ID Exam 1

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ID Exam 1
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2013-09-10 20:16:56
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Material for exam one
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  1. Divisons of dna viruses
    Single stranded vs double stranded and enveloped vs non enveloped
  2. Double Stranded enveloped DNA viruses
    • Herpes simplex virus type 1
    • Herpes simples virus type 2
    • Varicella Zoster virus
    • epstein barr virus
    • cytomegalovirus
    • Hepatitis B
  3. Divison of RNA virus
    • Single vs double stranded
    • For singled stranded positive vs. negative
    • Non-enveloped vs enveloped
  4. Aerobic Gram + cocci coagulase + custers
    staphylococcus aureus
  5. Aerobic Gram + coagulase - clusters
    Staphylococcus epidermidis and staphylococcus saprophyticus
  6. Aerobic gram + cocci in pairs
    • Enterococcus spp., alpha hemolytic strptococci,
    • and beta Hemolytic streptococci
  7. Aerobic gram-positive bacilli
    • Bacillus spp.
    • coynebacterium spp.,
    • gardnerella barinalis,
    • actinomyces spp.,
    • lactovavacillus acidophilus,
    • listeria monocytogenes,
    • nocardia spp.
    • rhodococcus equi
  8. Aerobic gram - bacilli
    enterocacteriaceae
  9. Aerobic gram - bacilli Coliforms
    • Escherichia coli
    • Klebsiella spp.
    • Enterobacter spp.
    • Serratia marcescens
    • Citrobacter spp.
  10. Aerobic gram - bacilli Non-coliform
    • Proteus spp.
    • Providencia stuartii
    • mroganella morganii
    • Salmonella spp.
    • Shigella spp.
  11. Aerobic gram - fermentors
    • Enterobacteriaceae
    • aeromonas hyprophila
    • Vibrio Cholerae
    • Pasterella multocida
  12. Aerobic gram - Non-fermentors
    • Pseudomonas aeruginosa
    • Acinetobacter spp.
  13. Gram _ fastidious
    • Haemophilus spp
    • campylobacter jejuni
    • Legionella pneumophilia
  14. Aerobic gram - cocci
    • Moraxella catarrhalis
    • Neisseria spp.
  15. Gram + anerobes
    • Clostridium spp.
    • peptostreptococcus spp.
    • Propionibacterium acnes
  16. Anaerobes Gram -
    • Bacteroides fragilis
    • Prevotella spp. 
    • Fusobacterium spp.
  17. Atypical Bacteria
    • Chlamydia spp.
    • Mycoplasma spp.
    • Legionella spp.
  18. Minimum Inhibitory concentration (MIC)
    the lowest concentration of an agent that inhibits the visible growth of an organism
  19. Minimum bactericidal Concentration (MBC)
    The lowest concentration of an agent that results in a 99.9% reduction in colony forming units.
  20. Methods for determining MIC
    • Macro-broth dilution
    • micro-broth dilution
    • agar dilution
    • kirby bauer disk diffusion
    • Epsilometer strip
    • automated system
  21. Breakpoint values
    • system developed to aid clinicians evaluate MIC results.
    • Breakpoint value is based on:
    • drug pharmacokinetics and pharmacodynamics
    • distribution of MICS of a population of bacteria
    • clinical efficacy
  22. Antibiogram
    summarize of bacteria suscepatibleity to antibiotics
  23. Limitations of MIC
    • Do not provide regarding the rate or extent of bactericidal activity
    • MIC are conducted with a standard incoulum
    • Media does not contain plasma proteins or complement
  24. Serum inhibitory and bactericidal titers-schilcter test
    Following a dose blood is obtained and serially diluted. Bacteria are added to the serum and the inhibitory and bactericidal titers recorded.
  25. Serum inhibitory titer (SIT)
    the largest dilution of a sample that inhibits the visible growth of an organism
  26. Serum bactericidal titer (SBT)
    the largest dilution of a sample that results in a 99.9% reduction in colony forming units.
  27. Interpretation of SIT and SBT
    • Larger dilutions contain less drug
    • SIT and SBT take individual pharmcokinetics into account
    • Can be used to evaluate antimicrobial therapy
  28. Time kill curves
    • provide data regarding the dynamics of antimicrobial activity
    • broth is inoculated with a test isolate at a standard inocula and a known amount of antibiotic 
    • Samples are removed from testing containers at predetermined time points and plated on agar
  29. Inappropriate antibiotic use by clinicians
    • overuse of broad-spectrum agents
    • used for the treatment of non-bacterial infections
    • inappropriate antimicrobial prophylaxis
  30. Lack of patient education or ineffective education
    • Failure to complete antimicrobial regimens
    • non-compliance
    • patient self-medication
  31. Widespread antimicrobial use in the food production industry
    • Nearly 1/2 of the antibiotic usage is in farm animals
    • increasing reliance on aquaculture
  32. Primary Resistance
    • Naturally occurring 
    • Prior antimicrobial exposure is not required
    • predictable
    • also refereed to as inherent, intrinsic , or native resistance
  33. Secondary resistance
    • develops following antimicrobial exposure
    • Not predictable
    • Also referred to as acquired resistance
  34. selection of resistant subpopulation
    • a bacterial population is comprised of isolated with varying MIC
    • Isolates with low MIC are easily killed
    • Resistant subpopulations remian grow
  35. Genetic alterations
    • Spontaneous mutiations
    • acquisition of new genetic material
  36. Strategies to precent the spread of antibiotic resistance
    • Patient education 
    • knowledge of local susceptibility patterns
    • prescriber education
    • develop guidelines for appropriate antimicrobial usage
    • vaccination 
    • Hand washing
  37. Positive Stand RNA virus enveloped
    • rubella 
    • west nile 
    • Hepatitis C
    • HIV
  38. Negative stand enveloped RNA virus
    • Influenza virus
    • Respiratory syncytial virus (RSV)
    • Mumps
    • measles
    • rabies
    • ebola
    • haunta
  39. Genome
    • Either DNA or RNA-NOT BOTH
    • Single stranded ss or double stranded DS
    • sommonly ds DNA or ss Rna
  40. SS RNA
    the positive stand can be used directly as a template for protein synthesis while the negative strand cannot.
  41. Capsid
    • Protein shell
    • helical-rod shaped or coiled
    • icosahedral-symmetrical
    • complex-not helical or icosaherdral
  42. Steps of viral replication
    • 1. Viral adsorption/attachment
    • 2. viral penetration
    • 3. Viral uncoating
    • 4. replication of the viral genomes and other viral components
    • 5. self-assembly of progeny viruses (viral replication)
    • 6. Release of progeny viruses
  43. Viral adsoprtion/attachment
    • attachment of virus to a host cell
    • viral attachment structures
    • cell surface proteins often hijacked by viruses
  44. Viral pentration
    passage of the complete virus from the target cell surface into the cytoplasm through the membrane
  45. Viral uncoating
    • disassembly of the complete virus
    • depend on enzymes from the infected cells
  46. abortive infection of the host cells
    • No progeny virus is produced
    • the virus enters a cell that lack necessary machineries for replication
    • a defective virus 
    • Cell death due to viral infection
  47. Latent infection of host cells
    viral genome is within the infected cell, but no progeny is produced until viral reactivation
  48. Persistent activation
    The infected host cell lives and continues to divide and function
  49. Lytic infection
    the infected host cell dies because its normal macromolecule metabolism is impaired the infecting virus aims to maximize viral replication.
  50. Fall-Spring seasonal viruses
    • Influenza A & B
    • Respiratory synacial virus
  51. Fall, spring
    Parainfluenza 1,3,4
  52. Spring Fall seasonal virus
    • West Nile Virus
    • enterovirus
  53. Winter Seasonal Virus
    Rotavirus
  54. All season virus
    • Parainfluenza 3
    • Noravirus
    • Adenovirus
    • Herpes Simplex 
    • Varicella zoster
    • Cytomeglovirus
    • HIV
  55. Herpesviridae
    • Replicate within the nucleus
    • The envelop contains antigenix glycoproteins that are species and tissue specific
    • Following primary infection, all herpes virus can enter into the latent phase and be activated at a later time throughout life
  56. Alphaherpesvirinae
    • Herpes simplex virus 1
    • Herpes Simplex Virus 2
    • Varicella Zoster Virus HHV-3
  57. Betaherpesvirinae
    • Cytomegalovirus HHV-5
    • Human herpes virus 6
  58. Gammaherpesvirinae
    • Epstein Barr Virus HHV4
    • Human herpes virus 8
  59. Common site of HHV 1
    oropharyngeal and labiofacial surfaces, other sites
  60. Common Site of HHV 2
    Genital squamous surfaces
  61. Transmission of HHV 1
    • Saliva to oropharyngeal and labiofacial surfaces
    • Some cases of skin-to-skin transmission
  62. Transmission of HHV 2
    Intimate sexual contact
  63. Presentation of HHV1 and HHV 2
    cutaneous herpes lesions that heal without scarring
  64. Latency of HHV 1
    Migrate through the sensory nerves fibers to the trigemental gangion and persists indefinitely in a dormant state
  65. Latency of HHV2
    • Migrate to the sacral neural ganglia. 
    • Reactivation rates are at least twice as high with HHV 1
  66. Immunocompromised Patients and HHV
    • Reactivate of HHV is only a problem for immunocompromised patients
    • Encephalitis and meningits are the main problems
  67. Varicella Zoster Virus-Chicken pox
    • Prutic vesicles progresses to ulcers, crust over and heal without scarring
    • mild symptoms and minimal sequalae
    • Virons travel by nerve fivers to regional sensory neural ganglions
  68. Varicella Zoster virus-Shingles
    • Reactivation of primary infection
    • Spreads from trigeminal or dorsal root ganglia back down nerve fibers to the skin producing painful cutaneous vesicles with a classic dermatome distribution
    • Can be very painful
  69. Human papillomavirus (HPV)
    • ds non-enveloped DNA virus
    • over 70+ strands
    • Induce hyperplastic epithelial lesion and malinancies
    • Most HPV warts of the hands and feet are transient and has no medical consequence
  70. sexually transmitted HPV
    • Anogenital wart: HPV 6 HPV 11
    • Carcinoma: HPV 16 HPV 18
    • Oral Cancer: HPV 13 and HPV 32
  71. Human Herpes 8 virus
    Kaposi sarcoma in severely immunocompromised patients. Specifically AIDs
  72. Exanthems
    • Widespread rash usually in children
    • Caused by viruses that spread hematogenously to skin and mucous membranes
  73. Coxasackie virus (hand-foot-and mouth disease)
    • Transmitted by direct contact with nose and throat discharge, saliva, fluid from blisters, or the stools of an infected person
    • most contagious during the first week; 3-7 days before system appear
    • transmission by inhalation or ingestion
  74. Other Coxasackie viruses
    • Herpangina
    • myocarditis
    • myostit
    • pericarditis
  75. HHV 6 Roseola
    • A high fever followed by a rash on neck trunk and thigh commonly seen in infants
    • transmission from saliva possible
  76. Measles Virus
    • ssRNA - enveloped viruses
    • transmission by sneezing/coughing droptlets
    • extremely infectious
    • Replicate in respiratory epithelial cells, then in lymphoid organce
  77. symptoms of measles
    • Rash
    • fever
    • upper respiratory tract symptoms
    • conjuncitivitis
    • Initial infection probably occurred 1-2 weeks prior
    • Once the rash appears the patient is not infectious
  78. Rubella Virus
    • ssRNA + enveloped viruses
    • Respiratory transmitted
    • Commonly called german measles
  79. Congenital rubella
    significant damages to fetus due to necrosis in fetus
  80. Smallpox
    • One of the most deadly viral infections in human history
    • Large ds DNA virus with complex genome
    • Caused by either of two virus variants
    • variola major and minor
    • No specific treatment the only prevention is vaccination
    • potentials as biologic weapon
  81. Transmission of smallpox
    • direct and fairly prolonged face-to-face contact
    • direct contact with infected bodily fluids or contaminated objects such as bedding or clothing
    • respiratory-uncommon
  82. Disease course of small pox
    • Incubation 1-2 weeks, asymptomatic, not contagious
    • Early symptoms, 3-4 days, high fever, malaise, head and body aches, and sometimes vomiting, may be contagious
    • Rash and pustules, 1-2 weeks very contagious
    • Resolution, 1 week contagious
  83. Rhinovirus
    • common cold
    • acid labile
  84. Coronavirus
    • common cold 
    • GI infection
  85. Adenovirus
    • common cold
    • GI infections
  86. Influenza virus (A & B)
    • Influenza
    • pneumonia
  87. Parainfluenza 1-4
    • common cold
    • pneumonia
    • croup in young children
  88. respiratory syncytial virus (RSV)
    Lower respiratory tract infections
  89. Human metapneumorvirus
    Upper and lower respiratory tract infections.
  90. SARS corona virus
    • Severe acute respiratory syndrome
    • Causes both upper and lower respiratory tract infections, muscle pain, fever
    • Highly contagious; 10% mortality
    • Originated from China & spread to N America
  91. Rotavirus-
    • Around winter months
    • Causes most cases of watery diarrhea in infants and young children in the US
    • Highly infectious 30%-50%
    • Dehydration with electrolyte imbalance is the most serious complication
  92. Adenovirus enteritits
    Clinically similar to rotavirus disease but has no seasonality
  93. Norovirus
    • affect children and adults-BUT NEVER INFANTS
    • year round
    • Can be non-enveloped can survive for days on inanimate surfaces
    • acute gastroenteritis
    • Oral fecal transmission
  94. Coronavirus and astrovirus
    Cause nosocominal and day care center outbreaks
  95. Mumps
    • ssRNA - enveloped viruses
    • Transmission by respiratory droplets followed by viremia
    • Usually affect children
    • Acute febrile infection and swelling on the parotid gland in 2/3 patents
  96. Complications of Mumps
    • Viral encephalitis 
    • Deafness
    • Male sterillity
  97. HSV encephalitis
    • Uncommon in immunocompetent patients
    • Usually occurs as a reactivation of latent HSV-1 that tracks into the cerebral cortex, producing a large necrotic mass
    • Progression is rapid and mortality is high
    • We have drug therapy for this
  98. Enteroviruses
    • ~75% of viral meningitis in the US 
    • usually a relatively benign and transient disease in children and young adults
    • coxsacki virus and echovirus
    • spread easily from person to person via fecal oral means
    • Often with annual summer-fall outbreaks
  99. Polio Virus
    • Very uncommon in the US
    • transmission by ingestion 
    • necrosis of spinal cord or brainstem motor neurons
    • Many asymptomatic but can cause flaccid paralysis
  100. Arbociruses
    • This family mostly comes from insects
    • Flavivirus
    • togavirus
    • bunyavirus
    • West Nile virus
  101. West nile virus
    • simple fever to meningits, encephalitis, and flaccid poliomyelitis paralysis
    • Long term encephalitic and paralytic disabilities
    • many fatalities-mostly elderly and immunocompromised patients
    • Detected by IgM and IgG in CSF or serum
  102. Infectious Mononucleosis
    • caused by Epstein Barr cirus
    • spread by saliva and infect B cells
    • primary infection in early childhood is usually asymptomatic 
    • Classical occurs in the young adult years
  103. Signs and symptoms of mononucleosis
    • sore throat
    • fever
    • tonsillitis
    • lymphadenopathy
    • splenomegaly
    • hepatitis
    • fatigue
    • malaise
  104. Other diseases Epstein barr virus
    • Nasopharyngeal carcinoma in Asians
    • Burkitts lymphoma Africa
  105. Chronic Fatigue Syndrome
    • Defined by clinical signs and symptoms rather than laboratory results
    • Presistent fatigue accompanied by:
    • fever
    • pharyngitis
    • tender lymphadenopathy
    • athralgia
    • myalgia
  106. Epstein Barr Virus (EBV)
    • Reactivation of latent EBV infection is linked to:
    • B cell CNS Lymphoma in AIDS patients
    • Post-transplant lympohoproliferative disorder (PTIF) in transplant patients
  107. Cytomegalovirus (CMV, HHV-5)
    The most common opportunistic viral infection in HIV and transplant patients
  108. Cytomegalovirus symptoms
    • Pneumonia
    • Hepatitis
    • encephalitis
    • esophagitis
    • enterocolitis
    • gastritis in HIV/AIDS patients
    • Retinitis
    • GI tissue damage 
    • graft damage in transplant patients
  109. Polyoma viruses
    JC virus and Bk virus
  110. Progressive multifocal leukoenocephalopathy (PML)
    a rare fatal and demyelinating CNS disease
  111. Parovirus 819
    Refractory anemia and pansytopenia(low WBC, RBC, and platelets)
  112. Rabies Virus ssRNA-
    • transmission by direct animal/human bite sometimes by respiratory tract by infected bat dropping
    • The virus replicate locally then move to the CNS through the peripheral neurons and then move to many organs through the autonomic nervous system
    • Disease course 1-8 weeks latent in the beginning but highly variable
    • Hallucinations, mental dysfunction, aggression, seizure, coma and death
    • Once symptoms begin death is inevitable
  113. Ebola Virus
    Hemorrhagic fever high mortality
  114. Marburg Virus
    • Hemorrhagic fever 
    • high mortality
  115. Hanta virus
    • Hemorrhagic fever with or without renal syndrome and pulmonary syndrome 
    • high mortality
  116. Beta lactamases
    • Produced by numerous gram+ and gram- microorganisms
    • Inactivate beta lactam antibiotics by splitting the amide bond of the beta lactam ring
    • Production of beta lactamases is either constitutive or inducible
  117. Microorganism with inducible beta lactamases
    • Enterobacter spp
    • Citrobacter freundii
    • Serratia marcescens
    • Pseudomonas aeruginosa
  118. Several agents are potent inducers of beta lactamases
    • Cefotaxime 
    • ceftriazidie
    • imipenem
    • Ceftazidime
  119. Extended spectrum beta lactamases (ESBL)
    • Active against all B-lactams except cephamycins, cefepime, and carbapenems
    • Inhibited by B-lactamase inhibitors
    • Most commonly found in K. pneumonia and E. coli
    • Genes are located on plasmids
  120. AmpC type B-lactamases
    • Active against all B-lactams except cefepime and carbapenems
    • not inhibited by b-lactamse inhibitors
    •  Most commonly found in K. pneumonia, enterobacter spp, C. freundii, M. morgannii, S. marcescens, and P. aeruginosa
    • Genes found on chromosomes and plasmids. Expression may be inducable
  121. Klebsiella pneumoniae carbapenemase (KPC)
    • Encoded for by the blaKPC gene
    • Extensive cross resistance with other classes of antibiotics
    • Only susceptible to colistin or tigecycline
    • Expression is independently associated with increased mortality
    • Standard susceptiblity testing may not identify KPC production
    • Use a modified Hodge test
  122. Strategies to overcome B-lactamase mediated resistance
    • Administer large doses of B-lactams to overwhelm the B-lactamases
    • Combine b-lactams with b-lactamase inhibitors such as tazobactam, clavulanate, and sulbactam.
  123. Aminoglycoside resistance modifying enzymes
    • Modification as the aminoglycoside is transported across the cell wall of the microorganism
    • Commonly observed among enterococci exhibiting high lavel aminoglycoside resistance
    • Chloramphenicol acetyltransferase
    • erthromycin estrase
  124. Alteration of the antimicrobial target or active site
    • 1. Penicillin-binding proteins (PBP)
    • 2. ribosomal binding sites
    • 3. Cell wall precursors
    • 4. DNA gyrases
  125. Alterations in bacterial cellular membranes
    • Porin channels-Change in #
    • Transport proteins
    • Effllux Pumps-proteins that actively pump agent out of the bacteria
  126. B-lactams Gram +
    • Most resistance is secondary to expression of PBP that bind B-lactams with low affinity
    • Staphylococcus are the only gram+ that produce B-lactamses
    • staphylococci can also express an altered PBP2a.
    • This is encoded for by the mec determinant found on the mobile staphylococcal chromosomal cassette mec elements
  127. Gram- B-Lactams
    • Most reistance is seondary to the production of B-Lactamses
    • developed in 4 waves:
    • 1. emergence of narrow spectrum penicillinases
    • 2. ESBL(resistance to extended spectrum cephalosporins, mainly K. pneumoniae
    • 3. CTX-M
    • 4.Carbapenemases
  128. Glycopeptides
    • High level resistance results from expression of operons that substitute a terminal d-lactate or d-serine for d-alanine
    • Reduced vancomycin affinity
    • Typically is only stable in the setting of continued vancomycin selective pressure
  129. Fluoroquinolones
    • Resistance reults secondary to accumulations of point mutations in topoisomerases
    • In general single point mutations result in low-level resistance-Mutant prevention concentration
  130. Methicillin-resistant Staphylococcus aureus (MRSA)
    • Common nosocomial pathogen
    • Isolation in the community is increasingly common especially among IVDU
    • Resitance is secondary to the production of an altered PVP
    • Resistance may be transferred via plasmids or transposons
    • Multiple resistance to many common anti-staphylococcal agents is frequently encountered
    • Treatment of choice is vancomycin
  131. Vancomycin Intermediate susceptibility(VISA)
    • VISA may be due to alterations in the cell wall and altered autolytic expression.
    • TMP/SMX may be a treatment option for VISA
  132. vancomycin resistant susceptibility(VRSA)
    VRSA isolates possessed mecA and vanA genes. This suggests transfer of resistance determinants from enterococci
  133. Penicillin resistant streptococcus pneumoniae
    • S. pneumoniae is a common cause of a variety of community acquired infections including otits media, pneumonia, sinusitis, and pneumonia
    • Overuse of antimicrobials in the community setting has overtime selected for resistant organisms
    • The prevalence of penicillin-resistant isolates in the United states has risen
    • The prevalence of penicllin resistance caries geographically and found more with people under the age of 6
    • Pneumococcal resistance to penicillin is the result of expression of modified penicillin binding proteins
    • Antimicrobial resistance in vitro does not necessarily translate into clincal resistance
    • In the case of pneumonia even high level PCN resistance among pneumococci has not been clearly associated with PCN failure
  134. Enterococcus
    • Increasingly common nosocomial pathogen
    • Intrinsically resistant to numerous antimicrobials including cephalosporins and TMP/SMZ
    • Monotherapy with penicillins or vancomycin are static
    • Combination therapy with an aminoglycoside is necessary for a cidal effect
    • acquired resistance to the penicillins is due to alterations is PBP
    • High level aminoglycoside resistance is conferred by the production of amino glycoside modifying enzyems
    • Isolation of vancomycin resistant strains is becoming increasingly problematic
  135. Three distinct genomic variants are responsible
    • Van A: Inducible high level resistance to vancomycin and teicoplainin
    • Van B: Inducible resistance to vancomycin susceptible to teicoplanin
    • Van C: constitutive resistance to vancomycin may be susceptible to teicoplanin
  136. treatment strategies for enterococcus
    • Vancomycin, linezolid, daptomycin. and streptogramins
    • Intermittent vs. continusous infusions of b-lactams and vancomycin
    • Tradition vs. once daily dosing of amino glycosides

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