Glossary
Clinical microbiology is the branch of laboratory medicine concerned with the detection, identification, characterization, and antimicrobial susceptibility testing of microorganisms associated with human disease.
This reference provides concise definitions of commonly encountered clinical microbiology terminology, diagnostic methodologies, organisms, laboratory tests, antimicrobial susceptibility concepts, quality practices, and biosafety terminology. It is intended as an educational reference for students, laboratory professionals, healthcare personnel, and others seeking a structured introduction to clinical microbiology.
Important: This reference is educational and is not a substitute for a laboratory’s validated standard operating procedures, applicable regulatory requirements, manufacturer instructions, or current professional standards. Diagnostic testing should be performed only by appropriately trained personnel using validated methods.
Fundamental Clinical Microbiology Terms
Aseptic technique
Practices designed to prevent unwanted microbial contamination during specimen handling, culture, testing, and related laboratory procedures. This includes wearing personal protective equipment (PPE) to prevent introduction of flora into the specimen.
Clinical microbiology
The laboratory discipline concerned with detecting, identifying, characterizing, and determining the antimicrobial susceptibility of microorganisms associated with human disease.
Colonization
The presence and multiplication of microorganisms at a body site without evidence that the organisms are causing disease.
Colony
A macroscopically visible population of microorganisms growing on a solid culture medium.
Colony-forming unit (CFU)
An operational measure of viable microorganisms capable of producing a colony under the conditions of a particular culture method.
Contamination
The unintended introduction or presence of microorganisms in a specimen, culture, reagent, instrument, or environment.
Culture
The growth of microorganisms in or on an artificial medium under controlled laboratory conditions.
Infection
The establishment and multiplication of an infectious agent within a host. Infection may occur without producing clinical disease.
Inoculum
A defined quantity of microorganisms introduced into a culture medium or test system.
Microorganism
A microscopic biological organism or infectious biological entity. In clinical microbiology, the principal groups include bacteria, fungi, protozoa, and viruses.
Mixed culture
A culture containing organisms from three or more microbial populations which diagnostically will not provide relevant information to the provider about the organism causing infection in the area.
Normal microbiota
Microorganisms that normally inhabit a particular body site without necessarily producing disease.
Opportunistic pathogen
An organism that can cause disease primarily when host defenses, anatomical barriers, or other protective conditions are compromised.
Pathogen
An infectious agent capable of causing disease in a susceptible host.
Pure culture
A culture containing one or two organisms likely representing the causative agent(s) of the infection.
Common Abbreviations
This section summarizes frequently used clinical microbiology abbreviations encountered in culture workups, susceptibility testing, and specimen processing.
| Abbreviation | Definition |
|---|---|
| AFB | Acid-fast bacilli |
| BAP | Blood agar plate |
| BBE | Bacteroides Bile Esculin Agar |
| BCYE | Buffered charcoal yeast extract agar |
| CAMHB | Cation-adjusted Mueller-Hinton broth |
| CHOC | Chocolate Agar |
| CNA | Colistin Nalidixic Acid Agar |
| CRE | Carbapenem Resistant Enterobacterales |
| CSF | Cerebrospinal fluid |
| CVA | Campylobacter Vancomycin Agar |
| GNR/GNB | Gram negative rod/Bacilli |
| GPC | Gram-positive cocci |
| GPR/GPB | Gram Positive rod/bacilli |
| IMA | Inhibitory Mold Agar |
| KPC | Klebsiella pneumoniae carbapenamse |
| LKV | Laked Kanamycin Vancomycin Agar |
| MAC | MacConkey agar |
| MIC | Minimum inhibitory concentration |
| MRSA | Methicillin Resistant Staph aureus |
| MSSA | Methicillin Susceptible Staph aureus |
| PBP2a | Penicillin binding protein 2a |
| PEA | Phenylethyl Alcohol Agar |
| PPE | Personal Protective Equipment |
| SAB | Sabourand Dextrose Agar |
| TSA | Tryptic soy agar |
| VRE | Vancomycin Resistant Enterococcus |
