Infectious Disease Flashcards
Shapes of Bacteria: rods
Bacillus
Salmonella tiphimurium
Bacillus anthracis
Shapes of bacteria: spheres
Coccus (sphere)
Ex: Streptococcus pneumoniae
Coccobacillus (between rod/sphere)
Ex: Yersinia pestis
Shapes of bacteria: others
Spirillum (rigid spirals)
Spirochete (undulating spirals)
Vibrio (comma shape)
Vibrio cholerae
Bacterial arrangements: cocci
Single
Diplococcus (pair)
Ex. Streptococcus pneumoniae, neisseria meningitidis
Streptococcus (chain)
Ex. Streptococcus pneumoniaeNeisseria meningitidis
Tetrad
Ex. Micrococcus luteus
Staphylococcus
Ex. Staphylococcus aureus
Bacterial staining
Gram-positive: stain blue
Gram-negative: stain red
Specialized stains:
Most useful is acid-fast stain
Bacterial Reproduction
Reproduce by binary fission
One circular chromosome per cell which doubles and the bacteria then splits to produce 2 bacteria
Bacteria: nucleoid
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
Bacterial cytoskeleton
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)
Bacterial exoskeleton
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
Common anti-microbial targets of bacterial exoskeleton
Murein synthesis (penicillin) Ribosomal proteins (gentamycin) DNA gyrase (ciprofloxacin)
Only bacteria that doesn’t have an exoskeleton
Mycoplasma:
Do not have necessary proteins to form the exoskeleton and are therefore amorphous
Gram-positive bacteria
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)
Levels of bacterial classification
Morphology, Metabolism, Antigenicity, Genetics
Bacterial classification: Morphology
Staining: gram stain positive vs. negative
Then,
Shape: coccus, bacillus, spirillum, coccobacillus, spirochete, vibrio
Bacterial classification: Metabolism
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
Bacterial classification: Antigenicity
Use of antibodies that are particular to certain bacteria
Bacterial classification: Genetics
Most commonly we use ribosomal DNA to look for highly conserved sequences particular to a family or genus
Virulence factors
Genetic traits that enhance the ability of bacteria to cause disease
Pathogenicity island
Large chromosomal regions that contain sets of genes that encode for virulence factors
Possible outcomes of new exposure
Transient colonization & clearance
Permanent Colonization
Disease
Strict Pathogens
Virulent bacteria that promote their growth at the expense of their host
Ex: mycobacterium TB
Neisseria gonorrhoeae
Plasmodium spp. (Malaria)
Rabies virus
Opportunistic bacteria
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
Commensal bacteria
Bacteria that does not harm nor benefit their host
Natural defense mechanisms for bacterial entry
skin, mucus, ciliated epithelium, and antibacterial secretions
Common ports of entry for bacteria
Ingestion, inhalation, trauma, needle stick, arthropod, & sexual transmission
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
Examples of bacteria that enter via inhalation
Mycobacterium spp. , Nocardia spp. , mycoplasma pneumoniae
Legionella spp., Bordetella, Chlamydophila psittaci
Chlamydophila pneumoniae, streptococcus spp.
Examples of bacteria that enter via trauma
Clostridium tetani
Examples of bacteria that enter via needlestick
Staphylococcus aureus
Pseudomonas spp.
Examples of bacteria that enter via arthropod bites
Rickettsia, ehrlichia, coxiella
Francisella Borrelia spp
Yersinia pestis
Examples of bacteria that enter via sexual transmission
Neisseria gonorrhoeae
Chlamydia trachomatis
Treponema pallidum
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
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
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
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)
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
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
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
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
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
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
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)
Microbial differentiation
Reversible changes in: Structure of surface macromolecules Organelle structure (like pilli) cell structure & organization (sporulation)
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
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
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
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
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)
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
Obligate intracellular pathogens
Chlamydia
Rickettsia
Facultative Intracellular Pathogens
Listeria Mycobacteria Shigella Salmonella EP E. Coli UP E. Coli
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)
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
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
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
Gram-positive bacterial infection: endotoxin-like response
Peptidoglycan & breakdown products (teichoic & lipoteichoic acid) –> released into the environment –> pyrogenic (fever) acute phase response
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
Enterobacteriaceae
Ubiquitous, free-living in nature
Facultative anaerobes, lactose fermentation (E. coli, Klebsiella, enterbacter, citrobacter)
Oxidase negative
Resistance to bile salts (salmonella, shigella)
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
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
Sepsis: overview
Pt has fever or low body temp
HR > 90
RR > 20 or PaCO2 < 32
WBC > 12K, <4K, left shift
Severe sepsis: characteristics
Hypoperfusion w/ associated organ dysfunction
Septic shock: characteristic
Hypotension despite adequate fluid resuscitation
Sources of Sepsis by gram (-) bacilli
Biliary tract GI tract (peritonitis, intestinal infarct) GU tract Infected pancreatitis Skin necrotizing infection Pneumonia Post-surgery
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
Host Defense Mechanism
Species, age Hygiene Gastric acidity Intestinal motility Enteric microflora Specific/non-specific immunity
Noninflammatory enteric infections
Involve enterotoxins
Watery diarrhea
No fecal leukocytes
Ex: V. cholerae & ETEC
Inflammatory Enteric Infections
Cell invasion & cytotoxins
Fecal leukocytes might be present
Ex: Shigella & Salmonella enteritidis
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)
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
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
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
Genome diversity in Bacteria
Vibrio cholera has 2 chromosomes (smaller one provides genes for toxin)
Others have linear DNA and plasmids (Borrelia)
Bacterial chromosome & extrachromosomal elements
Chromosomes:
Single circular DNA (except vibrio & borrelia)
Plasmids:
Many bacteria have plasmids, some have many copies, replicate along with chromosome
Bacterial gene regulation
Bacterial promoters will bind repressor molecules –> gene transcription
Sigma binds DNA which attracts RNAP
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
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
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
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)
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
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
Anaerobic bacteria
Many are commensal
Help w/ stabilization of bacterial flora
Guard against colonization by pathogenic organism from outside sources
Help digesting food
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)
Characteristic of anaerobic infection
Polymicrobial infections
Cause disease when spread by trauma of disease from mucosal surfaces to sterile tissues or fluid
Common type of anaerobic infection
RTI Brain abscess Intra-abdominal infection Gynecological infections (pelvic inflammatory disease) Skin & soft tissue infection Bacteremia Gastroenteritis
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
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
Complications/Diagnosis/Treatment of Ehrlichiosis/Anaplasmosis
CHF, Pericardial effusion
Renal failure
Immunosupression
Diagnosis:
peripheral blood smear: inclusions seen in WBCs (morulas)
Treatment: Doxycycline
Normal flora: mouth & URT
Staphylococcus Streptococcus Treponemes Enterobacteriaceae Candida
Normal flora: Skin
Staphylococcus Streptococcus Priopionibacter Candida Malassezia
Normal flora: Female urogenitial
Candida Enterococcus Lactobacillus Peptostreptococcus Staphylococcus Streptococcus
Normal flora: Lower GI tract
Bacteroides Clostridium Peptostreptococcus Enterobacteriaceae Enterococcus Pseudomonas Candida Blastocystis Entmoeba
Erysipelothrix rhusiopathiae
Gram + (gram variable)
Zoonotic (swine, turkey, fish) & soil
Presents w/ cellulitis (erysipeloid)
Treated w/ penicillin
HACEK: organisms
Haemophilus (parainfluenzae, aphrophilus, paraphrophilus) Actinobacillus actinomycetemcomitans Cardiobacterium hominis Eikenella corrodens Kingella
HACEK organisms: what they cause & Tx
Endocarditis
Eikonella (found in mouth, involved in clenched fist injury)
Treated w/ Ceftriaxone, Ampicillin-sulbactam, or fluoroquinolones
Capnocytophaga canimorsus
Filamentous gram - bacillus CO2 eating (requires high CO2 tension)
Found in human mouth & animal mouths (associated w/ bite injuries)
Spirochetes: general features
Slender, helical or planar wave
Highly motile & invasive
Double membrane w/ flagella in periplasmic space
Distantly related to gram + & gram -
Spirochete disease: general features
Cause widely disseminated disease (include CNS involvement)
Disease occurs in stages
Clinical manifestations are a result of host immunity
Mycobacteria: general features
Obligate aerobes
Slow growth
Waxy cell wall (made of glycolipid)
Mycobacteria cell wall
Above peptidoglycan layer, have arabinogalactan, mycolates, & acetyl lipids)
mycolates & acetyl lipids make up waxy coat –> makes these organisms acid-fast
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
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
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
Beta-lactams: groups
Penicillin
Cephalosporins
Carbapenems
Monobactams
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)
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)
Natural penicillins: available agents
Penicillin G (iv) Penicillin V (po) Procaine, benzathine (im)
Natural penicillin: spectrum of activity
Narrow-limited to: Gram (+) aerobes (Strept, Entero) Resistance in Strep pneumoniae & staph Some anaerobes Treponema pallidum POOR for gram (-)
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
Aminopenicillins
Combined w/ beta-lactamase inhibitor
Ex: amoxicillin or ampicillin
Improves gram (+) activity (staph) Broader gram (-) activity (Klebsiella) Improved anaerobic activity (Bacteroids)
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
Cephalosporins: general considerations
Ring structure less strained –> reduced tendency for hydrolyze & more stable penicillinase degradation
Acid & beta-lactamase stability
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
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.)
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
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
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
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
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
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%
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
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!!!)
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
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
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
Fungal morphology: Yeast
Round/oval that undergoes budding or fission; colonial growth is smooth
Fungal Morphology: Mold
Tubular structure (hyphae) that undergoes longitudinal extension & branching; colonial morphology is fuzzy
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
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
Dimorphic fungi
Fungi that can have both fungal morphology
Yeast form at 37 C
Mold form at 30 C
Ex: Histoplasma capsulatum, Coccidioides immitis
Reproduction in molds
Sexual state: teleomorph (perfect state)
Asexual state: anamorph (imperfect state)
Asexual form grows in culture & is the name we use clinically
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
Fungal culture
Sabouraud’s agar: 4% dextrose, at pH 5.5
Sugar & acidity discourage bacterial growth
Fungi grow very slowly in culture
Fungal identification in culture: yeast
Grows suspended in broth or on plates
Use metabolic reactions for specific organism identification
Fungal identification in culture: molds
Grow slowly & form conidia
Identify by conidial, hyphal, & colonial morphology
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)
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
Bactericidal: mathematical relationship
MBC less than or equal to MIC
Or 99.9% bacteria count reduction in 24 hrs
Bacteriostatic: mathematical relationship
MBC > 4x MIC
Tolerant: mathematical realtionship
MBC > 32x MIC
Bactericidal medications
Beta-lactams Aminoglycosides Vancomycin Fluoroquinolones Daptomycin Metronidazole
Bacteriostatic medications
Macrolides Tetracyclines Sulfonamides Clindamycin Linezolid Chloramphenicol
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
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
Antibiotic combinations: indifference
Combination is the sum of each alone
Antibiotic combinations: synergy
Combination better than the sum of each alone
Ex:
Ampicillin breaks down cell wall, allowing improved penetration of gentamicin into bacteria
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
Anti-microbial resistance: Intrinsic
An inherent attribute of a microbe
lacks necessary target
Ex:
Resistance of Enterococcus to cephalosporins
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
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
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
Mechanism for anti-microbial resistance: Decreased Antibiotic Access
Decrease Outer Membrane Permeability: Beta-Lactams
Decreased Cytoplasmic transport (influx): Aminoglycosides
Increased Efflux: Tetracyclines & Quinolones
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)
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)
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
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
Viral reverse transcriptase
Found in retro viruses
Converts RNA into DNA
Viral ds RNA transcriptase
Found in reo viruses
Copies dsRNA into ssRNA
Viral NTP phosphotransferase
Found in many enveloped virus
Phosphate exchange
Viral neuraminidase
Found in myxo & paramyxo virus
Cleaves cell surface sugars
Viral protein kinase
Found in myxo, retro, paramyxo, herpes
Phosphorylates proteins
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
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.
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
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
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
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”
Retroviruses: structure
Enveloped, with virus-specific membrane glycoprotein spikes.
Single-strand, dimeric RNA genome
Host tRNA
Reverse Transcriptase
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.
Human Retroviruses
Associated w/ leukemias (HTLVs) & AIDS (HIV)
HIV has a highly specific T4 lymphocytes/CD4 receptor
Viral genetics: recombination
Exchange of genes between 2 chromosomes by crossing over within regions of significant base sequence homology
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
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
RNA viral genome
All are ss except reoviridae
Positive stranded RNA viruses
retrovirus, togavirus, flavivirus, coronavirus, hepevirus, calicivirus, & picornavirus
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
Virus ploidy
All viruses are haploid except retrovirus (2 ssRNA)
RNA viral replication: location
Occurs in the cytoplasma
Except influenza & retrovirus
Viral envelopes: origin
Envelope is normally obtained by plasma membrane of a cell once it exits (except herpesvirses –> comes from nuclear membrane
Unenveloped viruses
Calicivirus, picornavirus, reovirus (RNA)
Parvovirus, adenovirus, papilloma, & polyoma (DNA)
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)
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
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)
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
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
