Culture-Based Diagnostic & Typing Methods – Vocabulary

A set of vocabulary flashcards covering microscopy, culture media, biochemical tests, and modern diagnostic methods from the HCS228 lecture.

Diagnostic Microbiology

The field focused on detecting and identifying pathogens in clinical samples and determining their disease potential and treatment options.

Typing

Laboratory methods used to distinguish different strains within the same microbial species.

Antimicrobial Susceptibility Testing

Procedures that determine which antibiotics inhibit or kill a particular microorganism.

Pathogenicity Profiling

Assessment of a microbe’s ability to cause disease, including its virulence factors.

Specimen

A clinical sample (e.g., blood, urine, swab) collected for laboratory analysis.

Macroscopic Observation

Visual examination of a specimen or culture plate without a microscope to note color, turbidity, volume, or visible parasites.

Microscopy

The use of microscopes to view microorganisms or cells that cannot be seen with the naked eye.

Bright-Field Microscopy

A common light microscopy technique in which specimens appear dark against a bright background.

Phase-Contrast Microscopy

Microscopy that enhances contrast in transparent specimens by amplifying differences in refractive index.

Fluorescence Microscopy

Microscopy that uses fluorescent dyes or tags to visualize specific structures or organisms under UV/blue light.

Electron Microscopy

High-resolution microscopy that uses electron beams (e.g., TEM, SEM) to visualize ultrastructure of microbes.

Gram Stain

Differential stain that classifies bacteria as Gram-positive (purple) or Gram-negative (pink/red) based on cell wall structure.

Crystal Violet

Primary purple dye used in Gram staining that binds negatively charged cell components.

Mordant (Iodine)

Substance that forms large complexes with crystal violet, fixing dye within bacterial cells during Gram staining.

Decolorizing Agent

Ethanol or acetone used in Gram staining to remove crystal violet–iodine complexes from Gram-negative cells.

Counterstain (Safranin)

Positively charged dye applied after decolorization to color Gram-negative bacteria pink/red.

Acid-Fast Stain (Ziehl-Neelsen)

Staining method for Mycobacterium spp. thatresist Gram staining due to waxy cell walls.

Peptidoglycan

Rigid polymer layer in bacterial cell walls; thick in Gram-positives, thin in Gram-negatives.

KOH Preparation

Direct fungal examination technique using potassium hydroxide to clear host material while leaving chitinous walls intact.

Calcofluor White

Fluorescent dye that binds chitin and cellulose, making fungi glow bright green-blue under UV light.

Trichrome Stain

Differential stain used to visualize protozoan parasites in stool samples.

Giemsa Stain

Blood smear stain commonly used to detect parasites such as Trypanosoma and Plasmodium.

Culture Medium

Nutrient-containing preparation that supports microbial growth in the laboratory.

Non-Selective Medium

General purpose medium (e.g., nutrient agar) that allows growth of most non-fastidious microbes.

Supplemented Medium (Chocolate Agar)

Medium enriched with lysed red blood cells to support fastidious organisms like Haemophilus influenzae.

Selective Medium

Medium containing inhibitors (e.g., antibiotics) that suppress unwanted microbes while promoting pathogen growth.

Differential Medium

Medium that reveals metabolic differences between organisms via color or pH changes (e.g., MacConkey agar).

Chromogenic Medium

Medium with enzyme substrates that release colored chromogens, allowing species-specific colony colors.

Blood Agar

Differential medium that displays hemolysis patterns (α, β, γ) produced by bacteria.

Mannitol Salt Agar (MSA)

Selective-differential medium containing 7.5 % NaCl and mannitol; identifies Staphylococcus aureus by yellow colonies.

CLED Agar

Cystine-lactose-electrolyte-deficient agar used for urinary pathogens; differentiates lactose fermenters.

MacConkey Agar

Selective-differential medium for Gram-negatives; lactose fermenters turn pink due to neutral red indicator.

Optochin Test

Disc diffusion test distinguishing optochin-sensitive Streptococcus pneumoniae from resistant α-streptococci.

Colony Morphology

Observable characteristics of colonies on agar—size, color, margin, elevation, hemolysis, mucoidity, etc.

Psychrophile

Microorganism that grows optimally at cold temperatures (<15 °C).

Mesophile

Microorganism with optimum growth around 20–45 °C; includes most human pathogens.

Thermophile

Organism thriving at temperatures >45 °C.

Obligate Aerobe

Microbe that requires oxygen for growth.

Obligate Anaerobe

Organism that cannot grow in the presence of oxygen.

Facultative Anaerobe

Microbe able to grow with or without oxygen, switching metabolism accordingly.

Microaerophilic

Organism requiring reduced oxygen levels (≈5 % O₂) for optimal growth.

Capnophilic

Microbe preferring elevated CO₂ concentrations.

Catalase Test

Biochemical test detecting catalase enzyme by observing bubble production from H₂O₂ breakdown.

Oxidase Test

Test for cytochrome c oxidase activity; positive colonies turn dark purple with reagent.

Coagulase Test

Assay differentiating Staphylococcus aureus (coagulase +) from other staphylococci via plasma clotting.

Indole Test

Biochemical test detecting tryptophan degradation to indole, turning red with Kovács reagent (positive in E. coli).

API Strip

Commercial panel of miniaturized biochemical tests yielding a 7-digit Analytical Profile Index for identification.

Vitek

Automated system that performs biochemical profiling and susceptibility testing of bacteria.

Great Plate Count Anomaly

Observation that plate counts vastly underestimate microbial numbers compared with direct microscopic counts.

MALDI-TOF MS

Mass spectrometry technique identifying microbes by protein ‘fingerprints’ without extensive culturing.

ELISA

Enzyme-linked immunosorbent assay used to detect specific antigens or antibodies in samples.

PCR / NAAT

Polymerase chain reaction or nucleic acid amplification tests that detect pathogen DNA/RNA directly.

Whole-Genome Sequencing

Determination of the entire DNA sequence of an organism, enabling precise identification and typing.