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This is the complete lecture note for MED406 Infectious and Tropical Diseases. You can read it online below, open it in the full viewer, or download the PDF for offline study. It pairs with the course's video lectures, so you can read and watch together.
Course code: MED 406 Course title: Infectious and Tropical Diseases Course credit load: 2 Units Series 1: Foundations of Infectious Diseases • Part 1.1: Epidemiology and Transmission of Infectious Diseases o Sub Part 1.1.1: Definitions and key concepts o Sub Part 1.1.2: Routes of transmission o Sub Part 1.1.3: Epidemiological measures and outbreak investigation • Part 1.2: Pathogenesis of Infectious Diseases o Sub Part 1.2.1: Aetiological agents and their characteristics o Sub Part 1.2.2: Host-pathogen interaction and virulence o Sub Part 1.2.3: The inflammatory response and sepsis • Part 1.3: Prevention and Control of Infectious Diseases o Sub Part 1.3.1: Immunisation and vaccines o Sub Part 1.3.2: Infection prevention and control o Sub Part 1.3.3: Antimicrobial stewardship • Part 1.4: Laboratory Diagnosis of Infectious Diseases o Sub Part 1.4.1: Microbiological techniques o Sub Part 1.4.2: Serological and molecular diagnosis o Sub Part 1.4.3: Interpretation of laboratory results
Introduction Infectious diseases remain the leading cause of morbidity and mortality in Nigeria and across sub-Saharan Africa. From childhood diarrhoeal illnesses and respiratory infections to malaria, tuberculosis, and HIV/AIDS, the spectrum of infectious and tropical diseases that clinicians encounter in Nigeria is broad, complex, and consequential. A sound understanding of the foundations of infectious diseases, including how pathogens cause disease, how they spread through populations, and how they can be prevented and controlled, is the essential starting point for effective clinical practice. The aim of this Series is to equip you with the fundamental knowledge needed to understand the epidemiology, pathogenesis, prevention, and laboratory diagnosis of infectious diseases. We shall commence by examining the key epidemiological concepts underlying infectious disease transmission and spread. Next, we will explore the pathogenesis of infectious diseases, covering aetiological agents, host-pathogen interaction, and the inflammatory response. Moving on, we will consider the strategies for prevention and control, including immunisation, infection control practices, and antimicrobial stewardship. Finally, we will address laboratory diagnosis, covering microbiological, serological, and molecular techniques. Series Learning Outcomes Upon completing this Series, you should be able to: • SLO 1.1: define key epidemiological terms and describe the major routes of transmission of infectious diseases, • SLO 1.2: describe the key epidemiological measures used in outbreak investigation, • SLO 1.3: classify the major aetiological agents of infectious diseases and describe their key characteristics, • SLO 1.4: describe host-pathogen interaction, virulence factors, and the pathogenesis of the systemic inflammatory response syndrome,
• SLO 1.5: describe the principles of immunisation, infection prevention and control, and antimicrobial stewardship, and • SLO 1.6: describe the major microbiological, serological, and molecular techniques used in the laboratory diagnosis of infectious diseases. 1.1 Epidemiology and Transmission of Infectious Diseases 1.1.1 Definitions and key concepts Infectious disease epidemiology studies the distribution and determinants of infectious diseases in populations. Key definitions: incubation period is the time between exposure to a pathogen and the onset of symptoms (during which the pathogen replicates); communicable disease is one that can be transmitted from person to person or from animals, insects, or the environment to humans; endemic describes a disease that is constantly present in a population at a predictable rate (for example, malaria in Nigeria); epidemic describes a higher than expected number of cases of a disease in a defined area and time period; and pandemic describes an epidemic that spreads across countries or continents. The basic reproduction number (R0) quantifies the average number of secondary cases generated by one infectious case in a fully susceptible population: an R0 above 1 indicates that the disease will spread, while an R0 below 1 indicates that it will decline. Herd immunity is achieved when a sufficient proportion of the population is immune (through vaccination or prior infection) to interrupt transmission and protect unimmunised individuals. The herd immunity threshold is calculated as 1 minus the reciprocal of R0. A disease that is constantly present in a population at a predictable rate is described as ________. The basic reproduction number R0 describes the average number of ________ cases generated by one infectious case in a fully susceptible population. 1.1.2 Routes of transmission
Infectious diseases are transmitted by several routes. Direct contact transmission involves physical contact between an infected and a susceptible person (skin-to-skin in scabies; sexual contact in gonorrhoea and HIV; droplet spray from coughing or sneezing landing on mucous membranes in influenza, COVID-19, and meningococcal disease). Indirect contact transmission involves a contaminated intermediate object or fomite (door handles, medical equipment, bed linen). Airborne transmission occurs when infectious particles remain suspended in the air for extended periods and are inhaled (tuberculosis, measles, varicella). Faecal-oral transmission occurs when food or water is contaminated with faecal material containing pathogens (cholera, typhoid, hepatitis A, amoebic dysentery, polio). Vector-borne transmission occurs through an intermediate arthropod vector: mosquitoes transmit malaria, dengue, yellow fever, and Zika virus; tsetse flies transmit African sleeping sickness; sandflies transmit leishmaniasis. Zoonotic transmission occurs when pathogens are acquired from animals: Lassa fever (rodents), rabies (dog bites), brucellosis (cattle and goats), and monkeypox. Tuberculosis, measles, and varicella are transmitted by the ________ route (infectious particles suspended in air). Malaria, dengue, and yellow fever are transmitted by the ________ route through mosquitoes. 1.1.3 Epidemiological measures and outbreak investigation Key epidemiological measures: incidence (the number of new cases in a defined population over a defined time period: measures the rate of occurrence of new disease), prevalence (the proportion of the population with the disease at a given time: includes both new and existing cases), attack rate (the proportion of exposed individuals who develop the disease: useful in outbreak investigation), and case fatality rate (CFR: the proportion of confirmed cases who die: measures disease severity). Outbreak investigation follows a systematic sequence: confirm the diagnosis and existence of an outbreak, establish a case definition, identify and count cases, describe the outbreak by time (epidemic curve), place, and person, generate and test hypotheses about the source and mode of transmission, implement control measures, and communicate findings. The epidemic curve (a histogram of cases by time of onset) distinguishes a common-source outbreak (a sharp peak from
a single exposure) from a propagated outbreak (a gradual rise from person-to-person transmission). ________ measures the proportion of a population with a disease at a given time (both new and existing cases). A sharp peak on an epidemic curve suggests a ________ outbreak from a single exposure. Figure 1.1: Routes of transmission of infectious diseases and key epidemiological concepts Pilot questions 1.1 1. Define incubation period, endemic, epidemic, and pandemic. (Linked to SLO 1.1) 2. Describe the six major routes of transmission of infectious diseases with one example each. (Linked to SLO 1.1) 3. Explain the basic reproduction number R0 and state its significance for disease control. (Linked to SLO 1.1) 4. Define incidence, prevalence, attack rate, and case fatality rate. (Linked to SLO 1.2)
5. Describe the steps of an outbreak investigation. (Linked to SLO 1.2) 1.2 Pathogenesis of Infectious Diseases 1.2.1 Aetiological agents and their characteristics Bacteria are prokaryotic organisms classified by Gram staining (Gram-positive: thick peptidoglycan cell wall staining purple; Gram-negative: thin peptidoglycan with outer lipopolysaccharide membrane staining pink), morphology (cocci, bacilli, spirochaetes), and oxygen requirement (aerobic, anaerobic, or facultative). Viruses are obligate intracellular parasites consisting of nucleic acid (DNA or RNA) enclosed in a protein capsid, which may be enveloped (HIV, influenza, hepatitis B) or non-enveloped (poliovirus, rotavirus). Enveloped viruses are more sensitive to drying and disinfectants. Fungi are eukaryotic organisms that cause superficial infections (dermatophytes causing tinea), subcutaneous infections (Sporothrix), and systemic infections in immunocompromised patients (Cryptococcus neoformans causing meningitis; Pneumocystis jirovecii causing PCP; Aspergillus causing invasive aspergillosis). Parasites include protozoa (Plasmodium species causing malaria; Entamoeba histolytica; Giardia lamblia; Trypanosoma; Leishmania) and helminths (roundworms such as Ascaris; tapeworms such as Taenia solium; flukes such as Schistosoma mansoni). Gram-positive bacteria have a ________ peptidoglycan cell wall and stain purple. Enveloped viruses such as HIV and influenza are more sensitive to drying and disinfectants than ________ viruses such as poliovirus. 1.2.2 Host-pathogen interaction and virulence Virulence refers to the ability of a pathogen to cause disease in the host and is determined by specific virulence factors: adhesins (surface molecules that mediate attachment to host cells), invasins (proteins that facilitate entry into host cells), toxins (exotoxins: proteins secreted by bacteria that cause specific damage such as the cholera toxin causing secretory diarrhoea or the
tetanus toxin causing spastic paralysis; endotoxin: the lipopolysaccharide of Gram-negative bacteria, which triggers the systemic inflammatory response), and enzymes that degrade host tissues (coagulase, hyaluronidase, proteases). Host defences against infection include physical barriers (intact skin and mucous membranes, mucociliary clearance, gastric acid), innate immunity (neutrophils, macrophages, natural killer cells, complement, interferon), and adaptive immunity (B lymphocytes producing specific antibodies; T lymphocytes mediating cell-mediated immunity, which is critical for intracellular pathogens such as Mycobacterium tuberculosis, Leishmania, and HIV). The balance between pathogen virulence and host defences determines the outcome of infection: elimination, latency, chronic infection, or death. ________ are surface molecules on bacteria that mediate attachment to host cells. The ________ (LPS) of Gram-negative bacteria acts as an endotoxin triggering the systemic inflammatory response. 1.2.3 The inflammatory response and sepsis
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