BMS171 Lecture 1: Microorganisms and Infections

• BMS171 Lecture 1 is an introduction to microorganisms and infectious diseases taught by Professor Eman El-Seidi at Galala University.
• The course is powered by Arizona State University for the Spring 2025 semester, and is part of the Faculty of Medicine.

BMS171 Assessment Breakdown:

• Final Term written exam constitutes 40% of the total grade.
• Practical exam constitutes 30% of the total grade.
• Quizzes/Assignments constitute 20% of the total grade.
• Mid Term exam constitutes 10% of the total grade.
• The total assessment is graded out of 75 marks.

Lecture Objectives:

• Identify microbial causes of human infections.
• Classify different microorganisms.
• Differentiate between eukaryotes and prokaryotes.
• Define the meaning of infection.
• Recognize the infection cycle.
• Identify the different sources, modes, and risk factors of infections.
• Explain the importance of carriers in infectious diseases.
• Identify the scheme for diagnosis of infectious diseases.
• Differentiate direct and indirect detection methods for diagnosis of infections.

Infectious Diseases:

• Infectious diseases are caused by pathogenic microorganisms including bacteria, viruses, fungi, protozoa, or parasites.
• Microbiology plays a vital role in healthcare by helping to identify infectious agents, understand infection spread, diagnose diseases, recognize specimen collection and transport, identify antimicrobial drugs, achieve disinfection/sterilization, recognize hospital-acquired infections, and implement immunization schedules.

What is Microbiology?

• Microbiology studies microorganisms (microbes with microscopic size), including bacteria, viruses, and fungi.
• Microorganisms are generally unicellular, for example, bacterial cell performs all functions for growth and replication.

Microorganisms of Medical Importance:

• Bacteria, protozoa, fungi and viruses fall under this category.
• Viruses can be classified based on DNA or RNA and whether they have an outer envelope.
• Bacteria are classified as Gram-positive, Gram-negative, or Acid-fast.
• Fungi can come in yeast (single-celled), mold (multi-celled), or dimorphic (yeast and mold) forms.

Microorganisms: Harmful vs Helpful

• Most microbes are beneficial and critical for human health.
• Skin, nose, mouth, gut, and genitourinary tract surfaces are covered with bacteria, fungi, and parasites.
• These organisms are critical for immune system maturation, metabolic functions like food digestion, and protection from unwanted pathogens.
• These organisms are referred to as normal flora or microbiome.
• Health is maintained if normal flora is balanced; disruption (naturally or via interventions like antibiotics) risks disease.

Classification of Microorganisms:

• Microorganisms are either prokaryotes (e.g., bacteria) or eukaryotes (e.g., fungi).

Prokaryotes vs. Eukaryotes:

• Prokaryotes have a primitive nucleus (nucleoid), eukaryotes have a true nucleus.
• Prokaryotes lack a nuclear membrane, eukaryotes possess one.
• Prokaryotes are unicellular, eukaryotes are multicellular.
• Prokaryotes are smaller in size, eukaryotes are larger.
• Prokaryotes lack mitochondria; eukaryotes have mitochondria.
• Prokaryotes respire through the cell membrane, eukaryotes through mitochondria.
• Sterols are usually absent in the prokaryotic cell membrane.
• Prokaryotes have 70S ribosomes, eukaryotes have 80S ribosomes.
• Bacterial cells are prokaryotes, fungal cells are eukaryotes.

Bacterial Cell Structures:

• Essential structures are chromosomes, cytoplasm/organelles, cytoplasmic membrane, and cell wall.
• Additional structures include flagella, pili (fimbriae), capsules, and spores.

Viruses and Prions:

• Viruses are the smallest infective agents, formed from nucleic acid (DNA or RNA) and a protein coat (capsid), some have a lipid envelope.
• Viruses are obligate intracellular parasites, and depend on a host cell for replication.
• Prions are infectious proteins without nucleic acid.

Fungi Classification:

• Fungi are complex eukaryotic organisms with cell walls, well-defined nucleus, mitochondria, Golgi bodies, and endoplasmic reticulum and can be single or multi-celled.
• Molds grow as hyphae (septate or non-septate).
• Yeasts grow as single cells.
• Dimorphic fungi grow as molds at 25°C and yeasts at 37°C.
• Examples include Aspergillus, Penicillium, dermatophytes (molds), Candida, Cryptococcus (yeasts), and Histoplasma (dimorphic).

Colonization vs. Infection:

• Colonization is the presence of microorganisms on the skin, mucous membranes, or in excretions without causing adverse clinical signs.
• Infection is the invasion and multiplication of an infectious agent in the host tissue.
• Disturbance to the physiological functions of the host due to infection is called an infectious disease.
• Not all infections will proceed to be infectious diseases.

Infection and Disease:

• Infection is the invasion of the human body by a microbe (bacteria, virus, fungus).
• Infectious disease is any disturbance to the physiological functions of the host due to an infection.
• Infection may or may not lead to disease based on the interaction between the microbe and the host's immune system.
• Bacteria uses virulence factors that allow bacteria to cause disease.
• The host uses an immune system to defend against infections.

Factors that determine the fate of infecting organisms:

• Host factors include age, immune status, chronic diseases, HIV, instrumentation, and certain treatments like immunosuppressive therapy or repeated blood transfusions.
• Microbial factors include microbial virulence, dose of infection, and presence of mixed infection.

Instrumentation and infection:

• Instrumentation (invasive procedures/devices) such as ventilators, urinary catheters, endoscopes and vascular assist the spread of infection.

Chain of Infection:

• Infectious Agent: Microorganism (germ or bug) that can cause harmful infections.
• Reservoir: Where the germ lives and grows, e.g., respiratory tract, equipment, environment, food, or water.
• Portal of Exit: How the germ leaves the infected person, e.g., sickness, diarrhoea, nose, mouth, sneezing, or coughing.
• Mode of Transmission: How the germ spreads from one person to another, e.g., hands, equipment, air, body fluids, or blood.
• Portal of Entry: How the germ enters another person, e.g., eyes, mouth, hands, open wounds, catheters, or feeding tubes.
• Susceptible Host: Person at risk of infection due to inability to fight it.

Sources of Infections can be endogenous or exogenous:

• Endogenous sources come from the patient's own microbial flora
• Exogenous sources include environmental sources and healthcare workers
• Endogenous infection is caused by the patient's normal flora introduced to sterile sites through trauma or disease such as E. coli causing urinary tract infections.
• Exogenous sources are microbes introduced from outside through humans, animals, insects, or environment.

Carriers and Exogenous Infections:

• A patient gets infected by an exogenous source from another ill person.
• Carriers are healthy people carrying a pathogen without symptoms, serving as infection sources.
• Carriers are dangerous due to being difficult to detect, unknown to the public, and freely mixing with others

Modes of Transmission:

• Direct Contact: Coming into contact with saliva, mucous, blood, or feces containing germs.
• Indirect Contact: Coming into contact with areas that have been contaminated by germs.
• Vector-borne: Being bitten by a tick or a mosquito carrying a disease-causing agent.
• Foodborne: Eating food contaminated with germs.
• Waterborne: Drinking or coming into contact with contaminated water.
• Microorganisms can be acquired through various routes, with some using multiple methods.
• Common healthcare facility transmission modes are contact, droplet, airborne, blood/needle prick, common vehicle, and vector transmission.

Contact Transmission:

• Contact transmission which is most important for nosocomial infections, can be direct (body surface to body surface) or indirect (contaminated object).
• Microorganisms can spread by direct contact via contaminated hands or physical contact during medical examinations.
• Hand hygiene is crucial and should be performed immediately after removing contaminated gloves.
• Indirect contact transmission involves a susceptible host coming into contact with a contaminated object; such as instruments, needles, or gloves that haven't been changed between patients.
• Healthcare settings should provide effective decontamination of medical equipment, and disinfect environmental surfaces to prevent transmission.

Droplet and Airborne Transmission:

• Droplet transmission occurs when microorganisms come into direct contact with mucous membranes and air travel a short distance.
• Droplet transmission occurs during talking, coughing, sneezing, or bronchoscopies.
• Large droplets travel short distances and require close contact.
• Examples include COVID-19, mumps, rubella, influenza, common cold, meningococci, and pertussis.
• Facial protection (surgical masks/face shields) can prevent droplet transmission.
• Airborne transmission occurs through small-sized particles that either remain suspended in the air for a long time over a long distance and requires no close contact.
• These bypass the upper respiratory tract and bronchial to infect the alveoli.
• Common airborne microorganisms are Mycobacterium tuberculosis, varicella-zoster virus, and measles.
• Healthcare workers (HCW immune) replace susceptible workers (HCW) through previous immunization or past infection to prevent cross-infection.

Transmission Via:

• Common vehicle where transmission may occur with contaminated food, water, medication and instruments.
• Vector-borne means that infectious agents may be transmitted through insects, mosquitoes, or sandflies for example.
• Infections can be prevented by breaking the five step chain: stop at the source, block the exit, disrupt the mode of transportation, protect the portal of entry, and increase the host's defenses.

Diagnosis of Bacterial Infections:

• Direct methods involve examining a specimen directly.
• Indirect include testing for antibodies.
• In direct, microscopic examination is usually done before processing specimens. Microbial Detection include non-culture or a culture technique.
• Direct examination involves microscopic and molecular methods (PCR)
• Indirect involves serological for antibody detection.

Direct Methods: Microscopic Examination involves:

• Stained/unstained sample preparations
• Different microscopes (light, dark ground, fluorescent, or electron).
• Unstained preparations such as wet preparations are used for microscopy to detect bacterial motility.
• Dark-ground microscopy detects Treponema
• Stained help in to detect size, shape, arrangement
• Different staining include gram-stain and acid-fast such as Ziehl-Neelsen or ZN Stain and Fluorescent such as auramine stains

Culture of Microbes:

• Culture Technique is used for isolation of the organism on artificial culture media, followed by identification for example useing bacterial colonies, and blood culture and broth.

Bacterial Identification:

• Bacterial identification is performed using different biochemical reactions such as detecting the presence of catalase, urease or oxidase and by molecular methods or antigen detection.
• Antibiotic sensitivity testing is done to find the proper choice to treat a bacterial infection and includes broths and antibiotics.