Molecular Epidemiology and Genomic Analysis Review

Vocabulary practice flashcards covering molecular epidemiology of infectious diseases, phylogenetics, high-throughput sequencing modalities, and genomic diversity mechanisms.

Molecular Epidemiology of Infectious Diseases (MEID)

A field that links microbial genetic relationships directly to host and contextual metadata to address urgent public health questions, distinguish outbreak dynamics, and inform disease transmission interventions.

Surveillance

A continuous and systematic process of collection, analysis, interpretation, and dissemination of descriptive health information used to monitor health problems and detect emerging outbreaks.

Metadata

The contextual data describing each sample, encompassing host information (such as age, sex, and ethnicity), temporal details (sampling time), spatial location, ward transfers, and clinical exposures.

Character Convergence

The independent development of identical genetic characteristics or mutations at the nucleotide level across distinct lineages, driven by chance events, natural selection, or horizontal gene transfer.

16S rRNA Gene

A highly conserved, slowly mutating ribosomal RNA gene that is robust against recombination and widely used to classify bacteria at higher taxonomic levels (such as genera within Enterobacteriaceae), but often lacks sufficient resolution to differentiate closely related outbreak strains like those of Escherichia coli.

PAM1

A point accepted mutation substitution model that models amino acid evolutionary changes assuming an evolutionary distance of $1$ substitution per $100$ amino acids.

PAM250

A point accepted mutation substitution model calibrated for greater evolutionary divergence that assumes $250$ substitutions per $100$ amino acids.

Sequence Alignment

A nucleotide-level optimization algorithm that compares multiple genomic sequences to identify the most probable substitutions, insertions, and deletion events separating them.

Hendrikson et al. Filtering Criteria

A four-step quality-filtering process that aligned reads to Vibrio cholerae strain N16961 while removing indel-containing and multimapping reads, excluded SNPs with $< 10\times$ coverage or present in $< 90\%$ of base calls, removed SNPs in duplicate regions of strain N16961, and discarded loci not present across all strains.

Distance-Based Tree Reconstruction

A computationally efficient phylogenetic reconstruction method (such as SNP distance) that condenses sequence divergence between samples into a single numeric value, offering speed and error-cushioning for large, divergent datasets at the expense of sequence-level character context.

Character-Based Tree Reconstruction

A phylogenetic method (such as maximum likelihood or maximum parsimony) that models expected changes over time at specific sequence positions, providing high resolution by retaining character context but requiring significantly more computational power and vulnerability to artifactual errors.

Bootstrapping

A statistical validation technique involving resampling alignment data with replacement to generate pseudo-replicate datasets, used to assess the consistency and robustness of phylogenetic tree topologies.

Bifurcating Tree Model

A phylogenetic model that assumes evolutionary lineages strictly diverge into two descendant branches with no subsequent gene exchange, thereby failing to capture reticulate events such as bacterial recombination and horizontal gene transfer.

Phylogenetic Network

A non-treelike representation of evolutionary relationships that explicitly models non-vertical events such as horizontal gene transfer, reassortment, and recombination, though often yielding noisier and more complex topologies to interpret.

Multi-Locus Sequence Typing (MLST)

A molecular typing method that characterizes bacterial isolates based on the sequence alleles of a specific set of conserved housekeeping genes to differentiate organisms at the strain level.

Secondary Analysis

The phase of high-throughput sequencing data processing where curated, quality-filtered reads are either aligned to a known reference sequence (reference mapping) or assembled without a guide (de novo assembly).

Reference Mapping

A rapid, low-resource secondary analysis method that aligns raw reads to an established reference genome, restricted to identifying variants in known regions and constrained by the assumption of high structural similarity to the reference.

De Novo Assembly

The computational reconstruction of a full sequence directly from overlapping reads without the aid of a reference genome, capable of discovering novel structural variants and genes but requiring high coverage, long reads, and substantial compute resources.

Tertiary Analysis

The specialized, question-driven phase of high-throughput sequencing analysis focused on specific biological interpretations, such as phylogenetic reconstruction, genome annotation, or mobile genetic element profiling.

Bakta

A modern bioinformatic tool developed as the successor to Prokka, used for rapid, standardized functional annotation of bacterial genomes by querying curated sequence databases.

MOB-suite

A bioinformatic software tool designed for the identification, typing, and reconstruction of bacterial plasmids from sequencing data, especially when plasmids are not fully circularized.

Nonamplified Probe Technology

A diagnostic method that employs labeled molecular probes to hybridize directly with complementary target nucleic acids without prior PCR amplification, meaning the detectable signal depends strictly on the initial target concentration in the specimen.

Point-of-Care (POC) Testing

Rapid diagnostic testing performed at or near the site of patient care (such as a hospital ward) rather than requiring specimen transport to an external centralized diagnostic laboratory.

Oxford Nanopore MinION

A portable, pocket-sized long-read sequencing device operated via a laptop that enables real-time, point-of-care genomic sequencing.

Second-Generation Sequencing

High-throughput short-read sequencing platforms (predominantly Illumina) characterized by high per-base accuracy and lower cost, but limited in their ability to resolve repetitive elements and large-scale structural variants.

Third-Generation Sequencing

Sequencing platforms (such as Oxford Nanopore and PacBio) that produce long reads capable of spanning complex repetitive sequences and resolving genomic structural arrangements, typically counterbalanced by higher per-read error rates.

Hybrid Assembly

A genome assembly strategy that combines the high per-base accuracy of second-generation short reads with the structural continuity and repeat-spanning abilities of third-generation long reads.

Gene Loss and Genome Reduction

An evolutionary process in pathogenic bacteria where non-advantageous or non-essential genes are systematically discarded over time to reduce the organism's metabolic and resource burden.

Genome Rearrangement

A mechanism of genomic variation involving changes in the physical order and orientation of genes along the chromosome, which can alter transcription rates by moving genes closer to or farther from promoter regions.

Gene Duplication

The generation of an extra copy of a gene within a genome, which can immediately increase transcription rates of the product and provide raw genetic material for divergence into a new functional niche.

Horizontal Gene Transfer (HGT)

The non-vertical lateral exchange of genetic elements between bacterial organisms via transformation, transduction, or conjugation, frequently transferring virulence traits or antimicrobial resistance.

Genomic Island (GI)

A contiguous cluster of genes within a bacterial chromosome or plasmid that often confers adaptive benefits (e.g., pathogenicity islands); recognized by distinct GC content, divergent codon usage, and flanking transposable elements or repeat structures.

Metagenomics

The direct genomic sequencing and analysis of collective DNA extracted from a complex community of microorganisms (such as the gut microbiota in Crohn's disease), providing total population profiles without requiring isolate culturing.

Isolate Sequencing

The targeted sequencing of a single, clonally purified bacterial strain, offering high-resolution characterization of specific genomic architectures, resistance genes, and point mutations disconnected from microbiome interactions.

H5N1 Avian Influenza

A highly lethal avian influenza subtype capable of bird-to-human transmission that serves as a non-human genetic reservoir with the potential to recombine with human-adapted influenza strains.

Reservoir of Infectious Agents

Any ecological niche, environmental source (such as soil, water, or food), animal population, or inanimate vector (like shared hospital ward equipment) where an infectious pathogen normally lives, multiplies, and spreads to human hosts.