Detection & ID of microorganisms Flashcards
advantages of molecular-based testing
fastidious organisms or time consuming to isolate
hazardous organisms
high volume tests
more sensitive
specimen collection
avoid contamination
proper equipment
maintain proper time & site of collection
positive control for PCR
DNA prepared from the same site & contains the organism of interest
negative control for PCR detection
DNA prepared from the same site but does not contain the organism of interest
Reagent blank for PCR detection
no DNA present whatsoever
amplification control
omnipresent template unrelated to target used to make sure PCR could show band if organism was present
acts as an internal control to amplify 16S rRNA region that is present in all bacteria
commonly IDed bacteria by molecular methods
Strep pneumoniae
S. agalactiae
Bordetella pertussis
Chlammydia trachomatis/ Neisseria gonorrhea
why detect S. pneumoniae by molecular methods
speed
if in the blood, it can progress very quickly
definitive lab diagnosis is made in 20 minutes
how S. pneumoniae is detected via molecular methods
hypbrid capture assay no DNA isolation look for target rRNA sequences hybrid DNA probe to RNA target the hybrid that is formed is resistant to the selection reagent
why detect S. agalactiae by molecular methods
recently is normal flora
can lead to post-natal infection of child
all pregnant women are screened & treated if positive
molecular methods are very sensitive!!
why detect C. difficile by molecular methods
speed
difficult to culture
determining normal flora vs active infection of C. difficile
if the PCR amplification products cross the threshold earlier than the cutoff its an active infection
later is normal flora
Chlamydia trachomatis/Neisseria gonorrhea (CTNG) testing by molecular methods
use the same assay for both organisms
not normal flora & any signal is an infection
can’t use for legal cases
high volume testing
Bordetella pertussis by molecular methods
nasopharyngeal swab, very difficult to culture
why detect mycobacterium by molecular methods
take up to 5 weeks to grow
very difficult to speciate
