Procedures/Guidelines For The Microbiology Laboratory

College of Physicians & Surgeons of Saskatchewan
Laboratory Quality Assurance Program
Procedures/Guidelines
for the Microbiology
Laboratory
January 2010
Table of Contents
Microbiology Procedures/Guidelines 2010 Edition
Page 1
QUALITY CONTROL IN MICROBIOLOGY LABORATORIES

Microbiology laboratories shall use quality control procedures to ensure the accuracy,
reliability and reproducibility of the various tests used in the isolation, identification and
antimicrobial susceptibility testing of microorganisms, and in the performance of
serological testing. The extent of quality control testing done will be determined by the
scope of clinical testing performed in each laboratory.
All laboratories performing microbiology shall have appropriate internal quality control
procedures using CLSI guidelines for antibiotic susceptibility testing and quality control
of media.
a)
The most recent update of the following CLSI documents should be followed:
(i)
M22 Quality Assurance for Commercially Prepared Microbiological

Culture Media
(ii)
M100 Performance Standards for Antimicrobial Susceptibility Testing
(iii)
M2
(iv)
M7
Methods for Dilution Antimicrobial Susceptibility Tests for
Bacteria that Grow Aerobically
(v)
M11 Methods for Antimicrobial Susceptibility Testing of Anaerobic

Bacteria
Performance Standards for Antimicrobial Disk Susceptibility Tests
b)
Identification panels should be quality controlled according to the manufacturer's

recommendations.
c)
ATCC organisms shall be used for proper quality control of media and of
antimicrobial susceptibility testing.
CLSI: Clinical and Laboratory Standards Institute
ATCC: American Type Culture Collection
All laboratories performing microbiology shall demonstrate and document their efforts to
meet the standards established by CLSI guidelines and quality control using appropriate
organisms.
Page 2
GUIDELINE FOR QUANTITATIVE INTERPRETATION OF GRAM STAINS

Background:
Microscopic examination remains the initial diagnostic test in the processing of
specimens in the clinical microbiology laboratory. The timely report of a Gram stain
result gives the physician important information about the presence and cause of
infection. The Gram stain has a broad staining spectrum and classifies bacteria as either
Gram-positive or Gram-negative. Despite the clinical importance of the Gram stain,
there are few available standards for the reading and interpretation of this test. The
assignment of semi-quantitative and quantitative values to the number of cells and
bacteria seen is clearly arbitrary, since published criteria for general use vary
dramatically(1-5). Although laboratories may report only semi-quantitative Gram stain
criteria, it is clinically important to have a standardized schema for assigning quantities of
cells and bacteria to individual semi-quantitative scores. Since several clinical studies
have shown that the presence of moderate to heavy amounts of pus and/or the presence of
bacteria on Gram stains correlates with the presence of infection(6-8), information reported
from Gram stains of specimens needs to be accurate.
Principle:
To review current practice in Canada and evidence from the literature to establish a
current best practice approach to the quantitative interpretation of Gram stains for all
types of clinical specimens.
Recommendation:
Although there are several published Gram stain reporting criteria, the Canadian
Coalition for Quality Laboratory Medicine recommends that:
Laboratories use:
o One set of interpretive criteria for all types of clinical specimens except for
sputa and vaginal smears for bacterial vaginosis.
o Separate published specimen rejection criteria for sputa.
o Standard criteria for diagnosis of bacterial vaginosis(9, 10).
Laboratories specify the criteria used when reporting Gram stain results to facilitate
interpretation by physicians.
Page 3
Gram Stain Quantification Criteria:

1) Grading System for Assessing Sputum Quality*:
i) Q score1:
Type of cell and #/low power field (x100)
Neutrophils:
<10
10 - 25
>25
Grade
0
+1
+2
Mucous present
+1
Squamous Epithelial cells:

10-25
>25
1
2
Rejection criteria: Reject specimens with an average score of 0 or less.

To determine average score, count the number of neutrophils and epithelial cells in up
to 20 fields and assign the appropriate positive or negative grade for each cell type in
each field. Total the individual grades and divide by the number of fields examined
to arrive at the average score.
*Grading system is only applicable to sputa from adults (>14 years)12, 13. Patients
who are neutropenic may not demonstrate purulence and a clinical history shall be
provided to the laboratory so that sputum specimens are not rejected.
ii) Number of Squamous epithelial cells (SEC)11.
Examine 20-40 fields under low power.
representative fields that contain cells.
Rejection criteria:
10 SEC / LPF
Acceptable:
<10 SEC / LPF
Average the number of cells in
NOTE: if number of PMN is 10X the number of SECs and there is 3-4+ of a single
morphotype accept the specimen for culture.
Page 4
2) All Other Specimen Types:

Epithelial or Polymorphonuclear (PMN)
Cells
Description
Number/LPF
1+, rare
<1
2+, few
1-10
3+, moderate
11-25
Microorganisms (bacteria, yeast/fungi)
Description
Number/OIF
1+, rare
<1
2+, few
1-10
3+,
11-25
moderate
4+, many
>25
4+, many
>25
Low-power field (LPF) (100); high-power oil immersion field (OIF) (1000).
Numbers are based on an average of 10 fields.
A thorough examination of all areas of the Gram-stained smear should be made
microscopically first under LPF (100) to observe any inflammatory cells and then
under OIF (1000) to observe bacteria.
NOTE: For fluid specimens where cytospin or similar preparations are used, the
quantification guidelines do not apply.
3) QA Criteria for Gram Stain Interpretation:
For scoring Gram stains a standard error classification schema is recommended as
follows:
MINOR ERROR:
Report the presence of polymorphs when not present
MAJOR ERROR:
Report the presence of an organism not present or;
Failure to report the presence of 1+ to 2+ polymorphs
VERY MAJOR ERROR:
Failure to report the presence of a microorganism
Failure to report the presence of 3+ to 4+ polymorphs
References:
1.
2.
Bartlett, JG, KJ Ryan, TF Smith and WR Wilson. 1987. Cumitech 7B, Lower respiratory tract
infections. Coordinating ed., J.A. Washington II. American Society for Microbiology,
Washington, D.C.
Evangelista, AT and HR Beilstein. 1993. Cumitech 4A, Laboratory diagnosis of gonorrhea.
Coordinating ed., C. Abramson. American Society for Microbiology, Washington, D.C.
Page 5
3.
Kruczak-Filipov P and RG Shively. 1992. Gram stain procedure. In: Clinical Microbiology
Procedures Handbook, Isenberg HD (Ed.), p.1.5.1-1.5.18, American Society for Microbiology,
Washington, D.C.
4. Martin RS, RK Sumarah and EM Robart. 1978. Assessment of expectorated sputum for
bacteriological analysis based on polymorphs and squamous epithelial cells: six-month study. J.
Clin. Microbiol. 8:635-637.
5. Murray PR, and JA Washington. 1975. Microscopic and bacteriologic analysis of sputum. Mayo
Clin. Proc. 50:339-344.
6. Thompson Jr RB, Miller JM. Specimen Collection, Transport, and Processing : Bacteriology. In:
Murray PR, Baron EJ, Jorgenson JH, Pfaller MA, Yolken RH (eds). Manual of Clinical
Microbiology 8th ed. 2003. American Society for Microbiology. Washington DC.
7. Chuard C, CM Antley and LB Reller. 1998. Clinical utility of cardiac valve Gram stain and
culture in patients undergoing native valve replacement. Arch. Pathol. Lab. Med. 122:412-415.
8. Ketai L, T Washington, T Allen and J Rael. 2000. Is the stat Gram stain helpful during
percutaneous image-guided fluid drainage? Acad. Radiol. 7:228-231.
9. Nugent RP, MA Krohn and SL Hillier. 1991. Reliability of diagnosing bacterial vaginosis is
improved by a standardized method of Gram stain interpretation. J. Clin. Microbiol. 29:297-301.
10. Schreckenberger PC. 1992. Diagnosis of bacterial vaginosis by Gram-stained smears. Clin.
Micro News. 14(16): 121-128
11. Clinical Microbiology Procedures Handbook 2nd Ed 2007
Isenberg HD (ed) p 3.2.1.20
12. Zaidi A.K., and L.B.R.eller. 1996. Rejection criteria for endotracheal aspirates from pediatric
patients. J Clin. Microbiol. 34: 352-354
13. Thakker JC, Splaingard M, Zhu J, Babe lK, Bresnahan J , Havens PL. Crit Care Med 1997 Aug;
25(8): 1997 . Survival and functional outcome of children requiring endotracheal intubation during
therapy for severe traumatic brain injury.
Page 6
Staphylococcus Identification Scheme

Gram Pos Cocci in clusters
Catalase positive
Latex Kit or Slide Coag
negative
report: coagulase
negative staphylococci
negative
positive
tube coag
colonial morphology
consistent with S. aureus?
positive
report: possible S. aureus (1, 3)
perform or refer out for Staph ID and sens
NO
YES
report: S. aureus (3)
tube coag 2
negative
report: possible S. lugdenensis (4)
1.
2.
3.
4.
positive
report: S. aureus (3)
Some colonies of MRSA and S. intermedius are clumping factor negative.

False positive Staph aureus results can be obtained with S. saprophyticus.
Remember to do an Oxacillin plate to rule out MRSA.
Refer for full staph identification.
Page 7
COAGULASE NEGATIVE STAPHYLOCOCCUS SPECIES (CNS)

Background:
Traditionally, medical technology students were taught that there were two types of
staphylococci. The first group was coagulase positive (ie. S. aureus) and caused
infection. The second group was coagulase negative staphylococci (CNS), and with the
exception of S. saprophyticus and S. epidermidis, did not cause infection.
As with all traditions, time brings change. Advances in medical technology have led to
more invasive techniques. Patients may have one or more of a variety of medical
devices, such as catheters and prosthetic device implants. Chemotherapy and
immunodeficient diseases have led to an increase in the number of immunocompromised
patients. IV drug users are at increased risk of infection due to CNS. These and other
factors have allowed CNS to take on a new role as a major nosocomial pathogen.
The majority of CNS isolates are found in hospitalized patients and are often resistant to
antibiotics. Methicillin resistant CNS are more frequently isolated than MRSA in a
facility. CNS is a predominant part of the normal skin flora, and may be present in a
specimen as a contaminant or a pathogen. Some species of CNS produce a slime layer,
allowing them to adhere to medical devices such as catheters, shunts, heart valves, graft
material, implants and artificial joints. These factors also make the organism more
difficult to treat, and difficult to determine clinical significance when isolated in a
specimen.
S. epidermidis is the most common nosocomial CNS. Infections include bacteremia,
post-operative cardiac infections, and infections of shunts, orthopedic devices and
prosthetic implants. It has been isolated in patients undergoing Continuous Ambulatory
Peritoneal Dialysis. There seems to be no clear standard on the reporting of S.
epidermidis in urines. It is a recognized pathogen in patients with prostatic infection,
prosthetic devices or post transplantation. It rarely causes urinary tract infections in
females.
S. saprophyticus is an important urinary pathogen, especially in young, sexually active
females. Males may also develop nonspecific urethritis. It can usually be quickly
differentiated from other CNS by using a novobiocin disk. S. saprophyticus is resistant,
while other CNS are sensitive.
S. lugdenensis was first described in 1988 in France. It is a CNS that can be
misidentified as S. aureus if the slide coagulase test is the only test used. The organism is
slide coagulase positive, tube coagulase negative, PYR positive and ornithine
decarboxylase positive. It is also very susceptible to penicillins. It closely resembles S.
aureus, in that it has similar virulence factors and produces similar types of infections.
Most reported infections are skin and soft tissue infections, and blood and vascular
catheter infections. The organism is part of the normal skin flora.
Page 8
S. schleiferi can also be misidentified as S. aureus if only the slide coagulase test is used.
It is slide coagulase positive, tube coagulase negative, PYR positive, and ornithine
decarboxylase negative. It too appears to be a significant opportunistic pathogen
associated with empyema, wound and IV catheter infections and bacteremia. As with S.
lugdenensis, many affected patients have defective immune systems due to underlying
disease.
S. haemolyticus has been reported to be the second most commonly isolated CNS and has
been isolated in endocarditis, septicemia, UTIs, bone, wound and joint infections.
Other CNS less commonly isolated include S. hominis, S. warneri, S. capitis, S. simulans,
S. cohnii, S. xylosus, and S. saccharolyticus.
Procedure:
A review of the literature suggests that CNS be identified to species:
o when isolated from normally sterile sites-blood, CSF and joint and other fluids.
Regarding blood cultures, a CNS isolated from one bottle only is considered to be a
contaminant. It is not necessary to identify or report susceptibility results. Laboratories
may store the isolate in case further testing is requested. Isolates from several bottles are
identified to species level. If the same species is isolated, it is a significant finding and
susceptibility testing should be performed. If different species are identified, it is
probably a contaminated set of cultures and susceptibility testing should not be
performed. CNS can be contaminants in CSF and other sterile fluids, therefore always
correlate with clinical information and direct gram smear results to determine the
significance of the isolate.
o when repeatedly isolated from wound specimens with a good gram smear (showing
the presence of GPC and WBC).
o when isolated from shunts, catheters, or prosthetic devices.
o to differentiate CNS from S. saprophyticus in midstream urines.
o when isolated from catheter or cystoscopy urine specimens
It is not appropriate or cost effective to do identification and susceptibility testing on
every CNS isolated. Each laboratory should look at their particular situation and
establish policies specific to their needs. If the CNS is isolated as part of the normal
flora, then it should be reported as such-normal flora. Although a review of the literature
and laboratory practice shows that there is consensus that full ID & susceptibility testing
is not always required, there is no absolute consensus as to when ID & susceptibility
testing should be performed. It remains the responsibility of the laboratory to look at
patient demographics, type of service, etc and decide on their policies. It is advisable to
consult with a Medical Microbiologist or Infectious Disease specialist when developing
these policies.
Page 9
References:
1. Identification of Commonly Isolated Aerobic Gram-Positive Bacteria pg 1.20.1-1.20.3 in
Handbook of Clinical Microbiology Procedures 1992. ASM Washington DC
2. Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A.
Pfaller, Manual of Clinical Microbiology, 9th ed., 2007 American Society
for Microbiology.
3. von Eiff C, Proctor, RA, Peters G. 2001. Coagulase-negative staphylococci in Post
Graduate Medicine online Vol 110 No 4 October 2001. www.postgradmed.com
4. Laboratory Detection of Oxacillin-resistant Coagulase-negative Staphylococcus spp. 1999.
Fact Sheet Issues in Healthcare Settings. CDC Atlanta GA.
5. Dowell EB, James. JF. Speciation of Coagulase Negative Staphylococci 2001 in
Contagious Comments, Vol XVI Number 2. The Childrens Hospital, Department of
Epidemiology, Denver CO.
6. Baron, EJ. Staphylococcus lugdenensis: Not your Fathers (or Mothers)
Coagulase-Negative Staphylococcus. 2003. www.antibiotic-consult.com
7. Ling, ML. Staphylococcus lugdenensis: Report of first case of skin and soft tissue
infection in Singapore. Singapore Med J 2000 Vol 41(4): 177-178
8. Canadian Paediatric Society. Coagulase negative staphylococci as pathogens:
Believe it or not? Canadian Journal of Paediatrics 1994: 1(2):61-3 Reaffirmed
April 2002.
9. CMPT Critique. M93-1 Urine Sample: Coagulase Negative Staphylococcus
(S. epidermidis) November 1999.
10. CMPT Critique M94-1 Deep Wound: Coagulase Negative Staphylococcus species
(Staphylococcus epidermidis) Feb 2000.
Page 10
BACTERIOLOGY CULTURE PLANTING PROCEDURES

Media Use:
Most media used in clinical bacteriology laboratories are commercially available, either
completely prepared or as dehydrated powder. The number and types used vary from
laboratory to laboratory depending on budgets, personnel and personal bias. Media
selection is governed by the specimen source. Media that allow growth of the majority of
potential pathogens from a particular source are used to recover the pathogen(s).
Inoculation and Isolation Techniques:
Traditional identification methods depend on obtaining isolated colonies. Many clinical
specimens contain a mixture of bacteria; therefore specimens are streaked to produce
single colonies of each organism type present. Isolation techniques include streaking the
inoculum with a wire loop or spreading with a glass rod, or, inoculating pour plates. The
choice depends on the material to be cultured, the result desired, and the laboratorys
preference.
Streak Plate:
The streak plate method is practical and fast. All streak plate methods are designed to
provide a continuous dilution of the specimen in order to give isolated colonies. Either a
stainless steel or nickel and chromium (Nichrome) wire or a plastic bacteriologic loop is
acceptable, although Nichrome should not be used for anaerobic bacteria. In the most
common method a portion of the specimen is deposited in one quadrant of an agar plate
free of moisture.
The method of transferring the inoculum to the plate depends on the specimen type.
Liquid specimens are usually inoculated by transfer with a sterile pipette or syringe and
needle. One or 2 drops are placed in the first quadrant of the plate. Urine is an exception
and must be plated quantitatively. (see below)
Specimens received on swabs can be planted directly by rolling the swab over an area
about 2 cm in diameter in the first quadrant of the plate.
Faeces and sputum are most easily inoculated by dipping a swab into the specimen rather
than attempting to use a loop to inoculate plates.
After implantation of the inoculum, a wire loop is flamed and cooled, or a sterile plastic
disposable loop is selected. The loop is held between the thumb and index finger and
passed at a 90 degree angle several times through the initial inoculum into the second
quadrant of the plate as illustrated in Figure 1 (streak area 1). The plate is turned 90
degrees, and the process is repeated, streaking into the third quadrant (streak area 2), and
finally after another 90 degree turn into the fourth quadrant (streak area 3). The loop
is flamed between quadrants unless the inoculum is light or the medium is selective or
inhibitory. When streak plates are used, the laboratory can report relative numbers of
Page 11
bacteria present, which may be helpful to the clinician, particularly if different organism
types are present.
Several methods of semi-quantitation are used (Figure 2a & b). Some laboratories use
very few, few, moderate or many; others use 1+ to 4+, based on the following criteria:
Score
1+
2+
3+
4+
Number of Colonies in Streak Area

1
2
3
<10
<10
<5
>10
<5
>5
>10
<5
>5
Quantitative Methods for Urine:

To determine urinary tract infection, the actual colony count of a urine specimen is
necessary (one colony equals one colony-forming unit, or CFU). For a colony count a
calibrated loop is used.
A calibrated loop of 1 or 10 l is dipped vertically into a well-mixed specimen. One
loopful is streaked down the center of a plate. Without flaming, cross-streaks at a 90
degree angle are made perpendicular to the original streak. Cross-streaks should be close
together and extend toward the edge of the plate.
1 l loop is commonly used in Clinical Microbiology laboratory for urine culture. In
some situations, as in urines obtained during cystoscopy, or by suprapublic aspirate
(SPA) culture using a 10l loop will be needed in order to identify a lower count of
bacteria. The number of colonies growing on the agar plate multiplied by the dilution
factor (103 if a 1 l loop is used and 102 for 10l loop) equals the number of CFU per
millimetre in the original specimen.
Culture Incubation:
Inoculated plates are incubated inverted to prevent the water of condensation from
dropping onto the agar surface, which can result in the colonies coalescing and is a safety
hazard.
The optimal growth temperature for most bacterial pathogens is 35C. Most bacteria
produce visible colonies in about 18 hours, although some require 48 to 72 hours.
Generally bacteria require a relative humidity of 70 to 80%. Most new incubators have a
water reservoir. If an incubator does not have a mechanism for humidity regulation, a
pan containing water kept at a constant level can be placed on the incubators lowest
shelf.
Many bacteria grow well in air but some need either increased CO2 (5 to 10%)
(capnophilic), decreased O2 and increased CO2 (microaerophilic), or anaerobic
Page 12
conditions. Carbon dioxide may be provided by a CO2 incubator, a candle jar, or a

container with a CO2 generating device. A candle jar is simply a wide-mouthed
container with a tightly fitting top. Inoculated media are placed in the jar. A lighted
candle is placed on top of the media, and the top is replaced.
Reference:
Clinical and Pathogenic Microbiology
Page 13
Figure 1
Figure 2a
Figure 2b
Page 14
URINE SPECIMEN PROCESSING

Background:
Urinary tract infections (UTI) are caused by a range of common bacteria, often derived
from the enteric or skin flora. Diagnosis of UTI is accomplished by semi-quantitative
culture of urine and antimicrobial susceptibility testing of potential pathogens present in
significant numbers. This procedure describes the collection of appropriate specimens
and their transport to the laboratory.
Specimen Collection and Transport:
Patient preparation: Instruct the patient to collect a mid-stream specimen of urine into the
specimen container provided. Mid-stream urine is used because the first few ml of urine
passed will contain skin flora from the urethral orifice and will yield potentially
misleading results. Pre-cleaning of the periurethral area is not recommended (Manual of
Clinical Microbiology 9th Ed.). The optimal timing for specimen collection is at the first
voiding of urine in the morning.
Collection, Handling, Storage: Urine is collected into sterile containers. These may be
sterile plain bottles or sterile bottles containing boric acid, which is bacterostatic and
limits overgrowth during transport. Specimens should be transported immediately to the
laboratory. If the delay between collection and culturing is more than 2 hr, specimens not
in preservative must be refrigerated.
Acceptable specimens: Midstream urines, catheterized urines, suprapubic bladder
aspirates and cystoscopy specimens, properly labeled and received within 24 hr of
collection.
Reject the following specimens, which are unsuitable for culture:
1.
Bedpan urines
2.
Condom/Texas catheter urines
3.
Specimen received in non-sterile container
4.
Bag urine
5.
Unlabelled and improperly labelled specimens
6.
Specimens that have leaked out of the container
Inform the ward or clinic when rejecting specimens.
Procedure/Media:
Media Plating Procedure:
1.
Mix urine well.
2.
Hold calibrated loop vertically and immerse the loop just below the surface of the
urine.
Page 15
3.
4.
Spread the urine over the surface of the agar plate as described in Bacteriology
Culture Planting Procedure. Media generally used are Blood Agar and
MacConkey agar or a single media that will support the growth of uropathogens.
Incubate plates aerobically overnight at 35oC.
Specimen Type
MSU
Catheterized urine
Bladder, Suprapubic or
Cystoscopy Urine
Calibrated Loop
Media
1 _l loop
Blood Agar (BA)
1 _l loop
MacConkey Agar
(MAC)
10 _l loop
Incubation
O2, 35C x 24 hrs
O2, 35C x 24 hrs
Dip 'n' Count Procedure:

1.
Mix urine well.
2.
Remove lid with the agar paddle from the dipslide container. Do not touch the
agar surfaces.
3.
Immediately (within 1 hour) dip paddle of dipslide into the urine so both sides of
agar paddle are immersed (fully covered). Alternately pour urine over both sides
of the agar paddle to cover both agar surfaces.
4.
Drain excess urine from the agar paddle by touching edge of paddle against the
edge of the collection container or drain by touching a filter/blotting paper.
NOTE: The agar on the paddle should not touch any other surface. DO NOT put
urine into the dipslide container. Excess urine in the container can re- inoculate
the dipslide, causing falsely increased bacterial counts.
5.
Replace lid and paddle into dipslide container. Label container.
6.
Send dipslide to the laboratory as soon as possible.
Interpretation of Cultures:
1.
2.
3.
Inspect the plates and dipslides for growth and determine the colony count (refer
to Standardization of the Colony Count for Urine Cultures).
Identify isolates of potential pathogens present in significant numbers according
to laboratory identification protocol.
Perform antimicrobial susceptibility tests according to the Antibiotic Reporting
Guideline and laboratory protocol.
Potential Pathogens in Urine Specimens:
Enterobacteriaceae such as E. coli, P. mirabilis. Klebsiella sp.
Pseudomonas aeruginosa
Staphylococcus aureus
Staphylococcus saprophyticus
Coagulase Negative Staphylococcus
-haemolytic Streptococci
Streptococcus pneumoniae
Page 16
Enterococcus spp.
Listeria monocytogenes
Yeast Candida species
These organisms are normally considered contaminants, but may be
significant upon repeat isolation:
Lactobacillus spp.
_-haemolytic Streptococci
Most Gram positive rods such as Diphtheroids
NOTE: ANY FEMALE WITH GBS BACTERIURIA IN ANY CONCENTRATION
DURING HER PREGNANCY SHOULD RECEIVE INTRAPARTUM ANTIBIOTICS.
(SOGC Clinical Practice Guideline No. 149, J. Obstet. Gynaecol. Can. 2004; 26:826832)
References:
Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A. Pfaller,
Manual of Clinical Microbiology, 9th ed.: American Society for Microbiology, 2007.
Page 17
STANDARDIZATION OF THE COLONY COUNT FOR URINE CULTURES

In order to standardize the interpretation of the colony count, the Microbiology Quality
Assurance committee recommends the adoption of the following criteria, as minimum
guidelines. These are based on the information gathered from the survey process, and
from the references provided.
Recommended Standardization of the Colony Count:
Detected Growth
In-dwelling Catheter
Midstream Urine
1l loop
In & Out Catheter

1l loop
1 organism isolated
<107 cfu/L
No significant
growth**
107 cfu/L
ID & Sens
107cfu/L
2 probable pathogens
in equal amounts
ID & Sens both
ID & Sens
predominant org only
1 org >107 cfu/L
2nd org <107 cfu/L
ID & Sens any

amount of growth
>107 cfu/L
ID & Sens both
probable
pathogens
1 org >107 cfu/L
2nd org <107 cfu/L
ID & Sens any

amount of growth
Mixed growth probable

contamination
Mixed growth probable

contamination
ID & Sens any

amount of growth
2 organisms isolated
2 organisms with
one predominate
organism
>2 organisms
Bladder Urine
Suprapubic or
Cystoscopy
10 l loop
ID & Sens any
amount of growth
ID & Sens any

amount of growth
**Exceptions include symptomatic males, adult females with urethritis, patients on

antibiotic therapy, patients with chronic or reoccurring infection, & children under 12
years of age. Isolates from specimens with positive leukocytes and/or nitrites will be
worked up when urine strip values are provided.
Calculation for the Interpretation of the Colony Count:
The colony count is multiplied by 1000 (when 1l calibrated loop is used) or 100 (when
10 l calibrated loop is used) to provide an estimate of the number of colonies per ml.
This number is multiplied by 1000 to equal the number of Colony Forming Units per
litre.
Page 18
References:
1.
College of Physicians & Surgeons of Alberta, Microbiology Laboratory Inspection Form,

(Edmonton: Laboratory Accreditation Program, 1995), criteria M.38.001, 002, page 12.
2.
A Joint Accreditation Program of the College of Physicians & Surgeons of B.C. and the B.C.
Medical Association, Accreditation Protocol Microbiology, (Vancouver: Diagnostic Accreditation
Program), criteria 30, 34, page 7.
3.
Baron Ellen, Peterson Lance, Finegold Sydney, Bailey & Scotts Diagnostic Microbiology,
(Toronto: Mosby,1994), 252.
4.
Kunan, White, Hua Hua, A Reassessment of the Importance of Low-Count Bacteriuria,

(Americian College of Physicians, 1993), 459.
5.
College of Physicians & Surgeons of Manitoba, (Winnipeg: Executive Assistant, April 1998).
6.
National Pathology Accreditation Advisory Council of Australia, Laboratory Assessment

Checklist Microbiology Section, (Canberra: Commonwealth Government Printer, 1987), criteria
6.4.3, page 12.
7.
Nicolle, Harding, Kennedy, McIntyre, Aoki, & Murray, Bacteriuria in Males, (Americian Society
for Microbiology, 1988), 1118.
8.
Shapiro Eugene, Infections of the Urinary Tract, (Yale University of Medicine, 1992), 165.
9.
Henry Isenberg, Clinical Microbiology Procedures Handbook, (Americian Society for

Microbiology/Washington, D. C., 1992), 1.17.7
Page 19
THROAT SWABS
Background:
Throat swab specimens are most commonly collected to diagnose infections caused by S.
pyogenes (Group A haemolytic streptococcus) and occasionally sequelae and should be
reported.
Throat swabs can also yield large (not pinpoint) colony-forming beta-hemolytic
streptococci harboring the Lancefield Group C or Group G antigen belonging to
Streptococcus dysgalactiae subsp. equisimilis.
They are associated with upper
respiratory tract infections similar to S. pyogenes, infections.
Cases of
glomerulonephritis and acute rheumatic fever have been reported. In work up of throat
swabs submitted for acute pharyngitis, Group C and Group G need to be reported.
Culture of any other suspected agents of disease such as: Arcanobacterium hemolyticum,
N. gonorrhoeae, C. diphtheriae shall be performed only at the request of the ordering
physician.
Specimen Collection:
A sterile swab is used to collect the throat swab from the posterior pharynx, tonsils and/or
inflamed areas. The swab is placed into the appropriate transport media, for C & S use
Modified Amies.
Storage Requirements: Place specimens at room temperature if to be processed within 2
hours, if processing to be delayed place into 4 C fridge.
Procedure\Media:
A. Processing of Specimens:
Culture: On the following media, and incubate plate as indicated:
Media
Blood Agar(BA) or selective media
such as Beta Strep Agar
Incubation
CO2 35C x 48 hours
AnO2 35C x 48 hours or /
AnO2 35C x 24 hours and then
CO2 35C x 24 hours
* Some institutions have better recovery incubating anaerobically.
Page 20
Commercial kits for Group A streptococcus (rapid direct tests) are also available. If a
laboratory implements the rapid direct test, two throat swabs should be collected. If the
rapid test is positive the second swab may be discarded; but if the rapid test is negative
the second swab should be cultured, because the sensitivity of these direct tests are
generally <100%.
B. Interpretation of Cultures:
The medium used to isolate S.pyogenes and other beta-hemolytic streptococci is sheep
blood agar with 5% blood, or selective agar containing agents that will suppress the
normal flora of the throat. Anaerobic incubation of the plates may enhance the betahemolysis, thereby making the colonies more easily detectable. If there are no colonies
demonstrating beta-hemolysis after 24 hours incubation, reincubate plates for another 24
hours. If beta-hemolysis is present, perform catalase and if negative, perform PYR &
latex agglutination testing.
C. Susceptibility Testing:
Antimicrobial susceptibility testing of these isolates is not required unless the patient is
known to be allergic to penicillin. Perform antimicrobial susceptibility tests according to
the Antibiotic Reporting Guideline and laboratory protocol.
Reporting Results:
Culture: Quantitate all significant isolates.
i.
ii.
iii.
If culture is negative, report out as 'No Group A, C or G Streptococcus

Isolated'.
If culture is positive for Group A Streptococcus, report 'Group A
Streptococcus Isolated'.
If either Group C or Group G Streptococcus is positive report out as
'Group C Streptococcus' or 'Group G Streptococcus Isolated'.
References
1. Isenberg et al, eds. Clinical Microbiology Procedures Handbook, ASM Press
Pfaller, Manual of Clinical Microbiology, 9th ed.: American Society for Microbiology, 2007.
Page 21
CONJUNCTIVAL SWABS
Background:
Conjunctival swabs are collected for the diagnosis of conjunctivitis. Swabs should be
sent from both the infected and non-infected eye. This allows comparison of flora and
helps determine pathogenity of any organisms isolated.
Swabs should be collected prior to the administration of drugs such as topical anesthetics
or antibiotics. The swab should be sent in Amies transport medium.
Procedure\Media:
a) Direct Examination of Gram stained
smear Note the presence of
polymorphonuclear cells and organisms. Quantitate as per Guideline for
Quantitative Interpretation of Gram Stains.
b) Culture on the following media, and incubate the plates as indicated.
Media
Blood Agar (BA)
ChocolateAgar (CHOC)
G. C. Selective Agar (neonates)
Incubation
CO , 35 C x 48 hours
CO2, 35oC x 48 hours
2
Interpretation of Cultures:
Examine the BA and CHOC plates after 24 hours and 48 hours incubation and the G.C.
plate after 48 and 72 hours incubation. Compare growth from infected and non-infected
eye cultures. This comparison will often provide hints of which organisms are pathogens.
Potential pathogens: S aureus. H.influenzae, M, catarrhalis, N. gonorrhoeae, S.
pyogenes, S. pneumoniae, Moraxella species, and P. aeruginosa . For other organisms, a
significant result is determined by the isolation of a moderate or heavy growth of an
organism that is seen as the predominant organism on the Gram stain. There should be
>1+ polymorphonuclear cells on the Gram smear. Full identification is required to the
species level for all significant organisms.
B. Susceptibility Testing:
Perform antimicrobial susceptibility tests according to the Antibiotic Reporting
Page 22
Guideline and laboratory protocol.

NOTE: There is no method for testing of topical agents.
Reporting Results:
a) Gram stained smear: Report with quantitation the presence of polymorphonuclear
cells and organisms.
b) Culture: Quantitate all significant isolates and report with antimicrobial
susceptibilities. If normal flora is also present, report with quantitation.
References:
1. Cumitech BA. Sep 1994. ASM Press, Laboratory Diagnosis of Ocular Infections
2. Bailey and Scott's Diagnostic Microbiology, 11th Edition 2002. Mosby Inc.
Page 23
SPUTUM /LOWER RESPIRATORY CULTURE

Background:
Lower respiratory tract specimens are primarily submitted for the detection of the
causative agent of pneumonia. The most common specimen type is expectorated or
induced sputum. Bronchial lavage, washes, brushings and transtracheal aspirates may
also be received but require additional handling procedures. The most common causative
agents of bacterial pneumonia are: S. pneumoniae, H. influenzae, S. aureus, M.
catarrhalis, K. pneumoniae, E. coli, and P. aeruginosa.
Collect expectorated or induced sputum into a sterile sputum container (early morning
specimens generally more suitable).
Storage Requirements: Specimens should be delivered promptly (within 2 hours) to
the lab. If a delay in processing is unavoidable the specimen must be refrigerated at 4 C.
Procedure/Media:
a. Assess the quality of the specimen as per Guideline for Quantitative Interpretation
of Gram Stains to determine acceptability for culture.
b. Culture on the following media, and incubate plate as indicated.
Media
Blood Agar(BA)
MacConkey Agar (MAC)
Chocolate Agar (CHOC)
Incubation
CO2,
35C x 48 hours
O2/CO2, 35C x 48 hours
CO2,
35C x 48 hours
Using a sterile swab or loop enter the specimen container and obtain a purulent portion of
the specimen. Plant each plate with the specimen following Bacteriology Culture
Planting Procedures.
After 24 hours incubation the plates are examined and if needed, tests are performed to
determine the organism(s) present. Any plates with significant growth of a potential
pathogen must be quantified, identified, and have susceptibility testing done. Plates
showing only normal flora are then reincubated for another 24 hours and re-read the
Page 24
following day. If any changes are noted do the appropriate testing required to identify the
organism(s) and perform sensitivity testing.
Perform antimicrobial susceptibility tests according to the Antibiotic Reporting Guideline
and laboratory protocol.
Reporting Results
a) Gram stained smear: If the specimen is suitable for culture, report the gram stain
smear result. Report with quantification the presence of polymorphonuclear cells,
squamous epithelial cells and organisms.
If the specimen is unsuitable for culture according to the Q score, report the gram
smear result and also comment: Gram smear indicates the sputum specimen is not
suitable for culture. Please resubmit. (refer to: Guideline for Quantitative
Interpretation of Gram Stains)
b) Culture: Quantify all significant pathogens and report with appropriate antimicrobial
susceptibilities. If only normal oral flora present, report with quantification:
"Growth of Oropharyngeal Flora.
Limitations Of The Procedure:
1) Poor quality specimen will not be cultured.
2) Procedure does not allow for isolation of other agents such as Legionella sp. Submit
urine specimen for antigen detection to the Saskatchewan Disease Control Laboratory
(SDCL). SDCL will culture Legionella sp. and/or bronchoalveolar lavage (BAL).
References:
Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A. Pfaller,
Manual of Clinical Microbiology, 9th ed., 2007: American Society of Microbiology
Page 25
EAR SWABS
Background:
Ear swabs are collected for the diagnosis of otitis externa. Otitis externa is a bacterial
infection of the external auditory canal usually caused by P. aeruginosa, S. aureus,
Group A streptococcus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella
catarrhalis or fungus/yeast. Tympanocentesis fluid is required for the diagnosis of otitis
media, which is cultured as a deep wound.
The ear swab should be collected using sterile swab and sent in Amies transport medium.
Procedure\Media:
a. Direct examination: Gram stained smear note presence of polymorphonuclear
cells organisms. Quantitate as per Guideline for Quantitative Interpretation of
Gram Stains.
b. Culture on the following media, and incubate plate as indicated.
Media
Blood Agar(BA)
Fungal Plate (ie: Sabouraud Dextrose
Agar, Fungal Selective Agar, Phytone)
Incubation
CO2, 35C x 48 hours
O2/CO2, 35C x 48 hours
O2, 30C x 48 hours
optional up to 4 weeks
CO2, 35C x 48 hours
Examine the culture plates after 24 and 48 hours incubation. Potential pathogens are S.
aureus, P. aeruginosa, Group A streptococcus, Haemophilus influenzae, Streptococcus
pneumoniae, Moraxella catarrhalis or yeast. For specimens from neonates only, identify
and report Gp. B. Strep. For other organisms, a significant result is determined by the
presence of a moderate to heavy growth of an organism which is seen as the predominant
organism on the Gram smear.
The Gram smear should also show 1+
polymorphonuclear cells. Fungal plates may be incubated at 30 for 4 weeks.
Page 26
Reporting Results:
a) Gram Stained smear: Report with quantitation the presence of polymorphonuclear
cells and organisms.
b) Culture: Quantitate all significant isolates and report with appropriate antimicrobial
susceptibilities. If normal skin flora is also present, report as normal.
References:
1. Cumitech 10. Dec 1979. ASM. Press, Laboratory Diagnosis of Upper Respiratory
Tract Infection
2. Bailey and Scott's Diagnostic Microbiology, 11th Edition 2002. Mosby Inc.
3. see Antibiotic Reporting Guideline - www.quadrant.net/cpss
Page 27
GENITAL TRACT SPECIMENS

Background:
Genital specimens are usually taken to diagnose infection or to rule out specific sexually
transmitted diseases. Certain pathogens are known to be associated with specific types of
genital infections. The physician will base the selection of culture requests on the type
and location of infection.
Cervical Swabs:
Specimens for N. gonorrhoeae are collected from the endocervical canal using a clean,
sterile swab, and are transported in Amies Charcoal transport medium.
Urethral Swabs:
Exudate from the urethra should be collected at least one hour after urination, using a
clean, sterile swab and transported in Amies Charcoal transport medium.
Vaginal Swabs:
Swabs from the posterior vaginal vault or vaginal orifice are collected and transported in
Amies transport medium. Vaginal swabs are not recommended for isolation of N.
gonorrhoeae from adults, but are indicated for the detection of Bacterial Vaginosis and
Candidal infections.
Group B Streptococcus (Streptococcus agalactiae) Screening for Pregnant Women:
A swab obtained from the combined vaginal and anorectal areas should be collected in
Amies transport medium. Cervical swabs are not recommended for isolation of this
organism.
Procedure/Media:
Direct Smear Examination (Gram Stain):
Gram stain of a vaginal swab is the most reliable method for the detection of
Bacterial Vaginosis, and is also sensitive for the detection of yeast. Follow the
Guideline for Laboratory Processing and Interpretation of Vaginal Specimens in the
Diagnosis of Bacterial Vaginosis and note presence or absence of yeats.
Other vaginal swab specimens (post op, post partum, recurrent no yeast): note
presence of polymorphonuclear cells and organisms. Quantitate as per Guideline for
Quantitative Interpretation of Gram Stains. Note the presence or absence of yeast.
Urethral: reliable for detection of Neisseria gonorrhoeae. Note the presence of
Page 28
polymorphonuclear cells and intracellular gram negative diplococci. Quantitate as per

Guideline for Quantitative Interpretation of Gram Stains.
Cervix: gram stain not indicated for Neisseria gonorrhoeae due to the presence of
normal flora.
Specimen Type
Vaginal - BV and yeast
Vaginal
Genital child
Cervix
Urethral
Rectal
Throat
Combined
Vaginal/Anorectal for
Group B Streptococcus
Media
Not cultured: direct stain
Blood Agar (BA)
Sabourauds Agar with Chloramphenicol
(Phytone)
Other media (Choc, MML) added per
clinical information post partum, post
op, recurrent vaginitis
Blood agar
Sabouraud agar
Modified Martin Lewis (MML)
Modified Martin Lewis (MML)
Group B Streptococcus Broth
Blood Agar (BA) subculture from broth
Incubation
CO2, 35C x 48 hours
O2, 30C x 48 hours
CO2, 35C x 48 hours

O2, 30C x 48 hours
CO2, 35C x 72 hours
CO2, 35C x 72 hours
CO2, 35C x 72 hours
CO2, 35C x 72 hours
CO2, 35C x 24 hours
CO2, 35C x 48 hours
Vaginal Cultures:
BA plates are examined at 24 and 48 hours: Growth of N. gonorrhoeae in any number is
significant. The significance of other organisms, is determined by pure or heavy growth
correlated with their presence as predominant organisms in the Gram smear. The Gram
smear should also show the presence of polymorphonuclear cells.
Cervical and Urethral Cultures:
CHOC and MML plates are examined at 48 hours and 72 hours for N. gonorrhoeae
colonies. Growth of N. gonorrhoeae in any number is significant.
Group B Streptococcus Screening:
The swab is inoculated into the GBS broth and incubated for 24 hours. Subcultures are
made from the broth to the BA plate and the plate incubated for 24 hours. The BA plates
are examined for strep-like colonies at 24 and 48 hours and the organism identified using
the laboratory protocol.
Page 29
Susceptibility testing is not performed for N. gonorrhoeae, Group B Streptococcus and
Yeast. For other organisms, follow the antimicrobial susceptibility tests according to the
Antibiotic Reporting Guideline and laboratory protocol, where appropriate.
All isolates of N. gonorrhoeae are referred to Saskatchewan Disease Control Laboratory
for susceptibility testing.
Isolates of Group B. Streptococcus from patients with a history of penicillin allergy will
need to be tested for susceptibility to erythromycin.
Reporting Results:
a.
Gram stained smear report with quantitation of polymorphonuclear cells and
organisms.
b.
Culture Report pathogens and normal flora with quantitation. Report
susceptibilities where appropriate.
c.
All isolates of N. gonorrhoeae must be confirmed by two methods.
References:
1. Bailey and Scott Diagnostic Microbiology, 11th Ed., Mosby Inc.
Pfaller, Manual of Clinical Microbiology, 9th ed., 2007: American Society of Microbiology
Page 30
GUIDELINE FOR LABORATORY PROCESSING AND INTERPRETATION OF VAGINAL SPECIMENS

IN THE DIAGNOSIS OF BACTERIAL VAGINOSIS
Background:
Bacterial vaginosis (BV) as a specific clinical entity has been recognized since the 1950s
and is characterized by increased, malodorous vaginal discharge. It is associated with
marked changes in microbial flora often described as a change in local vaginal ecology,
and a notable absence of inflammation. A reduction in Lactobacillus spp. and an increase
in Gardnerella vaginalis, several anaerobic species including Mobiluncus spp.,
Prevotella bivia, Peptostreptococcus spp. and others such as Mycoplasma hominis have
been described. The stimuli for these changes are very poorly understood. While BV is
often of only minor clinical consequence to the women affected, it is common and recent
work has heightened the importance of its recognition. It is clearly associated with
several obstetric and gynecologic conditions, most notably premature labour, and often
responds to antimicrobial therapy.
Clinical diagnosis of BV remains difficult despite the use of formalized clinical criteria
first proposed by Gardner and Dukes1 and formalized by Amsell.2 Criteria include visual
change in discharge, increase (>4.5) in pH, presence of clue cells (epithelial cells
coated with bacteria) in microscopic wet mount, and a fishy odor when discharge is
mixed with 10% KOH. The difference between Homogenous, grey-white adherent
discharge and normal discharge is often subtle and microscopy to detect clue cells is
rarely performed in Canadian primary care settings.
Laboratory diagnosis is essential and in recent years has focused on the morphologic
characteristics distinguishable on simple Grams stain of vaginal secretions.3,4 Culture for
Gardnerella vaginalis was advocated for many years but has been found to be poorly
predictive of clinical BV and culture for anaerobic organisms and Mycoplasma spp. is
impractical in the routine diagnostic laboratory.
Purpose:
Specimen Acceptability:
That the presence or absence of epithelial (clue) cells be reported to evaluate
specimen acceptability. If epithelial cells are absent, the specimen should be
considered inadequate or inappropriate for use.
Scoring System:
That the Nugent numerical scoring system on Gram-stained smears of vaginal
secretions be utilized.
That there be an age cut-off of >12 years and < 55 years for application of the
interpretive criteria of Bacterial Vaginosis by Q-score.
That although the Q-score in the pre-pubescent and post-menopausal age
Page 31
categories is of less value, if the microscopic picture is consistent with BV, but the
specimen specified as having been collected from a prepubescent individual, further
investigation is warranted and the results should not be ignored and be discussed with
the physician.
NOTE: The Nugent system was validated using smears made with a modified Gram
Stain4,5,6. This modified staining method recommended by Spiegel, utilizes a basic fuchsin
counterstain to minimize over-decolorization of gram-positive bacteria and to enhance
detection of gram-negative bacteria. It is acknowledged however, that the use of this
modified Gram Stain is not common practice in Canada.
NOTE: The wording of the score interpretations was suggested by Nugent and
subsequently endorsed.
Nugent Scoring System:
Gram-stained slides are examined under oil immersion (1000). Smears are observed
and quantitated for the presence of the following morphotypes:
Large gram-positive bacilli (Lactobacillus morphotypes)
Small gram-variable bacilli (Gardnerella morphotypes)
Curved gram-negative or gram-variable bacilli (Mobiluncus morphotypes)
The number of organisms seen is quantitated according to the following scale:
1 + = <1 organism per field
2 + = 14 organisms per field
3 + = 530 organisms per field
4 + = >30 organisms per field
A total numerical score is calculated by summing the scores for the three components
as indicated in the following table:
Lactobacillus
4+
Score
0
Gardnerella
4+
Score
4
Mobiluncus
4+
Score
2
3+
3+
3+
2+
2+
2+
1+
1+
1+
The total score is interpreted and reported as follows:

0-3
Gram stain indicates normal bacterial vaginal flora
Page 32
= TOTAL SCORE
46
Gram stain reveals altered vaginal flora that is not consistent with
bacterial vaginosis. This frequently represents a transitional stage. If signs
and/or symptoms persist, repeat testing is warranted
7 10 Gram stain consistent with bacterial vaginosis
References:
1.
2.
3.
4.
5.
6.
Gardner HL, Dukes CD. Haemophilus vaginalis vaginitis. A newly defined specific infection
previously classified "nonspecific" vaginitis. Am J Obstet Gynecol 1955;69:962-976.
Amsel R, Totten PA, Spiegel CA, Chen KC, Eschenbach D, Holmes KK. Nonspecific vaginitis:
diagnostic criteria and microbial and epidemiologic associations. Am J Med 1983;74(1):14-22.
Nugent RP, Krohn MA, Hillier SL. Reliability of diagnosing bacterial vaginosis is improved by a
standardized method of gram stain interpretation. J Clin Microbiol 1991;29(2):297-301.
Spiegel CA, Amsel R, Holmes KK. Diagnosis of bacterial vaginosis by direct gram stain of
vaginal fluid. J Clin Microbiol 1983;18(1):170-7.
Spiegel CA. Bacterial vaginosis. Clin Microbiol Rev 1991;4(4):485-502.
Spiegel CA. Bacterial vaginosis: changes in laboratory practice. Clin Microbiol Newsletter
1999;21:33-37.
Page 33
STOOL CULTURES
Background:
Enteric pathogens include Salmonella and Shigella sp., Campylobacter, E. coli 0157:H7,
Yersinia enterocolitica, Clostridium difficile, Aeromonas and Plesiomonas. Vibrio
(cholerae and parahemolyticus) are an important cause of diarrhea in other parts of the
world. S. aureus and Candida albicans may be found in pure cultures from patients on
broad-spectrum antibiotic therapy.
In adult patients who develop diarrhea 3 days after hospitalization,
C. difficile is the most common pathogen. Stools from these patients are tested for the
presence of C. difficile toxin only.
Specimens from outbreaks, as defined by Public Health must be sent to Saskatchewan
Disease Control Laboratory with the outbreak number.
When investigating patients suspected of being in a carrier state refer to the
Saskatchewan Disease Control Laboratory.
Freshly passed stool specimens should be transported to the laboratory within 30 minutes
of collection, and processed in 2 hours. If there is a delay in transport and/or processing,
the specimen should be transferred into a transport container with Cary-Blair medium.
Specimens should be up to the fill line in the transport container. Rectal swabs may be
adequate for the detection of pathogens in acute infections, but are NOT the preferred
specimens. Ensure that rectal swabs are for C & S, and not for isolation of N.
gonorrhoeae. Submit one specimen per stool sample, to a maximum of 2 stool samples,
ideally on separate days.
Stools for C. difficile toxin testing should be sent in a sterile container without transport
medium.
Unacceptable Specimens:
1. Specimens in containers with external contamination.
2. Specimens with contaminants such as urine or tissue paper.
3. Specimens not correctly identified will be rejected if the discrepancy cannot be
rectified.
4. Stool in SAF.
In all cases the ward or physician will be notified and a repeat specimen requested.
Page 34
Procedure/Media:
Culture on the following media, and incubate the plates as indicated.
Media
Xylose Lysine Deoxycholate (XLD),
Hektoen, Salmonella-Shigella (SS), or
Decoxycholate Agar (DCA) - selective for
Salmonella
Sorbitol MacConkey (SMA)
Campylobacter Agar
When requested or clinically indicated culture to:
Media
Blood Agar (BA) or Aeromonas selective
Thiosulfate Citrate Bile Salts Sucrose (TCBS)
- selective for Vibrio
Yersinia Agar (CIN)
Incubation
O2, 35C x 24 hours
O2, 35C x 24 hours
O2, 35C x 24 hours

Microaerophilic, 42C x 48-72 hours
Incubation
O2, 35C x 24 hours
O2, 35C x 48 hours
O2, 30C x 72 hours
Suspicious colonies of enteric pathogens should be subcultured and identified using the
laboratory identification system. i.e. conventional or automated methods as applicable.
Reporting Results:
Isolation of Salmonella, Shigella, Campylobacter, E. coli 0157:H7, Yersinia
enterocolitica, Plesiomonas, Aeromonas, and Vibrio are considered significant. A
pathogen specific negative report should be provided for each pathogen ruled out.
Antibiotic susceptibility testing is not done on E. coli 0157:H7 since its treatment is
associated with an increased risk of HUS and it is a self-limited disease. It is also not
done on Campylobacter and Yersinia sp, Aeromonas, Plesiomonas and Vibrio sp. For
Salmonella sp, the illness is also self-limited and the antibiogram is done and released
only in specific circumstances (elderly, immunosuppressed, infant (<2 years), severe
disease, presence of S. typhi).
If there is a concomitant isolate from a blood culture, antimicrobial susceptibilities should
be reported on the blood isolate.
* see Antibiotic Guidelines for more information
Page 35
References:
1. Bailey and Scotts Diagnostic Microbiology, 11th Edition., Mosby Inc.
2. Cumitech 12A Diagnosis of Bacterial Diarrhoea. 1992. ASM Press.
Page 36
INVESTIGATION OF INFECTIOUS DIARRHEA

Diarrheal illness is a significant health problem. Guidelines for testing of stool
specimens in the investigation of infectious diarrhea are based on current literature and
on guidelines from other Provinces (Ontario, Alberta and British Columbia, most
recently).
The most common guideline requires:
the clinical history indicating symptoms;
their duration;
recent travel;
antimicrobial use and;
any underlying medical conditions.
Bacterial Infections
a) Stool for C&S
Initially a single stool should be ordered in patients with symptoms of < 5 days
duration and where antibiotic associated diarrhea is not suspected. Stool for C&S
will detect Shigella sp, Salmonella sp, Campylobacter sp, Aeromonas and E. coli
0157. If other pathogens e.g. Vibrio sp or Yersinia enterocolitica are suspected, the
laboratory must be informed. If the first stool culture is negative, and symptoms
persist, a second sample may be submitted. Up to two specimens may be collected on
consecutive days. Stool for C & S should be submitted in enteric transport media or
Carey Blair transport media.
b) C. difficile toxin test should be ordered on patients who have diarrhea secondary to
antimicrobial use. Antibiotic associated diarrhea may occur up to 8 weeks after
antibiotics have been stopped. Testing should be performed on outpatients who have
recently been on antibiotics. A single sample should be submitted. If results are
negative but symptoms persist, a second sample may be submitted 5-7 days after the
first.
C. difficile is the most common cause of infectious diarrhea in hospitalized patients
who develop diarrhea >3 days after admission. C. difficile should be considered in
other cases of persistent diarrhea, in which no other causative agent has been
identified. Stool for C. difficile toxin testing should be transported in a sterile
container without preservative.
C. difficile is not a cause of disease in children under the age of one-year; therefore
testing should not be performed.
C. difficile toxin test should not be done as a test of cure.
c) Routine culture of stool, and O&P examination are not indicated in patients who
develop diarrhea > 3 days after admission to the hospital.
Page 37
Ova and Parasites Investigation

a) One stool sample is recommended for initial ova and parasite examination.
Specimens should be transported in SAF preservative
b) Additional samples may be examined, if clinically required, after the results of the
first examination are known. In special circumstances, e.g. patients with history of
travel to the tropics, immunocompromised patients, etc., please consult the
laboratory.
Two stool samples may only be requested in the following high risk cases:
patients with chronic diarrhea
returning travellers with diarrhea
other high risk categories of patients (e.g. immunosuppressed patients, patients on
steroids, male homosexuals)
.
Exclusions
These guidelines may not apply to the following:
To work up food borne outbreaks of diarrhea, need to refer to the provincial
laboratory to cover such agents as Bacillus cereus, Staphylococcus aureus and
Clostridium perfringens. The initial specimen should be stool sample, taken as soon
as possible. This result is used to determine the work up for food samples.
Where an infectious etiology is not a consideration.
If a laboratory is not able to perform these tests as part of the work-up, then the stool
should be referred to a reference laboratory to perform this level of testing.
References:
J. CLIN MICRO: Aug 93
Application of Rejection Criteria for Stool Cultures for Bacterial Enteric Pathogens. Fan
et al. Pages 2233-2235.
JAMA Feb 16, 1990 Vol: 263 #7
Inappropriate Testing for Diarrhoeal Diseases in the Hospital.
Siegel D.K., Edelstein P.M.
Am. J. of INFECTION CONTROL: Dec 88 Vol 16 #16
Yield of Stool Culture, Ova and Parasite tests and C. difficile determinations in
nosocomial diarrhoeas. Yanelli et at. Pages 246-249.
Page 38
DEEP WOUND, ABSCESS AND PUS SPECIMENS

Background:
Infections in deep wounds and abscesses are often caused by a mixture of aerobic and
anaerobic organisms.
Specimen collection and Transport:
Pus from an abscess or deep wound should be sent in a clean sterile container and/or an
anaerobic transport container.
Procedure/Media:
Direct examination of Gram stained smear-Note the presence of polymorphonuclear
cells, squamous epithelial cells and organisms. Quantitate as per Guideline for
Quantitative Interpretation of Gram Stains.
If Actinomyces sp. or Nocardia sp. is requested or suggested on gram stain (branching or
beaded gram positive organisms), the Modified Acid Fast stain should be performed. If
the Modified Acid Fast stain is not performed in your laboratory, refer to a reference
laboratory capable of isolating these organisms.
Culture on the following media, and incubate the plates as indicated.
Media
Incubation
Blood Agar (BA)
CO2 35C x 48 hrs
O2/CO2 35C x 48 hrs
CO2 35C x 48 hrs
Anaerobic Agar (BRUC)
AnO2 35C x 72-96 hrs
Other anaerobic agars as per laboratory protocol
If Actinomyces sp. requested or questioned on direct smear, incubate anaerobic media for
7 days.
Examine the aerobic plates daily for the total incubation time; and the anaerobic plates
after 48 hours and 4 days. Potential pathogens include such organisms as S. aureus,
Beta haemolytic streptococci, Pasteurella sp., Capnocytophaga sp. (animal bites)
Page 39
Eikenella sp. (human bites) , Enterobacteriaceae, P. aeruginosa, anaerobes. Correlate

with the results of the direct gram smear.
Deep Wound, Abscess
No
Are any of
them
listed?*
>3
How many
potential
pathogens?
Yes
<3
Minimal identification
and sensitivity screen
Is it a good
quality
specimen?
Consult others (supervisor or

MOC) to determine possible
significance
No
Yes
Full Work-up
ID and SENS as
appropriate
Report
Yes
Workup
required?
No
End
Potential Pathogens:
S. aureus
Beta haemolytic streptococci
Pasteurella sp.
Capnocytophaga sp. (animal bites)
Eikenella sp. (human bites)
Enterobacteriaceae,
P. aeruginosa
anaerobes
*Listed Organisms:
S. aureus - rule out MRSA
beta-hemolytic streptococci (groups A,
B, C, F, and G)
Yeast only when isolated in moderate to
abundant amounts (consult with MOC
or supervisor before reporting)
Pseudomonas species
Enterococcus species rule out VRE
Bacteroides fragilis group
Actinomyces israelii
Clostridium perfringens - if predominant
Page 40
Reporting Results:
Gram stained smear: Report with quantitation the presence of polymorphonuclear cells,
squamous epithelial cells and organisms.
Culture:
a. Negative report : No growth , Mixed aerobic flora, Mixed anaerobic flora, Mixed
aerobic and anaerobic flora Including Listed Organisms or Type of flora,
depending on site
b. Positive report: Report potential pathogens and sensitivities (as determined by
organism). Quantitate. Single isolates of anaerobes may require susceptibility
testing.
c. If organisms seen in the direct smear do not appear in culture, and anaerobic
specimen was not submitted, it might suggest that the organisms seen failed to
grow indicating the presence of fastidious or anaerobic organisms. It could also
indicate that the gram stain was interpreted incorrectly. It is helpful to re-check
the direct smear. If the gram stain is correct, the comment Organism(s) seen in
direct smear did not grow on aerobic culture, suggesting the presence of anaerobic
or other fastidious organisms or previous antibiotic therapy.
References:
1. Isenberg, H. 1992. Clinical Microbiology Procedures Handbook.
Microbiology. Washington DC.
American Society for
2. Miller, J.M. 1996. A Guide to Specimen Management in Clinical Microbiology. American

Society for Microbiology. Washington DC.
3. Murray, P.R. 1996. ASM Pocket Guide to Clinical Microbiology. American Society for
Washington, DC.
Page 41
SUPERFICIAL WOUND CULTURES

Background:
Superficial skin swabs are collected from lesions, open wounds, open abscesses, rashes.
Usual skin flora can contaminate the specimen if care is not taken to properly collect the
swab. Superficial swabs are not suitable for the recovery of anaerobes.
Specimens should be collected following appropriate skin decontamination to reduce the
presence of contaminating organisms. Specimens should be collected using a clean,
sterile swab and sent in Amies transport medium.
Procedure/Media:
A. Processing of Specimen:
Direct examination: Gram stained smear - note the presence of polymorphonuclear cells,
squamous epithelial cells and organisms. Quantitate as per Guideline for Quantitative
Interpretation of Gram Stains.
No. of
neutrophils
0
1-9
10-24
25
Quantity of cells per 10x (objective lens) microscopic field

Q-value for
Q-value for squamous epithelial cells present
neutrophils
in following no.
0
1-9
10-24
25
0
-1
-2
-3
0
(1)
0
0
0
1+
1
0
-1
-2
2+
+2
+1
0
-1
3+
+3
+2
+1
0
Attach Q-values to squamous cell and neutrophil quantities. Add the two Q-values
together. Specimens with positive Q-values are more likely to contain increased numbers
of potential pathogens and decreased numbers of potential contaminants. Specimens with
negative Q-values (or a Q-value of zero) are likely to be contaminated with the local
flora. Specimens with no squamous cells or neutrophils are scored as 1, allowing
neutropenic patients or those with necrotic or serous secretions to be processed as
acceptable.
NOTE: The first row of numbers in the table is the Q-value for squamous epithelial cells
only. The following four rows are the Q-values for the sum of the neutrophils and
squamous epithelial cells.
Page 42
Culture: On the following media, and incubate plate as indicated:

Media
Blood Agar (BA)
Colistin Nalidixic Acid Agar (CNA)/PEA
- optional
If tracheal swab or from chest tube site, add
Chocolate Agar(CHOC)
- optional
CO2
O2/CO2
CO2
CO2
Incubation
35C x 48 hrs
35C x 48 hrs
35C x 48 hrs
35C x 48 hrs
Examine the plates after 24 and 48 hrs incubation. Potential pathogens include S. aureus,
Beta hemolytic Streptococcus species, P. aeruginosa. A heavy, pure growth of other
organisms that is consistent with the predominant organism seen in the direct smear is
significant if there are 1+ polymorphonuclear cells seen.
Reporting Results:
A. Gram stained smear: Report with quantitation the presence of polymorphonuclear
cells, squamous epithelial cells and organisms.
If Q-score has a negative value, add a report comment such as: Microscopy of
Gram-stained smear indicates potential contamination with skin flora.
B. Culture:
a. Negative report: No growth or other normal type of flora dependent on site
as per laboratory protocol.
b. Positive report: Quantitate all significant isolates and report with appropriate
antimicrobial susceptibilities. If normal skin flora also present, report with
quantitation. Or, if other normal flora, report with quantitation.
References:
1. Isenberg, H. 1992. Clinical Microbiology Procedures Handbook, American Society for
2. Miller, J.M. 1996. A Guide to Specimen Management in Clinical Microbiology, American
Society for Microbiology. Washington DC.
Page 43
3. Murray, P.R. 1996. ASM Pocket Guide to Clinical Microbiology, American Society for
Pfaller, Manual of Clinical Microbiology, 9th ed., 2007: American Society of Microbiology;
Washington, DC.
Page 44
BLOOD CULTURE PROCEDURE

Background:
The detection of microorganisms in a patient's blood has diagnostic and prognostic
importance. When bacteria multiply at a rate that exceeds the capacity of the
reticuloendothelial system to remove them, bacteremia results. Bacteria enter the blood
from extravascular sites via lymphatic vessels. Blood cultures are essential in the
diagnosis and treatment of the etiologic agent of sepsis.
Specimen Collection:
1. Specimens must be collected aseptically following the laboratorys venipuncture
protocol.
2. A set is the total number of blood culture bottles drawn from two sites, with two
bottles taken from site 1 and one bottle taken from site 2. All three bottles are taken
during the same visit to the patient.
3. The table illustrates the optimum schedule.
Bottles/Set
Adult
Routine
or
ANY adult on
antibiotics
Adult
Endocarditis
FUO* on
antibiotics
Neonates
Children < 4 yrs.
Request for yeast

or candidemia
Site 1:
1 aerobic
1 anaerobic
Volume/Bottle
10 ml
7 ml
Site 2:
1 aerobic
Site 1:
1 aerobic
1 anaerobic
10 ml
Site 2:
1 aerobic
Site 1:
1 pediatric
10 ml
Site 2:
1 pediatric
1 aerobic
0.5-3 ml
10 ml
7 ml
# of Sets
0.5-3 ml
Timing
No time required between
draws from site 1 and site
2
1 hour**
The first set of three
bottles is drawn as above,
and an hour later, the
second set of three bottles
is drawn
NOTE: * FUO Fever of Unknown Origin (ie. 3 weeks of fever above 38C)
** In severe cases antibiotics may need to be started immediately after collection
of the first set.
Page 45
It is recommended to collect the blood just prior to administration of antibiotics.

Blood drawn through an intravenous or intra-arterial catheter is acceptable only if
the blood cannot be drawn from a peripheral venipuncture.
Volume:
1. The volume of blood drawn is dependent upon the blood culture system used. There
is much published evidence that a total volume of 30 ml per febrile gives optimum
recovery from adult patients.
2. The volume of blood is critical because the concentration of organisms in the
majority of bacteremias is low. In infants and children, the concentration of
microorganisms during bacteremia is higher than in adults; therefore, less blood is
required for culture.
3. The recommended blood to broth ratio is 1:5 to 1:10. Dilutions beyond 1:10 may
occur in blood cultures of infants and small children.
4.
Collect a maximum of 30 mls for adults, maximum of 5 mls for children, and any
obtainable amount for infants.
Unacceptable Specimens:
1. Bottles with external contamination.
2. Specimens incorrectly identified. In these cases the ward or physician must be
notified immediately and a repeat specimen requested.
Incubation:
For patients presenting with an unknown fever and if endocarditis is suspected, up to 3
weeks incubation may be required.
Materials, Equipment and Reagents: As per your laboratory procedure.
Procedure:
A.
Collection of Specimen
1. Remove flip caps from the blood culture vials and clean vial tops with an
alcohol swab.
2. Select the vein and prepare the arm using a double application of 70% alcohol
starting at the centre of the site and swabbing concentrically for 1 minute.
3. Allow the venipuncture site to dry.
Page 46
4. Do not touch the venipuncture site after preparation or prior to phlebotomy.

5. Perform venipuncture.
6. Transport directly to laboratory.
In the Laboratory
Proceed with incubation and subculture of the bottles as per the manufacturers
instructions for the system involved.
B. Detection and Work-Up of Positive Cultures
Gram Smear:
All bottles flagged as positive by the automated system, or detected as positive by
visual means such as turbidity, must be examined by preparation of a gram smear.
NOTE:
Results of gram smears must be called to the ward/physician stat.
Subculture:
Media
Blood Agar (BA)
ChocolateAgar (CHOC)
Anaerobic media eg. Brucella
Incubation
CO , 35 C x 48 hours
AnO2, 35oC x 72 hours
2
Identify isolates and perform susceptibility testing as per your laboratory protocol.
Reporting:
Negative No growth after 5 days incubation, or as per manufacturers instructions.
Positive Report organism with corresponding antimicrobial susceptibility.
NOTE: Organisms that are normal skin commensals such as coagulase negative
staphylococci, may be contaminants. The isolation of this type of organism in one
bottle/culture only may indicate contamination. This will need to be resolved by
discussion with the clinician. Reporting of contaminants may result in the inappropriate
use of antibiotics.
References:
1. CUMITECH 1C Blood Cultures 111 (2005)
CEREBROSPINAL FLUID AND STERILE BODY FLUIDS
Page 47
CEREBROSPINAL FLUID AND STERILE BODY FLUIDS

Background:
Bacterial meningitis is the result of infection of the meninges caused by aerobic or
anaerobic organisms. The specimens cultured include cerebrospinal and ventricular shunt
fluid.
Sterile body fluids include specimens such as joint, pleural, peritoneal and amniotic fluid.
CSF and other sterile body fluids may contain very few organisms per milliliter of fluid
and the concentration of the specimen is recommended. All isolates of sterile body fluids
must be reported.
Specimen Collection and Transportation:
CSF and other sterile body fluids should be collected in a sterile tube. For sterile body
fluids, if there is enough specimen, inoculate either an aerobic blood culture bottle or a
pediatric blood culture bottle. Process blood culture according to laboratory procedure.
Do not refrigerate the specimens collected.
PCR for Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae
on CSF specimens may be submitted upon request and review of the MHO.
Procedure/Media:
a) Preparation of CSF specimens
1.
Record volume and gross appearance of CSF, i.e., clear, bloody, cloudy,
xanthochromic. If the specimen is cloudy, a gram stain should be done
before the centrifugation.
2. Centrifuge the CSF specimen for Gram stain.
3. Centrifuge the specimen:
a. If the volume of fluid is >1 ml, centrifuge for 15 min. at 2500-3000 rpm
(1500 x g). The higher speed is preferred to sediment the bacteria.
b. Remove supernatent and vortex the sediment vigorously for at least 30
secs. This step is critical. Do not use a pipette to mix the sediment,
because the bacteria and cells may adhere to the sides of the tube and
cause false-negative findings.
c. If 1 ml is received, do not centrifuge but vortex the specimen.
4. Using a sterile pipette, inoculate the media and streak for isolated colonies. In
addition, add a single drop of fluid to the 4th quadrant of the plate and allow to
air dry. Do not streak out this drop of fluid.
Page 48
b) Preparation of Sterile Body Fluids

1. Briefly describe the appearance of the specimen, i.e., color, viscosity, lighttransmitting properties, and presence of a clot.
2. Centrifuge the specimen if >5 ml is received.
a. If the volume of fluid is >5 ml, centrifuge for 15 min. at 2500-3000 rpm
(1500 x g).
b. Remove supernatent and vortex the sediment.
c. If <5 ml is received, vortex.
c) Process specimens (both CSF and Sterile body fluids) with large clots as follows:
a. Pour sediment containing clotted material into a sterile tissue grinder. Add a
small volume (<0.5 ml) of sterile nutrient broth to the grinder, and gently
homogenize this mixture to disperse the clots and release any trapped bacteria.
b. OR, alternatively use a sterile stick, as clot adheres to stick, turn and wring
out the clot.
NOTE: Do not grind the clots if a fungal culture is also requested on the
sample. Tease the clots apart. Vigorous grinding can destroy fungal cells.
d) Direct Examination of Gram stained smear - Note the presence of
polymorphonuclear cells, epithelial cells and organisms. Quantitate as per
Guideline for Quantitative Interpretation of Gram Stains.
e) Culture on the following media, and incubate the plates as indicated.
Media
Incubation
CO2 35C x 72 hrs
CO2 35 C x 72 hrs
O2/CO2 35C x 72 hrs
CO2 35C x 72 hrs
Blood Agar (BA)

Anerobic plate (BRUC)
Blood Culture Bottle
* Thioglycolate broth (THIO)
*
CO2 35C x 7 days
If CSF: add the broth only when working up shunt infections.
a. CSF specimens: Examine the BA, MAC, CHOC and BRUC plates daily for 72
hours. In shunt infections, examine the THIO broth media daily for 7 days.
b. Sterile Body Fluids: Examine the BA, MAC, CHOC and BRUC plates daily for 48
hours. Anaerobic jars - examine at 48 hours and 72-96 hours before discarding.
Broth can be examined daily.
Page 49
c. Potential Pathogens include the organisms listed in the table below. Identify and
provide antimicrobials susceptibility on all microorganisms, regardless of the
amount isolated. Correlate with the results of the direct Gram smear.
CSF - Common organisms causing acute bacterial meningitis:
Age or condition
Organism(s)
Neonate < 30 d
Escherichia coli, Group B Streptococcus, Listeria monocytogenes,
Gram-negative bacilli, S. aureus
1-3 months
Gr. B Streptococcus, E.coli, Streptococcus pneumoniae, Neisseria
meningitidis, Haemophilus influenzae, L. monocytogenes
3 mo-18 yrs
Streptococcus pneumoniae, Neisseria meningitides, Haemophilus
influenzae
Young adult
Neisseria meningitidis
Adult
S. pneumoniae, N. meningitidis
Elderly
S. pneumoniae, N. meningitidis, Gram-negative bacilli, L.
monocytogenes
AIDS patient
Cryptococcus neoformans (fungi)
CNS Shunts
Coagulase-negative Staphylococci, Corynebacterium,
Propionibacterium, Gram-negative bacilli
NOTE: For CSF and Sterile Body Fluids Potential Pathogens include all isolates,
especially in immunocompromised patients.
C. Susceptibility Testing
As per laboratory protocol. For CSF follow the Antibiotic Reporting Guideline from
Microbiology Quality Asurance Committee.
Reporting Results:
A. Gram stained smear: Report with quantitation the presence of polymorphonuclear
cells, epithelial cells and organisms. Phone the results to the ward/doctor.
B. Culture: Report all isolates with quantitation and with the appropriate antimicrobial
susceptibilities. Note: subcultures from broths cannot be quantitated.
NOTE: A positive culture is a critical value, and must be phoned to the doctor STAT.
Procedure notes for sterile body fluids:
Although in the past the use of blood bottles for fluid collection has not been
recommended, recent studies suggest that the large sample volume that can be cultured
may improve the recovery of low numbers of organisms in fluids such as ascites. As
with any broth system, however, the fastest growing organism is often the only one
Page 50
isolated, jeopardizing the recovery of slow growers. When a broth is used, no direct
smear information is available, and, therefore, no assessment of the initial distribution of
organisms or inflammatory cells can be made. A smear can be prepared, however, at the
time of specimen procurement and submitted with the broth medium. Also, unless a
biphasic system is available, a broth culture delays by at least 24 h the preliminary
workup of organisms possible only from growth on solid media.
Limitations of the Procedure:
This procedure is not suitable for optimal recovery of all pathogenic microorganisms
found in sterile body fluids, including fungi, mycobacteria, parasites, or viruses.
Culture Negative CSF specimens from patients who have received antibiotics may be
sent to Saskatchewan Disease Control Laboratory for PCR, upon request of the MHO.
References:
2. Meredith F.T., Phillips H.K, and L. B. Reller, Clinical Utility of Broth Cutures of Cerebral
Spinal Fluid from Patients at Risk for Shunt Infections, 1997, JCM, 35:3109-3111
3. Dunbar, S.A., Eason R.A., Musher D.M., & J.E. Clarridge, Microscopic Examination and
Broth Culture of cerebral Spinal Fluid in Diagnosis of Meningitis, 1998 JCM, 36:1617
1620.
4. Sturgis C.D., Petersen L.R. & J.R. Warren, Cerebral Fluid Broth Culture Isolates: Their
Significance to Antibiotic Treatment, Am J Clin Pathol. 1997, 108(2): 217-221.
5. Performance Standards for Antimicrobial Susceptibility Testing; M100-S11 Vol. 21. No.1.
CLSI.
Page 51
Organism
Site
ANTIBIOTIC REPORTING GUIDELINE

Routine Report
Staphylococcus species
Wound/Sputum
Penicillin, Oxacillin, Cefazolin, Erythromycin
Blood
CSF
Urine
Eye/ear3
Blood
CSF
Sputum
Sterile sites4
Penicillin, Oxacillin
Penicillin, Oxacillin
Penicillin, Oxacillin, Cefazolin, Nitrofurantoin
Penicillin, Erythromycin, SXT
Wound
Blood
Urine
Wound
Sputum
Blood
CSF5
Sterile sites
Throat
Vaginal/Rectal
Ampicillin
Ampicillin, Gentamicin synergy12, Streptomycin synergy12
Ampicillin, Fluoroquinolone2, Nitrofurantoin
Urine
Wound/Sputum
Ciprofloxacin7, Norfloxacin7, Tetracycline7, Nitrofurantoin7, Cefazolin7

Ampicillin, Cefazolin and/or Cephalothin6, Gentamicin, SXT, Ciprofloxacin,
Amoxicillin-clavulanic acid
Ampicillin, Cefazolin and/or Cephalothin6, Gentamicin, SXT
Ampicillin, Cefazolin and/or Cephalothin6, Gentamicin, SXT, Ciprofloxacin,
Nitrofurantoin
Ampicillin, Gentamicin, Cefotaxime
Gentamicin, Fluoroquinolone2, Piperacillin
Streptococcus pneumoniae
Alpha hemolytic Streptococcus

Non-Strep pneumoniae
Enterococcus species
Beta hemolytic Streptococcus

(Groups A, B, C, F, G)
Enterobacteriaceae
Blood
Urine
Pseudomonas aeruginosa
Shigella species
Salmonella and Shigella species
Haemophilus species
Stenotrophomonas maltophilia
CSF
All sites
Stool
Systemic
Sputum
Eye/Ear3
Blood
CSF
CSF/Sterile
sites
Page 52
Penicillin
Penicillin, Erythromycin, SXT, Fluoroquinolone2
Penicillin, 3rd Gen Cephalosporin
Alternate
SXT1, Clindamycin9,
Vancomycin
Vancomycin, Clindamycin9
Vancomycin
SXT, Fluoroquinolone2
Cefuroxime, Clindamycin
Cefotaxime, Vancomycin
Cefotaxime8, Vancomycin8
Cefuroxime, Clindamycin
Vancomycin
Vancomycin
Penicillin, Clindamycin9, Erythromycin

Penicillin, Clindamycin9
Penicillin, Cefotaxime
Penicillin, 3rd Gen Cephalosporin, Clindamycin9, Erythromycin
Erythromycin7
Cefazolin7
Ampicillin, SXT, Fluoroquinolone2

Ampicillin, SXT, Fluoroquinolone2, 10
Ampicillin, SXT, Cefuroxime, Amoxicillin-clavulanic acid
Ampicillin, Cefotaxime
SXT11, Ceftazidime, Ciprofloxacin
Vancomycin
Clindamycin7,9, Erythromycin7,
Vancomycin
Cefotaxime5, Meropenem,
Piperacillin, Tobramycin, PipTazobactam
Ceftazidime, Tobramycin,
Meropenem, Pip-Tazobactam
Cefixime if resistant to SXT
Cefotaxime
Fluoroquinolone2,
Clarithromycin
Meropenem
NOTES:
Alternate antibiotics should be reported, only if the organism is resistant to two or
more first choice antibiotics, if the patient cannot tolerate those antibiotics or if the
patient is already on the antibiotic of choice.
For Entercoccus species, cephalosporins, aminoglycosides, clindamycin and
trimethoprim/sulfamethoxazole may appear susceptible in vitro but are not effective
clinically and should not be reported.
Oxacillin agar screen plate should be used for detection of Methicillin Resistant
Staphylococcus aureus (MRSA)
Vancomycin agar screen plate should be used for detection of Vancomycin Resistant
Enterococcus (VRE)
All enteric pathogens other than Shigella and Salmonella typhi: do not report
susceptibility, unless the patient is less than two years old, or is immunosuppressed.
For Salmonella and Shigella species, first and second generation cephalosporins may
appear susceptible in vitro but are not effective clinically and should not be reported.
-lactamase testing should be done on all isolates of: (1) Penicillin susceptible Staph.
aureus; (2) Haemophilus sp.; (3) N. gonorrhoeae; (4) M. catarrhalis; (5)
Enterococcus sp.isolated from sterile body sites; (6) anaerobic gram negative bacilli
(B. fragilis group).
1
SXT refers to trimethoprim/sulfamethoxazole

Fluoroquinolones should not be reported for patients <17 years of age or pregnant
women. Fluoroquinolones that may be used are Levofloxacin, Gatifloxacin,
Ciprofloxacin, or Moxifloxacin. Ciprofloxacin is not the drug of choice for Strep.
pneumoniae.
3
Guidelines for the interpretation of susceptibility testing of topical antibiotics are not
available. However, testing of eye or ear isolates using serum breakpoints may be
indicated as these infections may become systemic.
4
For Strep Viridans susceptibility testing must be done by an MIC method.
5
Potential inducible extended spectrum beta-lactamase producing species (ESBL),
Klebsiella pneumoniae, K. oxytoca, Escherichia coli, and Proteus mirabilis (bacteremic
isolates). These organisms produce beta lactamase enzymes that promote resistance to
broad spectrum beta-lactam antimicrobials, such as cefotaxime (<27mm), ceftriaxone
(<25mm), ceftazidime(<22mm), cefpodoxime (<17mm) and aztreonam(<27mm). Such
potential ESBL strains should be screened using the recommended disk diffusion or MIC
breakpoints. (MIC >1ug/ml for all antibiotics). The phenotypic confirmatory test using
ceftazidime and cefotaxime alone and in combination with clavulanic acid will confirm
ESBL producing strains. In all ESBL strains, the zone diameters should increase in the
presence of clavulanic acid. For all confirmed ESBL producing strains, the test
interpretation should be reported as resistant for all penicillins, cephalosporins, and
aztreonam. CLSI M100 Table 2A
6
Enterobacteriaceae -parentral (IV/IM) Cefazolin is generally used to treat in-patients,
and oral Cephalothin is generally used to treat out-patients.
7
Consider these susceptibility tests for patients with known Penicillin allergies. Consider
Cephazolin if patient is pregnant.
2
Page 53
CLSI recommends that all CSF isolates of S. pneumoniae should immediately be tested
by an MIC method for susceptibility for penicillin, 3rd gen Ceph and Vancomycin. Only
report 3rd gen Ceph and Vancomycin when penicillin is resistant.
9
Strains of Staphylococci and Streptococcus that are susceptible to Clindamycin, but
resistant to Erythromycin should be tested for inducible Clindamycin resistance using the
D-zone test. Erythromycin should be included in testing for this purpose, even if not
reported.
10
Resistance of Salmonella species to Nalidixic Acid may be used to predict the potential
for resistance to Fluoroquinolones.
11
Highly inherently resistant organism. SXT in high doses plus other antibiotics (if
susceptible) used.
12
Use of high-level aminoglycoside screening to predict synergy.
There are several reasons for prescribing two antimicrobial drugs together and one is to
achieve a synergistic effect. Bacterial synergy is seen between two drugs, which
individually are incompletely bactericidal, although acting together they completely kill
the inoculum. Enterococci are inherently resistant to aminoglycosides. However, strains
of enterococci with medium-level resistance (MIC < 2,000 g/ml) show synergistic
killing by a combination of penicillin/ampicillin and gentamicin. For enterococcal
infections of sterile sites such as blood the recommended therapy is a combination of
beta-lactam (e.g., ampicillin) or vancomycin combined with an aminoglycoside
(gentamicin or streptomycin). In the JCM 25:2443 - 2444 (1987)
Zervos et al.
demonstrated that growth in a single broth microdilution well containing gentamicin at a
concentration of 500g/ml predicted high level resistance to gentamicin (MIC > 2,000
g/ml).
Antimicrobial testing panels use a single concentration high-level
aminoglycoside as a synergy screen.
The ATB ENTEROC5 susceptibility test strip tests for high-level
gentamicin and
streptomycin sensitivity. The MicroScan choice is also based on the observation that in
the presence of high-level gentamicin resistance many isolates can be sensitive to
streptomycin. High-level gentamicin resistance indicates that there is resistance to
synergy to gentamicin, tobramycin, sisomicin and netilmicin, due to the presence of the
common bifunctional 6'-N-acetyltransferase and 2"-O-phosphotransferase enzyme. This
enzyme does not affect streptomycin. Thus streptomycin has its own screen.
From the January 2005, Performance Standards for Antimicrobial Susceptibility
Testing from CLSI (formerly CLSI) document M100 S15; Table 2D recommends the
following parameters for screening for high-level resistance
(HLR) to aminoglycosides among enterococci: ( i) agar dilution concentrations
gentamicin 500 g/ml and streptomycin 2000 gm/ml; endpoint any growth greater than
1 colony, (ii) broth microdilution, gentamicin 500 g/ml and streptomycin 1000 g/ml;
endpoint - any growth; (iii) disk diffusion concentrations gentamicin 120 gm disk and
streptomycin 300 gm/disk; endpoint 5mm = HLR, 7-9 mm inconclusive (use agar
dilution method), > 10 mm sensitive. In summary, enterococci isolated from sterile sites
should have antimicrobial susceptibility testing for ampicillin MIC, high-level screen for
gentamicin and streptomycin, and vancomycin screen.
Page 54
EXCEPTIONS
Any organism that does not present the typical antibiotic pattern for that organism should
have repeat testing (identification and susceptibility) performed +/or sent to reference
laboratory (ie. SDCL).
New resistance in a species never reported before (e.g. Streptococcus A resistant to

penicillin G).
Streptococci and enterococci:
Resistant to vancomycin
Do not need to re-test if isolate has intrinsic resistance (eg. E gallinarum)
Staphylococcus aureus:
Susceptible or intermediate to penicillin G without checking -lactamase
Resistant to oxacillin and sensitive to penicillin
Resistant to clindamycin and susceptible to erythromycin
Resistant to vancomycin
No need to re-test if resistant to oxacillin and susceptible to any or beta lactams. This
is expected and is handled by reflexing the interpretation of those organisms based on
the Oxacillin result.
Enterobacteriaceae:
Resistant to a third-generation cephalosporin when the strain is sensitive to
cephalothin
Resistant to ampicillin and susceptible to ticarcillin and cephalothin (check ampicillin
disk)
Salmonella:
Susceptible to ampicillin and resistant to cephalothin
Enterobacter and Serratia:
Susceptible to cephalothin, report as resistant
Klebsiella pneumoniae:
Susceptible to ampicillin, report as resistant
Pseudomonas aeruginosa:
Susceptible to cephalothin, nalidixic acid, or trimethoprim
Susceptible to ticarcillin and resistant to ceftazidime, or piperacillin
Haemophilus influenzae:
Susceptible or intermediate to ampicillin without checking -lactamase
Proteus mirabilis and Serratia marcescens:
Susceptible to nitrofurantoin
Page 55
LIMITATIONS
The following organisms do not have CLSI standards for susceptibility and interpretation.
If testing is performed, an MIC method should be used, and all interpretations must be
reported as "non-standardized".
These guidelines are for the use of various antibiotics in treatment of infections caused by
these organisms.
Pasteurella multocida
Penicillin remains the drug of choice. Ampicillin, SXT, Cefuroxime, Amoxicillinclavulanic Acid, Tetracycline and Fluoroquinolones also demonstrate good in vitro
activity.
For Pasteurella species Oxacillin, Macrolides, Aminoglycosides and 1st gen
Cephalosporins are not effective and should not be reported.
Listeria monocytogenes
Ampicillin, or Amoxicillin combined with an Aminoglycoside is the primary choice for
treatment. Co-trimoxazole is the alternative drug. Resistant to Cephalosporins
Moraxella catarrhalis
Most M. catarrhalis strains are beta-lactamase positive. Ampicillin, amoxicillin,
penicillin, and 1st generation cephalosporin therapy is not suggested. Recommended
therapy: generally susceptible to macrolides, SXT, cefuroxime, ceftriaxone, quinolones,
and amoxicillin/clavulanic acid. Flouroquinolones are not recommended in pregnancy or
individuals <17 years.
Bacillus sp.
Corynebacterium sp.
Eikenella sp.
Micrococcus sp.
Page 56
INTRINSIC ANTIMICROBIAL RESISTANCE IN SOME COMMON ENTEROBACTERIACEAE

Genus or species
Most strains are resistant to:
Buttiauxella species.
Cedecea species.
Citrobacter amalonaticus
Citrobacter freundii
Citrobacter diversus (C. koseri)
Edwardsiella tarda
Enterobacter cloacae
Enterobacter aerogenes.
Many other Enterobacter species.
Escherichia hermannii
Ewingella americana
Hafnia alvei
Klebsiella pneumoniae
Kluyvera ascorbata
Kluyvera cryocrescens
Proteus mirabilis
Proteus vulgaris
Cephalothin
Polymyxins, ampicillin, cephalothin
Ampicillin
Cephalothin
Cephalothin, carbenicillin
Colistin
Cephalothin
Cephalothin
Cephalothin
Ampicillin, carbenicillin
Cephalothin
Cephalothin
Ampicillin, carbenicillin
Ampicillin
Ampicillin
Polymyxins, tetracycline, nitrofurantoin
Polymyxins, ampicillin, nitrofurantoin,
tetracycline
Polymyxins, ampicillin, cephalothin
Polymyxins, cephalothin, nitrofurantoin,
tetracycline
Polymyxins, nitrofurantoin
Polymyxins, cephalothin, nitrofurantoin
Ampicillin, carbenicillin, cephalothin
Polymyxins,c cephalothin
Morganella morganii
Providencia rettgeri
Other Providenciaa species.
Serratia marcescensb
Serratia fonticola
Other Serratia species.
a
Most strains of Providencia stuartii are also resistant to cephalothin and tetracycline.
Serratia marcescens can also be resistant to ampicillin, carbenicillin, streptomycin, and
tetracycline.
c
Most Serratia species are resistance to polymyxins, but some strains have unusual
zones of inhibition, 10 to 12 mm or larger , even though they are resistant when tested
by other methods.
b
Reference: Antibiotics in Laboratory Medicine, Lorian 4th Edition
Page 57
PROCEDURE/METHOD STATISTICAL WORK-UP/VALIDATION STUDY GUIDELINES: MICROBIOLOGY

Work-up guidelines and definitions (change in method/instrument):
Work-up Element:
Definition:
CLSI or International Federation of Clinical
Chemistry (IFCC)
Minimum Data Requirements

(where appropriate):
1. Imprecision
Within run
Between run
The variation in analytical results demonstrated

when a particular specimen or aliquot is
analyzed multiple times or on multiple days.
Imprecision is expressed quantitatively by a
statistic such as standard deviation or coefficient
of variation.
2. Patient correlation
The correlation coefficient is a means to look for

a relationship, not agreement, between pairs.
Two methods may have a perfect correlation
throughout the measuring range but may not
agree in value ie.: one may be double the value
of the other.
Within run use preferably a

patient sample or pool close to
the decision levels with a
minimum of 10 data points.
Between run 20 results from
20 separate runs on 2 levels over
a 10-day minimum time period
using appropriate QC material
40 data points are recommended
with a minimum of 20 having
50% of the data points outside
the reference intervals, if
possible. Correlations should
involve comparison with an
acceptable reference method or
laboratory.
4 data points each in duplicate as
a minimum requirement, but 5
data points are preferred (over
reportable range). Linearity
studies are expected on an initial
method work-up and further
studies as defined by the College
guidelines
The minimum requirement is 40
data points for confirmation of
an established reference range
and 120 for the establishment of
a new reference range.
3. Linearity
(IFCC) The range of concentration or other

quantity in the specimen over which the method
is applicable without modification (CLSI) when
analytical results are plotted against expected
concentrations; the degree to which the plotted
curve conforms to a straight line is a measure of
the system linearity.
4. Reference range
validation
It is common convention to define the reference

range or interval of a laboratory test as the
central 95% interval bounded by the 2.5 and
97.5 percentiles of the selected patient
population. Validation of an established
reference range requires a minimum of 40
samples
Closeness of the agreement between the result of
5. Accuracy
Page 58
3 data points using acceptable
Applicability:
Qualitative
Quantitative
_
n=20
n=40
6. Sensitivity
7. Specimen Stability
8. Interference
a measurement and the accepted reference value

(true value of the analyte).
Measure of the ability of an analytical method to
detect small quantities of the measured
component. When concern is performance at
very low concentration it is useful to determine
the detection limit as influenced by imprecision.
The conditions of handling and storage which
permits the measurement and reporting of a
clinically relevant result.
The effect of any component of the sample on

the accuracy of the measurement of the desired
analyte
9. Organism
Identification
10. Antibiotic
sensitivity
Quantitative:
Page 59
reference material ie.: CEQAL

or CAP.
Sensitivity studies are only
required for those method which
have clinical relevance at values
close to 0 eg. PCR
Data required for specimens
known to be time sensitive.
Usually associated with rejection
criteria, eg. specimens >24 hrs in
transit or arrived in inappropriate
media.
Document the manufacturers
interference information. The
method should include a
disclaimer or a process for
dealing with a lipemic, icteric or
hemolyzed sample.
20 patient isolates worked up by
the new identification test in
parallel with an acceptable
reference method or laboratory.
In addition, for specimens likely
to possess complex flora, up to
20 common contaminants should
be included as negative controls.
See patient correlation above.
Appropriate CLSI standard
organisms should be tested in
principle, eg. see accuracy
above.
when clinically relevant
when clinically relevant
storage and transport

dependent
storage and transport

dependent
methods with known

interferences
methods with known

interferences
_
semi-quantitative only
_
semi-quantitative only
Work-up requirements when an instrument is moved from site A to site B: (it is assumed that the instrument has been in recent
use with acceptable performance).
Work-up Element:
1. Imprecision studies, QC only
2. Patient correlation
Minimum data requirements:

As above
10 data points, where feasible
Qualitative or semi-qualitative:
If site B has no previous experience
Work-up Element:
1. Organism Identification
2. Antibiotic susceptibility
Minimum data requirements:

10 patient isolates, up to 10 contaminants
As above
Page 60

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College of Physicians & Surgeons of Saskatchewan

Laboratory Quality Assurance Program

Microbiology Procedures/Guidelines 2010 Edition

QUALITY CONTROL IN MICROBIOLOGY LABORATORIES

M22 Quality Assurance for Commercially Prepared Microbiological

M100 Performance Standards for Antimicrobial Susceptibility Testing

M11 Methods for Antimicrobial Susceptibility Testing of Anaerobic

Performance Standards for Antimicrobial Disk Susceptibility Tests

Identification panels should be quality controlled according to the manufacturer's

Microbiology Procedures/Guidelines 2010 Edition

GUIDELINE FOR QUANTITATIVE INTERPRETATION OF GRAM STAINS

Microbiology Procedures/Guidelines 2010 Edition

Gram Stain Quantification Criteria:

Squamous Epithelial cells:

Rejection criteria: Reject specimens with an average score of 0 or less.

<10 SEC / LPF

Average the number of cells in

Microbiology Procedures/Guidelines 2010 Edition

2) All Other Specimen Types:

Microorganisms (bacteria, yeast/fungi)

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition

Staphylococcus Identification Scheme

Some colonies of MRSA and S. intermedius are clumping factor negative.

Microbiology Procedures/Guidelines 2010 Edition

COAGULASE NEGATIVE STAPHYLOCOCCUS SPECIES (CNS)

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition

BACTERIOLOGY CULTURE PLANTING PROCEDURES

Microbiology Procedures/Guidelines 2010 Edition

Number of Colonies in Streak Area

Quantitative Methods for Urine:

Microbiology Procedures/Guidelines 2010 Edition

conditions. Carbon dioxide may be provided by a CO2 incubator, a candle jar, or a

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition

URINE SPECIMEN PROCESSING

Microbiology Procedures/Guidelines 2010 Edition

Dip 'n' Count Procedure:

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition

STANDARDIZATION OF THE COLONY COUNT FOR URINE CULTURES

In & Out Catheter

ID & Sens any

ID & Sens any

Mixed growth probable

Mixed growth probable

ID & Sens any

ID & Sens any

**Exceptions include symptomatic males, adult females with urethritis, patients on

Microbiology Procedures/Guidelines 2010 Edition

College of Physicians & Surgeons of Alberta, Microbiology Laboratory Inspection Form,

Kunan, White, Hua Hua, A Reassessment of the Importance of Low-Count Bacteriuria,

National Pathology Accreditation Advisory Council of Australia, Laboratory Assessment

Henry Isenberg, Clinical Microbiology Procedures Handbook, (Americian Society for

Microbiology Procedures/Guidelines 2010 Edition

Microbiology Procedures/Guidelines 2010 Edition