Microbiology Units #1-5

Empiric Antimicrobial prescribing

occurs before pathogen id

Pathogen-directed therapy

occurs after pathogen id

Types of Direct Specimen Testing

immunoassay methods, molecular diagnostics, and stains

Rapid Diagnostic Testing

direct specimen testing, rapid test on colony growth, detection resistant genes

Rapid Diagnostic Testing Methods

immunoassays, molecular diagnostics, MALDI-TOF

Direct Specimen Testing

some can provide STAT results. tests come directly from patient

Direct Specimen Testing Determines

specimen quality, cell types present, and bacteria/yeast present

Gram Stain

differential stain that detects cells and bacteria/yeast present

Antigen Detection

uses immunoassay method using known antibody to detect unknown antigen. Enzyme/substrate reaction with color occurs. Strep pnuemo

Serology

Detects immune response to specific infectious diseases. Occurs in serum. Usually positive weeks after infection

Nucleic Acid Detection

detects DNA/RNA unique to a specific organism. Myco TB and West Nile Virus

Culture Incubation

18 - 24 hours at body temp (35 - 37 C)

Screen Culture

reports only specific pathogens from a specific source. Strep and Gonorrhea

Comprehensive Culture

reports all bacteria that is growing

Disinfection

pathogenic organisms destroyed but not spores

Physical Disinfection methods

boiling, pasteurize, UV light

Chemical Disinfection Methods

phenol, alcohol, detergents, bleach

Sterilization

all microbial life gets destroyed

Heat Sterilization Methods

incineration, bacti-cinerator (wire loops), autoclave (15/15 121 C)

Liquid Sterilization Methods

thin membrane filters for anything that is liquid

Air Sterilization Methods

high efficiency particulate air (HEPA) filter. Used in isolation room, safety hood, etc.

Sterilization QC Per Load

temperature and time

Sterilization QC Weekly

bacterial spores

Sterilization QC Semiannually

check gauges and recalibrate

Taking supplies out of lab

must be transported in separate bag so they don’t contaminate anything else

IDSA and ASM

help physicians appropriately and accurately use lab tests for diagnosis of infectious disease

General rule of Collection

quality specimen = quality data

Specimen Collection Information

timing, test requisition, proper container, site of infection, uncontaminated, quantity, and proper labeling

Urine Transport Media

Boric Acid

Stool Transport Media

Cary-Blair, formalin/polyvinyl alcohol

Blood Transport Media

sodium polyanethol sulfonate (SPS)

Swabs Transport Media

Stuart or Amies transport media, JEMBEC system

Freezing Specimen

for delays of four days or longer

Specimen Priority 1

critical and invasive specimen (fluid, brain, heart)

Specimen Priority 2

unpreserved specimens (tissue, suptum, feces)

Specimen Priority 3

specimen requiring quantitation (catheter tip, urine, tissue)

Specimen Priority 4

preserved specimen

More than 25 Epithelial cells/LPF

valid to reject specimen

Macroscopic Examination of Specimen

physical characteristics. Swab or aspirate, stool consistency, blood or mucous present, volume, and fluid clarity

Concentration Culture Setup

centrifugation for liquid specimen or filtration

Homogenization

tissue grinding

Decontamination Culture Setup

kills normal flora in a specimen to isolate organism. Mycobacteria

Venous

blood from vein

Capillary

blood from pricking skin

Central Line or PICC

blood from peripherally inserted central catheter

Arterial

blood from artery

Midstream Clean Catch

special cleaning before collection

Catheter

tube collects urine from bladder

Suprapubic

aspiration from bladder via needle. sterile

Voided

skin not cleansed before urine sample

Cerebral Spinal Fluid

surrounds brain and spine. Sterile

Synovial Fluid

cavity of joints. sterile

Pleural Fluid

lining of lungs. sterile

Pericardial Fluid

lining of heart. sterile

Peritoneal Fluid

lining of abdominal organs. sterile

Amniotic Fluid

surrounds a fetus. sterile

Bone Marrow

spongy tissue inside bones. sterile

Bronoalveolar lavage

fluid squirted into lungs then collected

Sputum

mix of saliva and mucus from lower resp tract

Nasopharyngeal

upper part of throat behind nose

Stool/Feces

waste from bowels and GI

Genital

reproductive organs

Abscess

collection of pus within tissue

Tissue

biopsy obtained

Nutrient Media

contains generic nutrients to enable growth of non-fastidious organisms

Nutrient Media Examples

Sheep Blood Agar or Blood Agar Plate

Enriched Media

contains complex substances for needs of specific species

Enriched Media Examples

Blood Agar Plate and Chocolate agar (heat lysed blood)

Selective Media

inhibits growth of selected organisms and allows growth of others

MacConkey Agar

inhibits gram positive and promotes gram negative

Phenyl-ethyl Alcohol Agar and Columbia Colistin Nalidixic Agar

inhibits gram negative and promotes gram positive

Mannitol Salt Agar

inhibits most except staphylococcus

Differential Media

grows different organisms with varying visual characteristics

Differential Media Examples

Blood Agar Plate (hemolysis) and MacConkey Agar (lactose ferment)

Enrichment Meida LIM Broth

designed to grow small numbers of particulate organism and suppressing others

Broth Media THIO

used in combination with agar. detects small aerobes, anaerobes, and microaerophiles

Isolation Technique

use sterile loop, inoculate non-selective then selective media

Obligate aerobe

requires oxygen to grow

Microaerophile

requires reduced oxygen and increased co2 to grow

Obligate Anaerobe

requires no oxygen present to grow

Facultative Anaerobe

not dependent on oxygen to grow

Capnophilic

requires increased co2 to grow

Psychrophiles

grow at 10-20 C

Mesophiles

grow at 20-45 C. most human pathogen

Thermophiles

grow at 50 - 200 C

pH Range for Growth

6.5 - 7.5 in buffered media

Moisture for Growth

70 - 80% humidity

Ambient air incubator

room air, generally 35 C. high humidity

CO2 incubator

5 - 10% Co2, mixed with room air, generally 35 C. high humidity

Anaerobic Incubator

5% H, 5-10% Co2, 85-90% N2. 35 C and high humidity

Anaerobic Culture Incubation

takes 5 - 7 days

Culture Day 1

Specimen processing, setup and incubate, preform gram stain, preliminary report

Culture Day 2

colony morphology, preform colony gram stain, biochemical testing, subbing of plates, setup id, preliminary report

Culture Day 3

final report. Organism id, quantitation, susceptibility, etc.

QC Media

CLSI requires 2 year record

Commercially prepared QC

exempt from QC in lab by certificate of manufacturer. However CHOC or high fail rate is still tested

Gram Positive

blue to purple. low lipid, thick cell wall of peptidoglycan

Gram negative

red to pink. high lipid, thin cell wall of peptidoglycan

Primary Stain

crystal violet for 1 minute.

Mordant

Grams Iodine for 1 minute.