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Microbiology > M1: CC1: Intro to Clinical Infectious Diseases > Flashcards

M1: CC1: Intro to Clinical Infectious Diseases Flashcards

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Biology 101 flashcards
1
Q

infectious etiologies (5)

A

bacteria (gram+, gram-, acid-fast, intracellular, others)
viruses (RNA, DNA)
fungi (yeasts, molds, dimorphic fungi)
parasites (protozoa, helminths, ectoparasites)
prions

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2
Q

nomenclature:

Genus and species (applies only to _)

Organism should be in _

Genus name should (be/not be) capitalized and the species name should (be/not be) capitalized (eg. _)

Genus name can be _ (eg, _)

Disease name should be _

Spp. is _ (eg, _); (do/do not) italicize it.

A

bacteria, fungi, and parasites

italics

be
not be
eg, Staphylococcus aureus

abbreviated after its first mention
eg, S. aureus

in normal print

an abbreviation for species
eg, Enterococcus spp
do not

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3
Q

micro-organisms:
colonizers

10^12 micro-organisms per human (consists of (more/fewer) human cells)

Most organisms are colonizers of _.

They prevent _.

There are many essential functions that bacteria have, such as _ and _

A

fewer

gut and skin

other more pathogenic bacteria from overtaking and hurting us

fermenting carbohydrates in our intestines
producing our essential Vitamin K

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4
Q

micro-organisms:
opportunists

These organisms (do/do not) normally cause any harm

However, _.

For example, when inserting a plastic catheter through the skin, _ can get access into the
bloodstream and cause _.

A

do not

at the wrong place at the wrong time they can cause disease

Staphylococci
bacteremia

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5
Q

micro-organisms:
pathogens

Some organisms are always (helpful/harmful) to us such as Ebola virus.

Our immune system is constantly _

A

harmful

at the look-out to neutralize them

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6
Q

how we can identify bacteria, viruses, fungi, & parasites:
appearance

Sometimes by _ (some parasites)

mostly by looking at a _ (bacteria)

or by _ (viruses)

A

naked eye

Gram stain through a microscope

electron microscopy

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7
Q

how we can identify bacteria, viruses, fungi, & parasites:
culture

grow the bacteria and fungi on _

viruses on _

A

media

cell culture

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8
Q

how we can identify bacteria, viruses, fungi, & parasites:
antigen recognition

By using _ that attaches to proteins of a specific micro-organism

By _ through the immune response of the host; detect _ in blood serum that are directed towards specific micro-organisms

A

fluorescent dyes (DFA = Direct Fluorescent Antibody)

serology
IgM and IgG antibodies

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9
Q

how we can identify bacteria, viruses, fungi, & parasites:
biochemical properties

Mostly useful for _ & some _

Tests of _ (coagulase activity in Staphylococci)

Tests of _, e.g. lactose fermentation in E. coli

A

metabolically active bacteria
fungi

enzymatic activity

carbohydrate fermentation/utilization

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10
Q

how we can identify bacteria, viruses, fungi, & parasites:
gene detection

_ of known viral or bacterial genetic sequences (GeneXpert for Mycobacterium tuberculosis in sputum)

Bacterial gene sequences analyzed with help of the _ (16S ribosomal DNA)

A

PCR: primer recognition

BLAST database

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11
Q

how we can identify bacteria, viruses, fungi, & parasites:
protein detection

_, rapidly becoming commonplace in medical microbiology laboratories.

A

Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS)

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12
Q

infectious differential diagnosis

A differential diagnosis is _.

First we have to decide between _ vs. _ causes of an illness.

If it is _, than we have to differentiate between _, _, _, or _organisms.

In order to perform the appropriate tests and treat the patient we often have to guess first, based on _, _, _ and _.

A

the list of possible diagnoses for the symptoms and signs of the patient

infectious vs. non-infectious

infectious
bacterial, viral, fungal, or parasitic

pattern recognition, exposures, incubation time and epidemiology

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13
Q

laboratory investigations:

The differential diagnosis can be shortened by use of appropriate investigations and the collection of specimens from the patient can allow:

1) _ to be made; the collection of specimens should ideally take place _ antimicrobials are given, since this will decrease the
chance of _

2) a prediction to which _ the organism is susceptible

A

precise microbiologic diagnosis
before
recovering the causative organism

antimicrobials

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14
Q

laboratory investigations:
caveat:

Many body sites have _

Therefore, cultures from body sites need to be interpreted in view of these _:

  • The _ is covered by coagulase negative staphylococci, corynebacteria, etc
  • The _, _, and _ are full of organisms
  • The _ is full of organisms
A

their own resident bacterial flora
colononizers

skin

mouth, pharynx and vagina

gut

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15
Q

The resident (colonizing) human microflora can obscure investigations into clinical infectious diseases:

The human _ and _ harbor 10^9 micro-organisms representing 700 species

The isolation of colonzers occasionally associated w/ disease states is (common/uncommon) in healthy persons

A

mouth and pharynx

common

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16
Q

Disease states associated w/ colonizers:

o viridans streptococci

o HACEK group organisms

o Fusobacterium spp.

o Neisseria meningitidis

o Candida albicans (yeast)

A

o endocarditis

o endocarditis

o bacteremias

o meningitis

o thrush

17
Q

if viridans streptococci or HACEK organisms (Haemophilus parainfluenzae, Aggregatibacter spp., Cardiobacterium hominis, Eikenella corrodens, Kingella kingae) stick to fibrin-platelet thrombi on damaged heart valves causing persistent bacteremia (positive blood cultures), then a life-threatening _ results

A

infective endocarditis

18
Q

If Neisseria meningitidis colonizing the pharynx of a college student passes to a new host with no prior adaptive immunity to the strain, invasion past the cribriform plate, proliferation in the CSF, and resulting inflammation results in a life-threatening _

A

bacterial meningitis

19
Q

Koch’s postulates (4)

A
  1. The microorganism must be found in abundance in all organisms suffering from the disease, but not in healthy organisms.
  2. The microorganism must be isolated from a diseased organism and grown in pure culture.
  3. The cultured microorganism should cause disease when introduced into a healthy organism.
  4. The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being the same as the original causative agent.
20
Q

Violation of Koch’s postulate #1:

The microorganism must be found in abundance in all organisms suffering from the disease, but not in healthy organisms.

A

Many diseases violate postulate #1 such as Clostridium difficile or Salmonella typhi (typhoid Mary) where humans can be colonized with the micro-organism without being ill (carrier state)

21
Q

Violation of Koch’s postulate #2:

The microorganism must be isolated from a diseased organism and grown in pure culture.

A

Viruses and prion diseases violate postulate #2

22
Q

Violation of Koch’s postulate #3:

The cultured microorganism should cause disease when introduced into a healthy organism.

A

It can be nearly impossible to test #3 if no animal model is available (HIV)

23
Q

If Koch’s postulates are not met but you want to implement a microorganism as the cause of a disease you need clinical judgment in conjunction with: (4)

A
  • Biostatistical tests of association
  • Serological surveys in human populations
  • Epidemiologic studies (case-control)
  • Molecular pathogenesis postulates
24
Q

Microbiologic testing in clinical bacteriology practice:
Qualitative

Patient specimen placed in _ to _

Result is expressed as _

Finalizing negative results takes from _ depending on growth rate of organism

Mostly reserved for analysis of _

Maximize _ at the expense of _

Examples (2)

A

nutritive broth
amplify small number of organisms present

positive for a specific organism or negative

5 to 42 days

sterile body sites (blood, CSF)

sensitivity
positive predictive value (false positives from contamination are common)

blood cultures
acid fast bacillus (AFB) cultures from sputum for Mycobacterium tuberculosis

25
Q

Microbiologic testing in clinical bacteriology practice:
Semi-quantitative

Specimen is directly _ (bacteria, mycobacteria, fungi)

to visualize you need at least _

Then specimen is directly _

Result is expressed as _

Finalizing negative results takes _

General-purpose culture _

Examples (2)

A

stained (Gram stain for bacteria, AFB for mycobacteria, calcofluor for fungi)

10^6 organisms per mL

plated on agar media (4-quadrant streaking)

negative/rare/light/moderate/heavy depending on how many quadrants show growth on agar plates

3-5 days

may help to decide whether the isolated organism is colonizing/contaminating only or significant enough to implicate it as the cause of the inflammation

wound cultures, sputum cultures

26
Q

Microbiologic testing in clinical bacteriology practice:
Quantitative cultures

Specimen can be directly _

to visualize you need at least _

Specimen of known _ is _

Result is expressed as _

A _ can help to decide whether the isolated organism is cause of the inflammation or not

Examples (3)

A

stained (Gram stain, AFB, calcofluor)

10^6 organisms per mL

volume
plated on agar media (lawn technique)

bacterial colonies (CFU =colony-forming units) per mL

predetermined CFU/mL cut-off (UTI’s > 10^5, ventilator-associated pneumonia > 10^5)

urine cultures
bronchoscopic lavage cultures (BAL)
skin biopsy cultures from burn patients

27
Q

_ or _ (infection of the bloodstream) is a most serious infection and may be secondary to _ (for example, _ & _).

The blood should normally be _

A

Bacteremia or fungemia

infections at other sites
urinary tract infection or pneumonia

sterile (free of circulating organisms)

28
Q

Blood culture collection:

The skin is _ and blood is collected and inserted into _ (enabling _).

These bottles contain _ to bind compounds (enhancing/inhibiting) microbial growth.

A

cleaned

bottles containing liquid media
enhanced growth of bacteria/fungi

resins

inhibiting

29
Q

Blood culture collection:

In order to increase the yield for Mycobacteria and some fungi, _ are used.

These are _ at high speed, _ immune cells containing intracellular organisms, and then _.

A

isolator blood cultures

centrifuged

lysing

plated on media

30
Q

Blood culture collection:

Blood should be collected from (#) different sites.

Blood from each site is collected in 2 bottles; one to support _ and another to support _.

Since the skin is covered by organisms, improperly collected blood cultures may be _ such as coagulase negative staphylococci.

Two samplings (2 sets of 2 bottles each) may _.

It is more useful to report the amount of positive (bottles/sets) than amount of positive (bottles/sets).

A

2

aerobic growth
anaerobic growth

contaminated with bacteria

differentiate between contamination and a true bacteremia

sets
bottles

31
Q

Other uses of blood (serum) for microbiologic diagnosis:

Direct microscopy to detect _ (Plasmodium falciparum (malaria), Babesia)

Detection of _ (Cryptococcus, Aspergillus, malaria)

Detection of _.

(Ig_) production may not be apparent at the time of the patient presenting to physicians; a _ sample (collected _) should be collected to detect _ and also changes in _

Detection of _ or _ by PCR (HIV, CMV)

A

organisms

fungal or parasitic proteins or antigens

antibodies (serology) against bacteria, fungi, viruses or parasites

IgM
“convalescent”
10-14 days after presentation
late-occurring IgM
IgG titer

viral RNA or DNA genomes

32
Q

Urine collection:

The skin around the urethral meatus may be contaminated with _.

Urine can be used for the detection of _ and _ such as Legionella pneumophila and Histoplasma capsulatum and for _ with
PCR (BK virus in kidney transplantation)

A

gastrointestinal tract flora

bacterial and fungal antigens
viral genomes

33
Q

Urine collection:

Aids in distinguishing a true urinary tract infection (UTI) from contamination:
• Presence of _ (inflammation indicates _)
• Absence of _ (presence indicates _)
• More than 100,000 _/mL urine (higher concentration of organisms make _ more likely)
• Only one kind of _ on urine culture (polymicrobial growth make _ more likely)

A

white blood cells
infection

epithelial cells
contamination from the meatus

bacteria
infection

bacteria
contamination from the meatus

34
Q

Cerebrospinal fluid (CSF):

The CSF bathes the _ and therefore, microbiologic examination of CSF may facilitate the diagnosis of _.

CSF can be tapped by a _ and, like blood, CSF should be _.

A cloudy appearance suggests the presence of _ as an _ response to _ infection.

A

meninges
meningitis

lumbar puncture
sterile

leukocytes
inflammatory
bacterial

35
Q

Cerebrospinal fluid (CSF):

  • A gram stain can immediately identify _ (high (specificity/sensitivity) but low (specificity/sensitivity)).
  • An India ink dye test can identify a _.
  • CSF can be cultured for: (3)
  • PCR of CSF can detect _ such as Herpes Simplex virus (HSV) and West Nile virus (WNV).
A

bacterial infection
specificity
sensitivity

Cryptococcus neoformans (fungus) infection

bacteria, fungi and viruses

viral gene targets

36
Q

Respiratory tract secretions:

_ is material spat out from the lower airways (not saliva).

Since it has to pass through the pharynx and mouth there is potential for it to be _

A

Sputum

contaminated with bacteria or fungi that are not truly causing disease.

37
Q

Respiratory tract secretions:

Bacteria and viruses can be grown or visualized from _.

A more invasive test is to obtain secretions directly from _ done by _. This makes oropharyngeal contamination by colonizing flora (more/less) likely.

Some diseases are best diagnosed by _ and/or _ such as Bordetella pertussis (whooping cough), Respratory Syncitial virus
(RSV) and influenza.

A

sputum

inflamed airspaces in the lung
broncho-alveolar lavage (BAL)
less

PCR
viral culture from nasopharyngeal swabs

38
Q

Stool (feces):

Microscopic examination can identify _.

Electron microscopy can identify some _ but this is not often done in clinical practice.

Culture can identify bacteria causing _; the use of selective media can differentiate _ from abnormal bacteria.

_ from some bacteria may also be found in the feces (C. difficile)

PCR can detect _ of bacteria (C. difficile) and viruses (enterovirus) that normally _.

A

parasites infecting the gut

viruses

gastroenteritis
normal gut flora

Toxins

toxin genes
do not colonize the gut

Microbiology (36 decks)

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