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Glossary with links to refresher pre-reading material
Glossary of terms used in this course
Glossary of terms & acronyms used in this course
Here is a list of terms used in this course – you can download this glossary from the bottom of this step to refer back to as you go through the course.
| Term/abbreviation | Definition |
|---|---|
| Acquired resistance | The resistance mechanisms a strain can acquire through changes in their genotype |
| AMR | Antimicrobial resistance |
| AST | Antimicrobial susceptibility testing |
| BLAST | Basic Local Alignment Search Tool |
| CARD | The Comprehensive Antibiotic Resistance Database |
| cgMLST | Core Group Multi-Locus Sequence Typing |
| CLI | Command Line Interface (sometimes called the Terminal) |
| DDBJ | DNA Database Japan |
| Disk diffusion method | A qualitative phenotypic AST |
| ENA | European Nucleotide Archive |
| Epigenetics | How gene expression is altered without direct changes to the underlying genome. However, in AMR research it is often used to refer to any resistance mechanism where the effect is on the gene expression level and not through chemical or target modification. This is the definition we will use in this course. |
| FAIR | Findable, Accessible, Interoperable, Reusable |
| Fasta | A file format to store sequence data, characterised by a > before sequence names in the file |
| FastQ | A file format for storing raw sequencing reads |
| FTP | File Transfer Protocol. A online data storage platform type |
| Galaxy | A cloud-based free bioinformatics analysis platform |
| Gene copy number | The number of times that specific gene is found in a genome |
| Genotype | The genetic material in an organisms gene or set of genes |
| GUI | Graphical User Interface |
| HGT | Horizontal Gene Transfer |
| HMM | Hidden Markov Models |
| INSDC | The International Nucleotide Sequence Database Collection |
| Intrinsic resistance | The natural resistance mechanisms a species has against certain antimicrobials |
| KMC | K-mer counting algorithm |
| Machine learning | A form of Artificial Intelligence which uses large datasets to find correlations and groupings |
| Meta-analysis | Combining data from multiple studies to gain greater insights |
| Metadata | Associated data that is linked to a genotype sample (e.g. host, location etc.) |
| MIC | Minimum Inhibitory Concentration |
| NCBI | The National Center for Biotechnology Information |
| NDM | New Delhi metallo-β-lactamase , a common family AMR genes |
| NLM-NCBI | National Library Medicine – National Center for Biotechnology Information |
| Phenotype | The set of characteristics that we observe which are due to the specific genotype of an organism |
| Point mutation | A specific single mutation in a gene or intergenic region |
| RGI | Resistance Gene Identifier (tool to access CARD) |
| SNP | Single Nucleotide Polymorphism. A synonym of point mutation |
| SNV | Single Nucleotide Variant. A SNP or an insertion/deletion of a single nucleotide |
| SRA | Short Read Archive (part of NLM-NCBI) |
| TB | Tuberculosis |
| VREfcm | Vancomycin-resistant Enterococcus faecium |
Option refresher pre-reading material
Below are some external links related to fundamental information such as antibiotics and genome sequencing. Much of this you might already know but if not, we suggest looking at these resources before you jump into the course.
Antibiotic classes and mechanisms of action
- https://apua.org/antibiotic-cards
- https://www.orthobullets.com/basic-science/9059/antibiotic-classification-and-mechanism
Genome sequencing and assembly overview
- Primer on genome sequencing and variant calling
- FastQ files overview
- Bacterial genome assembly and analysis primer
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Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis
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Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis
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