Lesson 1Antimicrobial susceptibility testing (AST) methods: disk diffusion, broth microdilution, automated AST systems — advantages, limitations, when to use eachDis section compare disk diffusion, broth microdilution, gradient strips, an automated AST systems, emphasizin test selection, setup, readin, quality control, an recognition of resistance mechanisms weh may miss by specific methods.
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 testingDis section outline quality control, validation, an biosafety fi molecular testin, includin verification of new assays, routine QC, contamination prevention, workflow separation, an compliance wid regulatory an accreditation 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 callingDis section introduce next-generation sequencin fi resistance surveillance, outlinin targeted amplicon workflows, WGS library preparation, sequencin, assembly, annotation, resistance gene callin, an basic quality control an data management steps.
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 cuesDis section explain best practices fi specimen receipt, blood culture collection an incubation, subculture techniques, an interpretation of colony morphology, linkin macroscopic features wid likely pathogens an contamination patterns.
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 carbapenemasesDis section focus pon rapid phenotypic carbapenemase detection, includin Carba NP variants an immunochromatographic lateral flow assays, wid emphasis pon performance characteristics, workflow integration, an result interpretation in clinical context.
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 interpretationDis section review major organism identification strategies, includin biochemical panels an MALDI-TOF MS, coverin sample preparation, instrument workflow, spectral interpretation, troubleshootin, an integration wid laboratory information 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 screeningDis section review phenotypic assays fi resistance, includin ESBL confirmatory tests, AmpC screenin, an carbapenemase assays such as mCIM, sCIM, an Carba NP, wid guidance pon algorithms an interpretation of complex patterns.
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 methyltransferasesDis section cover molecular workflows fi key resistance genes, detailin assay design, controls, an interpretation fi blaCTX-M, blaKPC, blaNDM, blaOXA-48-like, qnr, an 16S methyltransferases, plus integration wid phenotypic susceptibility 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 breakpointsDis section explain MIC interpretation usin CLSI an EUCAST breakpoints, highlightin conceptual differences, updates, dose-specific breakpoints, an strategies fi selectin an documentin appropriate standards in clinical laboratories.
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
