clinical lab med pt2

family of actinobacteria, acid fast gram positive, slow growing obligate aerobes w 3 main groups

mycobacteria

3 main groups of mycobacteria

mycobacterium tuberculosis (TB), mycobacterium leprae (leprosy), nontuberculous mycobacterium (NTM)

specimens to test for mycobacteria

mostly sputum, processed under biohood to prevent aerosolization

culture media used for mycobacteria

lowenstein-jensen, special for mycobateria (LJ) (egg based malachite green, needs 18-24days to grow)

middlebrook 7H10-7H11 (agar based, best for isoniazid resistant strains, 10-12d for growth)

acid fast staining methods

ziehl-neelsen: carbol fuschin and heat assisted staining, most commonly used

kinyoun: uses phenol and cold method (no heat), counterstain methylene blue or malachite green

fluorochrome stain: AFB yellow-orange fluorescense under UV, faster and more sensitive

acid fast bacteria look what color after a ziehl-nesslen method

red

other lab tests for myocbacterium that detects a pathoens genetic material (DNA or RNA) by amplifying specific sequences, making them easier to identify. used for rapid and accurate detection of infections like covid, STIs and certain bacteria

Nucleic acid amplification test (NAAT)

other test for mycobacteriam that is a blood test that detects TB infection by measuing interferon gamma released from T cells exposed to TB antigens. theyre more specific than TB skin test, esp in vaccinated ppl, and help dx latent and active TB

interferon-gamma release assays (IGRA)

considerations fro doing interferon-gamma release assays (IGRA) tests or Nucleic acid amplification test (NAAT)

multiple specimines needed, resistance testing for multidrug resistant TB

kinds of fungi and their structure

can be yeasts (candida) or molds (aspergillus)

eukaryotic cells w cell walls that have chitin, same structure as mammalian cells resulting in damage to the host while destroying the infection organism

opprotunistic in immunocomp pts

diseases can be superficial, cutaneous, sub q, and systemic

may need specialized testing referred to other labs

features of yeasts

unicellula, budding reproduction, look.creamy, smooth little colonies

features of molds

multicellular (hyphae), make spores (get into air and spread easier), fuzzy wooly colonies

specimens for mycology

any tissue or body lfuid (hair, skin scrappings, nails, urine, blood, tissue, bone marrow)

swabs are the least desirable

ensure proper collection for the specific site and transport quickly and carefully to precent aerolization

mycology direct microscopic examination methods

wet mount: sample put on slide, mixed w water/saline, covered w cover slip and observed for living cells (see living cells in natural environment, good for things that are alive like trich, sperm, and fungi but can see all the contaminants too

potassium hydroxide (KOH) prep: dissolves cellular material to reveal fungal elements (only leaves the fungi)

calcofluor white + KOH: fluorescent detection, helps you see it better

on gram stain what do fungi look like

stain purple/blue/black, show budding or hypae

what do fungi look like on acid fast stain

yeast stain purple, show budding/hyphae

what do clue cells mean

vaginitis (as opposed to yeast infection)

what do fungi look like on india ink (negative staining method, drop added to specimen to rapidly identify cryptococcus spp)

halo appearance

cryptococcus appearance

halo

candida albicans appearance

budding

aspergillus appearance

hyphae

gold standard for dx fungi, good for identification and susceptibility testing

culture media

use a general purpose, non selective media, use one w and w/o antibacterial and antifungal parts to prevent growth of contaminants. most commonly use sabouraund agar

can use enriched medium (sabouraud dextrose agar and sabouraud +BHI) or can use mycosel medium

if fungi grows in selective medium potato dextrose/flake what kind is it

saprophytic and dimorphic

if fungi grows in selective medium czapek dox what kind is it

aspergillus

if fungi grows in selective medium inhibitory mold what kind is it

dimorphic

if fungi grows in selective niger seed agar what kind is it

C neoformans

carb tests that combine enzyme activity and ability to use carbon/nitrogen for growth and sometimes fungal resistance (allows for rapid ID but not confirmatory)

assimilation tests

test that differentiates candida albucans by formation of germ tubes from yeast cells when incubated in serum

germ tube

test that grows specimens on a colorless media thatll undergo a color change based on enzyme activity

chromogenic agar

test that determines the ability of enzyme to breakdown substances (like hydrogen peroxide, urease, oxidase)

enzyme activity

test that tests for the production of acid end products

methyl red test

types of parasites

protozoa, helminths, arthropods

can infect GI tract, blood, urogenital tract, tissue

inc risk for parasitic infections

travel, immunosuppressed, refugee

site of infection for candida albicans infection

mouth and throat, vagina, invasive in blood stream

site of infection for candida auris infection

blood stream, wounds, ear, can be severe in hospitalized pts, often resistant to antifungal drugs

site of infection for cryptococcus neoformans infection

oral, vaginal, pneumonia-like cryptococcal meningitis, coccidiomycosis

specimen collection for parasites

stool sample is primary sample (3 samples, 1-2 days appart, within 10 days ova and parasite exma due to intermittent shedding)

dont contaminate w urine or water, get to lab in 24-48hrs (dont let them fish it out of the toilet after)

clean, dry, waterproof container w lid that should be refrigerated

blood samples for malaria

tissue/CFS/urogenital tract/sputum depending on suspected parasite

tape collection method for pinworms (enterobius vermicularis) (put scotch tape on perianal region to try to get eggs)

detection methods for parasites

macroscopic exam: not consistency (formed/soft/liquid) and presence of blood, mucus, or foreign materials

wet mounts: for trophozoites, ova, and larvae

concentration techniques: sedimentation by centrifuge or flotation using a reagent w high specific gravity (zinc sulfate)

staining: to confirm dx, reveal nuclear material and differentiate from background (can be iodine, trichrome (most commonly used), iron hematoxylin, or acid fast)

antigen detection: for giardia or cryptosporidium

molecular detection: limited use, mostly in reference labs

cellophane tape: for pinworms(put tape on butt to get pinworm eggs)

blood and tissue smears: thick and thin smears, thick has higher sensitivity, can be stained w Wright or Giemsa and examined (giemsa for malaria) can also see babesia, trypanosoma, loa loa)

the smallest, obligate infectious agents that require a host cell and reproduce via host machinery for propogation, transmission and infection

viruses

what environment are viruses found in and what are their structures

found in every environment (Ubiquitous)

have inner nucleis acid core (DNA/RNA + protein capsid ± lipid envolope

can lead to acute, latent, chronic, or oncogenic infections

virus specimens

type based on site: swabs, fluid, tissue samples

respiratory infection= nasopharyngeal swab or lavage

can use stool, urine, CSF, blood, bone marrow, other body fluids, tissue, lesions, vaginal, cerival, urethral

collect early in infection

gold standard to dx viruses

cell culture (incubate 1-4wks)

faster viral culture w immunofluorescence

shell vial assay

rapid viral tests

antigen detection tests (used fro flu, HIV, RSV, covid)

viral testing PCR based

molecular testing

viral test increasinly used for rapid dx

POCT

sites of infection of trichophyton spp

dermal infections

sites of infection of aspergilus infxn

lungs, visceral organs, brain, kidneys, heart, bone, GI tract, eyes, paranasal sinuses, skin, immunocomp pts