M1: CC1: Intro to Clinical Infectious Diseases Flashcards Preview

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

Flashcards in M1: CC1: Intro to Clinical Infectious Diseases Deck (38)
1

infectious etiologies (5)

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

2

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.

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

3

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 _

fewer

gut and skin

other more pathogenic bacteria from overtaking and hurting us

fermenting carbohydrates in our intestines
producing our essential Vitamin K

4

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 _.

do not

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

Staphylococci
bacteremia

5

micro-organisms:
pathogens

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

Our immune system is constantly _

harmful

at the look-out to neutralize them

6

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

Sometimes by _ (some parasites)

mostly by looking at a _ (bacteria)

or by _ (viruses)

naked eye

Gram stain through a microscope

electron microscopy

7

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

grow the bacteria and fungi on _

viruses on _

media

cell culture

8

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

fluorescent dyes (DFA = Direct Fluorescent Antibody)

serology
IgM and IgG antibodies

9

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

metabolically active bacteria
fungi

enzymatic activity

carbohydrate fermentation/utilization

10

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)

PCR: primer recognition

BLAST database

11

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

_, rapidly becoming commonplace in medical microbiology laboratories.

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

12

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 _.

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

13

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

precise microbiologic diagnosis
before
recovering the causative organism

antimicrobials

14

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

their own resident bacterial flora
colononizers

skin

mouth, pharynx and vagina

gut

15

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

mouth and pharynx

common

16

Disease states associated w/ colonizers:

o viridans streptococci

o HACEK group organisms

o Fusobacterium spp.

o Neisseria meningitidis

o Candida albicans (yeast)

o endocarditis

o endocarditis

o bacteremias

o meningitis

o thrush

17

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

infective endocarditis

18

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 _

bacterial meningitis

19

Koch’s postulates (4)

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

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.

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

Violation of Koch's postulate #2:
The microorganism must be isolated from a diseased organism and grown in pure culture.

Viruses and prion diseases violate postulate #2

22

Violation of Koch's postulate #3:
The cultured microorganism should cause disease when introduced into a healthy organism.

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

23

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)

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

24

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)

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

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)

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

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)

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

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

The blood should normally be _

Bacteremia or fungemia

infections at other sites
urinary tract infection or pneumonia

sterile (free of circulating organisms)

28

Blood culture collection:

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

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

cleaned

bottles containing liquid media
enhanced growth of bacteria/fungi

resins

inhibiting

29

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 _.

isolator blood cultures

centrifuged

lysing

plated on media

30

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).

2

aerobic growth
anaerobic growth

contaminated with bacteria

differentiate between contamination and a true bacteremia

sets
bottles

31

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)

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

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)

gastrointestinal tract flora

bacterial and fungal antigens
viral genomes

33

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)

white blood cells
infection

epithelial cells
contamination from the meatus

bacteria
infection

bacteria
contamination from the meatus

34

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.

meninges
meningitis

lumbar puncture
sterile

leukocytes
inflammatory
bacterial

35

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).

bacterial infection
specificity
sensitivity

Cryptococcus neoformans (fungus) infection

bacteria, fungi and viruses

viral gene targets

36

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 _

Sputum

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

37

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.

sputum

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

PCR
viral culture from nasopharyngeal swabs

38

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 _.

parasites infecting the gut

viruses

gastroenteritis
normal gut flora

Toxins

toxin genes
do not colonize the gut