vs. 2 mcg/mL
 Qualitative Susceptibilities:1
 Automated Broth Microdilution
(BMD):
 Inoculate card  Put in machine  Wait
 Tests organism to multiple concentrations
of multiple drugs
 Drugs in card determined by
manufacturer or card selected.
 Determines organism MIC to multiple
agents in single test
 Run time = 18-24 hours
 Pros: Easy, reliable, provides formal MIC
 Cons: Requires machine ($$$) and lacks
flexibility in agent selection.
Qualitative Susceptibilities:1,18
 Epsilometer test (i.e. E-test)
 Grow bug  Drop strip  look for
ellipse/strip intersection.
 E-Strip:
 Single agent
 Increasing concentrations
 One strip per plate.
 Has been at times to be more
accurate than automated broth
microdilution
 Pros: Easy to perform, ? Easy to
read, cheap
 Cons: One per plate, ? Easy to read
Susceptibilities:

 Summary:
1. Do you have qualitative, quantitative, or both?
2. If qualitative, was it performed via BMD, E-test, or Kirby-
Bauer?
3. If BMD or E-test, just how susceptible was the organism
(i.e. what was the MIC)?
 Select a therapy!
1. What is the narrowest spectrum agent that treats all
presently identified organisms?
Rapid Diagnostic Testing:17
Sensitivity vs. Specificity
Varies depending on testing method and specific test
 Sensitivity:  Specificity:

 If a person HAS the  If a person does NOT

disease how often will HAVE the disease how
the test be positive? often will the test be
negative.
 I.e.
 I.e.
 10 influenza
 10 patients
patients present
and are swabbed WITHOUT influenza
for EIA present and are
swabbed for EIA
 Rapid flu swab
 Rapid flu swab
(EIA) detects 5/10.
(EIA) detects 2/10
 Sensitivity = 50%  Specificity = 80%
 Rate of true positive vs.  Rate of true negative vs.
false negative. false positive.
Rapid Diagnostic Testing
(RDT):17
 Antibody testing:
 Agglutination testing:
 Antibodies (polyclonal or monoclonal) attached to latex beads and specimen
introduced.
 If lattice structure forms then antigen is present (antibody-antigen complexes)
 Typically tested from growth (not generally from direct specimen)
 Ex: S. aureus from plate growth
 Enzyme immunoassay (EIA)/Enzyme-linked immunosorbent assay
(ELISA):
 Antibody coated wells/trays  Specimen (antigen) introduced  Well
washed out  Second antibody introduced  well washed out  coloring
agent added.
 Wells that change color = positive for antigen.
 Typically tested direct from specimen
 Ex: Influenza A and B, Ag EIA (i.e. rapid flu swab)
Rapid Diagnostic Testing (RDT):1,17
 Polymerase Chain Reaction (PCR / NAAT):
 Testing done directly from collection specimen
 Target amplification system
 Amplifies SMALL sections of DNA using DNA polymerase and short oligonucleotide primers
for detection.
 If more than one primer used = improved sensitivity (multiplex PCR)
 Ex: Respiratory viral pathogen panel (Biofire TM)
 Blood Culture Identification Panel (BCID)
 GI Panel
 Meningitis/Encephalitis Panel
 C. diff, NAAT

 16S rRNA:
 Looks for specific section of ribosomal RNA that helps to identify specific organisms in a
specimen.
 Draws on LARGE bank of known sequencing vs. specific testing on specific platform
 Testing of direct specimen
Rapid Diagnostic Testing
(RDT):17
 Mass Spectrometry:
 Matrix-assisted laser desorption ionization time-of-flight
(MALDI-TOF)
 Thin smear on metallic slide
 Hit with pulses of laser
 Desorbed and deionized particles then accelerated through
electrostatic field and drifted through vacuum tube
 Contact mass spectrometers detector
 Different particles fly at different speeds which indicates the
presence of components of specific organisms
 Typically run off of organism growth
Rapid Diagnostic Testing
(RDT):19
 Accelerate Diagnostics – PhenoTM
 Gel electro-filtration (GEF)
 Sample loaded into gel well that contains pores smaller than bacterial cells
 Electric current applied which removes cellular debris to isolate/concentrate bacterial cells
 Electro-kinetic concentration (EKC)
 Cells are drawn to surface where analysis will take place by exposure to mild electric
charge.
 FISH (Fluorescence in-site hybridization)
 Cells exposed to probes with fluorescent tags looking for specific nucleic acid sequences.
 Fast phenotypic susceptibility testing
 Cell exposed to single concentration of agent and time lapse imaging correlates growth
patterns to MICs.
Learning Assessment:
1. T/F – Elevations in inflammatory biomarkers including (ESR, CRP, PCT,
and WBC) indicate the presence of an infectious condition.
2. Which of the following is a catalase positive, coagulase positive, latex
positive GPC?
 Staphylococcus aureus
 Streptotoccus pyogenes
 Staphylococcus epidermidis
 Streptococcus pneumoniae
3. Which susceptibility testing method provides a formal MIC? (circle all that
apply)
 Broth microdilution (BMD)
 Epsilometer test (E-test)
 Kirby-Bauer disk diffusion
References:
1. Rybak M, Aeschlimann JR. Laboratory tests to direct antimicrobial pharmacotherapy. In: Dipiro JT et al.
Pharmacotherapy: A Pathophysiologic Approach 7th ed. New York, NY: McGraw Hill Medical; 2008: 1715-
1730.
2. Pagana KD, Pagana TJ. Mosby’s Diagnostic and Laboratory Reference. 9th ed. Williamsport, PA: Mosby
Elsevier; 2009.
3. Simon L, et al. Serum procalcitonin and CRP levels as biomarkers of bacterial infection: a systematic review
and meta-analysis. CID 2004;39:206-217.
4. Simerville JA, Maxted WC, Pahira JJ. Urinalysis: a comprehensive review. Am Fam Physician.
2005;7(6):1153-1162.
5. Nicolle LE, Bradley S, Colgan R, et al. Infectious Diseases Society of American guidelines for the diagnosis
and treatment of asymptomatic bacteriuria in adults. CID 2005;40:643-54.
6. Kumar A, Roberts D, Wood KE, et al. Duration of hypotension before initiation of effective antimicrobial
therapy is the critical determinant of survival in human septic shock. Crit Care Med 2006;34(6): 1589-96.
7. Septimus E. Clinician guide for interpreting cultures. Centers for Disease Control and Prevention Web site.
http://www.cdc.gov/getsmart/healthcare/implementation/clinicianguide.html. Published April 7, 2015.
Updated April 7, 2015. Accessed October 5, 2016.
8. Mandell LA, Wunderink RG, Anzueto A, et al. Infectious Diseases Society of American/American Thoracic
Society Consensus Guidelines on the management of community-acquired pneumonia in adults. CID
2007;44:S27-72.
9. Solomkin JS, Mazuski JE, Bradley JS, et al. Diagnosis and management of complicated intra-abdominal
infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases
Society of America. CID 2010;50:133-64.
10. Kalil AC, Metersky ML, Klompas M, et al. Management of adults with hospital-acquired and ventilator-
associated pneumonia: 2016 clinical practice guideline by the Infectious Diseases Society of America and
the American Thoracic Society. CID 2016. doi: 10.1093/cid/ciw353.
References:

11. Stevens, DL, Bisno AL, Chambers HF, et al. Practice guidelines for the diagnosis and management of skin and
soft tissue infections: 2014 update by the Infectious Diseases Society of America. CID 2014. doi:
10.1093/cid/ciu296.
12. Lipsky BA, Berendt AR, Cornia PB, et al. 2012 Infectious Diseases Society of America Clinical Practice Guideline
for the diagnosis and management of diabetic foot infections. CID:54(12):e132-e173.
13. Bowler PG, Deurden BI, Armstrong DG. Wound microbiology and associated approaches to wound
management. Clin Microbiol Rev 2001;14(2):244-269.
14. Hall KK, Lyman JA. Updated review of blood culture contamination. J Clin Microbiol 2006;19(4):788-802.
15. Kallstrom G. Are quantitative bacterial wound cultures useful? J Clin Microbiol 2014;52(8):2753-2756.
16. Barenfanger J, Drake CA. Interpretation of gram stains for the nonmicrobiologist. Lab Med 2001;7(32): 368-
375.
17. Brooks GF, et al. Medical Microbiology 26th ed. New York, NY: McGraw Hill Medical; 2013
18. Rybak M, Vidaillac C, Sader HS. Evaluation of vancomycin susceptibility testing for methicillin-resistant
staphylococcus aureus: comparison of Etest and three automated testing methods. J Clin Microbiol 2013;51(7):
2077-81.
19. Accelerate Pheno System. Accelerate diagnostics. Available at:
http://acceleratediagnostics.com/products/accelerate-pheno-system/#features. Accessed December 30th,
2016.
Environmental Cleaning and
Disinfection

Bonnie Barnard, MPH, CIC, FAPIC

Interim Infection Preventionist
 Objectives
• Describe the process for cleaning patient
rooms daily and upon discharge
• Explain the importance of dwell/contact time
in relation to the use of disinfectants
• List at least five high touch items in the
patient’s environment that require special
attention to cleaning
Pathogens Survive on Surfaces

BMC Infectious Disease 2006

 Environment as Source of HAIs
20% of HAIs may be related to the environment
--William Rutala, PhD

Environmental cleaning in healthcare is only done

correctly 50% of the time
 Definitions
• Cleaning
– Removal of all soil from objects/surfaces
• Decontamination
– Removal of pathogenic microorganisms from objects to
ensure they are safe to handle
• Disinfection (Low, Intermediate, High)
– Elimination of many or all pathogenic organisms with the
exception of spores
• Sterilization
– Complete elimination of all microbial life, including spores
Spaulding Classification
 Processing “Noncritical”
Patient Care Objects
Classification: Noncritical objects will not come in
contact with mucous membranes or skin
that is not intact.
Object: Can be expected to be contaminated with
some microorganisms.
Germicidal action: Kill vegetative bacteria, fungi and lipid
viruses.
Examples: Bedpans; crutches; bed rails; EKG leads;
bedside tables; walls, floors and furniture.
Method: Low-level disinfection
 Regulations and Guidelines
• CDC Guideline for Environmental Infection Control (2003)
• Environmental Protection Agency (EPA)
– Pesticides
• Includes disinfectants and sterilants used on inanimate
objects and environmental surfaces
 Environmental Survival of Key Pathogens
on Hospital Surfaces

Pathogen Survival Time

S. aureus (including MRSA) 7 days to >12 months
Enterococcus spp. (including VRE) 5 days to >46 months
Acinetobacter spp. 3 days to 11 months
Clostridium difficile (spores) >5 months
Norovirus (and feline calicivirus) 8 hours to >2 weeks
Pseudomonas aeruginosa 6 hours to 16 months
Klebsiella spp. 2 hours to >30 months

Adapted from Hota B, et al. Clin Infect Dis 2004;39:1182-9 and

Kramer A, et al. BMC Infectious Diseases 2006;6:130
 Resistance of Microorganisms to
Disinfectants

Most Resistant
Prions
Bacterial spores (C. difficile)
Mycobacteria
Small, non-enveloped viruses (noro, polio, EV-D68)
Fungal spores
Gram-negative bacilli (Acinetobacter)
Vegetative fungi and algae
Large, non-enveloped viruses
Gram-positive bacteria (MRSA, VRE)
Enveloped viruses (Ebola, MERS-CoV)

Most Susceptible
 Understanding Chemicals
• Cleaner
• Cleaner/Disinfectant
• Disinfectant
– EPA Registered
• Special Products
– Stainless Steel
– Degreasers
 Low-Level Disinfection

Exposure time > 1 min

Germicide Use Concentration

Ethyl or isopropyl alcohol 70-90%
Chlorine 100ppm (1:500 dilution)
Phenolic UD
Quaternary ammonium UD
Improved hydrogen peroxide 0.5%, 1.4%
UD=Manufacturer’s recommended use dilution
 Ideal Disinfectant
• Broad spectrum • Easy to use
• Fast acting • Acceptable odor
• Remains wet • Economical
• Not affected by • Solubility
environmental factors • Stability
• Nontoxic • Cleaner
• Surface compatibility • Nonflammable
• Persistence

Rutala WA, Weber DJ. Infect Control Hosp Epidemiol 2014;35:855-865

 Surface Disinfectants

• Oxidant Based • Quaternary

– Bleach Ammonium Based
– Peracetic acid – High, low and no
– Hydrogen alcohol
peroxide
 Sodium Hypochlorite
Rutala, Weber. Am J Infect Control 2013;41:S36-S41

Advantages Disadvantages
• Bactericidal, tuberculocidal, • Reaction hazard with acids and ammonias
fungicidal, virucidal • Leaves salt residue
• Sporicidal • Corrosive to metals (some ready-to-use
products may be formulated with
• Fast acting corrosion inhibitors)
• Inexpensive (in dilutable form) • Unstable active (some ready-to-use
• Not flammable products may be formulated with
stabilizers to achieve longer shelf life)
• Unaffected by water hardness
• Affected by organic matter
• Reduces biofilms on surfaces • Discolors/stains fabrics
• Relatively stable (e.g., 50% reduction • Potential hazard is production of
in chlorine concentration in 30 days) trihalomethane
• Used as the disinfectant in water • Odor (some ready-to-use products may be
treatment formulated with odor inhibitors).
• Irritating at high concentrations.
EPA registered
 Improved Hydrogen Peroxide
Rutala, Weber. Am J Infect Control 2013;41:S36-S41

Advantages Disadvantages
• Bactericidal, tuberculocidal, • More expensive than most
fungicidal, virucidal
other disinfecting actives
• Fast efficacy
•
• Not sporicidal at low
Easy compliance with wet-contact
times concentrations
• Safe for workers (lowest EPA
toxicity category, IV)
• Benign for the environment
• Surface compatible
• Non-staining
• EPA registered
• Not flammable
 Quaternary ammonium compounds
Rutala, Weber. Am J Infect Control 2013;41:S36-S41

Advantages Disadvantages
• Not sporicidal
• Bactericidal, fungicidal, virucidal
• In general, not tuberculocidal and
against enveloped viruses (e.g.,
virucidal against non-enveloped
HIV)
viruses
• Good cleaning agents
• High water hardness and
• EPA registered cotton/gauze can make less
• Surface compatible microbicidal
• Persistent antimicrobial activity • A few reports documented asthma
when undisturbed as result of exposure to
• Inexpensive (in dilutable form) benzalkonium chloride
• Not flammable • Affected by organic matter
• Multiple outbreaks ascribed to
contaminated benzalkonium chloride
 Alcohol
Rutala, Weber. Am J Infect Control 2013;41:S36-S41

Advantages Disadvantages
• Bactericidal, tuberculocidal, • Not sporicidal
fungicidal, virucidal • Affected by organic matter
• Slow acting against non-enveloped viruses
• Fast acting (e.g., norovirus)
• Non-corrosive • No detergent or cleaning properties
• Non-staining • Not EPA registered
• Damage some instruments (e.g., harden
• Used to disinfect small surfaces
rubber, deteriorate glue)
such as rubber stoppers on • Flammable (large amounts require special
medication vials storage)
• No toxic residue • Evaporates rapidly making contact time
compliance difficult
• Not recommended for use on large surfaces
• Outbreaks ascribed to contaminated alcohol
 Phenolics
Rutala, Weber. Am J Infect Control 2013;41:S36-S41

Advantages Disadvantages

• Bactericidal, tuberculocidal, • Not sporicidal

fungicidal, virucidal • Absorbed by porous
• Inexpensive (in dilutable materials and irritate tissue
form) • Depigmentation of skin
• Non-staining caused by certain phenolics
• Not flammable • Hyperbilirubinemia in
• EPA registered infants when phenolic not
prepared as recommended
 Proper Use of Disinfectants
• Contact, dwell or ‘wet’ time
– 3-10 minutes
– Reapplication
– Applicator
• Considerations
– Cleaning ability
– Material compatibility
– Aesthetics (smell, residue)
• Spectrum of activity
• Safety
 High Touch Areas/Items
• Patient room
– Bedrail, side table, TV control, light switches
– Bathroom
• Nursing station
– Counter tops
• Electronic devices
– Keyboards
– Screens
– Cell Phones
• Equipment
– IV poles, beds, gurneys, wheelchairs, bedside commodes
 Shared Patient Care Equipment
• Vital signs
• Stethoscopes
• Point of care testing (glucose, INR)
• Therabands
• Physical therapy (gait belts, lift slings)
• Lift equipment
• Wheelchairs
• Transportation gurneys
 Keys to Success

• Standardize processes
• Assign responsibilities
• Training and skills validation
• Monitor and provide feedback
• Communicate
 Standardize processes

– Room cleaning checklist

– Clear delineation of responsibilities
– Extensive education with competencies
– Room cleaning assessment
 Terminal
Cleaning
Checklist

https://www.cdc.gov/hai/pdfs/
toolkits/environmental-cleaning
-checklist-10-6-2010.pdf
Cleaning/Disinfection Responsibilities

Item Frequency Product Responsible Comment

Party
Wheelchair After every use Sani-Wipe Transport Team
(purple top)
Gurney After every use Sani-Wipe Transport Team
(purple top)
IV Pump (in Weekly Sani-Wipe Nursing Orange top if
use) (purple top) Cdiff patient
IV Pole Weekly Sani-Wipe Nursing Orange top if
(purple top) Cdiff patient
Ventilator Weekly Sani-Wipe Respiratory Orange top if
(in use) (purple top) Therapy Cdiff patient

Etcetera…..
Training and Skills Validation
 Education for EVS Staff
• Provide an overview of the importance of HAIs in a manner
commensurate with their educational level using as many pictorial
illustrations as is feasible.
• Explain their role in improving patient safety through optimized
hygienic practice.
• Review specific terminal room cleaning practice expectations.
• Discuss the manner in which their practice will be evaluated. A
participatory demonstration of the monitoring method is very useful.

Source: CDC -
https://www.cdc.gov/hai/toolkits/appendices-evaluating-environ-cleaning.ht
ml
 Education for EVS Staff (cont’d)
• Provide them with information from the baseline
evaluation emphasizing or possibly exclusively showing
them results for those objects which have been most
thoroughly cleaned.
• Stress the non-punitive nature of the program.
• Inform them that their good performance will be broadly
recognized (i.e., beyond their department) and highlighted
within their department for others to emulate.
• Repeatedly reinforce the importance of their work, and
how it directly relates to the hospital’s goals and mission
and how it is appreciated by patients and plays a major
role in a patient’s satisfaction with the hospital.
Monitoring
 Monitoring Cleaning
• Direct practice observation
• Fluorescent marking
– Pre-cleaning placement
• ATP
– Post-cleaning measurement
 Cleaning Evaluation Monitoring Worksheet
https://www.cdc.gov/hai/pdfs/toolkits/environmental-cleaning-eval-worksheet-10-6-2010.xls
 Clean vs Dirty
• Separate storage areas Which one is clean?
• Ventilation issues
• Communication cues
 Most Common Problems
• Amount of time spent
• Dwell/contact times
• Number of wipes used
• Over-dilution of disinfectant (mixing)
• Confusion about responsibilities
• Turnover in EVS staff
• Infrequent monitoring of practices
• Training and competency
 It’s not just EVS….

From “Collaborate to Eradicate” Webinar – Jim Gauthier

 Special Situations
• Operating/procedure rooms
– Between cases
– Periodic ‘deep’ clean
• Discharge/terminal cleaning
• Isolation rooms
What can you do if you are still seeing infections (e.g., C.
difficile) and think you are doing a good job at cleaning?
 No Touch Environmental Disinfection
• Ultraviolet light
• Fogging systems
Y!
• Self disinfecting surfaces N L
E O
TIV
N C
J U
AD

NO ENVIRONMENTAL CULTURES FOR ROUTINE MONITORING

 Ultraviolet Light
• Continuous (UV-C)
• Pulsed-xenon

• Clostridium difficile
 Fogging System
• Hydrogen peroxide (H2O2)
– Aerosol
• 3-7% H2O2
• +/- silver ions
– Vaporized
• “Dry” gas
• 30% H2O2
 “Self Disinfecting” Surfaces
• Copper
• Triclosan impregnated surfaces
• Silver
Association for the Healthcare Environment

• Practice Guidance for Environmental Cleaning

– www.ahe.org
• Certificate of Mastery in Infection Prevention and
Control for Environmental Services
– Certified Healthcare Environmental Services
Technician
– Certified Healthcare Environmental Services
Professional
– http://www.ahe.org/ahe/lead/CMIP/index.shtml
 Resources
• Association for the Healthcare Environment
– Cleaning tools
• Environmental Protection Agency (EPA)
– Disinfectant information
• Guideline for Disinfection and Sterilization in Healthcare Facilities -
HICPAC
• Environmental Cleaning Toolkit (CDC)
https://www.cdc.gov/hai/prevent/prevention_tools.html
• APIC
– Topic Specific – Environmental Services
• http://www.apic.org/Resources/Topic-specific-infection-prevention
– Webinars
– APIC Text
• www.disinfectionandsterilization.org
 Summary
• Cleaning and disinfection of the health care
environment is critical to preventing
infections
• Products that are used for cleaning must be
used per the product’s IFU, which includes
attention to contact time and compatibility
with materials
• Staff who are responsible for cleaning need
to be trained with checklists and
competencies to ensure standardization of
practices
 Questions

Bonnie Barnard, MPH, CIC

907.212.4829
[email protected]
Evaluation Workshop
Station 1: EVS rounding and assessments

Station 2: PPE teaching and audits

Station 3: Handwashing teaching and audits

Communicating between facilities
Interfacility transfers
Precautions
Known MDRO infection/colonization

Communicate about local issues

Communicating with residents + families
Resident and family participation in precautions is key
Key to balancing homelike environment/resident
comfort and the safety of the group
Pro tips on how to talk to residents
What to do with residents who don’t follow the rules
What’s an outbreak?
More cases than your baseline
More cases than you’d expect in the given population
over the given time

Some disease-specific definitions:

One confirmed case of influenza in an LTCF
Anybody anywhere with smallpox
Outbreak investigation
 Make a line list
Notifications in here;
 Confirm your cases depends a little on how
much you know
 Check each one with your case definition

 Collect more data

 What are the symptoms?
 Who has been in contact with the patients?
 Where has the patient been (rooms, floors, special hospital areas)?
 Lab/microbiologic data

 Look for patterns among cases

 Take appropriate preventive action

What’s a line list?
Patient Name Date ill Symptoms Resident or Gender, age
staff?
Jim Halpert 12/30/16 Nausea, Resident M, 83
diarrhea
Dwight 12/31/16 Vomiting Resident M, 85
Schrute
Michael Scott 1/2/16 Abdominal Resident M, 90
pain, diarrhea,
vomiting
Pam Beesley 1/4/16 Nausea, Staff F, 82
vomiting,
diarrhea
Outbreak case definitions
Can be the same as normal for most conditions

In some cases, might make them looser:

“any diarrhea or vomiting” during a noro outbreak could
be a suspect case

Can use suspect/probable/confirmed lingo

Confirmed cases have supporting lab results
Probable cases meet the definition except no labs yet
Suspect have some suggestive symptoms, but not all
Data collection
May not be necessary for simple outbreaks

For more complex ones, consider possible modes of

transmission
Close contact: caregivers, partners, close friends ->
networks
Fomites: shared activities
Unsure/multiple: go broad with potential exposures
Stopping an outbreak
Interrupt transmission
 Must know how being spread
 Generally, promote hand hygiene and other basics

Use precautions and cohorting

 Staff and residents
 Disposable or cohorted instruments and equipment

Consider limiting group activities

Increase frequency of cleaning

Communicate with staff, residents, and visitors so they can help

by adjusting their behavior
Who to contact with an outbreak
Call Epidemiology- we can help!
269-8000

Management: show them your data

Communicate with staff, residents, and visitors

Don’t be scary
Provide directions (wear a mask, wash hands, etc.)
Influenza
Outbreaks of flu in long-term care facilities are
COMMON  have a plan!

Standard and droplet precautions for ill residents

Give antivirals and chemoprophylaxis to residents

Website has resources:

http://dhss.alaska.gov/dph/Epi/id/Pages/influenza/flu
info.aspx
Norovirus/ viral gastroenteritis
Contact precautions; consider cohorting and
cancelling group activities

Encourage ill staff to stay home

Resources available- many more online:

http://tn.gov/assets/entities/health/attachments/LTC
F_guidelines.pdf

https://www.cdc.gov/hai/pdfs/norovirus/229110a-norovi
ruscontrolrecomm508a.pdf
Outbreak Prevention and Prep
Vaccinate residents and staff!
Influenza
Chickenpox/ Shingles

Have records of vaccination/immunity status for

everyone

Have standing orders for antivirals/antibiotics in case

of an outbreak
Have a plan for when and how to cohort
 APIC
ASSOCIATION FOR PROFESSIONALS IN INFECTION CONTROL AND
EPIDEMIOLOGY
http://www.apic.org/About-APIC/About-APIC-Overview
What do they do?
• Collect, analyze, and interpret health data in order to track infection trends, plan
appropriate interventions, measure success, and report relevant data to public
health agencies.
• Establish scientifically based infection prevention practices and collaborate with
the healthcare team to assure implementation.
• Work to prevent healthcare-associated infections (HAIs) in healthcare facilities
by isolating sources of infections and limiting their transmission.
• Educate healthcare personnel and the public about infectious diseases and how
to limit their spread.
• Has groups for ACH, LTC, CAH, and ASC practitioners

State Chapter: Alaska Midnight Sun Chapter 065

 CDC
CENTERS FOR DISEASE CONTROL AND
PREVENTION
Who are they?
Under HHS, founded in 1946, headquartered in Atlanta, GA.
What do they do?
CDC works 24/7 to keep America safe from health, safety, security threats, both
foreign and domestic. Whether diseases start at home or abroad, chronic or
acute, curable or preventable, human error or deliberate attack, CDC fights
disease and supports communities
CDC presence
 SHEA
THE SOCIETY FOR HEALTHCARE EPIDEMIOLOGY
OF AMERICA
http://www.shea-online.org/
• Advances the science of healthcare epidemiology through research and
education.
• Translates knowledge into effective policy and practice.
• Mentors, trains and promotes professional development in healthcare
epidemiology.
• Collaborates and shares expertise with other organizations.
• Adheres to high ethical standards, promotes honesty and ethical principles in
the practice of epidemiology.
• Provide Guidelines and Expert Guidance Documents
 OTHER IMPORTANT GUIDELINE PRODUCERS
General Guidelines:
• HICPAC (Healthcare Infection control Practices Advisory Committee)
https://www.cdc.gov/infectioncontrol/guidelines/index.html

For construction/engineering:
• ASHE (American Society for Healthcare Engineering)
http://www.ashe.org/advocacy/orgs/fgi.shtml

For surgery-related stuff:

• AORN (Association of periOperaative RNs) https://www.aorn.org/
• AAMI (Assoc. for Advancement of Medical Instrumentation) http://www.aami.org/

Many state health departments have produced useful toolkits as well!

IN-STATE PARTNERS AND RESOURCES
MPQHF Mountain-Pacific Quality Health Foundation
http://mpqhf.com/corporate/

ASHNHA: Alaska State Hospital and Nursing Home Association

http://www.ashnha.com/

AK, Health and Social Services, Section of Epidemiology

http://dhss.alaska.gov/dph/Epi/id/Pages/hai/default.aspx

AK Division of Health Care Services, Health Facilities Licensing and Certification

http://dhss.alaska.gov/dhcs/pages/hflc/default.aspx
Data collection

 iAuditor

 iScrub
iAuditor

 Safety inspection product

 Build a checklist, which you complete on a

phone/tablet
 Can take and annotate pictures into the report
 Lots of smart design/complex checklist features

 Analyze in program

 Free and paid plans

iScrub- for iOS

 Hand Hygiene audit tool

 Can edit to add your facility’s areas,

employee types

 Exports to Excel
Options for Android

 SpeedyAudit
 Really nice format for doing the audits
 Also does PPE
 Free

 Paid options

 Bio-Rite AR- a hand hygiene trainer

Free analysis programs

 EpiInfo
 Doesn’t need to be installed
 Really, really easy descriptive stuff
 Can use data in a spreadsheet
 http://www.cdc.gov/epiinfo/index.html

 GraphPad
 Quickly does statistics for you
 http://graphpad.com/quickcalcs/
“Information” apps

 Infection Control Pocketguide (iOS)

 Infection Prevention (Android)

 Pathogen lookup- tells you the precautions
 Brings up a sign on how to do precautions
 PPE directions

 Quick LabRef (Android)

Other stuff

 Youtube!
 Decent video on how to clean a bathroom:
https://www.youtube.com/watch?v=yQrArIs74Ic
 There are others!

 I like ExcelJet for Excel help (some formulas

are real gamechangers)