1. Specimen Processing

The validity of results from the lab is directly tied to what

quality of the specimen

Accurate results can only reported if what

when the specimen is collected and processed according to strict guidelines and procedures

What happens without correct specimen collection instructions

specimens may be contaminated by normal flora from the surrounding areas (genital flora in urine, mouth flora in sputum) or be an incorrect specimen

When should specimens be collected and transported

collected before administration of antimicrobials and transported to the lab as soon as possible

What can decrease the chance of successfully culturing viable organisms

delay in transit time or exposure to the elements (excess heat or cold)

How does transport media preserve organisms

by maintaining pH, preventing dessication, and preserving organism numbers

What can increase the likelihood of isolating a pathogen

when specimens are collected at optimal times

What specimens are best collected first thing in the morning

urine and sputum

What can happen if clerical errors happen at any step of specimen processing

can lead to patient harm

What do you do if a clerical error is found in specimen processing

rejected and submitting location is contacted to recollect the specimen ensuring it is properly labelled

What is an exception when rejecting specimens

if specimen is a critical (invasive or impossible to recollect)

What happens to a mislabelled CSF or tissue

a waiver must be signed by the physician or nurse to take responsiblity for the error and ensure that the updated information provided is correct

What is another important step before processing occurs

checking the adequacy of the specimen

What happens if a specimen is collected improperly or it is not an appropriate specimen

results are unreliable

What are the requirements to ensure adequacy of the specimen

• appropriate collection devices

• sufficient quantity

• properly labeled with full name, ULI, pMRN, and source

• proper specimens that are the representative of the infected body site

• leak proof containers

• multiple specimens collected on different days

Examples of appropriate collection devices

sterile containers, appropriate transport media, preservatives

What happens to leaking specimens

rejected if non-critical

What happens to same day collections

often rejected based on specimen

Who develops the procedures for specimen processing

developed with microbiologists and senior staff to ensure that most pathogens are isolated

What do specimen processing procedures outline

which specimens require concentration, what media is required, what incubation atmospheres are necessary and how specimens will be stored after processing

What balance is necessary for specimen processing

cost and patient outcome

How is media chosen

chosen to ensure that most pathogens will grow while maintaining cost effectiveness

What are some examples of special “add-ons” that may be added to procedures

• patient diagnoses that will require additional media (TSS on a vaginal specimen requires culture, not just smear)

• specific physicians that require additional media or specific tests (eye specialist may require calcofluor white stain on all specimens submitted)

• patient symptoms that may require additional media, tests, or procedures (throat specimens with symptpm of rash will be held in CO₂ for a addition 24h)

What specimens are planted first once verified as acceptable and why are they first

STATs and priorities; must have their direct smears reported to physicians (by phone) within 1h and 4h respectively

For specimens not STATs and priorities, how are they planted, include an example

based on stability and possible batching (urine, sputum, and wound specimen planted before ova and parasite or dermatophyte specimens)

What are some specimens submitted to microbiology

swabs, liquids, or semi-solids in sterile containers

What order are specimens inoculated

onto media starting with non-selective/enriched media to more selective media then broths

If a direct smear is required, when should it be inoculated

should be inoculated first

How are swabs inoculated onto media/sterile slide

inoculated to an area the size of quarter

How are fluids inoculated

using a calibrated loop or sterile pipette

What happens prior to inoculation if large volumes of fluid is received

may be concentrated before inoculation

How are semi solids (stool, sputum) inoculated

using sterile swabs to an area the size of a quarter picking areas that appear bloody or purulent

How are urines and other specimens requiring quantification streaked

using a quantitative isolation technique using a calibrated loop

What is included in the incubation information for all primary media

temperature, atmosphere, and length of time the media must be incubated

What determines the storage of specimens after planting

by specimen type

Where are most specimens stored at and why

refrigerated, to try and keep bacterial growth at a minimum in case a specimen needs additional plates

What specimens do not require refrigeration and can be stored at room temperature

preserved specimens, such as stools for ova and parasite examination

Where are CSF and other sterile fluids commonly stored at

room temperature or even incubated in 35-37 degree with the primary plates

Why do we store CSF and other sterile fluids in that temp

it is common to isolate cold sensitive organisms from these types of specimens, so storage at 4 degrees could kill the pathogen

Why do we encourage bacterial growth of CSF and other sterile fluids

these specimens should not contain any bacteria so encouraging growth of organisms can be beneficial for isolation

Why is feces in SAF for feces culture unacceptable

SAF (sodium acetate-acetic acid-formalin) kills bacteria. It is meant for ova & parasites

Why is cervical swab in clear transport media for GC culture unacceptable

Amies/Stuart clear transport media lacks the nutrients and specialized atmosphere for N. gonorrhoeae

What specialized media is required for N. gonorrhoeae during transit

JEMBEC

Why is synovial fluid in syringe for sterile fluid culture unacceptable

needle hazard; fluids must be transferred into a sterile leakproof container or transport tube before transport

Why is unpreserved urine >24h for urine culture unacceptable

at RT, unpreserved urine allows fast-growing contaminants or normal flora to overgrow, while fastidious pathogens may die, making colony counts inaccurate

Why is a dry wound swab in sterile container (no media) unacceptable for surface wound culture

dessication (dryness) kills fragile bacterial cell walls. swabs require liquid or gel media to maintain moisture and pH

Why is appendix in 10% formalin unacceptable for tissue culture

formalin cross-links proteins and kills organisms. used for histopathology, not culture

What specimens are stored at 4 degrees (refrigerated)

• unpreserved urine

• sputum

• stool

Why do we refrigerate certain specimens

cold temps suppress metabolic activity, preventing normal flora from overgrowing true pathogens during delays

What specimens are stored at 22 degrees

• swabs (eye, wound, genital)

• fragile/cold-sensitive organisms (N. gonorrhoeae)

Why do we store certain specimens at 22 degrees

prevents cold-shock killing delicate organisms, less contaminated

What specimens are stored at 37 degrees

• CSF

• sterile body fluids

Why do we store certain specimens at 37 degrees

encouraging growth is useful

What is the target specimen of SAF

stool

What is the purpose of SAF

fixes and preserves protozoan trophozoites, cysts, and helminth eggs/larvae for microscopic examination

What is the target specimen of boric acid

urine culture

What is the purpose of boric acid

acts as a bacteriostatic agent that stabilizes bacterial counts for up to 25-48h at ET, preventing overgrowth w/o killing the organisms

What is the target specimen of clear transport media (Amies/Stuart)

general swabs

What is the purpose of clear transport media (Amies/Stuart)

isotonic, buffered semi-solid or liquid gel that prevents desiccation and maintains pH w/o nutrients (preventing overgrowth)

What is the target specimen of Cary-blair media

stool (enteric pathogens)

What is the purpose of Cary-blair media

low-nutrient, high-pH (8.4), transport medium that preserves fragile enteric pathogens (Salmonella, Shigella, Campylobacter) while limiting coliform overgrowth

What is the target specimen of charcoal-containing media

fragile fastidious organisms

What is the purpose of charcoal-containing media

neutralizes toxic fatty acids, peroxides, and metabolic byproducts present on swabs or in samples (N. gonorrhoeae, Bordetella pertussis)

What is the target specimen of JEMBEC system

genital swabs

What is the purpose of JEMBEC system

contains selective media (ex. modified thayer-martin) alongside a bicarbonate tablet that generates a CO₂ enriched environment inside a sealed bag

What are the target specimens of anaerobic transport system

deep wounds, aspirates, tissues

What is the purpose of anaerobic transport systems

sealed tube/jars containing oxygen-scavenging catalysts and indicators (resazurin/methylene blue) to maintain an anoxic environment

What are the target specimens of SPS (sodium polyanethol sulfonate)

blood, bone marrow, synovial fluid

What is the purpose of anaerobic transport systems SPS (sodium polyanethol sulfonate)

anticoagulant that prevents clotting, inactivates complement, inhibits phagocytosis, and neutralizes aminoglycoside antibiotics

What is the inoculation priority order of specimens

• STATs / critical priorities → CSF, invasive body fluids, tissue aspirates (direct smears requires phone within 1 and 4h)

• unpreserved routine samples → urines, sputum, wound specimens (susceptible to deterioration or overgrowth)

• preserved/batchable sam[les → stools in fixatives, fungal skin scrapings, viral

What are the purposes of direct smears

• specimen quality and adequacy audit

• early pathogen recognition

• guiding media selection

• internal quality control

Meaning of specimen quality and adequacy audit for direct smears

allow screening for saliva/oropharyngeal contamination in respiratory specimens

Meaning of early pathogen recognition for direct smears

identifies cellular morphology, gram reaction, and arrangements to guide initial empirical antimicrobial therapy days before final culture results

Meaning of guiding media selection for direct smears

direct observations may prompt the addition of specialized, selective, or anaerobic media

Meaning of internal quality control for direct smears

serves as a baseline to verify that isolates recovered in culture match the organisms seen in the original specimen

Definition of pharyngitis

inflammation of the mucous membranes of the throat/pharynx

Definition of pneumonia

infection causing infection of the pulmonary parenchyma

Definition of cystitis

inflammation of the urinary bladder

Definition of dysentery

inflammation GI disorder characterized by severe diarrhea with blood and mucous

Definition of pyuria

pus (wbc) in urine

Definition of dermatitis

skin inflammation

Definition of tonsillectomy

surgical removal of the tonsils

Definition of dysphagia

difficulty swallowing

Definition of rhinorrhea

free discharge of thin nasal mucous (runny nose)

Definition of colostomy

surgical creation of an artificial opening into the colon

Definition of keratitis

cornea inflammation

Definition of pyoderma

pus-forming skin infection