MI1.{3-9,11} | General Microbiology II: Laboratory Diagnosis, Specimens & Professionalism — Glossary

Technical measures that restrict viewing, editing, or releasing of patient laboratory data to authorised personnel only, protecting confidentiality.

Attitude, Ethics and Communication module mandated by NMC for MBBS curriculum; develops professional values, ethical reasoning, and communication skills across all clinical postings.

The proportion of exposed persons who develop disease during an outbreak; used to measure the impact of a specific exposure.

The average number of secondary cases generated by one infectious case in a completely susceptible population; determines whether an epidemic will grow (R₀>1) or decline (R₀<1).

Any waste generated in the diagnosis, treatment, or immunisation of humans or animals; must be segregated, treated, and disposed of per CPCB Biomedical Waste Management Rules 2016.

Inoculation of blood into enriched broth media (aerobic and anaerobic bottles) for detection of bacteraemia or fungaemia; gold standard for systemic bloodstream infection.

The right of a competent patient to accept or refuse medical procedures, including specimen collection, without coercion.

A semi-solid, reduced-pH transport medium that maintains viability of enteric pathogens (Salmonella, Shigella, Campylobacter) in stool specimens during transport.

A set of clinical and epidemiological criteria used to classify whether a person has the disease under investigation in an outbreak setting.

Cartridge-Based Nucleic Acid Amplification Test; a brand-agnostic term for enclosed real-time PCR systems (e.g., GeneXpert MTB/RIF) that simultaneously detect pathogen DNA and resistance mutations.

The sequential links — infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, susceptible host — that must remain intact for disease transmission.

An outbreak in which cases share a single exposure event at approximately the same time; produces a sharply peaked epidemic curve.

The ethical and legal obligation to protect identifiable patient health information from disclosure without the patient's explicit consent.

A laboratory result that indicates a life-threatening condition requiring immediate clinical action; must be communicated to the responsible clinician by direct telephone call without delay.

Enzyme-Linked Immunosorbent Assay; a plate-based technique using enzyme-labelled antibodies to detect and quantify antigens or antibodies in specimens.

A histogram displaying the number of new cases over time during an outbreak; its shape distinguishes common-source from propagated outbreaks and estimates exposure time.

The conceptual framework of agent, host, and environment whose interaction determines whether infectious disease occurs in an individual or population.

Indirect protection of susceptible individuals when a sufficient proportion of a population is immune, interrupting pathogen transmission.

An Indian law that criminalises disclosure of a person's HIV status without their informed consent, punishable by imprisonment and/or fine.

India's national disease surveillance network that collects weekly and immediate reports of notifiable communicable diseases from health facilities for public health response.

The number of new cases of a disease occurring in a defined population during a specified time period; reflects disease risk.

A microscopy technique in which India ink particles are excluded by the Cryptococcus neoformans capsule, producing a clear halo around the encapsulated yeast in CSF smear.

Sputum produced after inhalation of nebulised hypertonic saline, used when a patient cannot spontaneously expectorate; particularly useful for TB diagnosis.

A process by which a patient voluntarily agrees to a test or procedure after receiving comprehensible information about its nature, purpose, risks, and alternatives.

A software system that manages laboratory data — specimen tracking, test requests, results, and reporting — with access control to protect patient confidentiality.

A nucleic acid amplification method operating at a single temperature (~65 °C), suitable for point-of-care settings without a thermocycler.

A rapid strip-based test in which analyte migrates through a nitrocellulose membrane and produces a visible coloured line at the test zone when target antigen or antibody is present.

An egg-based solid medium used for primary isolation and culture of Mycobacterium tuberculosis; results take 3–8 weeks.

A selective and differential culture medium that inhibits gram-positive organisms and differentiates lactose fermenters (pink colonies) from non-fermenters (colourless).

Matrix-Assisted Laser Desorption/Ionisation – Time of Flight Mass Spectrometry; identifies microorganisms by analysing the unique protein mass fingerprint of a colony in seconds.

A legal requirement to report specified communicable diseases to designated public health authorities; overrides individual confidentiality but requires only minimum necessary information.

The lowest concentration of an antimicrobial agent that inhibits visible growth of a microorganism in vitro; forms the basis of susceptibility categorisation (S/I/R).

Urine collected after discarding the initial urinary stream; reduces contamination with periurethral flora for culture purposes.

The ethical and legal standard that only the minimum amount of identifiable patient information needed for a specific legitimate purpose should be shared or used.

DNA sequences (plasmids, transposons, integrons) capable of moving within or between genomes, frequently carrying antimicrobial resistance or virulence genes.

A PCR variant using multiple primer pairs in one reaction tube to simultaneously amplify and detect several target sequences from different pathogens.

National AIDS Control Organisation; the apex body in India for HIV/AIDS prevention and control, which sets protocols for HIV testing, counselling, and ART linkage.

High-throughput massively parallel sequencing technology that generates millions of short reads simultaneously, enabling whole genome sequencing and metagenomic pathogen identification.

The binding of a single-stranded labelled probe sequence to its complementary target nucleic acid sequence for detection purposes.

A public health process of informing the sexual or needle-sharing partners of a patient with a transmissible infection (especially HIV/STI) of their potential exposure, conducted with patient involvement and counsellor support.

A molecular technique that amplifies a specific DNA sequence exponentially using thermocycling and a thermostable polymerase, enabling detection of minute quantities of pathogen nucleic acid.

Circular extra-chromosomal DNA element in bacteria capable of autonomous replication; major vehicle for horizontal transfer of antimicrobial resistance genes.

The route by which a pathogen leaves the reservoir (portal of exit) or enters a susceptible host (portal of entry); e.g., respiratory droplets, skin breaks, mucous membranes.

Structured communication after a diagnostic test result to explain findings, their implications, treatment options, partner notification, and linkage to care.

Structured communication with a patient before a diagnostic test (especially HIV) to explain the test, its implications, address concerns, and ensure informed voluntary consent.

The proportion of a population with a disease at a given point in time (point prevalence) or during a period (period prevalence); reflects disease burden.

The consistent demonstration of ethical conduct, respect, competence, and accountability in clinical and laboratory settings, including in the absence of patients.

An outbreak sustained by person-to-person transmission over successive generations, producing a stepwise rising epidemic curve with waves corresponding to serial incubation periods.

PCR variant that detects and quantifies amplified product in real time using fluorescent probes, enabling measurement of pathogen load.

A chain-termination DNA sequencing method producing sequence reads up to ~1,000 bp; gold standard for targeted mutation detection (e.g., rpoB in MTB).

Situation–Background–Assessment–Recommendation; a structured communication framework used to convey critical clinical information efficiently and accurately between healthcare providers.

The proportion of susceptible close contacts (e.g., household members) who develop disease after exposure to a primary case within one incubation period.

Growth of ≥10⁵ colony-forming units per mL of a single organism in a clean-catch urine specimen, indicating true urinary tract infection rather than contamination.

Negative attitudes, discrimination, and social exclusion directed at individuals because of a health condition; particularly severe for HIV, TB, STIs, and mental illness; worsened by confidentiality breaches.

A non-nutrient gel medium that preserves bacterial viability in swab specimens without allowing multiplication, used for transport of throat, wound, and genital swabs.

A thermostable DNA polymerase from Thermus aquaticus that functions at PCR extension temperatures (~72 °C) without denaturing.

A set of infection control practices applied to all patient specimens and contacts regardless of known or suspected infection status, treating all as potentially infectious.

A buffered saline solution with protein stabilisers and antibiotics used to preserve viral particles in nasopharyngeal and other swabs during transport to the virology laboratory.

An immunoassay in which proteins separated by gel electrophoresis are transferred to a membrane and detected with labelled antibodies; used as confirmatory test for HIV.

A tube agglutination serological test detecting antibodies against Salmonella Typhi O and H antigens; limited by false positives from endemic baseline titres in India.

Differential stain using carbol fuchsin (hot) with acid-alcohol decolorisation; acid-fast bacilli such as M. tuberculosis retain the red dye on a blue background.

An infectious disease that can be transmitted between animals and humans, either directly or through an arthropod vector.