Modern Diagnostics in Medical Microbiology

Vocabulary practice flashcards covering modern medical microbiology diagnostics, workflows, instrumentation, PCR/qPCR metrics, tuberculosis drug resistance genetics, and next-generation sequencing technologies.

Traditional Culture Workflow

A four-step diagnostic procedure relying on live bacterial growth: 1) Inoculating clinical specimens onto selective and differential media, 2) Incubating under proper temperature and atmospheric conditions, 3) Reading plates for colony morphology and purity, and 4) Confirming identity and phenotypic antimicrobial susceptibility.

Hospital Microbiology Workflow

The end-to-end movement of a patient specimen through five distinct phases: Collection, Transport, Preprocessing, Diagnostics, and Patient Reporting.

LIMS (Laboratory Information Management System)

A software platform that connects bedside observations, the clinical laboratory, and the electronic health record by tracking a specimen's physical handling and data journey through order entry, accessioning, instrument interfacing, result verification, and reporting.

Accessioning

The second phase of the LIMS workflow where a received specimen is assigned a unique identifier, documenting receipt time, testing priority, and specimen status.

VITEK 2

An automated phenotypic identification and antimicrobial susceptibility testing (AST) system manufactured by bioMérieux that utilizes specialized cards filled with biochemical tests and antimicrobial dilutions, capable of processing up to 60 samples within 24 to 48 hours.

Real-Time PCR (qPCR)

A rapid molecular diagnostic technique that detects and quantifies target DNA or RNA in real time during thermal cycling using fluorescent dyes, yielding quantitative results in approximately 1 hour without requiring post-PCR gel electrophoresis.

End-Point PCR

Traditional PCR that detects the accumulation of target amplicon only after thermal cycling is complete, providing qualitative results that require post-PCR gel electrophoresis for visualization.

Cycle Threshold ($C_T$)

The thermal cycle number at which emitted fluorescence crosses the baseline threshold during qPCR; lower values denote higher starting pathogen load, whereas a value of 40 indicates no detection.

Pre-infectious Stage (SARS-CoV-2)

The early window of infection lasting 1 to 2 days, characterized by a weak positive qPCR result ($C_T = 33\text{--}40$) and a negative rapid antigen test.

Infectious Stage (SARS-CoV-2)

The active transmissible phase of infection lasting up to 10 days, marked by peak viral load, a strong positive qPCR result ($C_T = 1\text{--}33$), and a positive rapid antigen test.

Post-infectious Stage (SARS-CoV-2)

The late phase of infection lasting days to weeks during which non-infectious viral debris is shed, yielding a weak positive qPCR result ($C_T = 33\text{--}40$) and a negative rapid antigen test.

Pooled Testing

A testing strategy that combines samples from multiple patients (such as pooling 20 individuals into 4 batches) into combined RNA extractions and PCR runs to conserve reagents and accelerate population-wide screening during a pandemic; its efficiency is constrained by disease prevalence and dilution effects.

PrimeStore MTM®

An FDA-cleared molecular transport medium developed by Longhorn Vaccines & Diagnostics that inactivates infectious pathogens at collection and stabilizes microbial DNA/RNA for molecular testing without refrigeration.

BD BACTEC™ MGIT™ 960

An automated phenotypic broth-based culture system that monitors Mycobacterium tuberculosis growth in liquid media containing antibiotics; it requires live infectious cultures and takes 3 to 8 weeks to determine susceptibility.

rpoB Gene

A gene encoding the beta subunit of RNA polymerase in Mycobacterium tuberculosis; mutations within this gene (such as D435V, H445D, H445Y, and S450L) confer resistance to rifampin.

Rifampin Resistance-Determining Region (RRDR)

An 81-base-pair region spanning codons 507 to 533 within the Mycobacterium tuberculosis rpoB gene where approximately 91% of rifampin resistance mutations occur.

katG Gene

A gene encoding catalase-peroxidase in Mycobacterium tuberculosis; harboring mutations such as S315T confers resistance to the first-line antibiotic isoniazid.

pncA Gene

A gene encoding pyrazinamidase in Mycobacterium tuberculosis; mutations within this gene (such as K96R or Q122Stop) confer resistance to pyrazinamide.

gyrA Gene

A gene encoding DNA gyrase subunit A in Mycobacterium tuberculosis; mutations in this gene confer resistance to second-line fluoroquinolones such as ofloxacin.

rv0678 Gene

A gene in Mycobacterium tuberculosis associated with resistance to the bedaquiline class of antibiotics.

rrl and rplC Genes

Ribosomal genes in Mycobacterium tuberculosis whose mutations confer resistance to linezolid.

Targeted Gene Sequencing (TGS)

A genomic method where defined specific gene regions are amplified using PCR and indexed for parallel sequencing on NGS platforms, enabling high coverage depth ($500\text{--}{>}1000\times$) and multi-sample multiplexing at lower cost than whole-genome sequencing.

Heteroresistance

The coexistence of drug-susceptible and drug-resistant subpopulations of bacteria within the same clinical specimen, detectable via deep next-generation sequencing even when phenotypic cultures misidentify the isolate as fully susceptible.

PrimeSeq TB

A targeted next-generation sequencing workflow combining PrimeStore MTM collection, PrimeXtract DNA extraction, target PCR amplification, and Illumina MiSeq sequencing with DNAStar SeqMan NGen bioinformatics to detect antibiotic resistance mutations in Mycobacterium tuberculosis.

Molecular Diagnostics

Direct nucleic-acid-based testing platforms (such as real-time PCR, multiplex PCR, and next-generation sequencing) that detect both culturable and fastidious or non-culturable organisms and resistance genes within hours, providing same-day clinical results.