Infectious Disease Flashcards
(185 cards)
1
Q
Shapes of Bacteria: rods
A
Bacillus
Salmonella tiphimurium
Bacillus anthracis
2
Q
Shapes of bacteria: spheres
A
Coccus (sphere)
Ex: Streptococcus pneumoniae
Coccobacillus (between rod/sphere)
Ex: Yersinia pestis
3
Q
Shapes of bacteria: others
A
Spirillum (rigid spirals)
Spirochete (undulating spirals)
Vibrio (comma shape)
Vibrio cholerae
4
Q
Bacterial arrangements: cocci
A
Single
Diplococcus (pair)
Ex. Streptococcus pneumoniae, neisseria meningitidis
Streptococcus (chain)
Ex. Streptococcus pneumoniaeNeisseria meningitidis
Tetrad
Ex. Micrococcus luteus
Staphylococcus
Ex. Staphylococcus aureus
5
Q
Bacterial staining
A
Gram-positive: stain blue
Gram-negative: stain red
Specialized stains:
Most useful is acid-fast stain
6
Q
Bacterial Reproduction
A
Reproduce by binary fission
One circular chromosome per cell which doubles and the bacteria then splits to produce 2 bacteria
7
Q
Bacteria: nucleoid
A
DNA has a large amount of DNA that must be packed into the bacteria’s small body without the presence of a nucleus
Some unknown protein helps to condense DNA w/in bacteria
8
Q
Bacterial cytoskeleton
A
Have cytoskeletal components similar to eukaryotes and some unique proteins
MreB (homolog to actin) FtsZ (homolog to tubulin) Crescentin (Homolg to Intermediate filaments) MinD/ParA RhlB / RNase E
This is important for antimicrobial design (create a drug that target these structural proteins)
9
Q
Bacterial exoskeleton
A
Normally referred to as the murein sacculus
Other names: peptidoglycan, cell wall, or rigid layer
Function:
Giant molecule that envelopes the bacteria and protects from stress
Importance:
Environment is generally hypertonic, without exoskeleton the cell will swell –> lysis
10
Q
Common anti-microbial targets of bacterial exoskeleton
A
Murein synthesis (penicillin) Ribosomal proteins (gentamycin) DNA gyrase (ciprofloxacin)
11
Q
Only bacteria that doesn’t have an exoskeleton
A
Mycoplasma:
Do not have necessary proteins to form the exoskeleton and are therefore amorphous
12
Q
Gram-positive bacteria
A
Have a much thicker murein sacculus (stain gets trapped in this layer)
Contain specific polysaccharides in envelope
Teichoic acids polysaccharide:
covalently linked to the peptidoglycan layer or to the lipids of the cytoplasmic membrane
Difference between gram positive bacteria is based on the antigenicity of the teichoic acid **
Contain wall associated exoproteins:
Varies types
Function as a type-specific antigencity and virulence (important for host defense invasion)
13
Q
Levels of bacterial classification
A
Morphology, Metabolism, Antigenicity, Genetics
14
Q
Bacterial classification: Morphology
A
Staining: gram stain positive vs. negative
Then,
Shape: coccus, bacillus, spirillum, coccobacillus, spirochete, vibrio
15
Q
Bacterial classification: Metabolism
A
Anaerobic (fermentation) vs. aerobic (Respiration)
Can be facultative or obligate
Specific nutrients (e.g. fermenter of specific carbohydrates)
Production of certain metabolic products (e.g. acid, alcohols)
Specific enzymes (e.g. catalase
16
Q
Bacterial classification: Antigenicity
A
Use of antibodies that are particular to certain bacteria
17
Q
Bacterial classification: Genetics
A
Most commonly we use ribosomal DNA to look for highly conserved sequences particular to a family or genus
18
Q
Virulence factors
A
Genetic traits that enhance the ability of bacteria to cause disease
19
Q
Pathogenicity island
A
Large chromosomal regions that contain sets of genes that encode for virulence factors
20
Q
Possible outcomes of new exposure
A
Transient colonization & clearance
Permanent Colonization
Disease
21
Q
Strict Pathogens
A
Virulent bacteria that promote their growth at the expense of their host
Ex: mycobacterium TB
Neisseria gonorrhoeae
Plasmodium spp. (Malaria)
Rabies virus
22
Q
Opportunistic bacteria
A
an organism capable of infecting only when host defense are breached or compromised (some commensals are opportunistic)
Ex. Staph aureus
E. coli
Pseudomonas aeruginosa
Candida albicans
23
Q
Commensal bacteria
A
Bacteria that does not harm nor benefit their host
24
Q
Natural defense mechanisms for bacterial entry
A
skin, mucus, ciliated epithelium, and antibacterial secretions
25
Common ports of entry for bacteria
Ingestion, inhalation, trauma, needle stick, arthropod, & sexual transmission
26
Examples of bacteria that enter via ingestion
Salmonella spp, Shigella app. , Yersinia enterocolitica
enterotoxigenic E. coli, Vibrio spp. ,camplyobacter spp.
Clostridium botulinum, Bacillus cereus, Listeria spp, Brucella spp
27
Examples of bacteria that enter via inhalation
Mycobacterium spp. , Nocardia spp. , mycoplasma pneumoniae
Legionella spp., Bordetella, Chlamydophila psittaci
Chlamydophila pneumoniae, streptococcus spp.
28
Examples of bacteria that enter via trauma
Clostridium tetani
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Examples of bacteria that enter via needlestick
Staphylococcus aureus
Pseudomonas spp.
30
Examples of bacteria that enter via arthropod bites
Rickettsia, ehrlichia, coxiella
Francisella Borrelia spp
Yersinia pestis
31
Examples of bacteria that enter via sexual transmission
Neisseria gonorrhoeae
Chlamydia trachomatis
Treponema pallidum
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Bacterial colonization
Bacteria colonize if environment is suitable
If they are invading a normally sterile environment, this environment must be compromised in some fashion
Ex: In CF, the function of the ciliary mucoepithelial is comprosed allowing for pathogens to enter previously sterile locations
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Gram negative
Much thiner murein than gram positive (doesn't stain purple b/c the dye doesn't get trapped, must use safranin to get red color)
Have outer semi-permeable membrane outside the murein sacculus --> aqueous space is created between murein and outer membrane called periplasmic space
Lipoprotein: function to stabile outer membrane to murein
34
Periplasmic space
Unique to gram negative bacteria
Contain periplasmic proteins:
Proteins associated w/ murein: biosynthetic enzymes that create murein or immotile murein
Soluble proteins: carry nutrients across periplasmic space to the cytoplasm
Digestive enzymes: Larger molecules that enter the periplasmic must be digested into smaller ones to enter cytoplasm
35
Gram-negative bacteria: outer membrane
Unique to gram-negative bacteria
Specialized, asymmetric membrane, containing:
Lipopolysaccharide (all gram negative have this)
Outer membrane proteins (function as porins & adhesins)
Phospholipids is exclusively in inner leaflet and the outer leaflet is mostly LPS
Functions to:
Provide resistance to detergents & some antibiotics (you can use this to separate gram negative from gram positive)
36
Gram-negative bacteria: LPS function
Contribute to the virulence of gram negative bacteria in 2 ways:
Gram negative endotoxin is found exclusively in the lipid A portion
O-antigen:
Antigen properties help to differentiate between different subtypes of bacteria
Enhances virulence b/c it acts as an anti-phagocytic factor (its covers the enter cell making it difficult to phagocytose
37
Atypical cell walls
Some bacteria lack typical cell wall, these contain a waxy lipid (mycolic acid) bound to a thin layer of peptidoglycan
Provide for low permeability & high degree of resistance to chemicals
Stained w/ acid-fast stain
Ex: mycobacterium tuberculosis
38
Exoproteins
Found in both gram positive and gram negative bacteria
Made by membrane associated ribosome
Some remain w/ cell, others are released into the environment
Some of these proteins have a toxic enzyme (referred to as exotoxins)
Gram-negative bacteria have special mechanism to traverse both membrane to release exoproteins
39
Pili
Optional protein appendages
Function:
Some have specialized molecules that allow for adherence to host cell
Injection of bacterial protein into host cell
Virulence factor
40
Flagellum
Optional protein appendages
Function:
Motility
Ability to sense environment, helps to propel bacteria toward nutrients and away from toxins
H-antigen helps to identify subtypes of flagellated bacteria
41
Flagellar arrangements: nomenclature
Monotrichous: one flagellum found at the pole
Lophotrichous: when many flagella are found at the pole
Amphitrichous: various flagella found at both poles
Peritrichous: when flagella are found all over bacteria
42
Glycocalyx
Optional bacterial surface coating
Slime: if it is loosely organized & attached
Capsule: if highly organized, tightly attached
Usually made of polysaccharides
Anti-phagocytic (determines virulence)
Antigenic (antibody target)
43
Microbial differentiation
```
Reversible changes in:
Structure of surface macromolecules
Organelle structure (like pilli)
cell structure & organization (sporulation)
```
44
Sporulation
In normal environment, vegetative cell will undergo normal growth and multiplication
In nutrient deprivation, vegetative cell enters sporulation cycle
The cell structure changes to form endospore --> mother cell will lysis and release spore (which can live for many years)
If nutrients are introduced, then the spore will germinate and enter normal vegetative growth
45
Bacterial spore
Structural changes result in the formation of the spore coat (made from proteins) which protect the bacteria and importantly the chromosomal DNA
Coat protects against:
Drying, heat, chemicals, UV light, & mechanical stress
46
Pilus: formation
Gram-negative: on outer membrane there is a shaft (made of non covalent protein-protein interactions; arranged by chaperone/usher pathway
Gram-positive: The proteins are cross-linked and joined by covalent bond; organized by sortase enzyme
47
Chaperone/usher pathway
Pilins are exported to the periplasmic space
Chaperone proteins bind to pilins --> deliver it to usher proteins (outer membrane transmembrane protein)
Usher helps forms tip then the pilins brought by chaperone --> are assembled into a polymer in a specific order
48
Type III secretion
Resembles a molecular injection
Key factor in gram-negative pathogens
Expression/activity is highly regulated
Uses:
Facilitate uptake & invasion
Promote intracellular survival & replication
Lead to apoptotic death of cell
Ex: Shigella (to enter cell) Salmonella (promotion of uptake), E. coli (creates a docking system)
49
Pilus: important ones to remember
P pilli
assembly proteins (PapD & PapC)
adhesin (PapG)
Pilli that causes cystitis & pyelonephritis
Curli pili
assembly proteins (CsgBEG)
adhesin (CsgA)
Pilli that causes sepsis
50
Obligate intracellular pathogens
Chlamydia
| Rickettsia
51
Facultative Intracellular Pathogens
```
Listeria
Mycobacteria
Shigella
Salmonella
EP E. Coli
UP E. Coli
```
52
Exotoxins: types
```
Cytolytic: membrane disrupting toxins
alpha toxin (phospholipase C): degrades sphingomyelin & other phospholipids
```
Hemolysins: insert & disrupt erythrocytes
Pore-forming toxins: promote leakage of ions & water --> disrupt cell function, can lead to lysis (e.g. streptolysin O)
53
Exotoxins: structure
Mostly dimeric w/ an A & B subgroup
B subgroup: binds to cell surface receptor
A subgroup: transferred into the cell --> inducing toxic effect
Common targets include: ribosomes, transport proteins, & intracellular signaling
54
Superantigens
Special toxin that activate T cells by binding to both T cell receptor & MHC II on APC in the absence of an antigen
Results in a large release of interleukins (cytokine storm) including IL-1, IL-2, & TNF --> leading to dangerous autoimmune-like responses
Ex:
toxic shock syndrome toxin of Staphylococcus aureus, staphylococcal enterotoxins
erythrogenic A/C of Streptococcus pyogenes
55
Recognition & response of bacterial infection
Bacterial cell wall components acts as a signal of infection
Specifically, bacteria have PAMPs (pathogen-associated molecular patterns) that bind to TLR (toll-like receptor) --> production of cytokines --> immune response
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Gram-positive bacterial infection: endotoxin-like response
Peptidoglycan & breakdown products (teichoic & lipoteichoic acid) --> released into the environment --> pyrogenic (fever) acute phase response
57
Gram-negative bacterial infection: endotoxin
Endotoxin is only found in gram-negative bacteria
Endotoxin binds to receptors (CD14, TLR) on macrophages & B cells --> acute phase cytokines (IL-1, IL-6, TNF)
At low concentration --> vasodilation, fever, & acute inflammatory response
At high concentration --> leukopenia followed by leukocytosis, DIC, activation of complement, thrombocytopenia, decreased peripheral circulation & perfusion, shock, or death
58
Enterobacteriaceae
Ubiquitous, free-living in nature
Facultative anaerobes, lactose fermentation (E. coli, Klebsiella, enterbacter, citrobacter)
Oxidase negative
Resistance to bile salts (salmonella, shigella)
59
Antigens for classification of enterobacteriacae
O antigen: cell wall polysaccharide (identify strain w/in species)
K antigen: cell surface antigens
H antigen: flagellar protein
Pili: protein antigen
60
Common virulence factors in enterobactericae
```
Endotoxin
Type III secretion
Sequestration of growth factors
Resistance to serum killing (capsule, prevention of complement binding)
Antimicrobial resistance
Adhesins
Exotoxins
```
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Sepsis: overview
Pt has fever or low body temp
HR > 90
RR > 20 or PaCO2 < 32
WBC > 12K, <4K, left shift
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Severe sepsis: characteristics
Hypoperfusion w/ associated organ dysfunction
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Septic shock: characteristic
Hypotension despite adequate fluid resuscitation
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Sources of Sepsis by gram (-) bacilli
```
Biliary tract
GI tract (peritonitis, intestinal infarct)
GU tract
Infected pancreatitis
Skin necrotizing infection
Pneumonia
Post-surgery
```
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5 stages of sepsis
Local injury or infection
Systemic spillover of pro- & anti- inflammatory mediators
Development of Loss of regulatory control of proinflammatory responses (SIRS)
Inappropriate compensatory antiinflammatory response (CARS)
Ultimately can lead to multiorgan dysfunction syndrome
Sepsis happens when SIRS outweighs CARS
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Host Defense Mechanism
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Species, age
Hygiene
Gastric acidity
Intestinal motility
Enteric microflora
Specific/non-specific immunity
```
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Noninflammatory enteric infections
Involve enterotoxins
Watery diarrhea
No fecal leukocytes
Ex: V. cholerae & ETEC
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Inflammatory Enteric Infections
Cell invasion & cytotoxins
Fecal leukocytes might be present
Ex: Shigella & Salmonella enteritidis
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Penetrating Enteric Infections
Penetrate intact intestinal mucosa & multiply in lymphatic & RE cells
Febrile systemic illness w/ or w/out diarrhea
Fecal PMN
Ex: Salmonella typhi (Typhoid fever)
70
Evasion of immune system: Bacterial capsule
Most important virulence factor
Made of polysaccharide which is a poor immunogen
Makes it difficult for phagocytes to adhere to bacteria
Protects bacteria from destruction within the phagolysosome
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Evasion of immune system: intracellular pathogens
Intracellular growth that hides bacteria from detection
Require TH1 T helper cell to activate macrophages to kill or creat a barrier around the cell
They can avoid being killed intracellular by:
Blocking fusion of the phagolysosome
Resistance to bactericidal lysosomal enzymes
Ability to exit phagosome before coming in contact w/ lysosomal enzymes
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Evasion of complement system
Masking: antigenic variations that prevent antibody action
Inhibiting activation of complement: gram negative bacteria have an O antigen that prevents the complement system from reaching the plasma membrane
73
Genome diversity in Bacteria
Vibrio cholera has 2 chromosomes (smaller one provides genes for toxin)
Others have linear DNA and plasmids (Borrelia)
74
Bacterial chromosome & extrachromosomal elements
Chromosomes:
Single circular DNA (except vibrio & borrelia)
Plasmids:
Many bacteria have plasmids, some have many copies, replicate along with chromosome
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Bacterial gene regulation
Bacterial promoters will bind repressor molecules --> gene transcription
Sigma binds DNA which attracts RNAP
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2 Component Signal Transduction
Sensory kinase on the bacteria surface interact w/ small molecules and phophorylate downstream effectors including response regulator that can cause changes in the DNA by interacting to various sigma protiens
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Bacteriophages
Similar to a virus for bacteria
Insert RNA or DNA that then directly impact protein synthesis --> encapsidation and lysis
These are important for bacteriophage therapy as a potentially more potent treatment then traditional antibiotics
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Lysogenic conversion
Bacteriophage can carry gene for toxin and it can then inject these genes into normally non-toxigenic strands
Ex: Shiga toxin & diphtheria toxin
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Bacterial conjugation
Two bacteria bind via a pilus where the plasmid of one bacteria can be transferred into the other bacteria
Plasmid with the use of transposons can integrate into DNA and then also be transferred into another bacteria via same mechanism
This allows bacteria to transfer new traits to other bacteria (referred to as lateral genetic transfer)
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Transposons
Motile DNA elements ( from one site of a chromosome to a chromosome, plasmids, or phage genome)
Transposase: specific enzyme that mediates transposition of the cognate
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Development of bacterial resistance
```
By mutating:
Through errors of replication
Through DNA damage & error prone repair
Common mutations:
rRNA mutation (many antibiotic)
r-protein S12 mutation (streptomycin)
DNA Gyrase mutation (novobiocin, nalidixic acid)
```
By acquiring resistance genes
Transposon mediated: drug resistance genes produce enzymes that can alter the drug --> making them inactive
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Anaerobic bacteria
Many are commensal
Help w/ stabilization of bacterial flora
Guard against colonization by pathogenic organism from outside sources
Help digesting food
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Virulence factors of anaerobes
Adhesins (capsule & fimbriae)
Protection against phagocytosis (capsule, proteases that drgrade immunoglobulin)
Protection against oxygen toxicity:
Superoxide dismutase (inactivates superoxide)
Catalase (inactivates hydrogen peroxide)
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Characteristic of anaerobic infection
Polymicrobial infections
| Cause disease when spread by trauma of disease from mucosal surfaces to sterile tissues or fluid
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Common type of anaerobic infection
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RTI
Brain abscess
Intra-abdominal infection
Gynecological infections (pelvic inflammatory disease)
Skin & soft tissue infection
Bacteremia
Gastroenteritis
```
86
Human monocytic ehrlichiosis
Organism: E. charreensis
Tick vector: lone star tick
Location: mid atlantic, mid west, south central states
Disease: Leukopenia & thrombocytopenia, flu-like, fever/chills, headache, myalgias
Seen in CT
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Human Granulocytic ehrlichiosis
```
Organism: anaplasma phagocytophilum
Location: NE & North central USA, Europe
Vector: Deer tick
Resevoir: mice, chipmunks
Disease:
Febrile illness, Headache, myalgias, leukopenia, thrombocytopenia, rash in less than 10%
```
Seen commonly in CT
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Complications/Diagnosis/Treatment of Ehrlichiosis/Anaplasmosis
CHF, Pericardial effusion
Renal failure
Immunosupression
Diagnosis:
peripheral blood smear: inclusions seen in WBCs (morulas)
Treatment: Doxycycline
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Normal flora: mouth & URT
```
Staphylococcus
Streptococcus
Treponemes
Enterobacteriaceae
Candida
```
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Normal flora: Skin
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Staphylococcus
Streptococcus
Priopionibacter
Candida
Malassezia
```
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Normal flora: Female urogenitial
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Candida
Enterococcus
Lactobacillus
Peptostreptococcus
Staphylococcus
Streptococcus
```
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Normal flora: Lower GI tract
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Bacteroides
Clostridium
Peptostreptococcus
Enterobacteriaceae
Enterococcus
Pseudomonas
Candida
Blastocystis
Entmoeba
```
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Erysipelothrix rhusiopathiae
Gram + (gram variable)
Zoonotic (swine, turkey, fish) & soil
Presents w/ cellulitis (erysipeloid)
Treated w/ penicillin
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HACEK: organisms
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Haemophilus (parainfluenzae, aphrophilus, paraphrophilus)
Actinobacillus actinomycetemcomitans
Cardiobacterium hominis
Eikenella corrodens
Kingella
```
95
HACEK organisms: what they cause & Tx
Endocarditis
Eikonella (found in mouth, involved in clenched fist injury)
Treated w/ Ceftriaxone, Ampicillin-sulbactam, or fluoroquinolones
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Capnocytophaga canimorsus
```
Filamentous gram - bacillus
CO2 eating (requires high CO2 tension)
```
Found in human mouth & animal mouths (associated w/ bite injuries)
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Spirochetes: general features
Slender, helical or planar wave
Highly motile & invasive
Double membrane w/ flagella in periplasmic space
Distantly related to gram + & gram -
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Spirochete disease: general features
Cause widely disseminated disease (include CNS involvement)
Disease occurs in stages
Clinical manifestations are a result of host immunity
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Mycobacteria: general features
Obligate aerobes
Slow growth
Waxy cell wall (made of glycolipid)
100
Mycobacteria cell wall
Above peptidoglycan layer, have arabinogalactan, mycolates, & acetyl lipids)
mycolates & acetyl lipids make up waxy coat --> makes these organisms acid-fast
101
Tuberculoid response: characterized by & seen in
Good T cell response & activation of macrophages
Usual state of pts w/ reactivation type (pulmonary) TB & in tuberculoid leprosy
Histology: Caseous necrosis, scant mycobacteria
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Lepromatous response: characterized by & seen in
Defective T cell response & lack of macrophage activation
Usually seen in pts w/ lepromatous leprosy & miliary TB, disseminated mycobacterial infections in pts w/ AIDS
Histology: No necrosis, abundant mycobacteria
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Cell wall synthesis inhibitors: overall mechanism
Pentaglycl unit which enables cross-linking between strands & is the site where penicillin binding protein bind
Terminal D-alanine D-alanine where the antibiotics mimic or bind to prevent cross-linking by creating steric hindrance
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Beta-lactams: groups
Penicillin
Cephalosporins
Carbapenems
Monobactams
105
Penicillin: general considerations
Is bactericidal
No activity against atypical pathogens (true for all beta-lactam)
Poor penetration into human cells
Common mechanism for resistance (inactivation of penicillinase/betalactamase)
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Penicillin: clinical considerations
Well-tolerated
GI upset, diarrhea, allergic reactions are most common adverse effects, Allergic Rash: ~10% prevalence
Removed via kidney, basically no hepatic toxicity (must adjust for renal function)
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Natural penicillins: available agents
```
Penicillin G (iv)
Penicillin V (po)
Procaine, benzathine (im)
```
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Natural penicillin: spectrum of activity
```
Narrow-limited to:
Gram (+) aerobes (Strept, Entero)
Resistance in Strep pneumoniae & staph
Some anaerobes
Treponema pallidum
POOR for gram (-)
```
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Anti-staph penicillins
Agents:
Cloxacillin / Dicloxacillin: po
Nafcillin / Oxacillin: iv
Limited to Staphylococci, Streptococci
Activity decreased vs. Streptococci compared to PCN
Resistance in Staphylococci
(Methicillin-Resistant S. aureus, “MRSA”):
Change in PBP enzyme targets
Increasing in both community and hospital settings (>50% in most hospitals)
Hepatic elimination
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Aminopenicillins
Combined w/ beta-lactamase inhibitor
Ex: amoxicillin or ampicillin
```
Improves gram (+) activity (staph)
Broader gram (-) activity (Klebsiella)
Improved anaerobic activity (Bacteroids)
```
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Anti-pseudomonal penicillin
Mezlocillin / Piperacillin / Ticarcillin: iv
Combined with beta-lactamase inhibitor (Improves activity against Staphylococci, gram-negatives, and anaerobes)
Spectrum of Activity:
Less active against Gram-positive bacteria
Active against most Gram-negatives
Resistance becoming a more important issue for select strains of :
P. aeruginosa, Acinetobacter, Enterobacter spp.,
Beta-lactamase overproducing Klebsiella spp., E. coli,
Active against most anaerobes
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Cephalosporins: general considerations
Ring structure less strained --> reduced tendency for hydrolyze & more stable penicillinase degradation
Acid & beta-lactamase stability
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Cephalosporins: clinical considerations
Bactericidal
ALL cephalosporins have NO clinically reliable activity against enterococci
MOST cephalosporins have NO reliable activity against anaerobes
Well-tolerated and have minimal drug interactions
Usual adverse effects: GI-related
Approximately 2.5-5% of patients with documented penicillin hypersensitivity will also be allergic to certain cephalosporins
Most need to have doses reduced in moderate-severe renal dysfunction
114
1st generation Cephalosporins
Agents:
Cefazolin (Ancef): iv
Cephalexin (Keflex), Cefadroxil (Duricef): po
Most Gram-positives (except enterococci, MRSA)
Limited Gram-negatives (e.g., E. coli, Haemophilus spp.)
115
2nd generation Cephalosporin
Most important agent: Cefuroxime (Ceftin, Zinacef): po/iv
Spectrum of Activity:
Most Gram-positives (except enterococci, MRSA),
Some beta-lactamase producing Gram-negatives (e.g., Haemophilus, Moraxella, E. coli)
Cefoxitin, Cefotetan active against most anaerobes
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3rd generation Cephalosporin
Most common agents:
Oral:
Cefdinir (Omnicef)
Cefixime (Suprax)
Intravenous:
Ceftazidime (Fortaz)
Ceftriaxone (Rocephin)
Most gram-positives (except enterococci & MRSA)
Most gram-negatives (except Pseudomonas and certain strains of Enterobacter, Klebsiella, Citrobacter spp.)
Ceftazidime has antipseudomonal activity
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4th generation Cephalosporin
Cefepime
Spectrum of Activity:
Similar to 3rd Generation Cephs but:
Effective against Pseudomonas (like Ceftazidime)
Effective against some gram negative bacteria that are 3rd- generation cephalosporin-resistant
118
5th generation Cephalosporin
Ceftaroline (Teflaro)
Spectrum of Activity:
Gram Positives: Streptococcal spp. & Staphylococcus spp. (including MRSA!)
Gram negatives: Similar to 3rd Generation Cephs like ceftriaxone
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Aztreonam
Monobactam cell wall synthesis inhibitor
Spectrum of Activity
Gram-negatives: nearly all (including highly resistant strains)
No activity against Gram-positives, anaerobes, or atypical bacteria
Used on patient's with confirmed penicillin allergies
120
Carbapenems: clinical considerations
IV only: Imipenem (Primaxin), Meropenem (Merrem), Ertapenem (Invanz), Doripenem (Doribax)
BROAD-SPECTRUM: Active against nearly all Gram positive, Gram-negative, and anaerobic bacteria, No atypical antibacterial activity
Fungal superinfections may occur while on carbapenems
Risk of cross-allergenicity originally thought to be much higher than Aztreonam/Cephs for patients with PCN allergies...probably only ~5-10%
121
Imipenem/Cilastatin and Meropenem & Doripenem
Both dosed every 6-8 hours:
Cilastatin prevents enzymatic breakdown of imipenem in the kidneys (increases half-life and allows Q6-8H dosing)
Meropenem thought to have lower risk of seizures than imipenem…but controversial
Doripenem: slightly more potent than these other combination
122
Important consideration for Ertapenem
```
iv
Dosed QD (versus Q6-8H for imipenem and meropenem)
Should NOT be used if Pseudomonas spp. documented or suspected (no activity!!!)
```
123
MSSA: implication for beta-lactam use
Resistance via penicillinase:
resistant to PCN, aminoPCNs, extended-spectrum PCNs
Nafcillin, oxacillin, dicloxacillin have activity
Amox/clavulanate, Amp/sulbactam, pip/tazobactam have activity
Cephalosporins, Carbapenems have activity
124
MRSA: implication for beta-lactam use
Still has penicillinase:
resistant to PCN, aminoPCNs, extended-spectrum PCNs
Also altered PBP-2a
NO beta-lactams have activity against MRSA except Ceftaroline
125
Differences between fungi & bacteria
Fungi: eukaryote, larger cell size (2-15 micrometer), polysaccharide cell wall (glucans, mannans, chitin) & cell membrane contains sterols
Bacteria are prokaryotes, cell wall peptidoglycan, no sterols in cell membranes
126
Fungal morphology: Yeast
Round/oval that undergoes budding or fission; colonial growth is smooth
127
Fungal Morphology: Mold
Tubular structure (hyphae) that undergoes longitudinal extension & branching; colonial morphology is fuzzy
128
Reproduction in yeasts
More species go through budding
Mechanism: Initiated by localized enzymatic cell wall lysis, cell membrane bulges, nucleus divides & the 2nd nucleus moves into bud; cell wall is repaired between daughter & mother --> daughter cell breaks off
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Hyphae: characteristics
Can be aseptate or septate
Septae have pores that allow nutrient movement
Can be vegetative (obtain nutrients) or aerial (form conidia or sporangiospores
130
Dimorphic fungi
Fungi that can have both fungal morphology
Yeast form at 37 C
Mold form at 30 C
Ex: Histoplasma capsulatum, Coccidioides immitis
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Reproduction in molds
Sexual state: teleomorph (perfect state)
Asexual state: anamorph (imperfect state)
Asexual form grows in culture & is the name we use clinically
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Human defenses against Fungi
Most grow poorly at body temp
Skin & mucosal surfaces are effective barriers
Innate immunity provides initial protection (TLR 2, 4, 9 & C-type lectin receptors)
Cell-mediated immunity: is critical (require Th1 & Th17 response to decrease severity & incidence of fungal infections)
Humoral immunity: not important
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Fungal culture
Sabouraud's agar: 4% dextrose, at pH 5.5
Sugar & acidity discourage bacterial growth
Fungi grow very slowly in culture
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Fungal identification in culture: yeast
Grows suspended in broth or on plates
Use metabolic reactions for specific organism identification
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Fungal identification in culture: molds
Grow slowly & form conidia
Identify by conidial, hyphal, & colonial morphology
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Minimum inhibitory concentration (MIC): defined and how we determine it
Determined by adding bacteria to nutrient broth with serial dilutions of antibiotic, the point where there is no growth is the MIC
Can use an E test (an agar plate that has a pre-made gradient of antibiotic, the point specifically at the meniscus is the MIC)
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Minimum Bactericidal Concentration (MBC): defined and how we determine it
Once the MIC is determined, you take the same samples that show no growth and remove them from the antibiotic, plate the bacteria and look for growth. The concentration where there is no growth is the MBC
138
Bactericidal: mathematical relationship
MBC less than or equal to MIC
Or 99.9% bacteria count reduction in 24 hrs
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Bacteriostatic: mathematical relationship
MBC > 4x MIC
140
Tolerant: mathematical realtionship
MBC > 32x MIC
141
Bactericidal medications
```
Beta-lactams
Aminoglycosides
Vancomycin
Fluoroquinolones
Daptomycin
Metronidazole
```
142
Bacteriostatic medications
```
Macrolides
Tetracyclines
Sulfonamides
Clindamycin
Linezolid
Chloramphenicol
```
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Concentration-Dependent Killing
Eliminate bacteria when levels are well-above MIC in tissue
When ratio of drug to MIC increased further, greater killing occurs
Shown up to 64x MIC
Exhibits a “post-antibiotic effect”
Even when levels trail off, the bacteria are damaged and take some time to recover
Ex: Quinolones & Aminoglycosides
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Time-Dependent Killing
Killing occurs only when concentration is higher than MIC
Any levels >4x MIC generally do not add to the killing effect
```
Ex:
Penicillins
Cephalosporins
Aztreonam
Macrolides
Clindamycin
```
145
Antibiotic combinations: indifference
Combination is the sum of each alone
146
Antibiotic combinations: synergy
Combination better than the sum of each alone
Ex:
Ampicillin breaks down cell wall, allowing improved penetration of gentamicin into bacteria
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Antibiotic combination: antagonism
Inhibition of antimicrobial effect
Tetracycline is “static”, thus bacteria are inhibited but not
actively growing actively growing
Penicillin requires metabolically active bacteria to affect cell wall
Metabolic stasis induced by TCN protects bacterium from
killing effects of the ampicillin
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Anti-microbial resistance: Intrinsic
An inherent attribute of a microbe
lacks necessary target
Ex:
Resistance of Enterococcus to cephalosporins
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Anti-microbial resistance: Circumstantial
A difference between in vitro and in vivo effects of an antibiotic
May appear sensitive in lab, but resistance in clinical use
Ex:
Enterococcus can appear sensitive to TMP/SMX in vitro, but can take up environmental folate in vivo
Induction of a cephalosporinase in Enterobacter
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Anti-microbial resistance: Acquired
A change in the genetic composition of an organism so that a drug that was once effective is no longer active
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Genetics of resistance: mechanism
Antibiotics apply selective pressures for microbial survival
Microbes acquire traits that permit their survival
Gene modification can occur by several mechanisms:
Mutation: Spontaneous changes in the genetic code
Transformation: Acquisition of soluable DNA
Transduction: Acquisition from phage
Conjugation: Acquisition of new traits via plasmids
Transposition: Acquisition of new traits via transposons
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Mechanism for anti-microbial resistance: Decreased Antibiotic Access
Decrease Outer Membrane Permeability: Beta-Lactams
Decreased Cytoplasmic transport (influx): Aminoglycosides
Increased Efflux: Tetracyclines & Quinolones
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Mechanism for anti-microbial resistance: Drug Inactivation
Most common resistance mechanism seen
Generally acquired by exogenous genes
Enzymatic activity of bacteria alters the antibiotic to inactive state
Examples:
b-lactamase, Aminoglygcoside enzymes, Chloramphenicol Acetyl Transferase (CAT)
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Mechanism for anti-microbial resistance: Target Modification
```
Alters the target molecule such that it does not bind or is otherwise unaffected by the antibiotic
Ex:
Quinolones (Gyrase modification)
Rifampin (RNA polymerase mutation)
Macrolides (rRNA methylation)
β-lactams (PBP changes)
```
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Changes in Penicillin Binding Proteins: MRSA
Bacteria possess multiple transpeptidases
Function to cross-link the cell wall, Inhibition prevents cross-linking and accumulation induces autolysis
Community-acquired Methicillin-resistant Staphylococcus aureus (ca-MRSA)
Encoded on the gene complex “type IV Staphylococcalcassette chromosome” a.k.a. SCCmec gene
PBP 2': low β-lactam affinity, even to penicillins resistant to β-
lactamases
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Mechanisms of Antimicrobial Resistance: Target Bypass
The bacteria no longer need the enzyme targeted by the antibiotic to survive
Examples:
Trimethoprim: Enterococcus can use folate from the environment
Glycopeptides (Vancomycin Resistant Enterococci (VRE))
Vancomycin acts by blocking peptidoglycan synthesis
VRE use a d-ala to d-lactate instead of d-ala to d-ala
Three types: Van A, Van B, Van C
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Viral reverse transcriptase
Found in retro viruses
| Converts RNA into DNA
158
Viral ds RNA transcriptase
Found in reo viruses
| Copies dsRNA into ssRNA
159
Viral NTP phosphotransferase
Found in many enveloped virus
| Phosphate exchange
160
Viral neuraminidase
Found in myxo & paramyxo virus
| Cleaves cell surface sugars
161
Viral protein kinase
Found in myxo, retro, paramyxo, herpes
| Phosphorylates proteins
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Viral Life Cycle: components attachment
Attachment:
Always to specific cell surface receptors
Some receptors are highly tissue or cell specific; other receptors are present on many or even all cells
```
Ex:
HIV (CD4 antigen on T cells)
Rhino (ICAM-1 on upper respiratory epithelial cells)
Polio (Immunoglobulin-like receptors)
Influenza (Sialic acid)
Herpes Simplex (Heparan sulfate proteoglycans)
Rabies (Acetylcholine receptor)
Hepatitis B (IgA receptor)
```
Uncoating & penetration (Uncoating can occur at the plasma membrane, within an endosome, & at the nuclear membrane)
mRNA synthesis & translation
Viral genome replication
Virion assembly then release
163
Picornaviruses: structure
Single-stranded linear RNA genomes3' polyA, VPg protein at 5' end.
After entry and uncoating, a polyprotein is made, which self-cleaves to generate all necessary viral polypeptides.
164
Picornaviruses: life cycle
```
Specific cellular receptor
RNA serves as mRNA for viral proteins
VPg must be removed by cell proteases
RNA translated into one polyprotein, which undergoes post-translational modification into multiple polypeptides
Early host shutoff
RNA replication goes through minus strand intermediate
Assembly
Cell destruction and virus release
```
165
Orthomyxoviruses: structure
Single stranded RNA genome, negative polarity
Segmented 3. Enveloped virion, lipid derived from host
several surface antigens: hemagglutinin (HA), neuraminidase (N)
distinct viral proteins: Matrix, HA-2 subunits (functions in virus-cell attachment)Nucleoprotein (NP) - internal, core associated
Three RNA transcriptase proteins, internal
166
Orthomyxoviruses: life cycle
Attachment - mediated via HA and specific cell surface receptors
Internalization by HA conformational change and membrane fusion
RNA transported to nucleus
RNA replication requires host RNA polymerase II
Assembly and release by budding through cell membranes
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Retroviruses: basic characteristics
```
The only oncogenic class of RNA viruses - a major cause of cancers, especially
leukemias and lymphomas, in animals.
```
Likely to be important in some human cancers. (Can be oncogenic in two ways: insertional mutagenesis & transduction of host proto-oncogenes)
Transmitted both horizontally and vertically
Important replication strategy, involving integration into host genome and potential to transduce cellular genes
Many are defective - grow only with "helpers"
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Retroviruses: structure
Enveloped, with virus-specific membrane glycoprotein spikes.
Single-strand, dimeric RNA genome
Host tRNA
Reverse Transcriptase
169
Retroviruses: LIfe cycle
RNA genome has distinctive structure, with U3, U5, R sequences, and bound tRNA
3 genes: gag, pol, env.
RNA converted to double stranded DNA, with LTR's at both ends
Integration of DNA into host genome ("provirus")
LTR's contain genetic signals for
transcription initiation and polyadenylation
Integrated provirus is transcribed, and
RNA's processed in several ways.
Translation yields a variety of products important for virus life cycle.
170
Human Retroviruses
Associated w/ leukemias (HTLVs) & AIDS (HIV)
HIV has a highly specific T4 lymphocytes/CD4 receptor
171
Viral genetics: recombination
Exchange of genes between 2 chromosomes by crossing over within regions of significant base sequence homology
172
Viral genetics: complementation
When 1 of 2 viruses that infect the cell has a mutation that results in a nonfunctional protein. The nonmutated virus complements the mutated one by maing a functional protein that serves both viruses
173
VIral genetics: phenotypic mixing
Occurs when a cell is infected by 2 viruses; genome from virus A is partially coated with surface proteins of B & determines the infectivity of the mixed virus. Progeny of the virus will have virus A genetic material
174
RNA viral genome
All are ss except reoviridae
175
Positive stranded RNA viruses
retrovirus, togavirus, flavivirus, coronavirus, hepevirus, calicivirus, & picornavirus
176
viral genome infectivity
dsDNA & + strand ssRNA are infectious (do not require polymerase --> can be directly translated)
- strand ssRNA & dsRNA are non-infectious alone b/c they require enzymes from the host cell
177
Virus ploidy
```
All viruses are haploid
except retrovirus (2 ssRNA)
```
178
RNA viral replication: location
Occurs in the cytoplasma
| Except influenza & retrovirus
179
Viral envelopes: origin
Envelope is normally obtained by plasma membrane of a cell once it exits (except herpesvirses --> comes from nuclear membrane
180
Unenveloped viruses
Calicivirus, picornavirus, reovirus (RNA)
| Parvovirus, adenovirus, papilloma, & polyoma (DNA)
181
DNA viral characteristics
Include hepadna, herpes, adeno, pox, parvo, papilloma, polyoma
Are ds (except parvo) & linear (papilloma, polyoma, hepadna)
Are icosahedral & replicate in the nucleus (pox)
182
Cyclospora cayetanensis
Requires maturation outside of host to become infectious
Epi: transmission via fecally contaminated water or foods
Seen in children in low income countries, travelers
Pathogenesis: Localized to upper small bowel; invades small bowel epithelium within cytoplasmic vacuoles --> asexual & sexual replication in human host --> inflammatory response & mucosal infiltrate
Clinical: incubation is 1 week; frequent watery diarrhea which may be self-limited or prolonged; symptoms: anorexia, cramping, nausea, & weight loss
Diagnosis: Wet mount, modified acid fast staining of stool, autofluoresence under UV light
Treatment: SMX/TMP
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Trichuris trichiura
Eggs need to mature in soil before becoming infectious; ingestion of contaminated soil
Clinical: most infections are asymptomatic, symptoms due to mechanical imbedding of worms; symptoms: abdominal pain, weight loss, & rarely rectal prolapse; occasionally presents w/ anemia; eosinophila
Diagnosis: stool (lemon-shaped eggs w/ clear, bipolar prominence
Treatment: albendazole, mebendazole, ivermectin (combination therapy mebendazole + ivermectin)
184
Babesia microti
infection of RBCs with rupture
spleen critical in host defense; help with clearance and immune response
B cell response important for resolution of infection
Clinical:
most cases asymptomatic
splenectomy, older age, cell-mediated immune defect, HIV/AIDS,
anti-cytokine therapy defect predisposes to ↑ severity; most fatalities seen in these groups
incubation period: 1-4 weeks
malaise, chills, fever, N&V, myalgias & arthralgias
anemia, ↓ platelets, mild ↑ in liver enzymes, proteinuria
severe infection: jaundice, hemoglobinuria and renal failure
parasitemia can approach 85% in asplenic patients
can be chronic, asymptomatic parasitemia
185
Babesia: diagnosis & treatment
Diagnosis:
blood smears: ring forms, tetrads; serology, PCR
Treatment:
most infections probably resolve spontaneously in immunologically normal hostsif recognized should be treated
treatment:
atovaquone + azithromycin
clindamycin + quinine
exchange transfusion may be needed in severe disease may need long-term therapy in immunocompromised
