ABPath Medical Microbiology key terms

Baseline infection-control practices applied to every patient regardless of diagnosis, including hand hygiene, gloves, gowns, masks, and safe handling of sharps and body fluids. They replace the older category of universal precautions.

Additional isolation measures layered onto standard precautions when a specific route of spread is suspected or known, such as contact, droplet, or airborne precautions, sometimes with protective environment rooms for highly vulnerable patients.

A graded set of containment practices, equipment, and facility design requirements assigned to laboratories by the risk of the agents handled, ranging from BSL-1 for low-risk work to BSL-4 for dangerous agents with no available countermeasures.

A ventilated enclosure that uses directional airflow and high-efficiency particulate air filtration to protect the worker, the sample, and sometimes the environment from aerosols generated during handling of infectious material.

A clinical or laboratory activity that produces small infectious particles capable of traveling on air currents, such as centrifugation without lids, vortexing open tubes, or certain respiratory procedures, requiring heightened respiratory protection.

A single-occupancy patient room with negative pressure relative to surrounding areas and frequent air exchanges, used for diseases spread by tiny droplet nuclei that remain suspended and can be inhaled at a distance.

Scheduled testing of reagents, media, stains, instruments, and personnel performance against known standards to confirm that results are reliable before patient specimens are reported.

A program in which an outside agency sends blinded specimens of known or unknown composition to a laboratory, and the laboratory's results are compared with peer laboratories or reference answers to reveal systematic error.

A formal, often regulatory-required form of external quality assessment in which a laboratory analyzes challenge samples and must achieve an acceptable score to maintain accreditation or certification for that test.

Verification that each batch of prepared or purchased culture medium supports growth of intended organisms and inhibits or differentiates unwanted ones, using defined reference strains and documented growth or reaction endpoints.

Practices that prevent introduction of microorganisms into specimens, media, or patients, including hand hygiene, disinfection of collection sites, use of sterile containers, and avoiding contact between sterile and nonsterile surfaces.

Introduction of skin flora or environmental organisms into a blood culture bottle during collection, producing a false-positive result that can lead to unnecessary antibiotics, longer stays, and added cost.

The formal two-part naming system for organisms, with a capitalized genus followed by a lowercase species epithet, both italicized in print or underlined in handwriting.

A level in the hierarchical classification of organisms, such as domain, kingdom, phylum, class, order, family, genus, and species, where each level groups organisms sharing defining characteristics.

Grouping of organisms based on evolutionary relatedness, commonly inferred from conserved gene sequences such as ribosomal RNA, rather than on shared appearance or biochemical traits alone.

The permanently designated reference strain that anchors a species name, serving as the standard against which other isolates are compared when species boundaries are defined.

Obtaining a specimen in a way that excludes contaminating organisms from the collection site or environment, such as cleansing skin before venipuncture or avoiding normal flora when sampling a sterile site.

A defined group of blood culture bottles, typically one aerobic and one anaerobic bottle per collection, drawn from a single venipuncture and representing one sample for interpretation of positivity.

Assessment of a lower respiratory specimen by microscopic screening, such as counting squamous epithelial cells and neutrophils, to decide whether the sample reflects lung secretions or saliva contamination.

Documented conditions under which a laboratory will not process a specimen, such as an unlabeled container, a leaky transport device, a delay beyond stability limits, or a specimen unsuitable for the ordered test.

Movement of a collected sample to the testing laboratory under conditions that preserve the viability and relative abundance of pathogens, including temperature limits, time limits, and appropriate containers and transport media.

A buffered, often semisolid or reduced formulation that keeps fastidious organisms alive without allowing overgrowth by commensals during the interval between collection and culture.

A surface structure or molecule, such as pili, fimbriae, or specific adhesins, that lets a microbe attach to host cells and establish a foothold before tissue damage or invasion occurs.

A protein toxin actively secreted by a bacterium that damages host cells through a specific mechanism, often with high potency and a characteristic tissue target, and is typically neutralized by specific antibody.

Lipopolysaccharide in the outer membrane of gram-negative bacteria that triggers fever, inflammation, and shock through host pattern-recognition receptors, especially when released by bacterial lysis.

A microbial protein that cross-links immune receptors nonspecifically, causing widespread T-cell activation and massive cytokine release without requiring prior specific immune recognition of the organism.

An organized community of microbes attached to a surface and embedded in a self-produced matrix, which reduces antibiotic penetration and helps the organisms resist host defenses and clearance.

The lowest concentration of an antimicrobial agent that visibly prevents growth of a standardized bacterial inoculum under defined test conditions, used with breakpoints to classify susceptibility.

The lowest antimicrobial concentration that reduces the starting bacterial population by a defined large fraction, commonly 99.9 percent, reflecting killing rather than mere growth inhibition.

An agreed concentration threshold that separates organisms likely to respond to a given antimicrobial regimen from those likely to fail, set using pharmacokinetic, pharmacodynamic, and clinical outcome data.

A susceptibility method in which a strip containing a preformed concentration gradient is placed on an inoculated agar plate; the point where growth intersects the strip yields the inhibitory concentration.

A standardized susceptibility method in which antibiotic-impregnated paper disks are placed on an inoculated agar plate and the diameter of the growth inhibition zone is compared with validated interpretive criteria.

A culture formulation containing substances that suppress the growth of unwanted organisms while permitting the recovery of the target group, often combined with indicators that reveal characteristic colonies.

A culture formulation that allows colonies of different organisms to be distinguished by a visible reaction, such as color change, hemolysis, or gas production, while generally supporting growth of many species.

A culture formulation supplemented with nutrients such as blood, serum, or vitamins to support growth of fastidious organisms that fail on simpler media.

A sequential staining method that divides bacteria by cell wall structure; thick peptidoglycan retains the primary dye and appears purple, while thin walls lose it and take the counterstain, appearing pink.

A staining procedure using heat or a strong solvent to drive dye into waxy cell walls, which resist decolorization and appear red against a contrasting background, used to detect mycobacteria and related organisms.

An identification method that ionizes microbial proteins and compares the resulting mass spectrum with a reference library, giving a species-level identification within minutes from a single colony.

A molecular method that copies a specific microbial nucleic acid target many times so it can be detected, offering high sensitivity and speed, though contamination control and interpretation require care.

Determination of the complete genetic content of an organism, used for precise identification, resistance and virulence gene detection, and outbreak strain comparison at very high resolution.

Coordinated efforts to improve how antimicrobials are prescribed and used, aiming for correct drug, dose, duration, and route to optimize outcomes while limiting resistance and adverse effects.

A laboratory result indicating immediate danger to the patient, such as a positive blood culture or cerebrospinal fluid Gram stain, which must be communicated promptly to a responsible clinician with documentation.