MICROBIOLOGY

Commensal Microorganisms

Microorganism benefits

Host is not harmed or helped

Opportunistic Pathogens

Harmless microorganisms cause disease when opportunity is presented

Obligate (Strict) Pathogens

Always causes disease

Cellular (Prokaryotic)

Single celled

DNA genome

Independent replication (binary fission)

Peptidoglycan cell wall

Bacteria

Cellular (Eukaryotic)

Single celled (yeast) or multicellular (mycelium)

DNA genome

Independent replication

Chitin cell wall

Plasma membrane contains ergosterol

Absorb nutrients from dead/dying organic material

Fungi

Cellular (Eukaryotic)

Single cell (protista) or multicellular (animal)

DNA genome

Independent replication, often complex life cycle

• Mitosis or Sexual Reproduction

Parasites

Acellular

DNA or RNA genome

Completely host cell dependent replication

Viruses

Virus Relationship with Host Cells

Requires host to reproduce

• Some kill the cells they infect

• Some establish long-term infection of cells they infect

Highly specific to host

1-2 um

Singular, circular chromosomes in nucleiod

70S ribosome

No nucleus or membrane-bound organelles

No introns → mRNA processing

Prokaryotic

50 um

Multiple, linear chromosomes in nucleus

80S ribosome

Has nucleus and membrane-bound organelles

Eukaryotic

Three Domains

Archaea

Eukarya

Bacteria

Six Kingdoms

Animal

Plant

Fungi

Eubacteria (only pathogenic species of bacteria)

Protista

Archaebacteria (not pathogenic)

Grow outside human cell

Can produce many different virulence factors (species specific)

Communicate to form biofilms

Many potential drug targets

Clinical Outcomes of Bacteria

Why are there many effective drug targets for antibiotics?

Bacteria are prokaryotic so drugs can target them without affecting human (eukaryotic) cells

Harder to develop drugs w/o harming human cells

Strict or opportunistic (most) pathogen

Mycelium on body surfaces

Yeast on body surfaces and inside human cells

Clinical Outcomes of Fungi

Harder to develop drugs w/o harming human cells

Worms are harder to eliminate - can change exterior to evade immune system

Establish long-term infection

Complex life cycles with multiple hosts

Clinical Outcomes of Parasites

High mutation rates

Long-term/persistent or latent infections are possible

Harder to treat w/o harming human cells

Clinical Outcomes of Viruses

Prions

Misfolded, infectious proteins that cause healthy proteins to fold

Have no genetic material

Spread through contact with infected material

Resident Microbiota

More or less permanent

Transient Microbiota

Establish niche only briefly

Carrier State

Potentially disease-causing bacteria that are resident in some individuals

Sites Colonized by Microbiota

Skin

GI Tract (Stomach through Colon and Rectum)

Respiratory Tract

Vagina

Opening of the Urethra

Mouth/Oral Cavity

Sterile Body Sites

Blood

CSF

Pleural Fluid

Urinary Tract

Enclosed Cavities

Evolution of Human Microbiota

Sterile in Womb

Obtain microbiota during and after birth from mother’s vagina, environment, diet, interactions, etc.

Microbes that cross the placenta are…

ALWAYS pathogenic

16S rRNA Sequencing

Identify and classify bacteria by sequencing hypervariable regions of 16S rRNA gene and comparing genus-specific genetic signatures

Staphylococcus epidermis

Staphylococcus aureus

Examples of Microbiota on the Skin

Factors Contributing to Variation in the Skin Microbiota

Host phyiology

Environment

Immune System

Host Genotype

Lifestyle

Pathobiology

Normal microbione microorganisms in competition for survival in their ecological niche

Exclusionary Effect

Gut Microbiota

Influence development of immune system during childhood

Microbiota of Respiratory Tract

Many microbiota in nostrils

Few bacteria below the larynx due to cilia

LRT microbial communities are migrated from URT (VERY FEW)

Microbiota of the Genitourinary Tract

Urinary system = sterile

• EXCEPT last centimeter of the urethra

• Bacteria in sterile places = UTI

Microbiota adjusts to acidic environment of vagina

Yeast Infection

Disturbance in normal fungal vagina microbiota

Bacterial Vaginosis

Shift in pH and changes in the population of bacteria

Viruses Infecting Bacteria

• Activate immune responses via TLR signaling

Interact with host bacterial microbiota

• Modulate bacterial abundance

• Transfer DNA and modify bacterial fitness and virulence

Bacteriophages

Viruses Infecting Eukaryotes

• Cause acute and chronic infections

• Protect the host from viral infections and trigger the development of innate immunity

Eukaryotic Viruses

Viral genetic sequences whose identity/function we don’t know much about

Dark Matter

Human Virome

All viruses on human body NOT causing disease

Infection

Multiplication of organism in a host

Can have w/o disease

Carriers

Individuals with subclinical infection

• Active infection producing little to no symptoms

Disease

Infection causes damage and/or symptoms

Stages of Infection

1. Encounter

2. Entry and Establishment

3. Spread of Pathogen

4. Damage to Host Physiology (not always)

5. Outcome

Zoonotic Infections

Transmitted directly from animals to human host

Vertical Transmission

Mother → Fetus/Infant

Through placenta, birth, breastfeeding

Horizontal Transmission

Person to person (not vertical), from animal to person, from environment to person

Horizontal Routes of Infection (8 of them listed)

Skin-To-Skin

Genital/Sexual Transmission

Respiratory (Airborne)

Contact with Fomites

Salivary

Food and Water-Borne

Vectore-Borne

Bloodborne and other body fluids

Pathogenesis

How pathogen and host interact resulting in dysfunction

Steps for a microorganism to cause disease

1. Gain access

2. Must disrupt normal functioning

Endemic

Normal # of disease in population

Epidemic

Higher # than usual of disease in population

Pandemic

Epidemic that is widespread

Purpose of Immune System

Differentiate between self, non-self, and dangerous non-self to keep the body free from harm

Immune System Functions

1. Immunosurveillance “Seek and Destroy”

2. Maintain Homeostasis “Tolerate and Heal”

Cell Signaling (Extracellular vs Intracellular Signaling)

Extracellular domain detects pathogens

Intracellular domain initiates signaling cascade

Pattern Recognition Receptors (PRR)

Recognize characteristic microbial patterns associated with pathogens and cell damage

Pathogen Associated Molecular Pattern (PAMP)

Structures found on pathogens but NOT in human cells

Damage Associated Molecular Pattern (DAMP)

Intracellular elements found in the extracellular space

Binding PRRs Resulting Functions:

Phagocytosis (internalization and lysis)

Secretion of Soluble Mediators (Cytokines & Chemokines)

Alter Cellular Function

Soluble Mediator

Cytokines

Direct Immune Cell Migration

Soluble Mediator

Chemokines

Phagocytosis

• Macrophages, DC, Neutrophils

B Cells Secrete Antibody → ADCC

• Mast Cell, Basophil, Eosinophil, All Innate Immune Cells, Complement Proteins

Immune Effector Mechanisms in Response to Extracellular Pathogens

Kill Infected Cells

• NK, CD8+

CD4+ T Activation of Macrophages

Immune Effector Mechanisms in Response to Intracellular Pathogens

B Cells Effector Function

Antibody secretion into serum

• Block pathogens from binding to host cells

• Pathogen lysis via innate immunity

T Cells Effector Functions

Cytokine secretion: alter target cell function

• CD4+ and CD8+

Produce ALL blood cells and immune cells

• Leukocytes/Immune Cells/WBC

• Erythrocytes, platelets

Hematopoietic Stem Cells (HSC)

Ingest infected cells then kill themselves

Most abundant in blood

Migrate to tissues, not present in them

Can form extracellular trap

Pus = dead __________

Neutrophils

In ALL tissues, highly tissue-specific

Functions:

1. Phagocytosis: internalize and destroy

2. Secretion of Cytokines and Chemokines

   1. M1: pro-inflammatory (damage)

   2. M: anti-inflammatory (healing)

Macrophages

If pathocytosis didn’t occur __________ would be disrupted

Ingestion and killing of extracellular pathogen

Non-specific, kill infected cells that are lacking MHC

Kill via targeted release of lytic granules

Natural Killer (NK)

In tissues

Defense against allergies and parasites

Degranulation: release granules (histamine) to cause allergic reaction (alarm)

Mast Cell

In all tissues

PRR Activation → DC migrate to local lymph node

Captures antigen and presents it to T cells which then activate B cells

Connects innate and adaptive immune systems

Dendritic Cells (DC)

VERY specific

Directly kill infected cells

Binds with MHC I

CD8+

Activated/Deactivates other immune cells

Binds with MHC II

CD4+

LOCAL monitoring of fluid and tissues

Filter lymph

Bring antigens into contact with B and T cells

Lymph Nodes Functions

Monitors blood of whole body

Immune response to blood-borne antigens

Spleen Functions

Transports lymph through lymph nodes then back to blood

Lymphatics function

Macrophage Initiated Inflammatory Response Signs

Redness

Heat

Pain

Swelling

Function Loss

Macrophage Initiated Inflammatory Response Steps

1. PAMP Recognition by Macrophage

2. Release of Cytokines & Chemokines

3. Vasodulation

4. Influx of Fluids, RBC, WBC, Molecules

Antibody-coated target cell is destroyed by immune effector cells

ADCC: Antibody-Dependent Cellular Cytotoxicity

Three Main Functions of ALL Antibodies

1. Neutralization

2. Opsonization

3. Complement

Neutralization

Bind to pathogen to prevent binding of host receptors

Opsonization

Mark pathogen for destruction

Proteins released into blood and bind to pathogen to initiate lysis or phagocytosis

Cause destruction via:

1. Opsonization

2. Chemokines: bring immune cells to area

3. Membrane Attack Complex creates pores in cell membrane pf pathogen resulting loss of osmotic pressure → cell lysis

Complement

1. Pathogen Enters

2. Innate Recognition

3. Innate Effector Mechanisms Activated

4. Activation of Adaptive Immunity (B/T-Cell Activation)

5. Adaptive Effector Response

6. Pathogen Clearance

7. Memory Cells Remain

Typical Immune Response to a Pathogen

Immune Cells in BLOOD: Never Let Mom Eat Beans

Neutrophils

Lymphocytes

Monocytes

Eosinophils

Basophils

CBC with Differential:

EXTRACELLULAR INFECTIONS

BACTERIAL or FUNGAL infection, inflammation

• These can be intracellular

Pus

Neutrophils

CBC with Differential:

VIRAL infection

Lymphocytes

CBC with Differential:

Infection, INFLAMMATION

Monocytes

CBC with Differential:

Parasitic Infection or Allergy

Esosinophils and Basophils

Immune Cell Relative Leukocyte Count

Neutrophil > Lymphocyte > Monocyte > Eosinophil > Basophil

Antigen

Elements in any molecule/virus/cell that the adaptive immune system can mount a response against

Epitope

Part of antigen that the antibody or TCR recognizes

T Cell Receptor (TCR)

Recognizes antigen presented to T cells

Variable Region of Antibody

Interacts/Binds w/ Antigen

Determines antigen binding specificity

Constant Region of Antibody

Determines Effector Function

Allows antibody access to certain areas

Same for each antibody type regardless of specificity

IgA

Mucosal Surfaces

Tolerance

IgE

Parasites & Allergies

IgG

Most common serum antibody

Crosses placenta to protect fetus

IgM

Produced First

Activates Complement

IgD

Naive B Cells

NOT secreted