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Glossary of Microbiology 6

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mycobacterium: C content
60-90 C
GC content of DNA, mycobacterium
high GC content
mycobacterium
- gram stain
gram(+)
what is different about the peptidoglycan layer of mycobacterium?
peptidoglycan skeleton is covalently linked with arabinogalactan-mycolyic acid molecules
name three acid-fast stains
(1) Ziehl-Neelsen

(2) Kinyouns

(3) auramine / rhodumine
does mycobacterial cell wall confer relative resistance to acids and alkalis?
YES
does mycobacterial cell wall confer relative resistance to dehydration?
YES
mycobacterium tuberculosis complex (what 3 items)
(1) M. tuberculosis

(2) M. bovis

(3) M. africanum
M. tuberculosis
- habitat
- 1st route of transmission
humans

person-to-person by inhalation of droplets
M. bovis
- habitat
- 1st route of transmission
humans and wide range of animals

ingestion of contaminated milk from infected cows; airborne transmission
M. africanum
- habitat
- 1st route of transmission
humans (maybe animals)

inhalation of droplets
mycobacteria --> inc activation of CD4+ cells --> INC antibody production

effective in controlling mycobacterial disease?
NO
how long after infection with mycobacterium is the PPD positive?
4-6 weeks
what are the four types of cultivable NTM?
(1) photochromogens

(2) scotochromogens

(3) non-photochromogens

(4) rapidly growing mycobacteria
photochromogens
- definition
- two examples
only produce yellow carotenoid pigments after exposure to light; slow growers

M. kansasii, M. marinum
scotochromogens
- definition
- two examples
produce yellow carotenoids in the dark and light; slow growers

M. szulgai, M. scrofulaceum
non-photochromogens
- definition
- two examples
non-pigmented NTM; slow growers

M. avium complex, M. genovense
give three examples of cultivable NTM: relatively rapidly growing mycobacteria
M. fortuitum, M. chelonae, M. abscessus
name 4 possible drugs used to combat M. tuberculosis (standard regimen)
(1) Isoniazid

(2) Rifampin

(3) Ethambutol

(4) Pyrizinamide
M. tuberculosis: Isoniazid treatment
- MOA
- MOR
inhib mycolic acid synth

(1) mutation of gene for catalase (katG) that converts prodrug to active intracellular form

(2) mutation of gene for target enzyme involved in mycolic acid synthesis (inhA)
Isoniazid
- what type of administration for M. tuberculosis?
ORAL only
Isoniazid
- cleared how?
inactivated by acetylation in liver and acetylated derivative excreted in the urine
Rifampin
- MOA
- MOR
inhibits DNA-dependent RNA polymerase

mutation of target enzyme
list two important points about the pharmacology of Rifampin
(1) potent inducer of P450 enzymes; prominent drug-drug interactions with other hepatically metabolized drugs

(2) penetrates well into most tissues (turns urine and secretions orange)
what is the spectrum of Rifampin?
M. tuberculosis, staphylococci, Neisseria sp., Legionella sp., Brucella sp.
M. avium-intracellulare
- first line regiment
consists of a macrolide (azithromycin or clarithromycin) + ethambutal + rifabutin (rifampin derivative)
M. leprae
- regiment
dapsone (a sulfone) + rifampin for initial therapy followed by dapsone alone
anti-tuberculous regimens
- standard
- latent
standard therapy: INH + RIF + EMB + PZA for two months; INH + RIF for four months

latent (+ PPD with negative chest x-ray): INH alone for 9 months
what can you say about the lipid content of mycobacterial cell wall?
VERY HIGH
cord factor & LAM
aka trehalose dimycolate & lioarabininomannan

possible virulence factors in mycobacterial cell wall
how long can it take for mycobacteria to come up in culture?
up to 8 weeks!
M. tuberculosis
- reservoir
strictly human
M. avium
- reservoir
environmental
MTB complex
- pigmented?
no
during primary infection, before the development of hypersensitivity, m. tuberculosis growth is . . .
uninhibited
what's the main non-cultivable NTM to remember?
M. leprae
compare the CMI / humoral responses of tuberculoid and lepromatous leprosy
tuberculoid --> strong CMI but weak humoral antibody response

lepromatous --> strong humoral response but weak CMI
desc the lepromin skin test
tuberculoid --> reactivity to lepromin

lepromatous --> non-reactivity to lepromin
which relatively fast growing NTM is implicated in face lift and nail salon skin problems?
M. chelonae
What kind of media is Lowestein-Jensen?
selective agar
What kind of media is MGIT System?
broth medium
susceptible MTB strains
- definition
isolated from patients before treatment and contains less than 1% of the bacterial population resistant to any of the anti-TB drugs
how does M. tuberculosis become resistant to drugs?
NOT via plasmid pickup

YES via spontaneous mutation
toxicity for INH
rare but serious: idiosyncractic hepatotoxicity can result in massive hepatic necrosis

Also, peripheral neuropathy due to inhibition of vitamin B6
what is the most potent drug known for inducing cytochrome P450 enzymes?
rifampin
what are the two important interactions of rifampin?
(1) INC P450

(2) turns secretions orange
spectrum for rifampin
mycobacteria, staphylococci, legionella
EMB and renal failure
adjust dose to prevent ocular toxicity
what is a good second line mycobacterial drug to know?
especially know fluoroquinolone
compare the amount of mycolic acid in cell wall of nocardia to mycobacterium
nocardia has less
what are the two main examples of Nocardia species you want to remember?
N. asteroides complex, N. brasiliensis
where in general are nocardia species found?
environmental bacteria
what is the most common cause of actinomycosis?
actinomyces israelli
anaerobic actinomyces
- acidfast?
- produce what always?
- e.g.
no

produce granules

e.g. A. iraelli
DOCs for Nocardia?
sulfonamides, trimethoprim/sulfamethoxazole

others -- amikacin, tobramycin, ceftriaxone, imipenem
which aerobic actinomycetes have mycolic acid?
nocardia, rhodococcus, gordonia, tsukamurella, corynebacterium
which aerobic actinomycetes don't have mycolic acid?
streptomyces, actinomadura, dermatophilus, nocardiopsis, rothia, tropheryma, thermophilic actinomycetes
which bacteria are primarily responsible for decomposition of plant material?
nocardia
at what temp are viruses inactivated?
60C for 30 min for most

except 100 C for adeno, HBV, and scrapie

so to be safe, use 100 C for 30 min
1 M MgCl2 heat stabilizes what?
picornaviridae
1 M MgSO4 heat stabilizes what?
orthomyxoviridae and paramyxoviridae
1 M Na2SO4 heat stabilizes what?
herpetoviridae
which viruses remain localized in the respiratory tract?
(1) orthomyxoviridae

(2) paramyxoviridae

(3) coronaviridae
give two examples of cytocidal result of virus infection at the cellular level
poliovirus infection of nerve cells

rabies infection of nerve cells
cowdry type A intranuclear body
an inclusion body in nerve cells or in epithelial cells for herpes viruses
negri bodies
inclusion body within the nerve cell cytoplasm for rabies virus
guarnieri bodies
inclusion body in epithelial cells for smallpox or vaccinia virus in the cytoplasm
is viral attchment pH or temp dependent?
pH dependent, temp-independent
HIV
- attaches to which receptors?
T4 (CD4) receptors on T-helper cells, macophage subsets, and microglial cells in the brain

chemokine co-receptors such as CCR5 (for mac/monocyte-tropic strains) and CXCR4 (for lymphocyte-tropic) strains are also involved
Poliovirus
- attaches to which receptor?
attaches to a poliovirus receptor (PVI) which is similar to tissue-specific inter-cellular adhesion molecules (ICAM)
orthomyxoviruses and paramyxoviruses
- attaches to which receptors?
mucoprotein receptors in the respiratory tract
rabies viruses
- attach to which receptors?
nicotinic ACh receptors on neurons
Epstein-Barr virus
- attaches to which receptor?
C3d receptor on B lymphocytes
is penetration of viruses temp-dependent?
YES
transcription
- herpetoviridae, adenoviridae, papoviridae, and some parvoviridae use
cellular DNA-dependent RNA polymerase
transcription
- poxviridae utilize
viral DNA-dependent RNA polymerase
transcription
- arenaviridae, bunyaviridae, orthomyxoviridae, paramyxoviridae, rheoviridae, and rhabdoviridae use
virion-associated RNA-dependent RNA polymerase
transcription
- retroviridae use
a virion-associated RNA-dependent DNA polymerase
where does virus assembly occur for adenoviridae, papovaviridae, and parvoviridae?
nucleus
where does virus assembly occur for picornaviridae and poxviridae?
in cytoplasmic "cell factories"
where does virus assembly occur for herptoviridae?
nuclear membrane
where does virus assembly occur for orthomyxoviridae, paramyxoviridae, and rhabdoviridae?
cell surface membranes
how does virus release occur for picornaviridae and rheoviridae?
by cell lysis
how does virus release occur for orthomyxo, paramyxo, rhambdo, retro, and togaviridae?
budding from the cytoplasmic membrane
how does virus release occur for herpetoviridae?
through the ER and golgi
all animal DNA viruses replicate in the nucleus of the infected cell with the exception of
poxviridine (replicates in cytoplasm)
which DNA viruses are not naked?
herpetoviridae (obtains cell envelope from nuclear membrane of the virus-infected cell)

poxyviridae (complex lipid-protein mix on surface)

hepadnaviridae (lipoprotein-like material on their surface)
where do DNA viruses synth their DNA and assemble capsids? exception?
in the nucleus

exception: poxviruses
concerted assembly
- definition and three examples
concerted assembly -- viral particles are assembled around or in conjunction with the nucleic acid and in many cases the nucleic acid itself plays an important structural role in organizing the protein-protein interactions needed for particle assembly

e.g. retroviruses, vesicular stomatitis virus, poxviruses
sequential assembly
- definition and two examples
sequential assembly -- empty capsids are built first, then the nucleic acid is actively transported (packaged) into the capsids

e.g. adenovirus, herpesviruses
structural unit (of capsid)
structural units -- stable, multisubunit components of capsids that form prior to full assembly of the capsid
give two examples of viruses that require scaffold proteins
icosahedral capsids of adeno and herpesviruses require scaffold proteins
HSV VP16
HSV VP16 is a potent transcriptional activator that turns on HSV immediate early genes
HSV VHS
HSV VHS (virion host shutoff) is a ribonuclease that non-specifically digests mRNAs, shutting off host protein synth immediately after infection
viremia
viremia -- cell-associated or free infectious virus in the blood
list the neurotropic viruses
polio, rabies, HSV, VZV
feces
- major transmission route for which viruses?
enteroviruses, including poliovirus and hepatitis A
blood
- main route of spread for which viruses?
HBV and hemorrhagic viruses
semen
- main route of spread for which viruses?
herpesviruses and HBV
which viruses are mainly spread via breast milk?
mumps and cytomegalovirus
which viruses are mainly spread via skin lesions?
pox, varicella zoster virus, ebola, VZV
which viruses are mainly spread via genital lesions?
HSV, human papilloma virus (HPV)
what are the four classes of genes involved in pathogenesis?
(1) genes that are needed for replication in certain cell types

(2) genes involved in immune evasion

(3) genes involved in dissemination

(4) genes that produce toxic products
Th1 cells tend to promote what type of response?
proinflammatory and cell-mediated responses
Th2 cells tend to promote what type of response?
B cell development and antibody production
desc progression of Dengue Hemorrhagic Fever
Dengue Hemorrhagic Fever

- preexisting antibodies to a different serotype (from a previous infection) actually facilitate viral infection of monocytes by coating the viral particles with antibodies!
- infected monocytes then produce large amounts of pro-inflammatory cytokines which initiate a cytokine self-stimulating loop that culminates in severe leakage of the blood vessels and hemorrhagic fever
from where are Th cells derived?
derived from CD4+ precursor cells
what effect can the paramyxoviridae family of viruses have on the Jak/STAT signal transduction pathway?
can either degrade or alter Stat proteins to inhibit IFN signaling
antigenic shift is the hallmark of which virus?
influenza
T/F in the early stages of mycobacterium tuberculosis infection, before the development of hypersensitivity, microbial growth is uninhibited
T
PPD skin test
- what type of hypersensitivity rxn?
delayed-type hypersensitivity rxn (type IV)
tuberculosis rule of fives
droplet nuclei are 5 micrometers and contain 5 mycobacterium tuberculosis bacilli

patients infected with M. tuberculosis hav ea 5% risk of reactivation in the first 2 years and then a 5% lifetime risk

patients with "high five" HIV will have a 5 + 5% (10%) risk of reactivation per year!
what is required to grow M. leprae in the lab?
it's impossible to grow this bacterium on artificial media
do lepromatous leprosy patients show a positive lepromin skin test?
No, b/c they cannot mount a cell-mediated immune response (contrast with TL, which can)
what is the mech of action of EMB?
inhibits enzyme that complexes mycolic acid to cell wall component
what is the mnemonic for ethambutol adverse effects
ethane-butane flame torch, torching an eye (ocular toxicity)
which three drugs are used in the treatment of leprosy?
dapsone, rifampin, and clofazimine
rhodococcus equi
organism most commonly associated with human disease, particularly immunocompromised patients
thermophilic actinomycetes
aerobic actinomycete with no mycolic acid

responsible for hypersensitivity pneumonitis (an allergic rxn)
actinomyces israelii
- general characteristics (3)
- clinical manifestation
- treatment
general characteristics
- produce "sulfur granules"
- NOT acidfast
- anaerobic, gram+ filamentous branching rods

clinical manifestation:
- abscesses with draining sinus tracts

treatment:
- penicillin G and surgical drainage
OTE: what aerobic actinomycetete with mycolic acid is the main one to remember?
nocardia
how do you distinguish b/t actinomyces and nocardia?
only actinomyces forms sulfur granules (israelii) and only nocardia is acid-fast
list the criteria used to select an antibiotic for a patient
(1) is it effective for the organism causing the infection?

(2) Is it the least toxic of all available effective agents?

(3) Is it the least expensive of potentially effective and well tolerated drugs?

(4) Are there any considerations in an individual patient to a particular drug, such as allergy, potential drug interactions, history of lack of response, or intolerance?

Note: the drug(s) that best fulfill the first 3 considerations = DOC
list (4) bacteriostatic antibiotics
(1) tetracycline

(2) linezolid

(3) clindamycin

(4) macrolides
list (4) bactericidal antibiotics
(1) B-lactams

(2) fluoroquinolones

(3) aminoglycosides

(4) vancomycin
Describe what is meant when an organism is said to be "susceptible" or "resistant" to an antibiotic using the following terms: MIC, breakpoint, and serum concentration.
In general, an organism can be considered susceptible to an antibiotic if the MIC is <= 1/4 of the peak serum concentration achieved with the usual, safe doses. This concentration (i.e. 1/4 of the peak serum level) which separates susceptible from resistant bacteria is called the breakpoint.
S. pneumoniae, DOC
- pneumonia, hospitalized pt
- pneumonia, less serious
- meningitis
- pneumonia, hospitalized pt

Ceftriaxone (+ macrolide) or newer quinolone

- pneumonia, less serious

Amoxicillin or doxycycline or a newer quinolone

- meningitis

Ceftriaxone + vancomycin +/- rifampin until susceptibilities are known
S. pyogens, DOC
- pharyngitis
- skin/soft tissue
- pharyngitis

amoxicillin or penicillin G

- skin/soft tissue

penicillin G or dicloxaciliin or clindamycin
E. faecalis, DOC
- recurrent UTIs
- endocarditis
- recurrent UTIs

amoxicillin

- endocarditis

penicillin G or ampicillin + gentamicin
S. aureus, DOC
- skin/soft tissue infections
- bacteremia, endocarditis & osteomyelitis
- skin/soft tissue infections

MSSA: penicillinase-resistant penicillin

- bacteremia, endocarditis & osteomyelitis

MSSA: penicillinase-resistant penicillin
MRSA: vancomycin
N. gonorrhea, DOC
- gonococcal urethritis
Quinolone or ceftriaxone or cefpodoxime
E. coli, DOC
- UTI
- Hospital: bacteremia / serious infections
- UTI

TMP / SMX or quinolone

- Hospital: bacteremia / serious infections

3rd-generation cephalosporin
Klebsiella pneumoniae, DOC
- UTI
- Hospital: bacteremia / serious infections
- UTI

TMP / SMX or quinolone

- Hospital: bacteremia / serious infections

3rd-generation cephalosporin
Bacteroides fragilis group, DOC
- Intra-abdominal abscess
clindamycin or metronidazole or B-lactam/B-lactamase inhibitor
P. aeruginosa, DOC
- UTI (hospital)
- Bacteremia / other serious infection
- UTI (hospital)

quinolone

- Bacteremia / other serious infection

Aminoglycoside plus anti-pseudomonal penicillin, or ceftazidime, or cefipime, or imipenem, or aztreonam
C. difficile, DOC
- antibiotic-associated colitis and pseudomembranous colitis
Metronidozole

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