| Course Name | Molecular Pathology of Infectious Diseases |
| Course Code | 25CLG542 |
| Program | M. Sc. Clinical Genomics |
| Semester | 2 |
| Credits | 3 |
| Campus | Kochi |
Unit 1: Foundations of Infectious Disease Pathology
(9 lectures)
Introduction to infectious diseases and molecular pathology, Types of pathogens: Viruses, Bacteria, Fungi, Parasites. Host–pathogen interactions at the molecular level. Mechanisms of microbial adhesion, invasion, and colonization. Molecular basis of immune evasion by pathogens. Molecular determinants of virulence and pathogenicity. Role of microbiome in infectious diseases. Emerging infectious diseases: Molecular insights.
Unit 2: Molecular Mechanisms of Pathogenesis
(9 lectures)
Bacterial toxins (endotoxins, exotoxins): Structure and function. Viral pathogenesis: Mechanisms of cell entry, replication, and immune evasion. Host cell signalling manipulation by pathogens. Biofilms: Molecular formation and role in chronic infections.
Genetic variation and evolution of pathogens (mutation, recombination, horizontal gene transfer). Antigenic variation in viruses, bacteria, and parasites. Pathogen-induced inflammation and molecular mechanisms of tissue damage. Chronic infections: Molecular pathology (e.g., Tuberculosis, Hepatitis B/C). Zoonoses: Molecular mechanisms of cross-species transmission.
Unit 3: Molecular Diagnostics of Infectious Diseases
(9 lectures)
Molecular techniques for pathogen detection: PCR, qPCR, RT-PCR. Isothermal amplification techniques (LAMP, NASBA). Next-Generation Sequencing (NGS) for infectious disease diagnostics. Molecular typing and strain characterization (MLST, PFGE, WGS). Detection of drug resistance mutations (e.g., rifampicin resistance in TB). Point-of-care molecular diagnostics: Innovations and challenges. Viral load testing (e.g., HIV, HBV) and significance. Metagenomics and discovery of novel pathogens. Biosafety and quality control in molecular diagnostics.
Unit 4: Molecular Epidemiology and Surveillance
(9 lectures)
Principles of molecular epidemiology. Outbreak investigation using molecular tools. Genomic surveillance of emerging infections (e.g., SARS-CoV-2, Ebola). Phylogenetics and molecular evolution of pathogens. Antimicrobial resistance (AMR): Molecular detection and surveillance. Role of mobile genetic elements (plasmids, transposons) in AMR. Molecular barcoding and typing for epidemiological tracking. One Health approach and zoonotic disease surveillance. Global databases and molecular surveillance networks (GISAID, Nextstrain).
Unit 5: Molecular Strategies for Treatment and Prevention
(9 lectures)
Molecular targets for antimicrobial therapy. RNA interference (RNAi) and CRISPR technologies against pathogens. Vaccines: Design, mRNA vaccines (e.g., COVID-19 vaccines). Recombinant therapeutics. Host-directed therapies: Targeting host pathways to combat infection. Personalized medicine approaches for infectious diseases. Challenges in translating molecular findings into clinical practice. Future directions: Synthetic biology and infectious disease control.
Preamble
Molecular pathology of infectious diseases explores the molecular basis of pathogen virulence, host immune responses, and mechanisms underlying infection-associated tissue damage. Understanding the genomics, proteomics, and molecular interactions of infectious agents is crucial for developing modern diagnostic tools, therapeutics, and vaccines. This course emphasizes both the basic science and translational aspects of infectious disease pathology using cutting-edge molecular approaches.
Course Outcomes (CO)
CO1: Understand the molecular basis of infectious diseases and pathogen-host interactions.
CO2: Analyze molecular mechanisms driving pathogen virulence and immune evasion.
CO3: Apply molecular techniques for diagnosis and surveillance of infectious diseases.
CO4: Interpret genomic and epidemiological data to understand infectious disease outbreaks.
CO5: Evaluate modern molecular strategies for treatment, prevention, and control of infections.
CO6: Critically assess advances in synthetic biology, genomics, and molecular therapeutics in the field of infectious diseases.
Program outcome
PO1: Bioscience Knowledge
PO2: Problem Analysis
PO3: Design/Development of Solutions
PO4: Conduct Investigations of complex problems
PO5: Modern tools usage
PO6: Bioscientist and Society
PO7: Environment and Sustainability
PO8: Ethics
PO9: Individual & Team work
PO10: Communication
PO11: Project management & Finance
PO12: Lifelong learning
CO–PO Mapping Table:
| COs | PO1 | PO2 | PO3 | PO4 | PO5 | PO6 | PO7 | PO8 | PO9 | PO10 | PO11 | PO12 |
| CO1 | 3 | 2 | – | 2 | 2 | 3 | – | – | – | – | – | 2 |
| CO2 | 3 | 3 | 2 | 2 | 3 | 2 | – | – | – | – | – | 2 |
| CO3 | 3 | 3 | 3 | 3 | 3 | 3 | – | – | – | – | – | 3 |
| CO4 | 3 | 3 | 2 | 3 | 3 | 3 | – | – | – | – | – | 3 |
| CO5 | 3 | 3 | 3 | 3 | 3 | 3 | 2 | 2 | – | 2 | – | 3 |
| CO6 | 3 | 3 | 3 | 3 | 3 | 3 | 2 | 3 | 2 | 3 | 2 | 3 |
Program Specific Outcomes (PSO):
PSO1. Apply fundamental molecular biology principles to interpret clinical genomic data.
PSO2. Use molecular techniques (e.g., PCR, RT-PCR, sequencing) to detect genetic mutations and biomarkers.
PSO3. Analyze genotype-phenotype correlations in inherited and acquired disorders.
PSO4. Identify pathogenic variants from NGS data and interpret their clinical relevance.
PSO5. Correlate molecular pathways with disease mechanisms and therapeutic targets.
PSO6. Develop and validate diagnostic assays based on molecular biology principles.
PSO7. Utilize molecular biology to support pharmacogenomic profiling and therapy optimization.
PSO8. Integrate multi-omic data (genomic, transcriptomic, epigenomic) for personalized health solutions.
PSO9. Apply molecular knowledge to cancer genomics, infectious diseases, and rare genetic disorders.
PSO10. Translate molecular discoveries into clinical interventions through evidence-based practice.
CO–PSO Mapping Table:
| COs | PSO1 | PSO2 | PSO3 | PSO4 | PSO5 | PSO6 | PSO7 | PSO8 | PSO9 | PSO10 |
| CO1 | 3 | – | – | – | 3 | – | – | – | 3 | – |
| CO2 | 3 | – | 2 | – | 3 | – | – | – | 3 | – |
| CO3 | 3 | 3 | – | 2 | – | 3 | – | – | 3 | 2 |
| CO4 | 3 | – | – | 3 | 2 | – | – | – | 3 | 2 |
| CO5 | 3 | – | – | 3 | 3 | – | 2 | – | 3 | 3 |
| CO6 | 3 | 2 | – | 3 | 3 | 2 | 2 | 2 | 3 | 3 |
Evaluation Pattern: 50+50 = 100
| Internal Assessment – 50% | ||
| Periodical 1 | Exam | 20% |
| Periodical 2 | Exam | 20% |
| Continuous Assessment | Assignment/Test/Quiz | 10% |
| 50% | ||
| End Semester Examination- 50% | ||
| Theory Exam | 50% | |
| 50% | ||
| Total | 100% | |
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