Lesson 1Antimicrobial susceptibility testing (AST) methods: disk diffusion, broth microdilution, automated AST systems — advantages, limitations, when to use eachThis lesson compares disk diffusion, broth microdilution, gradient strips, and auto AST machines, stressing test choice, setup, reading, quality control, and spotting missed resistance in Namibian workflows.
Disk diffusion setup, reading, and limitationsBroth microdilution and MIC determinationGradient diffusion strips: use and caveatsAutomated AST platforms and alert rulesChoosing AST methods for special organismsLesson 2Quality control, validation, and biosafety considerations for molecular testingThis part outlines quality checks, proofing, and safety for gene tests, including new test checks, daily QC, stopping contamination, workflow splits, and meeting rules and standards.
Verification and validation of new PCR assaysInternal, external, and proficiency controlsPreventing amplicon contamination and carryoverUnidirectional workflow and lab zoningRegulatory and accreditation requirementsLesson 3Next-generation approaches: targeted amplicon sequencing, whole-genome sequencing (WGS) pipeline steps, assembly, annotation, resistance gene callingThis lesson brings in next-gen sequencing for resistance watch, covering targeted amplicon steps, WGS prep, sequencing, build, label, gene call, and basic quality and data handling.
Targeted amplicon design and library preparationWGS library prep, indexing, and run setupRead quality control and genome assembly choicesGenome annotation and resistance gene databasesReporting NGS findings and clinical relevanceLesson 4Specimen handling and culture: blood culture sets, incubation, subculture media and colony morphology cuesThis section teaches best ways for sample receipt, blood culture taking and warming, subculture tricks, and reading colony shapes, linking looks to likely bugs and contamination signs.
Pre-analytical variables and specimen rejectionBlood culture set collection and incubation rulesSubculture media selection and inoculation patternsReading plates and recognizing mixed culturesColony morphology clues to common pathogensLesson 5Rapid phenotypic methods and immunochromatographic assays for common carbapenemasesThis lesson spotlights quick phenotypic carbapenemase finds, like Carba NP types and strip tests, stressing performance, workflow fit, and result reading in patient care.
Principles of rapid phenotypic carbapenemase assaysCarba NP and derivatives: setup and readoutImmunochromatographic tests for KPC, NDM, OXA-48Sensitivity, specificity, and common interferencesAlgorithmic use with culture and molecular testsLesson 6Organism identification methods: biochemical panels, MALDI-TOF MS workflow and interpretationThis part reviews main bug ID ways, biochemical kits and MALDI-TOF MS, covering prep, machine steps, spectrum reading, fixes, and linking to lab systems.
Design and interpretation of biochemical identification panelsMALDI-TOF sample prep for bacteria and yeastsAcquisition parameters and spectral quality controlDatabase matching, score cutoffs, and reportingCommon pitfalls and discordant ID resolutionLesson 7Phenotypic assays for resistance detection: ESBL confirmatory tests, modified Hodge test, Carba NP / mCIM / sCIM for carbapenemases, AmpC screeningThis lesson reviews phenotypic resistance tests, ESBL confirms, AmpC screens, carbapenemase checks like mCIM, sCIM, Carba NP, with tips on plans and tricky pattern reading.
ESBL screening and confirmatory synergy testsPhenotypic detection of plasmid-mediated AmpCmCIM and sCIM workflows and interpretationCarba NP and related carbapenemase assaysIntegrating phenotypic and genotypic findingsLesson 8Molecular workflows: targeted PCR assays for blaCTX-M, blaKPC, blaNDM, blaOXA-48-like, qnr, 16S methyltransferasesThis section covers gene test flows for key resistance, design, controls, reading for blaCTX-M, blaKPC, blaNDM, blaOXA-48-like, qnr, 16S changers, plus linking to sensitivity data.
Primer and probe design for resistance targetsDNA extraction methods and inhibition controlSingleplex vs multiplex PCR assay strategiesResult interpretation and limit of detectionReconciling PCR results with AST phenotypesLesson 9Interpreting MICs and breakpoints: CLSI vs EUCAST differences and how to select appropriate breakpointsThis lesson explains MIC reading with CLSI and EUCAST cut-offs, differences, updates, dose cut-offs, and picking and noting right standards in clinical labs.
MIC concepts, ECOFFs, and clinical breakpointsKey differences between CLSI and EUCASTDose-specific and infection-site breakpointsUpdating and version control of standardsDocumenting breakpoint choices in the lab
