Infectious Disease Flashcards

1
Q

Shapes of Bacteria: rods

A

Bacillus
Salmonella tiphimurium
Bacillus anthracis

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2
Q

Shapes of bacteria: spheres

A

Coccus (sphere)
Ex: Streptococcus pneumoniae

Coccobacillus (between rod/sphere)
Ex: Yersinia pestis

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3
Q

Shapes of bacteria: others

A

Spirillum (rigid spirals)

Spirochete (undulating spirals)

Vibrio (comma shape)
Vibrio cholerae

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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

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5
Q

Bacterial staining

A

Gram-positive: stain blue

Gram-negative: stain red

Specialized stains:
Most useful is acid-fast stain

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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

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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

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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)

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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

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10
Q

Common anti-microbial targets of bacterial exoskeleton

A
Murein synthesis (penicillin) 
Ribosomal proteins (gentamycin)
DNA gyrase (ciprofloxacin)
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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

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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)

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13
Q

Levels of bacterial classification

A

Morphology, Metabolism, Antigenicity, Genetics

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14
Q

Bacterial classification: Morphology

A

Staining: gram stain positive vs. negative

Then,
Shape: coccus, bacillus, spirillum, coccobacillus, spirochete, vibrio

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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

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16
Q

Bacterial classification: Antigenicity

A

Use of antibodies that are particular to certain bacteria

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17
Q

Bacterial classification: Genetics

A

Most commonly we use ribosomal DNA to look for highly conserved sequences particular to a family or genus

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18
Q

Virulence factors

A

Genetic traits that enhance the ability of bacteria to cause disease

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19
Q

Pathogenicity island

A

Large chromosomal regions that contain sets of genes that encode for virulence factors

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20
Q

Possible outcomes of new exposure

A

Transient colonization & clearance
Permanent Colonization
Disease

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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

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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

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23
Q

Commensal bacteria

A

Bacteria that does not harm nor benefit their host

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24
Q

Natural defense mechanisms for bacterial entry

A

skin, mucus, ciliated epithelium, and antibacterial secretions

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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
29
Examples of bacteria that enter via needlestick
Staphylococcus aureus Pseudomonas spp.
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Examples of bacteria that enter via arthropod bites
Rickettsia, ehrlichia, coxiella Francisella Borrelia spp Yersinia pestis
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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
33
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
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Facultative Intracellular Pathogens
``` Listeria Mycobacteria Shigella Salmonella EP E. Coli UP E. Coli ```
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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
56
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)
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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
``` 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)
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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
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Genome diversity in Bacteria
Vibrio cholera has 2 chromosomes (smaller one provides genes for toxin) Others have linear DNA and plasmids (Borrelia)
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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
78
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
79
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
81
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
82
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)
84
Characteristic of anaerobic infection
Polymicrobial infections | Cause disease when spread by trauma of disease from mucosal surfaces to sterile tissues or fluid
85
Common type of anaerobic infection
``` RTI Brain abscess Intra-abdominal infection Gynecological infections (pelvic inflammatory disease) Skin & soft tissue infection Bacteremia Gastroenteritis ```
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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
``` Staphylococcus Streptococcus Priopionibacter Candida Malassezia ```
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Normal flora: Female urogenitial
``` Candida Enterococcus Lactobacillus Peptostreptococcus Staphylococcus Streptococcus ```
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Normal flora: Lower GI tract
``` 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
``` Haemophilus (parainfluenzae, aphrophilus, paraphrophilus) Actinobacillus actinomycetemcomitans Cardiobacterium hominis Eikenella corrodens Kingella ```
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HACEK organisms: what they cause & Tx
Endocarditis Eikonella (found in mouth, involved in clenched fist injury) Treated w/ Ceftriaxone, Ampicillin-sulbactam, or fluoroquinolones
96
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 -
98
Spirochete disease: general features
Cause widely disseminated disease (include CNS involvement) Disease occurs in stages Clinical manifestations are a result of host immunity
99
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
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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
102
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
103
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
104
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)
106
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
110
Aminopenicillins
Combined w/ beta-lactamase inhibitor Ex: amoxicillin or ampicillin ``` Improves gram (+) activity (staph) Broader gram (-) activity (Klebsiella) Improved anaerobic activity (Bacteroids) ```
111
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
113
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
116
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
119
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
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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
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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
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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
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Tolerant: mathematical realtionship
MBC > 32x MIC
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Bactericidal medications
``` Beta-lactams Aminoglycosides Vancomycin Fluoroquinolones Daptomycin Metronidazole ```
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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 ```
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Antibiotic combinations: indifference
Combination is the sum of each alone
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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
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Viral ds RNA transcriptase
Found in reo viruses | Copies dsRNA into ssRNA
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Viral NTP phosphotransferase
Found in many enveloped virus | Phosphate exchange
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Viral neuraminidase
Found in myxo & paramyxo virus | Cleaves cell surface sugars
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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
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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.
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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 ```
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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
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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
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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.
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Human Retroviruses
Associated w/ leukemias (HTLVs) & AIDS (HIV) HIV has a highly specific T4 lymphocytes/CD4 receptor
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Viral genetics: recombination
Exchange of genes between 2 chromosomes by crossing over within regions of significant base sequence homology
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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
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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
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RNA viral genome
All are ss except reoviridae
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Positive stranded RNA viruses
retrovirus, togavirus, flavivirus, coronavirus, hepevirus, calicivirus, & picornavirus
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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
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Virus ploidy
``` All viruses are haploid except retrovirus (2 ssRNA) ```
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RNA viral replication: location
Occurs in the cytoplasma | Except influenza & retrovirus
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Viral envelopes: origin
Envelope is normally obtained by plasma membrane of a cell once it exits (except herpesvirses --> comes from nuclear membrane
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Unenveloped viruses
Calicivirus, picornavirus, reovirus (RNA) | Parvovirus, adenovirus, papilloma, & polyoma (DNA)
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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)
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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)
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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
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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