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functions of clinical laboratory

diagnosis or confirm diagnosis of infectious disease
guidance of treatment
outbreak detection
support for infection control
collect and collate data/info: trends in resistance, antimicrobial susceptibility summaries
epidemiological studies


what do clinical microbiologists provide advice on?

appropriate specimen collection and transport
interpret test results
patient management - recommendations on antimicrobials


why is it important to understand how the clinical lab works?

need to give the lab the appropriate specimens
decrease frustration
cost effective use - choose test wisely
want physicians to provide clinically relevant information such as allergies or the type of wound/body part/symptoms the sample was collected from


general workflow of lab

susceptibility testing/ molecular testing
reporting/ documentation


requisition form

must have physicians name and contact info

patients name, birthday, unique identifier such as health card number or passport number

specimen type
method of collection - how it is collected determines how it is processed
time/date of collection
required analysis

relevant clinical info - allergies


things to consider for specimen collection

- will the specimen provide useful information - if you're not prepared to change the patients management based on the results then don't do it
- choice of the actual specimen to take
- instructions for collection by patient if required
- transport time to lab - may need transport media
- quality of the specimen
- risk of false positives/negatives
- specimens that required being cultured are never put in formalin


Accessioning of the sample

process of identifying the specimen

is the specimen properly labeled? does the requisition info match the specimen label?

was it properly collected

time/date of collection

is it being processed or rejected

is it STAT/life threatening

received specimens must be coded and entered into the LIS system


criteria for specimen rejection

missing information

info on specimen does not match requisition

specimen is too old- improper transport

swab or media is expired

inappropriate specimen

poor quality specimen

specimen is leaking

duplicate specimens

cant be from physician or their family member


things to consider for transport of specimens

transport time to the lab
type of specimen (swab, urine, blood, stool, fluids, scrapings)

transport media: maintain viability but inhibit growth, Cary Blair Transport Media, SAF (parasites)



processing of specimens

types of specimen: swab, fluid, stool, blood

what tests are required: culture, molecular point of care (POC), serology, microscope (gram stain, AFB stain)

additional processing such ad decontamination or centrifugation if required

what media

incubation conditions: CO2. low O2 high O2, 37 degrees, 42, etc.


why are molecular diagnostics not great for bacterial identification?

good or viral diagnosis but huge cost for bacterial diagnosis and not super effective because the culture is often more sensitive than the actual PCR itself
molecular diagnostics also does not provide susceptibility information


sputum/specimen grading

Q0- very poor quality: oropharyngeal contamination determined via microscope

Q1- poor quality: oropharyngeal contamination but specimen is still processed - results to be interpreted with caution

Q2- good quality
Q3- very good quality


interpretation/identification and turn around times

microscopy: 30mins-same day
Point of Care (POC): rapid streptococcal antigen test in an hour or less
direct MALDI-TOF: same day
Culture: 24hr to 3 weeks
Serological: same day/ week
molecular: same next day for diagnosis but same/next week for epidemiological studies
susceptibility testing: 24-72 hours or longer for mycobacterium


antimicrobial chemotherapy

use of drugs to combat infectious agents including antivirals, antibiotics, antifungals, and antiparasitic

most are derived from naturally occurring compounds some may be semi-synthetic or synthetic


differential toxicity

drug is more toxic to the infecting organism than to the host


spectrum of activity

broad vs narrow

broad kills a lot of different organisms

narrow kills a select group - try to use these if possible


minimum inhibitory concentration (MIC)

minimum concentration of the antibiotic required to inhibit the growth of the organism


minimum bactericidal concentration (MBC)

minimum concentration required to kill the organism


bacteriostatic vs bactericidal drugs

bacteriostatic drugs inhibit the organism - MBC is higher than MIC

bactericidal drugs - kill, MIC and MBC are the same


time dependent killing vs concentration dependent killing

time dependent killing: goal is to maximize exposure of the drug to the bacteria - dont care how high the concentration is just want to maintain the MIC for as long as possible - dosed more frequently bc want to keep it stable

Concentration dependent killing: goal is to maximize the concentration of the drug - only need to dose one or two times per day



antimicrobial agents are given prevent an infection - do this before a surgery for example



antimicrobial agents are administered to treat an existing infection


therapeutic index
+ examples of drugs with low therapeutic index

therapeutic dose/ effective dose

drugs with a low therapeutic dose may require therapeutic drug monitoring to ensure drug levels are both effective at treating the infection and not killing the patient



the ideal antibiotic

no/low toxicity to the host
low probability of having resistance mechanisms
does not induce hypersensitivities in the host eg penicillin
rapid and extensive distribution to the tissues
relatively long half life but not too long
free of interactions with other drugs
convient for administration


empiric therapy

some infectious disease require immediate treatment - need to prescribe a drug before getting test results back

make a prescription based on:
- epidemiology (most probable diseases and etiologies)
- severity of the disease
- local rates of resistance

once the organism is identified the treatment should be adjusted - narrowed is possible or a new drug given if the first guess was wrong


advantages and disadvantages of combination therapy

- treating polymicrobial infections
- initial empiric treatment
- synergy - 1 +1 = 4
- may prevent the emergence of resistance (this is the case with TB)

- may be antagonistic - 2+2=1
- cost
- increased risk of side effects and drug-drug interactions
- usually not required for maximum efficacy


what influences you choice of antibiotics

activity against isolated or suspected organism
acute vs chronic disease
antibiotic history of the patient - can't give the same one more than once in 3 months
site of infection
mode of administration/toxicity/cost
metabolism and excretion
duration of treatment / frequency of dose
local rates of resistance
concomitant medications that may react with antibiotic


re-infection vs reoccurrence

reinfection = same infection by different organism

reoccurrence = same infection by same organism - could indicate drug resistance


antimicrobial resistance

resistance = the inability to kill or inhibit the organism with clinically achievable drug concentrations

resistance can be innate such as gram negatives are resistant to vancomycin because it only works on gram positives - don't really care about this stuff

resistance may be acquired through: mutation and acquisition of DNA
this results in: up/down regulation of things such as efflux pumps or OMPs, expanded spectrum of enzymatic activity (beta lactamases), and target site modification


antimicrobial selection of resistance

the use of antibiotics doesn't create resistance it selects for it

have a colony of bacteria (billions of mutations happening in the genome) and one of them mutates to modify something in the cell that will resist the effect of antibiotics
the treatment with the antibiotics selects for that mutation

then have a resistant population develop