Comprehensive Microbiology Laboratory Diagnosis & Therapy Vocabulary

A curated vocabulary list summarising essential laboratory diagnostic tests, microbial characteristics, serological assays, molecular techniques, and first-line treatments covered throughout the lecture notes. Each flashcard pairs a key term with a concise definition, enabling efficient review of core microbiology concepts for exam preparation.

Specimen Collection

First step in laboratory diagnosis; obtaining appropriate clinical material (blood, CSF, urine, swab, etc.) before antimicrobial therapy.

Gram Stain

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

Acid-Fast Stain (Ziehl-Neelsen)

Staining technique used to detect mycobacteria and other acid-fast organisms that retain carbol-fuchsin despite acid-alcohol decolourisation.

Albert Stain

Special stain for demonstrating metachromatic granules in Corynebacterium diphtheriae.

Dark-Ground Microscopy

Optical method for visualising thin, live organisms such as spirochaetes by illuminating them against a dark background.

Phase-Contrast Microscopy

Microscopy that enhances contrast of transparent specimens, useful for observing living bacteria without staining.

Fluorescence Microscopy

Technique employing fluorochrome-labelled antibodies or dyes to detect microorganisms or antigens under UV light.

Antigen Detection

Direct identification of microbial proteins or polysaccharides in clinical specimens using methods like ELISA, latex agglutination, ICT, DFA.

Molecular Diagnosis

Detection or amplification of microbial DNA/RNA (e.g., PCR, RT-PCR, real-time PCR, probes) directly from specimens.

Culture Media

Artificial nutrient substrates (broth or agar) supporting microbial growth for isolation, identification, and susceptibility testing.

Selective Medium

Culture medium containing inhibitors that suppress unwanted flora while allowing target pathogens to grow (e.g., TCBS for Vibrio).

Enrichment Broth

Liquid medium that favours growth of low-number pathogens over commensals before plating (e.g., Selenite F for Salmonella).

Biochemical Identification

Use of metabolic reactions (indole, citrate, urease, TSI, etc.) to characterise and identify bacterial species.

Automated Identification (MALDI-TOF / VITEK)

Instrument-based platforms that rapidly profile organisms via protein mass spectrometry or biochemical cards.

Antimicrobial Susceptibility Testing (AST)

In vitro determination of pathogen’s sensitivity or resistance to antibiotics (e.g., disk diffusion, MIC, automated panels).

Serology

Laboratory detection of pathogen-specific antibodies (IgM/IgG) or antigens in patient serum.

Typing Methods

Techniques (phage typing, PFGE, MLST, genotyping) used to differentiate strains for epidemiology.

Electron Microscopy (EM)

High-resolution imaging method for direct visualisation of viruses or ultrastructural details.

Immunoelectron Microscopy

EM technique that uses specific antibodies to enhance visualisation of viral particles.

Histopathological Inclusion Bodies

Intracellular structures (e.g., Negri, Lipschütz) seen by light microscopy indicative of viral infection.

ELISA (Enzyme-Linked Immunosorbent Assay)

Enzymatic immunoassay for qualitative or quantitative detection of antigens or antibodies.

Indirect Immunofluorescence (IF)

Assay where patient antibody binds antigen, detected by fluorescent anti-human Ig; used for viruses, rickettsiae.

ICT (Immunochromatographic Test)

Rapid lateral-flow assay providing point-of-care detection of microbial antigens or antibodies.

HAI (Hemagglutination Inhibition)

Serological test measuring antibody ability to prevent viral hemagglutination of RBCs (e.g., influenza, dengue).

Complement Fixation Test (CFT)

Classical serologic assay detecting antigen–antibody complexes by consumption of complement.

PCR (Polymerase Chain Reaction)

In vitro enzymatic amplification of specific DNA sequences for detection or identification of pathogens.

Reverse Transcriptase PCR (RT-PCR)

PCR preceded by reverse transcription to amplify RNA targets (e.g., RNA viruses).

Real-Time PCR

PCR format that monitors amplification in real time, enabling quantification of microbial load.

Animal Inoculation

Method of viral isolation using live animals (e.g., newborn mice) to demonstrate infectivity.

Embryonated Egg Culture

Classical virology technique inoculating virus into chick embryo membranes or cavities for isolation (influenza, pox).

Tissue Culture

Growth of viruses in organ, explant, or cell-line cultures (primary, secondary, continuous).

Blood Culture

Incubation of patient blood in broth (e.g., BACTEC) to recover bloodstream pathogens.

BACTEC / BacT-ALERT

Automated systems detecting microbial CO₂ in blood culture bottles for rapid positivity.

Widal Test

Tube agglutination assay measuring antibodies (TO, TH, AH, BH) for serodiagnosis of enteric fever.

Slide Agglutination Test

Rapid method using antisera to confirm serotype of cultured Salmonella colonies.

Modified Duke Criteria

Clinical, microbiologic, and echocardiographic parameters used to diagnose infective endocarditis.

HACEK Group

Slow-growing, fastidious gram-negative coccobacilli (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella) causing IE.

Weil-Felix Test

Heterophile agglutination of Proteus OX strains detecting anti-rickettsial antibodies.

Indirect Immunofluorescence Assay (IFA)

Gold-standard serology for rickettsial and scrub typhus infections detecting species-specific antibodies.

56-kDa Antigen ELISA

Recombinant antigen-based ELISA for diagnosis of scrub typhus.

BCSA Blood Culture (Castaneda)

Biphasic brain–heart infusion medium for isolation of Brucella from blood/bone marrow.

Standard Agglutination Test (SAT)

Serological assay detecting Brucella IgM antibodies in patient serum.

Leptospira EMJH Medium

Semisynthetic medium supporting slow growth of Leptospira species at 30 °C for weeks.

Microscopic Agglutination Test (MAT)

Reference serovar-specific assay for leptospiral antibodies using live organisms.

GlpQ Assay

Immunoblot detecting antibodies to recombinant GlpQ protein for relapsing fever Borrelia.

HIV ELISA

Screening test detecting anti-HIV antibodies; results in 2–3 h.

Rapid HIV Tests

Lateral-flow or filter-based assays giving HIV antibody results in <30 min.

Western Blot

Supplemental assay detecting antibodies to specific HIV proteins for confirmation.

p24 Antigen

HIV capsid protein detectable in serum early (12–26 days) during window period.

HIV RNA Load

Quantitative measure of plasma viral RNA by RT-PCR; best marker for therapy monitoring.

NS1 Antigen (Dengue)

Non-structural protein 1 detected in serum from day 1 of fever; early specific marker.

MAC-ELISA (Dengue)

IgM antibody-capture ELISA recommended in India for dengue diagnosis after day 5 of fever.

Real-Time RT-PCR (Dengue)

Highly sensitive assay detecting and quantifying dengue viral RNA and serotype.

Tetravalent Dengue Vaccine (CYD-TDV)

Live attenuated chimeric yellow-fever/dengue vaccine (Dengvaxia) licensed in 2015.

MAC-ELISA (Chikungunya)

IgM-capture ELISA with high sensitivity/specificity for chikungunya virus infection.

Peripheral Thick Smear

Concentrated blood film detecting malaria parasites; more sensitive than thin smear.

HRP-II Antigen

Histidine-rich protein specific to Plasmodium falciparum detected by RDTs.

Artemisinin Combination Therapy (ACT)

First-line treatment for falciparum malaria combining artemisinin derivative with partner drug.

LD Bodies

Amastigote forms of Leishmania donovani seen inside macrophages on Giemsa stain.

rk39 ICT

Rapid immunochromatographic test detecting antibodies to rk39 antigen for visceral leishmaniasis.

Og4C3 Antigen

Circulating filarial antigen detected by ELISA/ICT in Wuchereria bancrofti infection.

Diethylcarbamazine (DEC)

Drug of choice for lymphatic filariasis; kills adult worms and microfilariae.

Germ Tube Test

Serologic-free test where Candida albicans forms germ tubes in serum within 2 h at 37 °C.

CHROMagar Candida

Differential medium producing species-specific coloured colonies for rapid Candida identification.

ESBL

Extended-spectrum β-lactamase conferring resistance to penicillins and cephalosporins in Enterobacteriaceae.

String Test (Vibrio cholerae)

Viscous mucoid string formed when colonies emulsified with sodium deoxycholate, indicating V. cholerae.

Kanagawa Phenomenon

β-Haemolysis of Vibrio parahaemolyticus on high-salt Wagatsuma agar correlating with pathogenicity.

Copro-antigen ELISA

Stool assay detecting Entamoeba histolytica lectin antigen for amoebiasis diagnosis.

HBsAg

Hepatitis B surface antigen; first marker to appear; indicates current infection or carrier state.

Anti-HBc IgM

Antibody to HBV core antigen; marker of acute or recent Hepatitis B infection.

HBV DNA

Molecular marker indicating active replication; quantified to monitor antiviral therapy response.

HCV Core Antigen

Protein detected by automated immunoassay as cheaper alternative to HCV RNA for active infection.

Direct-Acting Antiviral (DAA)

Small-molecule drug targeting HCV NS3/4A, NS5A, or NS5B proteins achieving >90 % SVR.

Metronidazole (ALA)

Nitroimidazole tissue amoebicide—first-line drug for amoebic liver abscess.

Hydatid PAIR

Percutaneous Puncture, Aspiration, Injection, Re-aspiration technique treating hepatic hydatid cysts.

Protein A

Surface protein of Staphylococcus aureus that binds Fc portion of IgG; detected for identification.

ASO Titre

Antistreptolysin-O antibody level indicating recent Streptococcus pyogenes infection.

Nagler Reaction

Opaque zone on egg-yolk agar surrounding Clostridium perfringens due to α-toxin lecithinase activity.

HTIG

Human tetanus immunoglobulin used for passive immunisation and treatment of tetanus.

Medusa Head Colony

Filamentous edges of Bacillus anthracis growth on agar due to chained bacilli.

McFadyean Reaction

Polychrome methylene blue stain showing purple capsule of B. anthracis against blue bacillus.

Tzanck Smear

Cytology exam showing multinucleated giant cells in HSV or VZV lesions.

Paul-Bunnell Test

Heterophile antibody agglutination of sheep RBCs used in infectious mononucleosis diagnosis.

Optochin Sensitivity

Inhibition halo around ethylhydrocupreine disk identifying Streptococcus pneumoniae.

Satellitism (H. influenzae)

Growth of tiny colonies around Staphylococcus aureus streak on blood agar due to factor V release.

Fried-Egg Colony

Mycoplasma pneumoniae morphology on PPLO agar with dense centre and translucent periphery.

GeneXpert MTB/RIF

Cartridge-based NAAT detecting Mycobacterium tuberculosis and rifampicin resistance in 2 h.

Line Probe Assay (LPA)

Hybridisation test identifying MTB complex and mutations conferring first/second-line drug resistance.

Regan-Lowe Medium

Charcoal-blood agar enriched medium for Bordetella pertussis culture.

Cetrimide Agar

Selective medium isolating Pseudomonas aeruginosa via suppression of other flora.

Neuraminidase Inhibitors

Antivirals (oseltamivir, zanamivir) blocking release of influenza A & B virions; effective within 48 h.

IS481 PCR Target

Insertion sequence used in PCR assays to detect Bordetella pertussis DNA.

NP Swab (COVID-19)

Nasopharyngeal specimen collected for SARS-CoV-2 RT-PCR or antigen testing.

Convalescent Plasma

Therapeutic transfusion of antibody-rich plasma from recovered COVID-19 patients.

RdRp Gene

RNA-dependent RNA polymerase target for confirmatory SARS-CoV-2 RT-PCR assays.

Lipschütz Bodies

Eosinophilic intranuclear inclusions characteristic of HSV infection in Tzanck smear.

Negri Bodies

Eosinophilic cytoplasmic inclusions in rabies-infected neurons, diagnostic post-mortem.

CSF Latex Agglutination

Rapid antigen test for encapsulated bacteria (S. pneumoniae, H. influenzae type b, N. meningitidis).

pp65 Antigenemia

Detection of CMV lower-matrix protein in leukocytes indicating active cytomegalovirus infection.

VDRL Test

Flocculation assay detecting reagin antibodies for syphilis screening; quantitative titre follows therapy.