Introduction to Microbiology & Infectious Diseases Flashcards
What is mycrobiology?
study of microscopic organisms
What are the 3 domains? What are the kingdoms and their role
bacteria, archaea, eukarya.
bacteria - many species are important in human health and disease
archaea - no known role in human disease, several species - “normal flora”
protista - includes protozoan (single celled) parasites
plantate
fungi - Important cause of human disease, especially in ICH (immune compromised host)
animalia - Includes multi cellular parasites – ‘worms’
Bacteria, protista, fungi, animalia are the four causing disease.
What are communicable diseases, zoonotic diseases, and opportunistic infections?
Communicable diseases – diseases passed between people through close proximity, social or intimate contact
Zoonotic diseases – diseases transmitted from animals to man
Opportunistic infections – infections caused by micro-organisms that require impaired host defenses to establish infection
How do you name all living things?
All living things have two names
Generic (genus name)
Specific (species name)
Staphylococcus aureus
S. aureus = proper abbreviated name (italicized)
Staph. aureus = common abbreviation ((italicized)
Proper scientific names are italicized.
Staphylococcus sp. = an unnamed species in the genus Staphylococcus
Stapylococcus spp. = multiple species of the genus (italicized) Staphylococcus
Staphylococci – generic term referring to the genus, not italicized
Why do names change for micro-organisms?
Molecular biology continues to challenge our understanding of the relationship between organisms – as new information becomes available, we discover that many organisms have been incorrectly assigned to a genus, thus requiring reassignment and renaming.
What classifies a bacteria?
Single celled organisms – prokaryotes
Contain both DNA and RNA
Usually have a cell wall
May have a capsule
Do NOT have:
A nucleus
Mitochondria
Other membrane bound organelles
What is an atypical bacteria?
Mycoplasma Lack a cell wall Chlamydia Lack peptidoglycan in cell wall Obligate intracellular parasite, require ATP from host Rickettsia Obligate intracellular parasites, require ATP from host Most transmitted by arthropods
What are the characteristics of fungi?
Possess both DNA and RNA
Have a defined nucleus and cell wall
Contain membrane bound organelles
All fungi are capable of asexual reproduction
Most fungi are also capable of sexual reproduction
Fungi capable of both asexual and sexual reproduction have different names for the asexual and sexual states.
What are the two major types of fungi?
Yeast – small, round, unicellular
Mold – grows in the form of filaments (hyphae) that form a tangled mass (mycelium). Often referred to as filamentous fungi - “fuzzies”
What classifies viruses?
Small organisms containing either DNA or RNA but not both
Capable of growth and reproduction ONLY when inside another cell
Lack systematic nomenclature
Viruses causing human disease are commonly named after the disease they cause OR the locality in which they were first isolated.
Measles virus, Mumps virus
West Nile virus, Ebola virus
Classification
DNA vs RNA
Single or double stranded or segmented nucleic acid
ss DNA viruses ds DNA viruses ss RNA viruses ds RNA viruses segmented RNA viruses
What are prions?
A non-living infectious agent, comprised only of protein
Transmit a misfolded protein state – abnormal protein induces normal proteins to covert to the misfolded state
Newly misfolded proteins convert more proteins into the prion state…and so on
Altered proteins are highly stable and accumulate causing tissue damage, dysfunction and cell death
What are parasites?
Organisms adapted to life in (endoparasites) or on (ectoparasites) higher organisms.
Includes single and multicellular (including macroscopic) organisms
Often have complex life cycles
Protozoans – single celled, eukaryotes
Helminths – multicellular organisms, micro or macroscopic (‘worms’)
Roundworms, tapeworms and flukes
How are bacteria organized?
How do we organize bacteria? Shape and organization Oxygen requirements Spore formation Staining patterns - these first ones are simple lab tests Metabolic processes Immunologic features Genetics these last ones are more complicated testing
What are the shapes?
coccus - round, diplococci are two round together, streptococci are multiple in a chain, staphylococci are triangle bunches of forms together.
bacilli - coccobacilus are oval, bacilus is oval and elongated like a rectangle with rounded edges,
vibrio - looks like a bean
what are the oxygen requirements?
Strict aerobes – require normal atmospheric levels of oxygen to grow
Facultative – grow in both aerobic and anaerobic environments. Use either aerobic or anaerobic metabolism (fermentation or anaerobic respiration) to generate energy. Anaerobic energy generation is less efficient than aerobic metabolism.
Aerotolerant – use only fermentative metabolism but are not killed in the presence of oxygen
Microaerophilic – require oxygen tensions to grow but at levels less than 21%; often require increased levels of CO2 (capnophilic).
Strict anaerobes – no growth in the presence of oxygen; some species are killed by oxygen.
Thioglycollate broth - test used, Tube1 – no growth at top – anaerobic
Tube 2 – only growth at top – aerobic
Tube 3 - Uniform growth throughout – aerotolerant
Tube 4 – growth throughout but best at top - facultative
Tube 5 – best growth near top of tube but not right at surface - Microaerophilic
What about spore formation? why do they do spores and what’s so bad about them?
The formation of spores is an important feature of some species of bacteria. Spore formation is typically a feature of gram positive bacilli.
Generalization: Spores are not formed by:
Medically important cocci
Medically important gram negatives
Aerobic spore forming bacilli
Bacillus spp: anthrax, food poisoning
Anerobic spore forming bacilli
Clostridium spp: tetanus, botulism, C. difficile
Spores help organisms survive times of adversity.
Lack of nutrients
Lack of moisture
Lack or excess of oxygen
Exposure to heat, radiation, toxic chemicals
Spores can survive for very long periods of time – perhaps thousands of years!
Responsible for disease transmission from food, environment, or other individuals.
Anthrax, Tetanus
Clostridum difficile infection
Responsible for disease relapse despite treatment.
Clostridium difficile relapses
What about bacterial staining?
Stains are chemical dyes that interact with molecules in the cell wall of the organism
Different types of bacteria take up stain differently (or not at all) based on structure.
Staining features help with rapid identification
General stains – general purpose: Identify presence and morphology of bacteria
Differential stains – different organisms take up stain differently: categorization of organisms based on staining characteristics
Special stains
Stains to identify specific bacterial features
Stains used for hard to visualize organisms
What are the general stains and differential stains?
General (Simple) stains – methylene blue
Differential stains
Gram stain: differentiates most bacteria into gram positive or gram negative based on cell wall structure
Acid Fast Stains: used for staining Mycobacteria and Nocardia - waxy material in cell walls repels gram stain
What is gram stain?
Differential stain – gram positive, gram negative, gram variable
Why is the gram stain so important in microbiology?
Crystal violet is retained by gram positive cell walls.
Crystal violet is NOT retained by gram negative cell walls. Safranin (pink) is used as a counterstain to visualize gram negatives.
You fix, then use crystal violet, the gram positive will retain this, you treat them with iodine and there will be decolorization with this, the negative will turn back clear and the gram positive will stay purple. Then you counter stain using sfranin (pink) which will then make the gram negative appear pink while the positive remains pruple.
Staining characteristics are based on major differences in cell wall structure – these characteristics correlate with other important features:
Ecology
Antibiotic susceptibility
Gram positive - have thick cell wall, no outer envelope
Gram negative have a thinner cell wall with outer envelope, that’s why the gram negative repels the dye, because it has that outer envelope.
How many organisms do you need to see gram stain?
In order to see organisms on a gram stain, there must be at least 104 to 105 organisms per ml.
Gram staining will also demonstrate human cells – this is critically important when staining specimens from NON STERILE sites where bacterial are expected to be present.
We can detect the presence of an inflammatory response (numerous pus cells – PMNs) which is indicative of true infection rather than contamination or colonization.
What’s a pathogen, infection, and disease?
A few more definitions
Pathogen: a micro-organism that has potential to cause disease
Infection: invasion and multiplication of pathogenic micro-organisms
Disease: infection causes damage to host tissues or function
NOTE: infection does not always = symptomatic disease
What’s pathogenicity, virulence, and virulence factors?
Pathogenicity
The ability of an infectious agent to cause disease
i.e. can this organism make you sick?
Virulence
Quantitative ability of an agent to cause disease
i.e. how easily can it make you sick / how sick can it make you?
Virulence factors
Features of the organism that confer virulence.
What is a biofilm?
A microbial community adherent to a surface
Bacteria adhere to a surface and secrete a gel like matrix comprised of protein, polysaccharides and DNA
Matrix entraps other cells
With growth of the microbial community
Signal molecules allow communication between individual organisms
Channels develop to transport nutrients and waste
Small portions may break off and migrate to establish a new community
Problems:
Poor antibiotic penetration into biofilm
Protects bacteria from host defenses
Obstruction of catheters
What sort of environment do microbes live in?
Air
Viruses, fungi and bacteria can cause respiratory illnesses
Water
Surfaces waters can be heavily contaminated with bacteria from soil run-off, sewage, animals
Natural water organisms: Pseudomonas
Soil organisms: Gram negatives
Intestinal flora (man and animals)
Salt water: vibrios and other ‘halophiles’ (salt tolerant organisms)
Soil – contains high levels of bacteria, as well as smaller numbers of fungi and protozoa. High numbers of anaerobic organisms in soil.
Pathogenic organisms found in soil are responsible for infections following injuries.
Soil (and food grown in soil) can be contaminated by intestinal flora of animals or man when excrement is used as fertilizer.
Where do microbial entities live in and on us?
Our indigenous microbial flora (AKA microbiota) is the most important source of micro-organisms causing human disease.
All body surfaces with contact with the external environment have resident microbial flora.
Composition of resident flora is determined by local conditions: temperature, pH, nutrient availability, oxygen tension, cell surface receptors etc.
What’s going on on the skin of us?
Microbial numbers are variable Common isolates: Coagulase negative Staphylococci, coryneform bacteria / diphtheroids, micrococci, proprionibacteria (Gram positive cocci and bacilli) Staphylococcus aureus Higher levels of bacterial growth are found in: Moist areas Around hair shafts Apocrine glands – gram negatives Damaged skin: excema, psoriasis Occluded skin
What are the microbes like in our respiratory tract?
Extensive bacterial flora in the upper resp tract.
Mostly gram positive cocci in healthy people.
Fibronectin on the cell surfaces provides binding sites for gram positive cocci and allows them to outcompete gram negatives in healthy people.
With illness increased salivary proteases, fibronectin is cleaved off and gram negatives move in replacing the gram positive cocci.
Neisseria, Moraxella, Strep pneumoniae etc. can colonize the nasopharynx for periods of time and may result in systemic infection, or may be cleared by the host defenses.
Few microorganisms below the larynx
In normal adults, airways below the main bronchi should be free of micro-organisms.
Individuals with lung damage from smoking, CF, bronchiectasis etc. will have:
Bacterial colonization in deeper airways
Greater variety of organisms and pathogens
Hemophilus
Staph aureus
Pseudomonas
Burkholderia / Stenotrophomonas.
What is the microorganism like in the gastrointestinal area?
Stomach: low pH results in few organisms
Reduced gastric acid from disease or drugs results in increased colonization
Small intestine: high motility limits microbial colonization to ~103-104 organisms per ml
Impaired motility increased colonization
Large intestine: slow motility, anaerobic conditions result in high bacterial numbers.
Anaerobe to facultative ratio = 10 to 1.
Anaerobes: Bacteroides, Clostridia, anaerobic streptococci
Facultative enteric gram negative bacilli
Enterococci, Yeast
Bacteroides fragilis: 109-1010/ ml; E coli: 105-106/ml
what’s the flora like in the genital tract?
Vagina – flora varies with age
Child: Enteric GNB, staphylococci, yeast
At puberty, estrogen induces glycogen production by vaginal epithelial cells: promotes growth of lactobacilli
Lactobacilli metabolize glycogen to lactic acid which produces a low pH environment that inhibits growth of many other species.
Group B streptococci
Menopause – flora reverts to predominance of Gram negative enteric bacilli
Why is normal flora important
‘Normal flora’ can cause disease….
When normal host defenses (barriers) are breached and it ends up where it is not meant to be.
Colonic flora – urinary tract infections
Colonic flora – peritonitis and intra-abdominal abscesses
Skin flora – wound infections, boils, abscesses
Oral flora - endocarditis
Pathogens may colonize non sterile sites and from there invade causing diseases.
Meningitis – typical bacterial pathogens first colonize nasopharynx
Pneumonia – typical pathogens may colonize nasopharynx
MRSA may colonize skin before giving rise to boils and soft tissue abscesses.
Group A strep colonizes skin before causing erysipelas.
Disruption of normal flora and replacement with other organisms may cause disease
Bacterial vaginosis
Clostridium difficile diarrhea
How do infections begin?
Where do the bugs come from?
Infection arising from bacterial flora
Infections arising from external sources
Other people or animals, environment, food, water etc.
How organism get into the body?
Direct contact – skin to skin, mucosa to skin or mucosa.
Indirect contact – organisms are carried on ‘fomites’ to the body
Ingestion – from food or water, accidental ingestion (hands to mouth)
Transcutaneous
Inoculation of organisms across normal skin
Arthropod vectors
Inoculation of organism across damaged skin
Iatrogenic – surgical wounds, injections
What are the vectors of arthropods and what is the vertical transmission often?
Vectors Typically arthropods Pathogen can be passively carried or can complete part of its life cycle in the arthropod Vertical transmission Mother to child In utero During delivery Via breast milk
How does inhalation of pathogens occur?
Droplet – inhalation of droplets
Large particles which travel only short distances
Deposited in upper airways or large bronchi
Airborne – inhalation of droplet nuclei
Small airborne particles, can remain airborne for long periods and travel large distances
Can be inhaled all the way to alveoli
Most particles produced when sneezing, then coughing, then talking but by far the most sneezing, over 100,000 compared to just over 1000 coughing and just under 100 talking.
most colds passed with sneezing
How do bugs cause disease
Penetration of normal anatomic barriers
Healthy skin and mucosa form effective barriers to most pathogens.
Damage to normal defense mechanisms
Skin trauma or disease
Mucosal ulcers, damage or inflammation
Ineffective mucociliary function – impaired cilia activity, abnormal mucous production
Impaired gag and cough reflex
Impaired immune function – humoral and cellular immunity
Colonization often precedes infection
Compromised normal flora increases likelihood of colonization by pathogens
What is adhesion?
Most infections begin with adhesion of a microbe to a specific epithelial surface
Non specific interactions: hydrophobic / lipophilic mediated adhesion, capsules, slime layers, biofilm
Specific interactions: adhesin - receptor
Group A strep: fimbriae contain M protein and lipoteichoic acid which binds to fibronectin on epithelial cell surfaces.
Staph aureus: fibronectin binding protein binds to fibronectin
E coli is a common cause of UTI – but only some strains cause UTI (uropathogenic strains) - P fimbriae bind to galactose containing glycolipids and glycoproteins on epithelial cells
Measles virus: Hemagglutinin protein binds to CD46
After adherence, invasion and spread or remain on epithelial surface (symptoms caused by elaboration of toxins, or local effects on cells. )
What are the different types of invasion of epithelial surfaces?
What happens after invasion?
Transcytosis – across superficial epithelium to subepithelial space
Phagocytosis by host cells with intracellular survival
Induced engulfment by non phagocytic cells (triggers local rearrangement of host cell cytoskeleton)
Organisms remain locally in area of penetration
Spread into and via lymphatics
Spread hematogenously
Spread as hitchhikers in professional macrophages
How are tissues injured with disease?
Tissue injury
Direct invasion of cells cell damage, death
Induction of apoptosis / necrosis
Induction of damaging host immune responses
Autoimmune responses – microbial antigens cross react with host proteins: e.g. Rheumatic fever: cross reactions between endocardium and synovial membrane and Group A strep cell wall antigens.
Hypersensitivity reactions
Granuloma formation
Toxic shock syndrome
Sepsis
What are exotoxins?
toxins released from bacterial cells
Enzymes that damage and kill cells (disruption of neutrophils releases enzymes that themselves cause tissue damage)
Enzymes that degrade extracellular matrix (promoting bacterial growth and spread)
Toxins that disrupt cell function / intracellular signalling pathways
Superantigens – activate massive numbers of T cells
Bacterial enzymes (exotoxins) Collagenase – breaks down collagen, disrupts connective tissue and promotes spread of infection. Coagulase – works with plasma factors to coagulate plasma. Aids in development of fibrous walls around sites of Staphylococcal infections which protects bacteria from host defenses and walls of the infection resulting in focal abscess formation.
Hyaluronidases – enzymes that hydrolyse hyaluronic acid which is important to the integrity of connective tissue. Aids in the spread of infection through tissues.
Streptokinase – (fibrinolysin) – dissolves coagulated plasma, thought to aid in spread of infection.
Hemolysin – dissolves red blood cells
Streptolysin O – causes hemolysis
What are endotoxins?
Toxic components of the bacterial cell wall
Lipopolysaccharide is the classic endotoxin found in gram negative cell walls
Peptidoglycan also has endotoxin properties
Endotoxins non specifically trigger inflammatory reactions
Cytokine release
Activation of alternate complement pathway
Leading to: fever, hypotension, shock, DIC and death
What are the signs of infection, with some plus or minuses?
Local features of infection 4 cardinal signs of inflammation: Erythema / redness (rubor) Swelling (tumor) Tenderness (dolor) Heat (calor)
Plus or minus:
Loss of function
Drainage of pus
Other symptoms specific to tissue involved
What are systemic features of infection as well as non specific symptoms?
Systemic features of infection
Fever – increased body temperature
May be preceded by chills / rigors
Tachycardia – increased pulse rate
Temperature and pulse usually increase in parallel
Certain pathogens may not increase the pulse to the expected degree (Pulse – temperature deficit)
Non specific symptoms: myalgias (muscle aches), arthralgias (joint pain), headaches, nausea, vomiting, lethargy, malaise, anorexia
What are some features suggesting sever infection? (sepsis/septic shock)
Tachypnea and respiratory alkalosis – rapid breathing, blows off excess CO2
Hypotension
Altered level of consciousness
End organ damage – renal failure, liver failure
What are some inflammatory markers?
Inflammatory markers
In acute infection metabolism switches from an anabolic (protein building) state to a catabolic (protein breakdown) state. Structural proteins are converted to acute phase reactants which have roles in host defense, inflammation or anti-inflammation
C reactive protein
Fibrinogen and other coagulation proteins
Ferritin
Complement proteins
Etc.
How do we treat infections?
- Supportive care:
Fluid replacement
Drugs to maintain blood pressure - Surgical care:
Address the source of infection: debride, drain and repair - Antimicrobial agents: antibiotics, antifungals, antivirals etc.
- Adjunctive therapies:
Intravenous immunoglobulin
Hyperbaric oxygen therapy
Immunomodulatory therapy - Preventative measures: infection control and public health considerations
Infection control precautions
Tracing and treatment of contacts where appropriate
What are the basic principles of antimicrobial treatment?
- Empiric or directed therapy?
- Choice of antibiotic
Disease / pathogen considerations
Patient considerations
What is empiric vs directed therapy?
- Empiric therapy
Exact organism is unknown (but a considered judgment can often be made as the potential organisms involved)
Therapy often must cover a variety of pathogens (broad therapy)
Empiric therapy is important in severe infections as delay results in increased mortality. - Directed therapy
The organism is known
The antibiotic susceptibility may be known
Therapy should generally be targeted (narrowed).
What makes an antibiotic appropriate or not?
Terms like “strong”, “potent” and “weak” are not really relevant
More appropriate is whether or not:
The antibiotic is from a class that will be effective against the pathogen (spectrum of activity)
The specific organism will respond susceptible to the antibiotic (susceptibility)
The antibiotic can get to the site of infection in sufficient concentrations to work (pharmacokinetics: absorbtion, tissue distribution etc.)
What are the spectrums of activity for antibiotics?
Antibiotic therapy can be broad spectrum or narrow spectrum
Broad spectrum means that the antibiotic or combination of antibiotics used covers a wide range of pathogens.
Broad spectrum coverage cause more problems with resistance and suppression of normal flora.
Broad spectrum is desirable when:
We don’t know the pathogen and a wide range of pathogens may be involved.
The infection is polymicrobial.
Narrow spectrum means that only a limited range of pathogens is covered.
Narrow spectrum is desirable whenever broad spectrum therapy is not required (narrow spectrum should be the default option)
What can help with determining empric vs directed therapy?
Appropriate cultures should be taken prior to initiation of empiric therapy so that the patient can later be converted to directed therapy.
Tissue samples are preferable to swabs.
Open biopsies are more reliable than percutaneous biopsies.
In patients with suspected, non life threatening infections it is generally ok to wait for initial results to be sure a satisfactory sample has been obtained.
What is bacteriostatic vs bactericidal agents?when are each indicated?
Bactericidal vs bacteriostatic activity
Bacteriostatic agents stop growth but do not kill. Depend on host immune response to assist in control of infection.
Bactericidal agents kill organisms.
Bactericidal therapy is desirable when:
The infection involves critical tissues (CNS, vegetations) or very serious infections.
Bacteriostatic therapy is desirable when:
Killing organisms may release toxins.
Generally we should AVOID combining a static and a cidal agent.
What is pharmokinetics?
Pharmocokinetics
Will the antibiotic get to the site of infection in adequate levels to be effective?
Some tissues are more challenging: brain / cerebrospinal fluid, bone, vegetations
The size and polarity of antibiotics affects how well they are distributed in tissues
Includes things such as absorption, tissue distribution, metabolism and excretion
What are some patient factors in your choice of antibiotics?
Toxicity
Underlying disease may make certain antibiotic choices less desirable
Chronic renal failure – avoid nephrotoxic agents
Route
Is the patient able to take oral medications?
Are we confident oral medications will be retained an absorbed?
Administration
Number of doses per day
Adherence decreases with the number of doses required per day
Allergy and intolerances
Certain drug classes may need to be avoided because of allergy
Intolerances may be able to be overcome with supportive care
what happens with antibiotic overuse/misuse?
Antibiotics are NOT helpful in viral infections
Overuse of antibiotics has many adverse outcomes
Development and spread of antibiotic resistance is directly related to antibiotic use.
Infections become more challenging and costly to treat
Allergic reactions
Intolerance
Toxicity
Altered normal flora – overgrowth with pathogens
What is the key principle for antibiotic use?
Use the narrowest spectrum agent possible for the shortest duration appropriate to resolve the infection.
