5, 26 Sample Collection

Exam 2 lecture 26

what are the different methods used in lab diagnosis

direct examination and culture, photype identification, and molecular detection and identification

what is the responsibility of the clinician

collect and submit appropriate samples with specific requests and history

what is the responsibility of the microbiologist

interpret the results in relation to information supplied

what does a negative report not mean

does not mean the etiological agent is not present

what are some reasons why the bacteria may not grow in a negative report

bacteria was overgrown by contaminants, bacteria died on the way to the lab, animal stopped shedding the bacteria before sample was taken

what does a positive result not mean

it does not establish a diagonsis

what is needed for interpretation of a positive result

clinical signs, vaccination, history, normal flora

sample directly from affected site

collect early after onset

sample clinical cases and in contact animals

take from lesion edge, with some normal tissue

use aseptic technique

inform the lab if treatment has started

submit enough

avoid cross contamination

use PPE is zoonosis is suspected

principles of sample collection

what tools are used to colelct from anaerobic bacteria

fine needle aspiration, post mortem swabs, swabs

suitable specimens for anaerobic culture

normally sterile fluids

surgical specimens

deep abscess contents

aspirates from deep wounds

blood

unsuitable specimens for anaerobic culture

saliva

vaginal or cervical specimens

feces

tracheal swabs

naso-tracheal aspirates

colostomy

skin wound swabs

voided urine

what conditions suggest anaerobic bacteria

foul smell

deep infections from penetration of mucosal surface

necrotic tissue, gangrene

gas in tissue

bite wounds

advantages of immunology and serology

high throughout capacity

rapid

low cost

ease of use

example of immunology and serology test

elisa

disadvantages of immunology and serology

detection limit for organisms/antigens with low abundance

difficulties in generating selectove antibodies

what shows bacteria in elisa test

change of color

steps of pcr

1. denaturing

2. annealing

3. extension

types of pcr

conventional, multiplex, reverse transcription, real time, microarrays

what is pcr based on

nucleic acide (DNA/RNA) amplification

advantages of pcr

rapid

small amount of sample needed

can detect fastidious, in culturable, slow growing, dangerous pathogens

high specificity and sensitivity

disadvantages of pcr

expensive, primers vary in specificity

what is the advantage to whole genome pcr

provides the most detail, unambiguous information

how is the information retrived with MALDI-TOF

laser beam, cloud of particles, then mass spectrometery

what are the advantages of MALDI-Tof

rapid

easy interpretation

low overall operating costs

disadvantages of MALDI-TOF

detection limit for low abundance, normal flora may overlap, high initial cost

use sterile instruments

collect appropriate tissue size (1 cm³)

place samples in seperate, leak proof containers

use sterile, screw cap jars

collect post mortem asap

if transport is delayed use transport medium

guidelines for tissues and organs

fluids better than swabs

larger volume is higher detection

avoid dry swabs'

uses guarded swabs when needed

guidelines for swabs and discharge

collect directly from rectum

rule fo thumb amount

transport medium

leak proof container

transport immediately

Guidelines for feces

as soon as mastitis is observed

do not wash udder unless heavily soiled

disinfect with 70% alcohol on teat ends

clean furthest teat first then nearest

hold sterile bottle nearly horizontal

discard first stream

guidlines for milk

what is the best way to collect urine

cystocentesis

where should abscess specimen be taken from

edge of abscess, not center

disinfect intact elstions with 70% alcohol

aspirate pustules/vesicles

swab ulcer bases

biopsy wounds

pluck hair if ring worm

guidelines for skin lesions

what is cell growth in culture determined by

temperature, hydrogen ion concentraion, availability of moisture, atmoshpheric composition, osmotic pressure

what is liquid media used in

test tubes, bottles, flasks

how do bacteria grow in liquid media

uniformly, production of turbidity, some aerobic and those with flagella form a thin film

what media doesnt contain agar

liquid media

what does a liquid media contain

yeast extract, peptone, sodium chloride, nutrients

what is the agar content of semi solid agar

0.2-0.5%

what is semi solid agar used for

demonstrating bacterial motility

what agar concentration does solid agar have

1-3%

what bacteria is basal media used for

non-fastidious

what does blood agar plate show

hemolysis but zone of clearing/ staph infections

what does the macconkey agar plate show

gram negative bacteria that ferment lactose

what does eosin methylene blue plates show

e. coli

what do zylose lysine deoxycholate plates show

salmonella

what do brilliant green agar plates show

salmonella or e coli depending on color

what do mueller hinton agar plates show

antimicrobial sensitivity

what do mannitol salt agar plates show

staph infections

what do sabouraud dextrose plates show

fungal growth