By

Maha Fathy

3/12/2011

Maha Fathy 2 3/12/2011

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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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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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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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

Table (1): Collection, transport and storage of common clinical specimens

Type of specimen Patient

preparation Container and Special instructions

Transportation to

Lab

Storage before

processing

Abscess, wound,

ulcer

Wipe area by

sterile saline (or

alcohol 70% if

intact skin)

In deep lesions:

Aspirate material from wall with sterile

syringe and needle or excise tissue and

transfer aseptically into sterile container

with anaerobic transport.

Superficial:

A swab (preferably moisten with sterile

transport medium) is passed deeply into

wound bed

Within 24 hours/

Room Temp.

24 hours/ Room

Temp.

Burn Wound Removal of debris

with saline

Biopsy specimen removed from an area

suggestive of infection, after

debridement, down to and including

viable bleeding tissue in a sterile

container (for quantitative culture)

Immediately/ Room

Temp.

Process as soon as

received

Blood culture Disinfect

venipuncture site

2 Blood culture bottles (aerobic and

anaerobic) per set

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)

Within two hours/

Room Temp.

Incubated at 37oC

on receipt

IV catheters Disinfect skin

before removal

Sterile screw-cap container (for

semiquatitative and quantitative

cultures)

Immediately/ Room

Temp.

Process as soon as

received

CSF Disinfect skin

before aspiration

Aspirate with sterile lumbar puncture

needle and aseptically transfer into

sterile screw-cap tubes (3 or 4 tubes)

Immediately/ Room

Temp.

up to 6 hours/37oC

(For viruses keep at

4 oC up to 3 days)

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Body fluids (pleural,

peritoneal, synovial

Disinfect skin

before aspiration

Aspirate with sterile aspiration needle

and aseptically transfer into sterile

screw-cap container

Immediately/ Room

Temp.

Process as soon as

received

Throat Ordinary throat swab (preferably

moistened with transport medium)

Immediately/ Room

Temp. (avoid

dryness).

Within 24 hours/

Room Temp.( if

transport medium is

used)

Process as soon as

received.

24 hours/ Room

Temp. ( if transport

medium is used)

Nasopharyngeal

specimens

Pernasal short flexible swab is

introduced through nose to the

nasopharynx

Immediately/ Room

Temp. (avoid

dryness).

Within 24 hours/

Room Temp.( if

transport medium is

used)

Process as soon as

received.

24 hours/ Room

Temp. ( if transport

medium is used)

Lower respiratory

specimens:

Sputum

Induced sputum

Patient rinse or gargle

with water before

expectoration of

sputum

Collected directly into sterile screw-cap

container ( patient should cough deeply to

produce lower tract specimen)

Within two hours/

Room Temp.

24 hours/4oC

Endotracheal

aspirate

Bronchoalveolar

lavage (BAL)

Protected

specimen brush

(PSB)

Sterile screw-cap container Within two hours/

Room Temp.

24 hours/4oC

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Gastric aspirate In the early morning,

with patient still in

bed, before

eating, introduce

nasogastric tube;

lavage 50 ml sterile

water, sample

Sterile screw-cap container (For the detection of Mycobacterium

tuberculosis in patient who is unable to

produce sputum)

Immediately/ Room

Temp.

Must be neutralized

with sodium

bicarbonate within

1 hour of collection

Mid stream urine Clean area

thoroughly with soap

and water and rinse

thoroughly;

holding the labia

apart (in female)

begin voiding; after

several ml have

passed, collect

sample without

stopping flow

Sterile screw-cap container

Immediately/ Room

Temp.

Within 24 hours/4oC

24 hours/4oC

Indwelling catheter Disinfection

collection port with

alcohol 70%

Aspirate 5-10 ml urine with sterile

syringe and needle and transfer

aseptically into Sterile screw-cap

container

Immediately/ Room

Temp.

Within 24 hours/4oC

24 hours/4oC

Feces Clean leak proof container, use transport

medium if transport will exceed 1 hour

Immediately/ Room

Temp.

72 hours/4oC

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.

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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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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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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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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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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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Appendix

Indirect Diagnosis Direct Diagnosis

Indirect diagnosis

Direct diagnosis

Conventional Microbiological methods

Immunological methods

Molecular methods

Direct microscopic

examination

Patient (suspected

infectious disease)

Inoculation into suitable

culture media

Pure culture isolation

Conventional Identification:

microscopy, biochemical

reactions, animal

inoculation

Antibiotic

susceptibility testing

Immunological direct

diagnosis

(Direct Ag or toxin

detection):

IF, ELISA, particle

agglutination

Molecular direct

diagnosis

(Direct nucleic acid

detection with or

without amplification):

Nucleic acid

Hybridization &

PCR

Detection of humoral

immune response i.e

antibody detection

tests

(Serological tests e.g.

ELISA, IF)

Clinical specimen: (e.g.

Blood, CSF, CSF, feces,

urine, ….. )

tissue biopsy, ,...

Immunological

Identification:

agglutination,

immunofluorescence,

……

Molecular

Identification:

hybridization,

PCR

Flow Chart for Diagnosis of Infectious Diseases

Detection for

cell mediated

immune

response (e.g.

skin tests)

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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 102-10

3 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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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- 10

6 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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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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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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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, 12

th

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.