Microbiology - MLS 334: Exam 1 Objectives

Define Microbiology

Specialized area of biology that encompasses tiny life forms that are microscopic such as; microbes, bugs, germs, microorganisms. It is one of the largest and most complex biological sciences

Taxonomy

The orderly classification and grouping of organisms

Classification

Arrangement of organisms into groups

Nomenclature

Assigning names to various taxonomic rankings for each microbial species

Identification

Discovering and recording traits of organisms so they can be put into taxonomic scheme

Infection

Invasion and multiplication of microorganisms within a host

Carrier

Person may harbor a pathogen that can be transmitted to others without eliciting disease themselves

Colonization

Bacteria on our body surface that does no illicit an immune response or disease

Normal Flora

Organisms that exist in a symbiotic relationship with the host. Skin, Upper Respiratory Tract, Gastrointestinal Tract and Female Genital Tract

Examples of Normal Flora: Skin

Propionibacterium acnes and Staphylococcus epidermidis

Examples of Normal Flora: URT

Streptococcus viridans, Moraxella catarrhalis, diptheroids

Examples of Normal Flora: GI

Lactobacillus spp., Escherichia coli, Clostridium spp.

Examples of Normal Flora: Female Genital Tract

Diptheroids (Corynebacterium spp.), Streptococcus, Peptococcus, Lactobacillus

Ways to Classify Infectious Disease

1. Microbiological: pathogens or causative agent

2. Clinical: Clinical Manifestation

3. Epidemiological: Transmission and Reservoir

How to use basic Classification in Microbiology

Genotype and Phenotype: Media, Gram stain, morphology, biochemical characteristics, antimicrobial resistance patterns

How to use Hierarchical Classification from largest to smallest

Domain (largest), Kingdom, Phylum, Class, Order, Family, Genus, Species (smallest)

What is the chain of infection?

1. Pathogen 2. Reservoir 3. Portal of Exit 4. Mode of Transmission 5. Portal of Entry 6. Susceptible host

Infectious Disease Periods

1. Incubation Period: no signs or symptoms

2. Prodromal period: vague, general symptoms

3. Illness: most severe signs and symptoms

4. Decline: declining signs and symptoms

5. Convalescence: no signs or symptoms

Disease Prevention Measures: Individual

1. Hand Hygiene

2. Food and water safety

3. Condom Use

Disease Prevention Measures: Community

1. Sanitation

2. Water safety

3. Blood-donor screening

4. Isolation and quarantine

Rules of Nomenclature

1. Use binary names: Generic and species -> (Escherichia coli) slanted

2. Capitalize: Genus always capitalized, species never capitalized

3. Italicize: All taxa italicized and underline if handwritten

4. Initials: Full name first time in paper and abbreviated to initial capital letter followed by species (E. coli)

5. Common names: Lowercase, non italic -> streptococcus

Hand Hygiene

1. Providers perform hand hygiene less than half the time they should

2. Can be washing your hands with soap and water or alcohol-based hand sanitizer

3. The Joint Commission has a large document for this

STI Prevention Measures

Abstinence, Vaccination, Condoms, Testing, Monogamous, Limit sex partners, do not douche, do not abuse alcohol or drugs

Contact Tracing

Contacts of infected individuals are identified, then investigated and notified

- Helps with spread by notifying individuals who may need to quarantine

Case Finding

Actively searching for infected inidividuals

- COmmunity screening programs

- May include contact tracing and screening for STI's

Safety Organizations

OSHA, EPA, CDC, JACHO, CLSI, WHO

OSHA

Occupational Safety and Health Administration

EPA

Environmental Protection Agency

CDC

Center for Disease Control and Prevention

JACHO

Joint Commission on Accreditation of Healthcare Organizations

CLSI

Clinical Laboratory Standards Institute

WHO

World Health Organization

What are Standard Precautions?

Measures taken to protect hospital personnel from bloodborne infections

Droplet Transmission

Close repiratory contact or exposure of mucus membranes/respiratory secretions

Airborne Transmission

Infectious agents that can remain airborne for long periods of time and long distances

Contact Transmission

Direct or indirect contact with patient or environment

Risk Groups

1. Risk Group 1 (No or Low Individual or Community Risk): Microorganism unlikely to cause human or animal disease

2. Risk Group 2 (Moderate Individual Risk, Low Community Risk): Pathogen can cause human or animal disease but unlikely a serious hazard to lab workers. May cause infection but effective treatment and preventative measures available and spread is limited

3. Risk Group 3 (High Individual Risk, Low Community Risk): Pathogen can cause serious human disease but does not ordinarily spread from person-to-person. Treatment and preventative measures available

4. Risk Group 4 (High Individual and Community Risk): Pathogen can cause serious human disease and can be easily transmitted from person-to-person (directly or indirectly). Treatment not always available

BSL-1

- No potential for exposure to pathogenic material or biohazards

- Lab work conducted on open bench top

- General safety guidelines followed

- Example: College Chemistry and Biology Labs; Organisms: Bacillus subtilis

BSL-2

- Level 1+ more restrictions

- Agents pose a moderate potential hazard for employee and environment: not normally aerosolozed

- Most Clinical Labs: Employees need specific training

- Access to lab is limited

- Immunizations required (Hep B and TB)

Example organisms: HBV, HIV, Salmonella spp

BSL-3

- Level 2+ more

- Work with pathogens that are indigenous or exotic (M. tuberculosis, St. Louis Encephalitis virus) - potential for aerosol transmission and inhalation

- Clothing and access controlled

- Negative air pressure: directional air flow

BSL-4

- Level 3 + more

- Agents are dangerous and high risk of lethality

- Transmitted by aerosols or unknown

- Isolated lab

- Separate room for changing clothes before entering lab

- Use Class III BSC

- Wear positive protective suit to perform lab work

- Mainly research

- Examples: Marbug and Congo-Crimean hemorrhagic fever

Chemical Storage

- Never store alphabetically

- Never store acids and bases together

- Acetic acid and sulfuric acid should never be stored with oxidizing agents

- Flammable chemicals should be stored in a flammable cabinet

- Bulk chemicals should be stored in a certain area

Symbiosis

Two different organisms living together, usually advantageous to both

Commensalism

Microorganism benefits, host is not harmed

Mutualism

Both microorganism and host benefit

Parasitism

Microorganism benefits, host is harmed

Resident Microbiota

- Organs, tissues and fluids should not contain microbes

- Areas of the body that are exposed to the outside environment will harbor resident microbes (normal flora)

Transient

Microbes that occupy the body for a short amount of time

Resident

Microbes that have established "residence"

Microbial Flora Composition

- Nutritional factors

- Antibacterial substances: fatty acids, lysozyme, bile

- Environment: Gaseous atmosphere for low oxidation/reduction potential

- Low pH: Femal genital tract, GI tract of breast-fed infacts

- Moist or dry: most microorganisms prefer moist areas examples skin folds

Sterile Sites

Internal Organs and Tissue: Heart, Liver, Kidneys, Lungs, Brain and Spinal Cord, Muscles, Bones, Ovaries/Testes, Glands, Sinuses, Middle and Inner Ear and Internal eye

Fluids within Organ Tissue: Blood, Urine in bladder, ureters and kidneys, CSF

Skin Flora

- Skin surface and hair follicles

- Apocrine sweat glands: Secrete substances metabolized by bacteria

- Normal flora colonize skin surface and prevent pathogens from colonizing

Common Microorganisms found in Skin Flora

- Candida spp.

- Micrococcus spp.

- Staphylococcus spp.

- Clostridium spp.

- Propionibacterium spp.

- Diphtheroids (Corynebacterium spp.)

Mouth Flora

- Supports anaerobic growth: low oxidation reduction potential

- Buccal mucosa and tooth surface: microorganisms produce acids which can lead to tooth decay

Common microorganisms found in Mouth Flora

Streptococcus mitis

Streptococcus sanguis

Streptococcus salivarius

Streptococcus mutans

Respiratory Tract Flora

- Upper Respiratory Tract

- Lower Respiratory Tract: normally considered sterile and cilijary epi cells and mucus help protect

GI Flora

- Esophagus, stomach, small intestine and colon

- Environment favors anaerobes

- Beneficial relationship: Ferment wastes to generate vitamins and digestive enzymes

- Stomach normally sterile: acidic pH and exceptions such as endospores, H. pylori, parasitic cysts

- Antibiotics can alter usual flora

Genitourinary Flora

Sterile: Kidneys, Bladder, Fallopian Tubes

Nonsterile: Vagina and Distal cm of urethra

Role of Microbial Flora in Infectious Disease

Disease:

- Opportunistic Infections~ Host environment change and weakened immune system

- Trauma

- Immunosuppressed host~ Drugs, Chemotherapy, Radiation, Immune system defects

Protection: Normal microbial flora prime immune system

- Flora block colonization of pathogens

- Inhibitors: sterile environment antibiotics

Pathogenicity

Ability for an organism to produce disease

Opportunistic pathogen

Host resistance low and generally do not cause disease

True pathogen

Disease in immunocompetent hosts

Latrogenic infection

Infections from medical treatments or procedures and HAI

Different Routes of Transmission

Airborne, Fecal-Oral, Close contact: direct contact (congenital sexual person-to-person droplet), wounds, cuts, bites, arthropods and zoonoses

Virulence

- Ability for a microorganism to cause disease

- The number of organisms required

- Virulence factors: Capsules, Toxins, Adhesive fimbriae, ability to survive intracellularly

Host Resistance

- Physical barriers (First line of defense): Intact skin

- Cleansing mechanisms: Liquid movement such as tears, urine, mucus secretion, Cillia which clear debris through locomotion

- Low pH: Acidic and stomach, vagina

- Antimicrobial substances: fatty acids on skin, hydrochloric acid (HCl) in stomach, Lysozymes, Immune proteins~ IgA, LMW cationic proteins, complement, interferon

- Indigenous microbial flora

- Phagocytosis

- Inflammation: Accumulation of phagocytic cells and release mediators~ Erythema, Edema, Pus

- Enzymes digest foreign particles, injured cells and debris

Phagocytosis

- Primary mechanism against extracellular bacteria: PMNS, Macrophages

- Diapedesis: Movement of PMNS from blood vessels into tissues

- Chemotaxis: Chemically directed movement of PMNS to needed area

Steps of Phagocytosis

1. Attachment: organism to phagocyte; PMNS have various receptors (Fc portion of IgG1, IgG2 and C3b of complement) - opsonin

2. Ingestion: surrounds attached particles; enclosed in phagosome -> fuses with lysosomes -> degranulation

3. Killing: increased metabolic activity in PMNS (respiratory burst); increase glycolysis and acid and hydrogen peroxide production; release enzymes~ bactericidal effect

* Not effective for intracellular pathogens

Mechanisms to Resist Phagocytosis

- Capsules

- Prevent fusion of phago-lysosome

- Leukocidins

- Inhibit chemotaxis

Innate Immunity

- Natural, nonspecific immunity

** Physical barriers, chemical barriers, Phagocytosis

Adaptive Immunity

- Specific

- Humoral -> B lymphocytes

- Cell-mediated -> T lymphocytes

-Types of acquired immunity: passive acquired where mom passes antibodies to baby. active acquired is where your own body has a response to a specific antigen like directly (disease) or vaccination

Humoral Immunity

- Initiated by antibodies or immunoglobulins

- 5 classes of antibodies: IgG, IgM, IgA, IgD, IgE

IgG

70-75%, crosses placenta

IgM

10-15%, first antibody produced, largest antibody

IgA

15-20%, secreted by mucus membranes

IgD

<1%, signals B cell receptors

IgE

<1%, clearance of parasites and allergies

Primary antibody response

- IgM

- Peak in 1-3 weeks then decline

- Gradually changes to IgG or IgA

Secondary (anamnestic immune response)

Rapid increase in IgG and IgM plays minor role

Lab Screening for Primary vs Secondary Immune Response

- IgM: current or recent

- IgG: previous

Cell-Mediated Immunity

- Protects against intracellular pathogens

- T-helper cells (CD4+) Lymphokines -> activate macrophaes and other phagocytes

- Cytotoxic T cells (CD8+) Kill infected cells

Patient Sign Definition

Objective evidence of disease from an observer

Patient Symptom Definition

Subjective of disease sensed by patient

Laboratory Signs of Infection

- Elevated WBC:

~Bacterial - increased PMNS (neutrophils) left shift possible

~Viral Increased lymphocytes

~Elevated ESR

~Increased C-reactive protein

~High lactic acid level may indicate sepsis

-Septicemia: bacteria multiplying in blood

Prokaryotic Cell Structure

- No membrane bound nucleus

- Ribosomes (RNA and protein) found free in cytoplasm and attached to cytoplasmic membrane

- 70S ribosomes complex -> disassociate into 50S and 30S

- Svedberg (S) units are sedimentation rates during high-speed centrifugation

- Values NOT additive, because they bind, they lose surface area

- Endospores: survival, highly resistant, will not stain

Cell Envelope Structures

Membrane and structures that surround the cytoplasm

- Bacteria: plasma membrane and cell wall

Some bacterial species produce capsules and slime layers

Plasma Membrane (Cell Membrane)

- Phospholipid bilayer: Embedded proteins

- Made up of phospholipids and proteins: No sterols

- Functions as an osmotic barrier

Cell Wall has 4 categories

1. Gram positive cell wall

2. Gram negative cell wall

3. Acid-fast cell wall

4. Absence of cell wall

Capsule

Some pathogenic bacteria produce a surface polymer that acts as a protective covering

Gram Positive Cell Wall

- One major layer

- Composed of peptidoglycan, teichoic acid, lipoteichoic acid, mycolic acis and polysaccharides

- Thick (20-80nm)

- No outer membrane

- Narrow periplasmic space: jelly like material between peptidoglycan and cytoplasmic membrane

- Penetrable to molecules

Peptidoglycan

Also known as murein

Polymer that has interlocking chains of two amino sugars

- N-acetylglucosamine (NAG)

- N-acetylmuramic acid (NAM) + pentapeptide (5 amino acids)

- Together for a peptidoglycan monomer

Gram Positive Cell Wall Functions

Peptidoglycan: prevent osmotic lysis

Teichoic acid: cell wall strength

Surface proteins: vary in different bacteria

- Function as enzymes

- Function as adhesions

Periplasm: nutrient breakdown

Gram Negative Cell Wall

- Two major layers

- Composed of Lipopolysaccharide (LPS), Lipoprotein, Peptidoglycan, Porin Proteins

- Tinner (8-11 nm)

- Contains an outer membrane (unique to g=)

- Large periplasmic space

- Less penetrable to molecules

Gram Negative Cell Wall Functions

Peptidoglycan: prevent osmotic lysis

Outermembrane: semipermeable -> retains certain enzymes, prevents certain toxic substances from entering (penicillin G, lysozyme)

LPS: add strength to outer membrane

Surface proteins: vary in different bacteria

- Function as enzymes

- Function as adhesions

Periplasm: nutrient breakdown

Acid-Fast Cell Wall

Waxy layer of glycolipids and fatty acids

- Mycolic acid: strongly hydrophobic

Organisms might show up lightly gram positive

Acid-fast stain

- Carbolfuchsin and acid-alcohol decolorizer; Mycobacterium spp. Nocardia spp. and other bacteria decolorize with acid-alcohol

Absence of a Cell Wall

Plasma membrane has sterols

Lack of rigid cell wall

- Pleomorphic variability in shape

Henera Mycoplasma and Ureaplasma

Surface Polymers

Capsule and Serologic typing

Surface Polymers: Capsule

Polysaccharides or polypeptides

Help bacteria evade phagocytosis

Does not stain-> appears "halo" like

Surface Polymers: Serologic typing

Remove capsule by boiling and detects somatic antigens

Cell Appendages

Flagella, Pili and Fimbriae