Lecture 1 - Microbiota & Bacteriology PDF

MICROBIOLOGY Spring 2025  PURPOSE: Understand the ORGANISM and how it causes disease to be prepared to diagnose and intervene to help your future patients Basic Concepts  Principles of Infection...

MICROBIOLOGY Spring 2025  PURPOSE: Understand the ORGANISM and how it causes disease to be prepared to diagnose and intervene to help your future patients Basic Concepts  Principles of Infection Host exhibiting adverse response to the presence of an infecting organism Infection Infectious Disease Presence & multiplication of an organism within a host Interaction between an organism & host  Types of infection Primary infection Secondary infection First infection by an organism 1 4 Superimposed infection of a different pathogen in an already infected host Reinfection Nosocomial infection Subsequent infection by the same organism 2 5 Infection acquired during a hospital stay or at a medical facility due to infection from the environment, instruments, prosthetics, etc. Reactivation Iatrogenic infection Organism lies dormant in the body & becomes active at a later date under 3 6 Physician induced infection due to therapy different conditions Includes immune suppression from chemotherapy  Stages of infection Replication after attachment to host cells Needs to avoid/overcome host defenses Facilitates adherence of the Production of toxins or microbe to the host enzymes that destroy Requires surface structures host immune response or virulence factors Morphology changes to Adhesins, fimbriae, pili surface antigens Evasion of Invasion & Colonization Adhesion host defenses multiplication Ability to resist Adherence of the phagocytosis and other microorganism to the host host defenses Specific interaction Requires production of between the microbe & virulence factors host in which a bond is Toxins, cell surface formed proteins, capsule, enzymes Human Microbiota Human Microbiota Formerly called microbial flora Composition Bacterial – mostly Fungi Parasites Viruses – rare Varies with age, geography & external factors Diet Systemic health Contact lens wear  Origin of microbiota Colonized by many different species Colonized by ~100 different microbial species Total organism load of ~100 trillion Variable throughout life Sterile until birth Organismal load Fetus is in sterile environment until birth Once exposed to microorganisms in environment, must create a host-microbe relationship Changes throughout life Changes throughout different stages of life & varying environmental conditions Region, diet, age  Host-organism relationships Symbiosis / Mutualism Parasitism Relationship between 2 or more Relationship in which one species organisms where each benefits from benefits at the expense of the other the presence of the other Carrier state Potentially pathogenic organism Commensalism establishes residence on the body Relationship in which the organism Possible to transmit to a different host benefits, but no benefit or harm is May be resident or transient organisms done to the host  Microbiota Resident flora Organisms that have established a niche at a particular body site May occupy indefinitely Transient flora Acquired from environment Establish a brief residency at a particular body site Often replaced by resident flora Microbiota Microbial flora NOT ESSENTIAL to life Animals can be reared in complete absence of microbes Do not develop adaptive immune system in the same manner Plays a role in maintaining normal health & functioning Suppression of normal flora creates a void that allows for colonization by opportunistic organisms  Microbiota Blood, bodily fluids, tissues Generally sterile Occasionally organisms introduced by trauma or during childbirth Frequently leads to infection Filtered out by pulmonary capillaries or reticuloendothelial system Microbiota Skin Predominantly dry, slightly acidic & aerobic environment High microbial colonization Increased prevalence on moist skin areas Axillae, perineum, between toes Resistant to bactericidal effects of skin lipids & fatty acids Difficult to eliminate with scrubbing Especially when colonization occurs in pilosebaceous units Conjunctiva Similar distribution to skin in lower numbers Inhibited by flushing effects of blinking & high lysozyme content of lacrimal secretions Microbiota Digestive tract Oral cavity High number or organisms Mouth & pharynx highly colonized by facultative & anaerobic bacteria, saliva contains mixed organisms Stomach Few organisms capable of surviving gastric acid & peptic enzymes Small intestines Scant flora in small intestines Lower ileum begins to resemble colon Microbiota Digestive tract Colon Most abundant & diverse microbiota in the body Mostly anaerobic organisms, some facultative Variable based on diet High meat diets have increased Bacteroides species & other gram-negative Bacilli compared to diets high in fish or vegetables Feces of adults comprised of ≥25% bacteria by weight Research evaluating gut microbiome & role in obesity Microbiota Respiratory tract Upper respiratory tract External 1cm of anterior nares have flora similar to skin Nasopharynx similar to mouth Sinuses generally free of organisms Lower respiratory tract Protected by epithelial cilia & movement of mucociliary blanket Only transient organisms gain access to trachea & larger bronchi Microbiota Genitourinary tract Urinary tract Distal 1cm of urethra colonized by organisms derived from perineum Rest of urinary tract sterile Vaginal flora Flora varies per life stage During childbearing years Predominantly anaerobic & microaerophilic organisms Pre-puberty & post-menopause Mixed, non-specific organisms  Microbiota Role in health & disease Positive Negative Contribute to normal microbial defenses Imbalance leads to opportunistic infection & toxin degradation Overproduction of resident flora leads to Assists in maturation of immune system infection Prevents colonization by potentially Transient flora may proliferate to cause harmful organisms infection Synthesis of vitamins & nutrients Infectious Disease Pathogenesis Ability of a microbe to produce disease Often used to describe or compare species True pathogen Organism able to cause disease in a healthy, immune-competent individual Opportunistic pathogen Organism that causes disease only in immune-compromised state Often found in normal microbiota Virulence Relative ability of a microorganism to cause disease or the degree of pathogenicity Often used to describe or compare strains within a species Measured by the number of organisms needed to produce a disease state Virulence factors allow microorganisms to persist in host & cause disease Evade or overcome host defenses  Immunity Host defenses to infection 1 Physical barriers 2 Cleansing mechanisms 3 Antimicrobial substances Enzymes, antibodies, β-lysins, interferon 4 Indigenous microbial flora 5 Phagocytosis 6 Inflammation 7 Immune response  Immunity Microbial resistance factors to host defenses 01 Ability to resist phagocytosis Surface structures 02 Adhesins 03 Intracellular survival & proliferation Production of toxins & enzymes 04 Exotoxins Endotoxins Microbial immunity Production of toxins & enzymes Disease only noticeable if tissue damage occurs Ability of organisms to produce harmful agents or induce host-driven immunologically mediated damage increases invasiveness & virulence Toxins Poisonous substances produced by an organism to interact with host cells Disrupt normal host metabolism & cause harm Exotoxins Produced by gram positive & gram-negative organisms Secreted by organism into extracellular environment or by cell lysis Allow direct spread of organism Endotoxins Portion of the gram-negative outer cell membrane NOT a component of gram-positive organisms No enzymatic activity No specificity in their activity against the host Clinical manifestations of infectious disease Universal signs of infection Fever / heat Pain Redness Swelling Body area & offending organism produce different signs & symptoms Considerable overlap Bacteriology  Eukaryotic vs Prokaryotic Cells Eukaryotic Large, complex structures 10-100µm Highly compartmentalized Contain a true nucleus, organelles, & cytoskeleton Cell membranes separate organelles from each other Plant, animal cells Eukaryotic vs Prokaryotic Cells Prokaryotic Smaller No nucleus or membrane bound organelles More complex cell envelope Plasma membrane to regulate what enters the cells Nucleoid Bacterial DNA – circular molecule arranged loosely within the cell Number depends on growth conditions Rapidly growing cells have more nucleoids Multiple copies are identical Ribosomes to synthesize proteins Prokaryotic cells Cell envelope Multi-layer structure Protects organism from environmental stresses Components Cell / plasma membrane Cell wall Capsule & gylcocalyx Cell appendages Flagella Pili Fimbriae Cell envelope Plasma membrane Phospholipid bilayer with embedded proteins No sterols present Exception: Mycoplasma Osmotic barrier Location of electron transport chain Cell envelope Cell wall Maintains shape Prevents bursting from high osmotic pressure within Different morphologies based on gram staining characteristics Gram-positive Gram-negative Acid-fast (modified gram-positive cell wall)  Cell envelope Cell wall staining Purpose Allow for visualization of cells Distinguish characteristics of cells for recognition Gram-positive Crystal violet stain adheres to the thick peptidoglycan layer Process 1. Stain with crystal violet dye for 60 seconds Gram-negative 2. 2. Wash off & flood with iodine Crystal violet washes off, safranin solution for 60 seconds binds to cell wall 3. 3. Wash off & decolorized with 95% alcohol 4. 4. Counter-stain with safranin for 30 seconds Cell envelope Gram-positive cell wall Composition Cytoplasmic membrane Phospholipid bilayer with embedded proteins Thick peptidoglycan layer Protective Wall techoic acid – anchored to peptidoglycan Leipoteichoic acid – anchored to plasma membrane Portfolio Designed Gram-negative cell wall Composition Cytoplasmic membrane Periplasmic space Gel-filled space containing proteins & enzymes Thin peptidoglycan layer Contains murein lipoprotein Outer membrane Phospholipid bilayer Contains lipopolysaccharides Function Barrier to hydrophobic compounds & harmful substances Contains porin proteins which allow water-soluble molecules to enter the cell Provides attachment sites Gram-negative cell wall Lipopolysaccharide (LPS) Components O-specific side chains Outer oligosaccharide units Variable lengths specific to different organisms Play a role in adherence of organism to host cell Core polysaccharides Anchor sections together Lipid A Disaccharide which anchors LPS to the cell wall Endotoxin When cell lysed, fragments released into circulation lead to non-specific symptoms Cell envelope Acid-fast cell wall Composition Modified gram-positive cell wall Thin peptidoglycan layer Mycolic acid – waxy layer of glycolipids & fatty acids bound to exterior wall Forms a strongly hydrophobic lipid shell altering its permeability Stains red/pink Mycobacterium species Cell envelope Glycocalyx Capsule Condensed, well-defined layer Protective barriers to host immune recognition Gram positive & gram negative Function as virulence factors by helping to evade phagocytosis Composed of polysaccharide polymers or polyproteins Slime layer Loosely associated with the cell Protective Prevents desiccation Assists in adherence of bacteria to surfaces  Cell envelope Cell appendages Flagella Pili Motility organ Protein filaments that rotate to allow the Non-motile, long, hollow protein bacterium to be motile tubes Types Allow connection of bacteria & DNA Monotrichous – extend from one end exchange Lophotrichous – occur on one end in tufts Peritrichous – occur on all sides of the bacterium Fimbriae Polar – single flagella occurring at both ends of the bacterium Non-flagellar, sticky, proteinaceous, hair- like appendages Adhere bacterial cells to each other, or to environmental surfaces Cell appendages Prokaryotic cells Genetic material Nucleoid Attached to mesosome in the cell membrane Contains DNA material Generally single, continuous circular molecule Number depends on growth conditions Rapidly growing bacteria have multiple copies Plasmids Extrachromosomal, circular, double stranded (ds) DNA located in the cytoplasm Not essential for bacterial cell growth Number depends on species Self-replicating Passed to daughter cells via binary fission or transferred during conjugation Prokaryotic cells Cytoplasmic structures No membrane bound organelles Ribosomes Free-floating in cytoplasm & attached to cytoplasmic reticulum Synthesize proteins 70s Dissociate into 50s & 30s subunits Endospores Produced by some species in response to harsh environments Small, dormant, asexual spores Become vegetative when harsh conditions removed Bacterial Morphology Bacterial morphology Shape Cocci Spherical, kidney-bean, or lancet-shaped Bacilli Rod shaped, ends may be blunt, tapered or rounded Spirochetes Spiral shaped Vibrios Comma shaped Filamentous Elongated, thin Pleomorphic Size Variable depending on shape 0.1 - 5µm Cocci: 1µm Bacilli: 0.5-1 x 3µm Spirochetes: 0.3-0.6 – 1-3µm Bacterial morphology Arrangement Singular Cocci or bacilli Coccobacilli Elongated / oval shaped organism Pairs: diplo- Clusters: staphylo- Chains: strepto- Side-by-side: palisading Only in bacilli organisms Bacterial morphology Gram positive organisms Cocci Bacilli No spores Streptococci Corynebacterium Staphylococci Listeria Enterococcus Spores Bacillus x Clostridium Gram negative organisms Cocci Bacilli Spirochetes Borrelia Neisseria All others Leptospira Moraxella Treponema Other forms Acid fast No cell wall Chlamydia Mycobacterium Mycoplasma Bacterial Metabolism  Physiology of bacterial growth Environmental factors necessary for bacterial growth pH Neutral pH is ideal for most bacteria Temperature Psychrophiles Grow best at cold temperatures (10-20°C) Found mostly in arctic seas Thermophiles Grow best at high temperatures (50-60°C) Found mostly in hot springs Mesophiles Grow best at moderate temperatures (20-40°C) Most bacteria adapted for survival in human hosts Environmental gaseous composition Aerobes Anaerobes Physiology of bacterial growth Atmospheric requirements vary based on organisms Normal atmosphere 21% O2 & 1% CO2 Aerobic Survive in the presence of O2 Anaerobic Grow without O2 Microaerophilic Require reduced O2 levels – 5-6% atmospheric O2 Capnophilic Require increased CO2 levels – 5-10% enrichment Physiology of bacterial growth Oxygen Highly reactive & forms toxic byproducts in the presence of electrons Ability to break down byproducts dictates whether bacteria can survive in presence of oxygen Enzymes Catalase Breaks down hydrogen peroxide into water & oxygen 2H2O2  2H2O + O2 Peroxidase Breaks down hydrogen peroxide into water H2O2 + O2  2H2O Superoxide dismutase Breaks down superoxide radicals O2- + O2- + 2H+  H2O + O2  Bacterial oxygen requirements Environment Metabolism Enzymes Glycolysis, TCA cycle, Catalase Obligate aerobes Need O2 for growth electron transport Peroxidase chain Superoxide dismutase Aerobic Require reduced levels of Microaerophilic Glycolysis oxygen to survive Aerobic organisms that Glycolysis Facultative Catalase can survive for short Fermentation in the anaerobes Superoxide dismutase periods without O2 absence of O2 Anaerobic, but can survive Aerotolerant in the presence of O2 Fermentation Superoxide dismutase Anaerobic anaerobes Do not use O2 for metabolism Cannot survive in the Obligate anaerobes Fermentation None presence of O2  Physiology of bacterial growth Metabolism Fermentation Respiration / Glycolysis Anaerobic process Aerobic process Obligate & facultative anaerobes Obligate aerobes, facultative anaerobes Organic compound is electron acceptor Molecular oxygen is electron acceptor Less efficient Anaerobic respiration possible using other organic/inorganic substance as final electron acceptor More efficient Physiology of bacterial growth Energy parasites Steal ATP from the host Obligate intracellular organisms Unable to synthesize ATP through metabolic pathways Organisms Chlamydia & Rickettsia Bacterial Growth Physiology of bacterial growth Binary fission replication Chromosome replicates & moves to opposite sides of the cell Cell elongates Plasma membrane pinches to separate cell into 2 identical daughter cells Horizontal gene transfer Generation / doubling time Average time required for a population to double in size Variable per organism E. coli = 2o minutes Mycobacterium = 24 hours Physiology of bacterial growth Bacterial growth curve Lag phase Cells preparing to divide Exponential phase Replication of cells in a steady state New material being synthesized at a constant rate Stationary phase Represents exhaustion of nutrients or accumulation of toxic products Growth (replication) ceases Population numbers remain constant Death phase Number of nonviable cells exceeds number of viable cells Generally occurs slower than the exponential phase Biofilms Communities of organisms bound to each other & a surface Secrete a complex sugar/protein matrix Often composed of numerous species Functions Persistence of infection Protection from killing via host immune system & antimicrobial agents Communicates with each other via quorum sensing Cell maintenance & division Horizontal gene transfer Host-pathogen interactions Biofilm behavior Biofilms Form on numerous surfaces Occur naturally Teeth Wounds Joints Prosthetic devices Estimated that ~65% of infections associated with biofilms Device associated Contact lenses Contact lens cases Non-device associated Bacterial Genetics Genetic recombination Purpose Processes for introducing genetic variability into the population Types Transformation Transduction Conjugation Genetic recombination Conjugation F+ cell transfers DNA to F- cell via pili Pilus produced by F+ cell Requires close contact Recipient synthesizes complementary DNA Generally plasmids transferred Hfr cells F factor integrated in bacterial chromosome instead of a plasmid Results in increased rates of conjugation in a population Genetic recombination Transduction Transfer of bacterial genetic material via a bacteriophage Injects DNA from donor into recipient cell Phage instructs new cell to synthesize its DNA Bacterial cell lyses releasing phage Takes phage & bacterial DNA to infect new cells Lytic phage Causes lysis of the host bacterium Temperate phage Phage DNA incorporated into recipient DNA after infection Cell then passes on phage genome to progeny & enters into lytic cycle Bacteria may express phage characteristics Genetic recombination Transformation Naked DNA taken up into cell Recipient must be competent Bacterial enzymes break DNA strands into fragments Incorporated by recombination Can replicate in the cytoplasm & be transferred to daughter cells Other bacterial genetic mechanisms Mutations Transpositions Replacements Insertion sequences Deletions Transposons Insertions Inversions Spontaneous Restriction enzymes Enzymes produced by bacteria to cut or restrict incorporation of foreign DNA into bacterial genome at specific sequences Bacteria methylate their DNA at the same sequence Protective mechanism Used in biotechnology to create sites for new genes Other bacterial genetic mechanisms Mutations Transposons Result in differences in parent & progeny Mobile genetic elements allowing for genetic variability Some pieces of DNA able to jump from one Error in DNA replication location to another Changes in DNA code which often Insertion sequences results in the change of a coded Code for 1 gene only protein or prevention of protein Bacterial genome often consists of synthesis many insertion sequences Rates increase in certain Transposons environmental or physical changes Contain multiple genes Single nucleotide change  single amino Often carry antibiotic resistance genes acid within protein change May be located on bacterial Insertions or deletions  disruption of chromosome or on plasmids gene or frame shift mutations creating incomplete or inaccurate proteins