Glossary - Clinical and AMR Terms

Index: Glossary Index · Hubs: MOC - Clinical Microbiology · MOC - Antimicrobial Resistance (AMR)

Infection and clinical syndromes

Infectious Disease — clinically apparent illness resulting from infection.
Bacteraemia — viable bacteria in the bloodstream; may be transient and asymptomatic.
Sepsis — life-threatening organ dysfunction caused by a dysregulated host response to infection.
Septic shock — sepsis with circulatory and metabolic failure requiring vasopressors.
HAI / nosocomial — healthcare-associated infection, acquired ≥48 h after admission.
Community-acquired — present or incubating before admission.
Empirical therapy — treatment started before the organism and susceptibility are known.
Definitive / targeted therapy — treatment after identification and susceptibility results.
De-escalation — narrowing therapy once results allow. See Antimicrobial Stewardship.
Prophylaxis — antimicrobial given to prevent, not treat, infection.

Specimen adequacy — whether the sample can answer the question (e.g., sputum vs saliva). See Microscopy.
Contamination — organism introduced during collection or processing, not from the patient.
Sensitivity / specificity — test properties independent of prevalence.
PPV / NPV — predictive values; depend on prevalence. See Model Evaluation in Clinical Microbiology.
Gold / reference standard — the imperfect comparator a new test is judged against.
Turnaround time — collection to reported result; the clinically decisive metric.
Selective reporting — deliberately withholding broad-spectrum susceptibilities to steer prescribing.

MIC — minimum inhibitory concentration.
MBC — minimum bactericidal concentration; kills rather than inhibits.
Breakpoint — MIC or zone value separating S, I, R; set by EUCAST or CLSI.
ECOFF — epidemiological cut-off separating wild-type from non-wild-type; for surveillance, not therapy.
S / I / R — susceptible / susceptible at increased exposure / resistant.
Disk Diffusion — zone-diameter method. Broth Microdilution — reference MIC method.
Very major error — false susceptible; the most dangerous category of error.
Major error — false resistant. Minor error — involves the I category.
Antibiogram — cumulative institutional susceptibility summary guiding empirical choice.

AMR — survival at normally inhibitory drug concentrations.
Intrinsic vs acquired — inherent to the species vs newly gained.
MDR / XDR / PDR — multidrug-, extensively-, pan-drug-resistant.
Tolerance — survives without growing; MIC unchanged.
Persistence — a non-inherited subpopulation surviving exposure.
Heteroresistance — resistant subpopulation within an apparently susceptible isolate.
Cross-resistance — one mechanism covering several drugs. Co-resistance — several genes carried together.
ESBL — extended-spectrum β-lactamase. AmpC — cephalosporinase, often inducible.
Carbapenemase — hydrolyses carbapenems (KPC, NDM, VIM, OXA-48). CRE / CPE — carbapenem-resistant / carbapenemase-producing Enterobacterales.
MRSA / VRE — methicillin-resistant Staphylococcus aureus / vancomycin-resistant enterococci.
ESKAPE Pathogens — the six organisms dominating resistant hospital infection.
Resistome — the full set of resistance genes in an organism or community.
Fitness cost — biological price of resistance, often erased by compensatory mutation.

Incidence / prevalence — new cases per time / existing cases at a point.
R₀ / Rt — basic / effective reproduction number.
Herd immunity threshold — coverage needed to interrupt transmission (~1 − 1/R₀). See Vaccination.
Outbreak / cluster — more cases than expected / cases linked in time, place, or genome.
Standard vs transmission-based precautions — universal measures vs pathogen-specific additions.
One Health — human, animal, and environmental health as one system.