Specimen Processing

Agents include those that have no known potential for infecting healthy people

Bacillus subtillis is the representative organism

Precautions include standard good laboratory practices

Biosafety Level 1 (BSL-1)

Agents are those most sought in Clinical specimens

• Associated with disease that is preventable and treatable

Staphylococcus aureus or Escherichia coli are some of the many representative organisms

Precautions include using a biosafety cabinet, training laboratory personnel in handling pathogenic agents, and the use of primary containment equipment

Biosafety Level 2 (BSL 2)

Agents associated with serious or lethal disease and could be treatable

Mycobacterium tuberculosis is one of the representative organisms in this group

Precautions include the same as BSL-2 and -1, but need to also include engineering controls that control air movement of the room, adequate PPE

Biosafety Level 3 (BSL 3)

Agents that are highly likely to cause serious or lethal disease and is generally not known to be treatable or preventable

Ebola virus is one of the representative organisms in this group

Precautions are the same as above but also need to include decontamination of personnel and all materials before leaving the facility

Procedures are performed under maximum containment (Class III BSC) and preferably the laboratory is in a facility of its own

Biosafety Level 4 (BSL-4)

Encloses a workspace to protect the user from aerosol exposure to infectious agents

Air is sterilized by either heat, ultraviolet light or by passage through a HEPA filter

Class 1: Allows room air to pass into the cabinet and only sterilizing the air that is exhausted out

Class 2: Sterilizes air that flows over the infectious material as well as the air that is exhausted out

Class 3: Air coming in and going out of the cabinet is filter sterilized and infectious material is handled with rubber gloves that are attached and sealed to the cabinet

Biologic Safety Cabinet

Impervious lab coat, disposable gloves, masks

Microbiology PPE

What phase of illness should culture specimens be collected during?

Acute Phase

Before any antimicrobial antifungals and antivirals are administered

When should specimens be transported to the lab

Within 2 hours of collection

Sealable, leak proof, separate section for paperwork

Specimen containers

Transport media

Stuart or Amies medium

Anticoagulants that can be used for specimen preservation

SPS (Sodium polyanethol sulfonate) at a 0.025% concentration should be used (blood culture media)

Heparin can inhibit gram-positive organisms and yeast but can be used for viral cultures

Anticoagulants to not use for transport media

Citrate, EDTA

Urine, stool, viral cultures, sputum, swabs, and foreign devices

Stored at 4 C

Serum may be frozen for

One week at -20 C

Tissues or specimens for long-term storage should be frozen at

-70 C

Label does not match requisition form

Specimen is not labeled

Specimen was transported at the improper temperature

Specimen was not transported in the proper medium

Quantity not sufficient for testing

Specimen is leaking out of the container

Specimen exceeded 2 hours post collection without correct preservation

Specimen was received in a fixative, like formalin

Specimen has orders for anaerobic culture from a site known to have anaerobes as normal flora

Specimen is dried

Specimen would produce information of questionable medical value

Specimen rejection

Inoculation allows for what analysis of colony growth

Semi-Quantitative

What is used for cultures like urine where quantity needs to be defined

Calibrated loop

One colony represents 1000 CFUs

Used for every urine culture

0.001 calibrated loop (green loop)

One colony represents 100 CFUs

Only utilized for invasive urine collection (Catheter, nephrostomy, bladder, surgery)

0.01 calibrated loop (Blue loop)

Organisms that utilize oxygen for growth and will grow in ambient air conditions

Pseudomonas, Neisseria, and Brucella (strict)

Aerobic

Most clinically significant organisms fall in this category

Able to grow in the presence or absence of oxygen

Staphylococcus, Escherichia, and Corynebacterium

Facultative anaerobic

Unable to use oxygen and can be lethal to some organisms

Anaerobic organisms that do not utilize oxygen but are not killed are considered aerotolerant

Clostridium, bacteroides, and peptosteptococcus

Strictly anaerobic

Organisms that thrive in areas of lower oxygen levels but not entirely anaerobic

Campylobacter species is the primary example of a microaerophilic organism

Microaerophilic

Routine cultures in carbon dioxide incubators

3-5% CO2 and at 35-37C

Haemophilus and Neisseria are examples of capnophilic organisms

Require around 5-10% CO2

Anaerobes require a s pecial gas mixture and are kept at 37 C

5-10% Hydrogen, 5-10% CO2, and 80-90% Nitrogen

Co2 incubators do what to the media causing it to change color prematurely

Acidify

Values beyond the abnormal limits and life threatening

Positive blood culture

Sterile body fluid critical

Clostridium difficile first time positive

Streptococcus pyogenes from a surgery patient

Positive acid-fast stain

Positive cryptococcal antigen test

Detection of a select agent - Brucella, Franciscella

Detection of a significant pathogen: MRSA, CRE

Critical (Panic) Values