Medical Microbiology: Human-Microbial Interactions

• Medical microbiology is a subdiscipline of microbiology
• Medical microbiology studies microorganisms that cause human disease, including diagnosis, treatment, epidemiology, and immunology
• Not all microorganisms cause infection; some benefit the human host

Beneficial Human-Microbial Interactions

• Microbiota refers to all microorganisms present in or on the human body
• Microbiome refers to the genomes of all microorganisms present in or on the human body
• Each person harbors 10-100 trillion symbiotic microbial cells, mainly in the gut
• The human body hosts over 10,000 different microbe species
• Up to 90% of all diseases can be traced back to gut health and the microbiome
• There are 10 times as many outside organisms as human cells in the human body
• The genes in the microbiome outnumber human genes by about 100 to 1
• The human gene catalog has approximately 22,000 genes
• The human gut microbiome contains 3.3 million non-redundant genes
• Individual humans are 99.9% identical in terms of the host genome
• Individual humans differ from one another by 80-90% in terms of the microbiome
• The human microbiota consists of bacteria, archaea, fungi, and viruses
• Genetics, environment, and diet affect the composition of an individual's microbiota
• Each body site has different microbes that perform different functions
• Commensal microorganisms are those that live on the body

Types of Beneficial Human-Microbial Interactions

• Gut microbes digest complex carbohydrates into short-chain fatty acids (SCFAs)
• SCFAs provide energy and support gut health
• Gut bacteria produce essential vitamins, such as vitamin K and B vitamins
• Microbes assist in the absorption of minerals like calcium, magnesium, and iron by modifying the gut environment
• Exposure to commensal microbes trains the immune system
• Training helps the immune system distinguish between harmful pathogens and harmless microbes
• Gut bacteria produce molecules that reduce inflammation and maintain immune balance
• Microbes compete with harmful pathogens by occupying niches
• Competition involves consuming available nutrients and producing antimicrobial compounds
• Skin microbiota, such as Staphylococcus epidermidis, helps maintain skin barrier integrity
• Microbiota protect against colonization by harmful pathogens
• Microbial metabolites strengthen gut and respiratory mucosal barriers
• Metabolites prevent the invasion of pathogens
• The microbiota communicates with the central nervous system via the vagus nerve
• Communication involves immune signaling and microbial metabolites
• Gut microbes produce neurotransmitters like serotonin, dopamine, and gamma-aminobutyric acid (GABA)
• The neurotransmitters influence mood and mental health
• Certain microbes degrade harmful substances, such as dietary toxins, xenobiotics, and carcinogens
• Gut microbes influence the metabolism of medications, impacting their efficacy and toxicity

Microbes and Disease

• Microbial pathogenesis is the process by which microbes cause disease
• Each pathogen has its own unique pathogenesis factors

Koch’s Postulates

• The suspected pathogen must be found in every case of disease but not in healthy individuals
• The suspected pathogen can be isolated and grown in pure culture
• A healthy test subject infected with the pathogen must develop the same signs and symptoms of the disease
• The pathogen must be re-isolated from the new host and must be identical to the original pathogen

Stages of Pathogenesis

• Exposure to the pathogen occurs through contact

• Exposure comes from various sources

• Host tissue access is required for infection

• Adhesion of the pathogen involves the pathogen adhering is accomplished through adhesin factors

• Invasion by the pathogen spreads pathogens throughout tissues facilitated by exoenzymes and toxins

• Virulence factors aid in evading the immune system

• Infection is the pathogen's successful multiplication in the host

• Infections described as local or systemic based on their extent

• A local infection is confined to a small area of the body, typically near entry

• A systemic infection occurs when a pathogen disseminates throughout the body

• A primary infection, caused by one pathogen, can lead to a secondary infection by another pathogen

Pathogenic Mechanisms

• Bacteria’s pathogenic mechanisms involve endotoxins (LPS in Gram-negative bacteria, causing inflammation), exotoxins (secreted proteins that damage host cells), adherence mechanisms (adhesins for attachment), and immune evasion (capsules and antigenic variation)
• Viruses hijack host cellular machinery for replication and induce host cell lysis or immune-mediated damage
• Fungi pathogenic mechanisms include mycotoxin production (e.g., Aspergillus flavus) and opportunistic infections (e.g., Candida albicans in bloodstream infections)
• Parasites employ immune evasion (e.g., Plasmodium species in malaria) and nutrient competition (e.g., Ascaris lumbricoides in intestinal infections)

Examples of Disease by Class of Pathogen

• Tuberculosis caused by Mycobacterium tuberculosis
• Staph skin infections
• Toxic shock syndrome caused by Staphylococcus aureus
• Influenza & respiratory illness
• HIV/AIDS, targets CD4+ T cells, causing immunodeficiency
• Candidiasis: Yeast infections
• Aspergillosis: Pulmonary disease
• Malaria is caused by Plasmodium species
• Giardiasis is an intestinal infection caused by Giardia lamblia

Host Factors in Infection and Disease

• The human body defends with physical, chemical, and anatomical barriers
• The barriers provide natural resistance to pathogen colonization and infection

The Host Immune Response

• Innate immunity provides a rapid, non-specific response

• Mediated by phagocytes

• Macrophages, dendritic cells, and neutrophils engulf and destroy pathogens

• Pathogen-Associated Molecular Patterns (PAMPs) are on pathogen surfaces

• Examples of PAMPs are peptidoglycan (in bacterial cell walls), lipopolysaccharide (LPS) in gram-negative bacteria and flagellin (a protein in bacterial flagella)

• Pattern Recognition Receptors (PRRs) on phagocytes recognize PAMPs

Stages of Phagocytosis

• Bacteria engulfed
• Phagosome forms
• Phagosome binds to the lysosome to form a phagolysosome
• Lysosomal enzymes degrade the pathogen
• Debris is released

Adaptive Immunity

• Two important characteristics are specificity and memory
• Specificity is the adaptive immune system's ability to target specific pathogens
• Memory is its ability to quickly respond to pathogens previously seen

Classifications of Adaptive Immunity

• Natural active immunity is adaptive immunity that develops after natural exposure to a pathogen Natural passive immunity involves the natural passage of antibodies from a mother to a child before and after birth
• Artificial active immunity is from vaccination and involves the directed exposure of weakened or inactivated pathogens
• Preparations consist of key pathogen antigens.

Treatment of Infections

• Antibiotics target bacterial pathogens
• Antifungals target fungal pathogens
• Antivirals target viruses
• Antiparasitics target parasites that cause infection
• Antibiotics are metabolites made by microorganisms to inhibit or kill other microorganisms

The following are various antibiotics and their microbial sources:

• Bacitracin comes from Bacillus subtilis
• Polymyxin from Bacillus polymixa
• Erythromycin from Streptomyces erythreus
• Tetracycline from Streptomyces rimosus
• Vancomycin from Streptomyces orientalis
• Penicillin from Penicillium chrysogenum

Antibiotic Resistance

• Genes for antibiotic resistance have always existed in nature
• A sample of E. coli from 1946 contained plasmid genes for resistance to streptomycin and tetracycline
• Resistance plasmids (R-plasmids) have been found in non-pathogenic soil bacteria

How Antibiotic Resistance Arises

• Resistance from natural processes and human activities
• Intrinsic resistance, genetic mutations, HGT (horizontal gene transfer)
• Human-driven accelerates the development and spread
• Overuse, agricultural Use, inadequate Infection Control, global Travel and Trade

Impacts of Antibiotic Resistance

• Treatment failures, increased mortality, economic costs

Preventing Antibiotic Resistance

• Rational Antibiotic Use involves using antibiotics only when prescribed and completing the full course
• Hygiene and Infection Control involve proper hand hygiene, sterilisation & improved sanitation
• Research and Development should focus on new antibiotics, vaccines, and alternative treatments
• Global Surveillance involves monitoring resistance trends to guide treatment & public health policies

Bacteriophage as an Alternative Treatment for Bacterial Infections

• Can combat antibiotic resistance
• These viruses specifically infect and kill bacteria addressing multidrug-resistant infections
• Phage can infect and lyse antibiotic-resistant bacteria without harming the host's normal microbiota
• Target Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae

Phage can bypass traditional resistance mechanisms because they target bacterial surface receptors

• Phage-antibiotic synergy (PAS) has been observed - Phage enhances antibiotic efficacy by disrupting biofilms or resensitising bacteria
• Lysins break down bacterial cell walls, leading to rapid bacterial lysis, effective against Gram-positive bacteria
• Agriculture: use as alternatives to antibiotics in livestock and poultry, reducing antibiotic use
• Food Safety involves targeting foodborne pathogens (e.g., Listeria, Salmonella, E. coli)
• Used in environmental to control antibiotic-resistant bacteria

Challenges in Phage Therapy

• Host specificity, resistance development, regulatory hurdles, and delivery methods

Diagnostic Microbiology

• Process of laboratory identification of what microorganism is causing an infection

• Direct pathogen detection is the gold standard

• Challenges include that some bacteria are harder to grow or take a long time to grow

• May lead to use of incorrect antibiotics which can increase the risk of AMR

• May also lead to unnecessary treatments for patients

Techniques

• Microscopy involves direct observation of pathogens (e.g., Gram staining for bacteria)
• Culture Methods involve growth on specific media (e.g., blood agar for Streptococcus)
• Molecular Diagnostics involves PCR for pathogen-specific genes (e.g., Mycobacterium tuberculosis)
• Serological Tests detect antibodies or antigens (e.g., ELISA for HIV)
• Rapid Tests are lateral flow assays for point-of-care diagnostics (e.g., COVID-19 antigen tests)