1. By
Maha Fathy
3/12/2011

2. Medical Microbiology is the branch of science that is concerned with
the study of microorganisms which produce disease (bacteria, mycoplasma,
chlamydiae, rickettsiae, fungi, viruses and parasites), the response of the
host to infection, and the control of infectious disease.
Medical Microbiology Laboratory plays an integral role in the
practice of infection control because it defines one of the major components
of the disease process, which is the agent. Within microbiology laboratory
different techniques are used to evaluate agent-host interactions, to evaluate
potential reservoirs within the facility, and to analyze the relatedness of
microorganisms for epidemiologic purposes.
Medical Microbiology Laboratory Diagnostics
When a patient is being evaluated for infection, it usually requires a
thorough history and physical examination, microbiological assessment, as
well as other diagnostic tests. Microbiologic assessment includes different
measurements that may help to diagnose/ identify the infection or to evaluate
the stage of an infectious disease or process.
In general there are two methods that are helpful in diagnosing or staging
infections: Direct and indirect methods (see Appendix).
Direct methods are used to demonstrate the presence of the causative
microorganism or one of its components or products (antigens, toxins,
nucleic acids) in clinical specimens.
Indirect methods depend on detection of the host response to infection;
either humoral immune response (antibody detection) or cell mediated
immune response (e.g. skin tests).
I. Specimen Collection and Transport
Specimen collection and transport to the laboratory is an essential part of
the microbiologic workup. Improperly selected, collected, or transported
specimens can generate misleading data that may result in inappropriate
patient management.
A. Proper Specimen Collection and Transport
It is the microbiologist’s responsibility to provide clinicians with the
required instructions for optimum collection techniques and transport
information. These instructions should include safety considerations,
appropriate anatomic collection site, collection, transportation and labeling
instructions in addition to any special instructions for specific patient
preparation before collection.
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3. For optimum collection and transport of different specimens the following
should be considered:
1. Appropriateness of specimen for suspected pathogen or disease
process, or both
2. Sufficient quantity of specimen
3. Appropriate timing: appropriate specimen for disease stage and
ideally, collect specimen in acute or early stage of the illness before
antimicrobial therapy is initiated
4. Appropriate collection technique (prevent contamination by
endogenous) and appropriate container: In general, all specimens
should be collected aseptically and placed in sterile containers.
5. Prompt delivery to laboratory is required to prevent death of suspected
pathogen or overgrowth by other organism(s). In case of delayed
transport, special preservatives or holding media are used to ensure
viability of some fastidious agents
6. Appropriate specimen labeling so that the specimen can be matched
with the specimen requisition.
Many slips in collection can alter the results including:
 Inadequate specimen
 Inappropriate specimen
 Wrong timing
 Wrong container
 Introduction of contaminants
Delay in transport can lead to:
 Death of fastidious organisms due to changes in environmental
conditions e.g. temperature, pH and oxygen requirements
 Overgrowth of pathogens by fast growing commensals
 Variation in bacterial count
To avoid:
 Culture at bed side: In some cases specimens may be placed
directly into culture media (e.g., blood cultures, genital cultures).
 Use of transport media, preservatives or holding media
 Special handling techniques may be necessary for some specimens
such as those for anaerobic culture.
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4.  Adjusting temperature conditions during storage: some specimens
may be refrigerated (e.g., urine, stool, sputum) while others should
be maintained at 37oC (e.g. CSF).
Golden rules for proper specimen collection and transport
1.Ensure adherence to safety precautions
 Use the appropriate personal protective equipment (gloves,
laboratory coat, and face wear)
 Containers should be leak proof, transported in a sealable bag
with a separate compartment for paperwork
 Avoid transporting syringes with needles attached
2.Instruct patient to overcome fear in painful procedures and to ensure
cooperation and participation
3.Consider number of specimens (e.g., blood cultures and acid-fast
bacilli smears)
4.Avoid contamination from endogenous flora by means of appropriate
site preparation
5.Select collection site properly, consider if fastidious organisms or
organisms with special oxygen requirements are expected and if the
site has endogenous flora. (e.g., a cervical swab is an unacceptable
specimen for anaerobic culture, whereas an endometrial aspirate is
acceptable)
6.Collect adequate volume
7.Consider transport media (to protect environmentally sensitive
organisms, avoid use of dry swabs)
8.Label specimen properly (patient name, identification number, source,
date, and time of collection) and include provisional diagnosis and
other reliable clinical data in the specimen requisition
9.Handle and transport specimen properly
 Promptly transport to laboratory, preferably within 2 hours
 If processing is delayed, store the specimen properly in the
appropriate temperature. urine, stool may be refrigerated; never
refrigerate genital, eye, or spinal fluid specimens
B. Specimen Requisition
It is an order form sent to the laboratory along with the specimen in a
separate section from the specimen bag. Sometimes this requisition can be
sent electronically if the hospital information system offers computerizes
orders. A complete requisition should include the following:
 Patient name
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5.  Hospital identification number
 Age
 Gender
 Collection date and time
 Ordering clinician
 Exact nature and source of the specimen
 Provisional diagnosis
 Current antimicrobial history
C. Rejection of Specimens
Processing improperly selected, collected, or transported specimens can
generate misleading data that may result in inappropriate patient
management; ideally the specimen should not be processed and should be
recollected; examples include:
1. Prolonged transport without proper preservation
2. Improper or leaking container
3. Duplicate specimens on the same day for same request (except
blood)
4. Poor-quality clinical specimens (particularly expectorated sputum)
5. Insufficient quantity or the specimen is dried up.
6. Information on specimen label does not match that on requisition
form
7. The specimen was sent in a fixative e.g. formalin (it will kill
microorganisms)
8. Specimens of questionable medical value e.g. Foley catheter tip.
D. Common Clinical Specimens
Table (1) demonstrates the collection, transport and storage of common
clinical specimens submitted to medical microbiology lab
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6. Table (1): Collection, transport and storage of common clinical specimens
Patient Transportation to Storage before
Type of specimen Container and Special instructions
preparation Lab processing
Abscess, wound, Wipe area by In deep lesions: Within 24 hours/ 24 hours/ Room
ulcer sterile saline (or Aspirate material from wall with sterile Room Temp. Temp.
alcohol 70% if syringe and needle or excise tissue and
intact skin) transfer aseptically into sterile container
with anaerobic transport.
Superficial:
A swab (preferably moisten with sterile
transport medium) is passed deeply into
wound bed
Burn Wound Removal of debris Biopsy specimen removed from an area Immediately/ Room Process as soon as
with saline suggestive of infection, after Temp. received
debridement, down to and including
viable bleeding tissue in a sterile
container (for quantitative culture)
Blood culture Disinfect 2 Blood culture bottles (aerobic and Within two hours/ Incubated at 37oC
venipuncture site anaerobic) per set Room Temp. on receipt
Adults, obtain 10 to 20 ml per set;
infant, 1 to 2 ml per set;
2 to 3 sets withdrawn from separate sites
within 24 hrs preferably during febrile
episode.(for endocarditis, two sets from
two sites over 2 hours)
IV catheters Disinfect skin Sterile screw-cap container (for Immediately/ Room Process as soon as
before removal semiquatitative and quantitative Temp. received
cultures)
CSF Disinfect skin Aspirate with sterile lumbar puncture Immediately/ Room up to 6 hours/37oC
before aspiration needle and aseptically transfer into Temp. (For viruses keep at
sterile screw-cap tubes (3 or 4 tubes) 4 oC up to 3 days)

7. Body fluids (pleural, Disinfect skin Aspirate with sterile aspiration needle Immediately/ Room Process as soon as
peritoneal, synovial before aspiration and aseptically transfer into sterile Temp. received
screw-cap container
Throat Ordinary throat swab (preferably Immediately/ Room Process as soon as
moistened with transport medium) Temp. (avoid received.
dryness). 24 hours/ Room
Within 24 hours/ Temp. ( if transport
Room Temp.( if medium is used)
transport medium is
used)
Nasopharyngeal Pernasal short flexible swab is Immediately/ Room Process as soon as
specimens introduced through nose to the Temp. (avoid received.
nasopharynx dryness). 24 hours/ Room
Within 24 hours/ Temp. ( if transport
Room Temp.( if medium is used)
transport medium is
used)
Lower respiratory Patient rinse or gargle Collected directly into sterile screw-cap Within two hours/ 24 hours/4oC
specimens: with water before container ( patient should cough deeply to Room Temp.
expectoration of
 Sputum produce lower tract specimen)
sputum
 Induced sputum
 Endotracheal Sterile screw-cap container Within two hours/ 24 hours/4oC
aspirate Room Temp.
 Bronchoalveolar
lavage (BAL)
 Protected
specimen brush
(PSB)
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8. Gastric aspirate In the early morning, Sterile screw-cap container Immediately/ Room Must be neutralized
with patient still in (For the detection of Mycobacterium Temp. with sodium
bed, before tuberculosis in patient who is unable to bicarbonate within
eating, introduce produce sputum)
nasogastric tube;
1 hour of collection
lavage 50 ml sterile
water, sample
Mid stream urine Clean area Sterile screw-cap container Immediately/ Room 24 hours/4oC
thoroughly with soap Temp.
and water and rinse Within 24 hours/4oC
thoroughly;
holding the labia
apart (in female)
begin voiding; after
several ml have
passed, collect
sample without
stopping flow
Indwelling catheter Disinfection Aspirate 5-10 ml urine with sterile Immediately/ Room 24 hours/4oC
collection port with syringe and needle and transfer Temp.
alcohol 70% aseptically into Sterile screw-cap Within 24 hours/4oC
container
Feces Clean leak proof container, use transport Immediately/ Room 72 hours/4oC
medium if transport will exceed 1 hour Temp.
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9. II. Microbiological Diagnostic approaches (See appendix)
A. Direct Methods
1. Direct detection of infecting organism by microscopy
2. Cultivation, identification and antimicrobial susceptibility testing
of infecting organism
3. Direct detection of specific antigens by immunological methods
4. Direct toxin detection assays
5. Direct detection of nucleic acids of infecting agents by molecular
techniques
B. Indirect Methods
1. Detection of antibodies produced by the patient in response to an
infecting organism ( serodiagnosis)
2. Detection of cell mediated immune response
Microscopy
Microscopic examination of a Gram stained film made directly from the
clinical specimen is the most common procedure conducted to directly
examine a clinical specimen for the presence of microorganisms (i.e.,
bacteria or fungus). Acid-fast stains are very useful in identifying
Mycobacterium spp. (AFB, or acid-fast bacillus)
Why Microscopic Findings are important?
• Usually available in the same day or even within hours.
• Give an idea about the quality of the specimen.
• Can direct primary antibiotic therapy.
• Some clinical syndromes can be diagnosed based on results of
microscopic examination
Cultivation and Identification
The specimen is placed into or onto special media to cultivate the
organisms in separated colonies (isolation). Once the microbe grows,
identification can be made by colonial morphology, microscopic
examination of growing organisms and different identification tests
depending on some biological characteristics of microorganisms.
Sometimes identification of isolated organisms can be made by
immunological or molecular techniques.
Isolation and identification is the conventional diagnostic approach and is
considered the gold standard for diagnosis although it is time consuming
and can be problematic in certain situations.

10. Examples of the common problems facing isolation:
‘No Growth’
• Non cultivable organisms
• Intermittent discharge of microorganisms
‘Pathogen or Colonizer?’
• Quantitative culture: for detection of significant bacterial growth
• Ancillary findings including: Abundance of pus cells and
Predominance of one bacterial morphology
Antigen detection
Several test methods may be used for antigen detection including
agglutination tests, immunofluorescence, and enzyme-linked
immunosorbent assay (ELISA). Serum, body fluids, and other clinical
specimens may be used for antigen testing.
Methods are designed to detect the entire agent (e.g., virus) or part of the
agent (e.g., bacterial cell wall structures).
These tests may be helpful in early diagnosis when cultures are not yet
positive or are not possible.
Example: detection of antigens causing bacterial meningitis in CSF
(Haemophilusinfluenzae, Streptococcus pneumoniae, Neisseria
meningitides)
Direct Toxin detection assays
Example: Detection of Toxin A and/or B in stool for diagnosis of
Clostridium difficile associated disease.
Molecular techniques
Since it is often difficult and sometimes impossible to grow and identify
pathogens in culture, identification methods based on molecular
diagnosis are widely used. Nucleic acid –based diagnostic procedures
become more widely used because (a) nucleic acids can be isolated from
infected tissues; (b) can be measured, (c) nucleic acid sequence is unique
for each pathogen; and (d) nucleic acid sequence can be amplified to be
analyzed.
Polymerase chain reaction (PCR): It is a method for copying and
amplifying specific DNA sequences up to one million (106) fold.
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11. It can be used to find very low quantities of an infectious agent present in
a clinical sample by increasing the quantity of a specific nucleotide
sequence contained within the organism by a process of directed DNA
synthesis.
Indirect diagnosis
Antibody detection (serodiagnosis)
Antibody detection is an indirect method of identifying infection by
assessment of the humoral host response (antibody production) to the
invading microorganism. Results may be reported qualitatively (positive
or negative) or quantitatively (titers). A positive antibody titer does not
necessarily indicate active infection but may represent a previous
infection. For diagnosis of active infection we depend upon the detection
of rising titers of IgG antibodies in two consecutive serum samples or the
presence of high titers of IgM antibodies.
Detection of cell mediated immune response
Sometimes we depend upon the detection of cell mediated immune
response for diagnosis of infections e.g. positive tuberculin test or detection
of in vitro interferon gamma production for diagnosis of Mycobacterium
tuberculosis infection.
III. Antimicrobial Susceptibility Testing
 AST is done to assist in the selection of appropriate antimicrobial
therapy.
 It should be done by a standard technique (e.g CLSI
recommendations). The standardization should include the
methodology, selection of tested antimicrobials, interpretation of
results and reporting format.
 AST has also been used as a simple method to differentiate between 2
isolates of the same species
Many methods can be used as:
 Disc diffusion Method
 MIC assay by tube dilution method
 E-test
Choose of different antibiotics for testing depends on:
 Identification of the isolated organism
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12.  Type of infection whether Community acquired or hospital acquired
 Infection site
 Age of the patient
 Other conditions of the patients
The Testing List: should include agents of proven efficacy which have
acceptable in vitro test performance taking in consideration minimizing
emergence of resistance
Reporting:
 Reported agents must be pre tested unless reporting based on testing
another agent provides a more accurate result
 Agents of comparable results need not be duplicated in testing;
however the report should include footnotes indicating the agents that
usually show comparable interpretive results
Verification of patient results:
 The antimicrobial susceptibility results consistent with the
identification.
 The results follow established activity rules, e.g. 3rd generation
cephalosporins are more active than 1st or 2nd generation
cephalosporins against enterobacteriaceae.
 The isolate is susceptible to those agents for which resistance has not
been documented.
Detection of Multi-drug resistant organisms (MDROs)
Identification of MDR organisms: depends on either phenotypic or
genotypic characteristics:
Phenotypic Characteristics: e.g.
 Identification of MRSA by detecting resistance to Oxacilline or
Cefoxitin disc.
 Identification of Penicillin resistant pneumococci and VRE using MIC
assays.
 Testing Gram-negative bacilli for the production of new β lactamases
as ESβLs and Carbapenenemase
Genotypic Characteristics: e.g.
 Detection of mecA gene that mediate oxacillin resistance in MRSA.
 Detection of van (A&B) genes that mediate vancomycin resistance in
VRE.
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13. IV. Typing (Determining organism relatedness)
A variety of methods are used to determine the epidemiological relatedness
between microorganisms including phenotyping and genotyping methods.
1. Phenotyping methods
These methods can differentiate between different strains. They may be
based on antigenic structure (serotyping), biologic characteristics
(biotyping), susceptibility to antimicrobial agents (antibiogram or
resistotyping), bacteriocin (colicin typing) or bacteriophages (phage
typing).
Some of these methods as serotyping, biotyping and antimicrobial
resistance profile are easy to be done and can determine different strains
rather than confirming strain relatedness.
2. Genotyping methods:
A number of molecular methods have been developed for typing: e.g.
 Pulsed- Field gel electrophoresis (PFGE)
 Restriction fragment length polymorphism (RFLP)
 PCR - based typing methods
These genotypic methods have very high typability and discriminatory
power and can confirm difference or relatedness between two isolates of
the same species. However they require expensive equipment and trained
staff.
V. Microbiologic Workup, Communication and Reporting
The microbiologist should decide what is clinically relevant regarding the
specimen workup. He should judge what organisms should look for and
report. It is essential to recognize what organisms constitute normal flora
and what constitutes a potential pathogen. Indiscriminate reporting of
normal flora can lead to unnecessary use of antibiotics and emergence of
resistant organisms. In final analysis the results should be compared with
the suspected diagnosis. The clinician should supply the microbiologist
with all reliable information (e.g. recent travel history, animal exposure,
radiographic findings……) so that the microbiologist can use this
information to plan the appropriate workup and interpret the analysis
results.
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14. The microbiologist professional obligation necessitates communicating
their findings to health care professionals responsible for treating the
patient. The microbiologists should avoid confusion and misunderstanding
should not use abbreviations. They should provide final reports with clear
cut conclusions. Appropriate interpretative findings can be included in the
written final report along with the specific result e.g. “suggest
contamination at collection”.
Certain critical results must be communicated to the clinicians
immediately. Each microbiology lab should prepare a list of these critical
results in consultation with the medical staff. Common critical results
include:
 Positive CSF Gram stain or culture
 Positive blood culture
 Gram stain suggestive of gas gangrene
 Positive acid fast stain
 Positive blood film for malaria
 Detection of a significant pathogen e.g. MDRO, legionella, brucella…
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15. Appendix
Flow Chart for Diagnosis of Infectious Diseases
Direct Diagnosis Indirect Diagnosis
Patient (suspected
infectious disease)
Clinical specimen: (e.g.
Detection of humoral Detection for
Blood, CSF, CSF, feces,
immune response i.e cell mediated
urine, ….. )
antibody detection immune
tissue biopsy, ,...
tests response (e.g.
(Serological tests e.g. skin tests)
ELISA, IF)
Direct microscopic
examination
Immunological direct Molecular direct
Inoculation into suitable diagnosis diagnosis
culture media (Direct Ag or toxin (Direct nucleic acid
detection): detection with or
IF, ELISA, particle without amplification):
agglutination Nucleic acid
Hybridization &
Pure culture isolation
PCR
Conventional Identification: Immunological Molecular
microscopy, biochemical Identification: Identification: Antibiotic
reactions, animal agglutination, hybridization, susceptibility testing
inoculation immunofluorescence, PCR
……
Conventional Microbiological methods Indirect diagnosis
Immunological methods
Direct diagnosis
Molecular methods
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16. Role of Microbiology Lab in Infection Control
Goals of Microbiology Laboratory in IC:
1. Microbiological diagnosis of healthcare associated infections.
2. Determining antibiotic susceptibility pattern of isolated strains and
detection of MDROs
3. To assist in epidemiological investigations (surveillance): both at
endemic level and for outbreak investigations.
4. It helps in situations requiring environmental sampling
Microbiological diagnosis of HCAIs
The diagnosis of HCAIs has 2 important functions. The first is clinical- for
optimally managing the infected patients. The second is epidemiological –
knowledge of the infective agent can lead to finding its source and route of
transmission. This allows IPC staff to stop spreading of infection.
Microbiological diagnosis of common HCAIs:
Urinary tract infections:
 Quantitative urine culture is commonly used to differentiate
significant bacteriuria from false positive cultures related to
contamination during specimen collection.
 The value of ≥105 CFU of bacteria /ml of urine in non catheterized
patients was chosen because of its high specificity for diagnosis of
true infection, even in asymptomatic individuals. In catheterized
patients the value of 102-103 is considered significant
 Simple and rapid preliminary screening tests can be used to exclude
normal samples to avoid such labor work of their further full
examination.
 Commercially available dipstick tests can be used to predict
bacteriuria based on nitrate reduction or peroxidase production by
variety of bacteria or by esterase production by leukocytes.
Healthcare associated pneumonia
 Diagnosis of HAP remains a major challenge.
 HAP is suspected based on some clinical criteria
 Usually a positive quantitative culture is required to confirm the
diagnosis.
 It is important to obtain all cultures prior to antibiotic administration.
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17. In patients with suspected HAP without mechanical ventilation:
It is recommended to obtain sputum for Gram stain and culture plus two
blood cultures at least 15 minutes apart. A sputum specimen is considered
representative of deep respiratory secretions when there is ≥ 25
neutrophils and less than 10 epithelial cells on Gram stained microscopy
examination.
In mechanically ventilated patients:
Endo tracheal aspirate for quantitative culture plus two blood cultures are
recommended. The significant threshold for tracheal aspirate quantitative
culture is considered 105- 106 cfu/ml.
In patients undergoing fiberoptic bronchoscopy, cultures of BAL are
considered significant with growth of at least 104 cfu/ml.
For specimens obtained via protected brush the significant threshold is
considered 103 cfu/ml.
Intravascular device infections:
The challenge of identifying the source of sepsis, particularly in critically
ill patients, makes the clinician point strongly toward an IVD as the
source of a septic episode.
 If purulence is seen in combination with signs and symptoms of
sepsis, it is highly likely the patient has IVDR BSI.
 The presence of inflammation or purulence at the catheter insertion
site is usually uncommon in patients with IVDR BSI.
 Definitions for IVDR colonization, local infection, BSI are based
upon microbiologic confirmation.
IVD colonization:
It is defined by a positive culture (semiquantitative or quantitative) of the
implanted portion or portions of the IVD together with absence of signs of
local or systemic infection.
Local IVD infection:
It is defined by a positive culture (semiquantitative or quantitative) of the
removed IVD or culture of pus or thrombus from the cannulated vessel
together with clinical evidence of infection of the insertion site.
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18. IVD Related BSI:
If the IVD is removed:
 positive culture (semiquantitative or quantitative) of the removed
IVD or a positive culture of the catheter hub or infusate or culture
of pus or thrombus from the cannulated vessel together with one or
more positive blood cultures, ideally percutaneously drawn,
concordant for the same species.
If the IVD is retained:
 If quantitative blood cultures are available, cultures drawn both
from the IVD and a peripheral vein (or another IVD) are both
positive and show a marked step-up in quantitative positivity
(≥five-fold) in the IVD-drawn culture.
 If automated monitoring of incubating blood cultures is available,
blood cultures drawn concomitantly from the IVD and a peripheral
vein show both are positive, but the IVD-drawn blood culture turns
positive more than 2 hours before the peripherally-drawn culture
Surgical site infections:
Identification of SSI is based in most situations on clinical criteria as
many SSIs are clear such as when there is purulent drainage and fever or
other sign of infection. Yet, in some instances, infections are not quite so
obvious and need microbiological workup for identifying infectious
agents and its antibiotic susceptibility pattern.
II. Antibiotic Susceptibility testing and detection of MDROs
In addition to the clinical role of determining antibiotic susceptibility
testing, it can also help in planning antibiotic policy and designing the
local antibiotic formulary. Resistance patterns should be reported
periodically. These reports should be available for clinicians for the
design of empirical therapy.
III. Surveillance of HCAIs and outbreak investigations
The microbiology laboratory plays a pivotal role in both endemic and
epidemic epidemiology. It should produce routine reports of bacterial
isolates to help IPC staff in surveillance studies as allowing them to make
incidence graphs for specific pathogens, hospital units or settings. These
graphs enable to identify any new isolates and discover the beginning of an
outbreak. Also Microbiology lab can assist in the identification of an
outbreak by confirming organism identities and retrieve and review
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19. archival data to determine if an outbreak situation actually exists.
Sometimes the IPC staff requires additional tests to clarify endemic or
epidemic situations e.g environmental sampling or detection of
colonization of patients or HCWs.
IV. Microbiologic Environmental Sampling
Key concepts:
 Microbiologic environmental testing is not generally
recommended.
 Environmental culturing can be costly and may require special
laboratory procedures.
 In most cases no standards for comparison exist.
Rationale for routine environmental monitoring:
In limited situations “routine” environmental sampling may be indicated
including:
 Biologic monitoring of sterilization processes.
 Monthly cultures of water and dialysate in hemodialysis units.
Microbiologic air sampling:
 There are no recommendations regarding routine microbiologic air
sampling.
 It can be indicated where there is documented or high potential for
healthcare-acquired aspergillosis.
 Settling plates should NOT be used.
 Volumetric air sampling devices, sampling a constant rate of
airflow, can be used for testing.
Special Environmental Testing:
Environmental testing may be indicated when epidemiological
investigation suggests that a source or reservoir of microorganisms may
exist.
Testing may involve:
 personnel,
 medical devices
 air
 water, food
 surfaces
The type of sampling:
 Swab-rinse sampling: uses a template to swab a standardized area.
 Rinse-sampling involves direct immersion of an item if it can be
totally exposed to a rinse solution.
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20.  Impression plating is a method where the culture media is placed
directly onto the surface being tested.
 Liquid or water testing: more difficult than solid surfaces and
requires a quantitative culture, agar spread method, membrane
filter method
Minimal requirements for microbiology Lab in control of
HCAIs (IIFIC Basic Concepts of Infection Control, 2nd edition- revised 2011)
1. Each health care facility should have a microbiology lab or has access
to a nearby one.
2. Should be available every day including holidays, ideally on a 24-hur
basis, at least for Gram stain.
3. Should be able to examine most common clinical samples particularly
those of utmost of clinical value and those of life threatening
infections (blood, CSF, urine, stool, wound exudates, respiratory
specimens) and perform serological tests for BBPs. (HIV, HBV,
HCV).
4. Should be able to identify common microbial agents causing HCAIs
to species level in addition to other agents causing some severe
community acquired infections.
5. Should be able to perform antibiotic susceptibility testing by
standardized disc diffusion method.
6. Should be able to do basic typing methods (biotyping, serotypin).
7. Should have quality assurance procedures (both internal and external
quality control) (national or international).
8. Should have a medical microbiologist with good communication skills
with clinical and IPC staff.
9. May have the ability to perform simpler genotyping methods or have
access to genotypic methods at central or regional labs for
epidemiologic investigations.
References:
1. Forbes BA, Sahm DF and Weissfeld AS, Bailey & Scott’s Diagnostic Microbiology, 12th
edition, 2007, Mosby Elsevier.
2. Kalenic S, The Role of Microbiology Laboratory, IFIC Basic Concepts of Infection
Control, 2nd edition-revised 2011.
3. Keroack MA and Rosen-Kotilainen H, Microbiology/Laboratory Diagnostics, APIC Text
of Infection Control 1999, Washington DC.
4. Ritter J, Clinical Microbiology, APIC Text of Infection Control 2005, Washington DC.
5. Ritter J, Laboratory diagnostics, APIC Text of Infection Control 2005, Washington DC.
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