Microbiology > 06- Lab specimens > Flashcards

06- Lab specimens Flashcards

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1
Q

Pre-Analytical Errors

A

wrong test, order entry, pt-specimen misidentification, quality of sample collection poor, wrong container, inappropriate storage and transport

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2
Q

Essential Test Information

A
  • Unique identification of the patient
  • gender, age, DOB
  • test ordered
  • date and time of collection
  • who requested the test- most responsible physician
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3
Q

Penicillin Allergy

A

for specimens such as throat swabs and vaginal-rectal swabs for group B strep, the lab will do additional testing if the pt is known to be penicillin allergic.

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4
Q

Clinical Information

A
  • penicillin allergy
  • anatomic location of specimen
  • CSF shunt vs CSF
  • Animal bite for a wound swab
  • Travel Hx
  • Pregnancy
  • Immunocompromised
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5
Q

Patient Identifiers

A

full name, hospital accession number, OHIP number, DOB

Ask patient name and DOB or if unconscious, verify with hospital bracelet

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6
Q

Labelling Specimens

A

Label the specimen at the bedside. Label with patient ID, ensure that specimen label and contents of tube match, ensure information is legible, that the contents are visible, and that the barcode can be read.

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7
Q

Four Steps to Prevent Errors

A
  1. take labels to the patient
  2. take a moment to check patient identifiers. always check 2 unique identifiers
  3. write time of collection and your initials on the label
  4. Label immediately after collection
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8
Q

Maximizing the ability to isolate a pathogen

A
  • collect specimen before the patient begins Abx
  • choose the correct specimen container
  • collect the maximum volume of specimen
  • collect when the organism is most abundant
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9
Q

Transport media

A

designed to preserve the pathogen if there is a delay in getting it to the lab. there are different transport media for bacteria vs viruses vs parasites. some transport media have resins to bind to Abx.

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10
Q

Minimizing contamination with normal flora

A
  • disinfection of skin

- midstream urine culture

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11
Q

Infection Control and safety

A
  • follow infection control precautions when collecting specimens
  • routine practices for all specimens
  • additional precautions depending on pt Sx or organisms
  • be aware of outbreaks and novel strains where airborne precautions are recommended for collection.
  • never re-cap, bend, break, or cut needles. dispose in sharps container. do not transport syringes with a needle to the lab
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12
Q

Novel infections

A

have a higher biosafety risk. additional precautions for collection, enhances laboratory precautions for processing.

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13
Q

Storage

A

minimize storage- transport to lab promptly. if delayed, store at the appropriate temperature; either room temperature or 2-8 degrees (depending on the specimen) to reduce growth or maintain viability of specimen.

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14
Q

Transport

A

all specimens should be transported to the lab within 2hrs. STAT specimens should be transported within 1hr.

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15
Q

STAT Specimen

A

significant specimen where rapid results are essential for appropriate management, and results could be life-threatening. Lab can provide results rapidly.
eg. Spinal fluid, tissue/wound culture if necrotizing fasciitis suspected

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16
Q

Bad Specimens

A

hemolyzed blood, delayed specimen, not enough of a specimen, leaky specimen, wrong container

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17
Q

Secondary bacteremia

A

from lung, urinary, meningeal, soft tissue infection, central line

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18
Q

primary bacteremia

A

from endovascular; eg. endocarditis mycotic aneurysm.

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19
Q

amount of blood drawn for culture

A

the most important factor in detecting the pathogen. the yield is proportional to the amount of blood.
the ratio of the volume of blood to the volume of the broth in the blood culture bottle is important to allow adequate dilution of the blood to prevent inhibition of growth if the pt is on Abx

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20
Q

Adult Blood volume to draw

A

8-10mL per bottle

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21
Q

Diagnosing endocarditis with blood culture

A

collect blood over a period of time to demonstrate continuous bacteremia. at least 2 positive cultures of blood samples drawn >12hrs apart or all 3, a majority of >/= 4 separate cultures of blood

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22
Q

Blood Culture Contamination

A

usually occurs during the collection process. has a negative impact on patient care.
difficult for clinicians to know the pathogen requiring Tx
increase in hospital length of stay
increase in costs for Abx, investigations, etc.

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23
Q

Steps to decrease blood culture contamination

A
  1. Skin preparation (choose the right disinfectant. need contact time of the disinfectant on the skin)
  2. Bottle preparation (the rubber septum is not protected by the cap on the bottle. disinfecting the septum with alcohol reduces contamination)
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24
Q

most common breaks in technique

A

not allowing disinfectant to dry completely, not disinfecting bottle septum, palpating the site of puncture after cleaning with non-sterile finger, placing blood specimen on non-sterile surface

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25
Peripheral blood culture vs draw from a line
increase in false positives with blood culture draw, catheter draw. only take a culture from a catheter if you suspect line-related infection or if the person is a very difficult draw.
26
Blood culture instruments
the blood culture bottles are placed in the instrument ASAP. it incubates the bottle at 35 degrees, mixing the bottles. a continuous detection system looks for an increase in CO2 or a decrease in O2. as soon as growth is detected, it alarms.
27
Gram Stain
portion of blood placed on a slide, dried, and stained. includes a primary stain (crystal violet). a decolorizer removes the primary stain from gram negative bacteria (d/t increased lipid content). secondary stain (safranin) is taken up by gram negative bacteria.
28
Vitek-2 identification system
rapid method involving biochemical and other reactions to identify a wide range of organisms. identification usually 6-8hrs
29
MALDI-TOF
novel method for rapid identification of microorganisms. laser pulses hit a sample of the grown bacteria or yeast, small ionized molecules are released and quantified based on mass, resulting in a pattern unique to each organism. results available in 20mins
30
Urine cultures
one of the most common lab specimens. cultures should only be done if pt is symptomatic with dysuria, hematuria, urgency, fever, rigors, back pain.
31
asymptomatic bacteruria
positive urine culture in a patient without Sx. common in diabetics, elderly women, LTC residents; up to 50% of catheterized pts. Treating this increases antibiotic resistance, risk of subsequent UTIs, risk of C.diff, and SEs from antibiotics, so we don't treat it.
32
Non-Invasive urine specimens
clean catch midstream specimens, catheter, ileal conduit, bagged specimen (peds)
33
Invasive urine specimens
cytoscopic, ureteral, percutaneous nephrostomy, supra-pubic aspirate
34
Midstream urine culture
prone to contamination from bowel, vagina, and urethral flora. void first part of urine into toilet and then, without stopping, collect midstream portion to prevent ureteral contamination.
35
Foley catheter specimen
never obtain specimen from the catheter bag- highly contaminated!! never send the tip of the foley catheter. obtain sample by aspirating from sampling port, using aseptic technique.
36
Urine sample contamination
presence of 3 or more organisms indicates contamination. can occur at time of collection, if the specimen is refrigerated, or if transport is delayed for more than 24hrs.
37
Swabs from superficial ulcers for culture?
no! swabs are prone to both false positive and false negative results. don't routinely obtain swabs during surgical procedures when tissue samples can be collected. ideally send the specimen, and not a swab of the specimen.
38
Best specimen for wound cultures
fluid or tissue
39
taking a swab from a wound
open areas are usually contaminated; clean the area with sterile water or non-bacteriostatic saline with a sponge or gauze. always sample the advancing margin. pus may not grow anything, as the organism may be dead.
40
Antimicrobial resistance
occurs when microbes develop resistance to antibiotics.
41
MRSA
methicillin-resistant staphylococcus aureus | screened via nares and rectum/peritoneum
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VRE
vancomycin resistant enterococcus | rectal swab
43
ESBL
extended spectrum beta-lactamase
44
CPE
Carbapenemase-producing Enterobacteriaceae rectal swab resistant to almost all Abx and include resistance to all penicillins, cephalosporins, carbapenems, and all other antibiotic classes.
45
MDR
pseudomonas
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Candida auris
yeast | nares, groin, axilla, rectum
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Surveillance swabs
ordered based on risk factors, known exposure, previous colonization/infection
48
Lab detection of antibiotic resistance
lab selects a media that will preferentially grow the resistant organisms. Abx and other components are added to prevent the growth of susceptible organisms and other organism groups.
49
Bacterial causes of infectious diarrhea
salmonella, shigella, campylobacter, yersinia entercolitica, shigatoxin producing E.Coli, C. diff, vibrio cholera, aeromonas, plesiomonas
50
Viral causes of infectious diarrhea
norovirus, adenovirus, astrovirus, enterovirus
51
Parasitic causes of infectious diarrhea
giardia, entamoebahistolytica, dientamoeba fragilis, tapeworms, nematodes, cryptosporium, cyclospora
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Green Lidded Stool Container
bacteria
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Yellow lidded stool container
parasitology
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Orange lidded stool container
C. diff, virus detection
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Positive stool culture rejection criteria
C.diff: formed stool from a patient <1y/o incorrect transport media in a hospitalized pt admitted for >72hrs
56
Diagnosis of enteric pathogens
routine stool culture still performed at most hospitals.
57
Molecular Assay
detects salmonella, shigella, campylobacter, yersinia entercolitica, shiga-toxin-producing e.coli. advantage over stool culture is that it has a much greater sensitivity to pick up organisms that are often in low numbers and not very stable. culture still needed to isolate pathogens for genotyping and susceptibility testing
58
Sterile fluids
collected by a physician. considered irretrievable specimens (eg. CSF, pleural fluid, joint aspirate, pericardial fluid, vitreous fluid)
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Inoculation of media
portion of the sediment is inoculated onto media. media is chosen to help grow different types of bacteria.
60
Incubation of media
media is incubated at 35 degrees in different atmospheres (eg. 5% CO2, anaerobic, etc)
61
Invasive Meningococcal Disease
thrombosis and gangrene of fingers, hemorrhage of adrenals, macular and non-blanching petechial rash
62
critical call notification
life-threatening results are called to the nurse/physician involved in the care of the patient by the lab.
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Diagnosis with sterile fluids
- gram stain of CSF, culture - molecular detection using PCR in CSF - aspiration or biopsy of skin lesion for IMD
64
listeria monocytogenes
cause of meningitis in older and immunocompromised patients. | detected with MALDI-TOF
65
nasopharyngeal swabs
used to detect influenza A & B, parainfluenza, respiratory syncitial virus, rhinovirus, enterovirus, metapneumovirus, and adenovirus
66
Respiratory Viral Detection
involves viral culture, antigen detection, immunofluorescent methods, and molecular assays.
67
Immunofluorescence
cells from the patient are placed on a glass slide in wells. fluorescent labelled antibodies to the virus is added. if the virus is present, fluorescence is detected using a fluorescent microscope.
68
throat swabs
sample the inflamed area of the back of the throat and the tonsils, avoiding other areas.
69
Sputum
first morning sputum often produces the best sample. pt should rinse mouth, remove dentures, and cough into the container. potential for contamination with mouth flora.
70
Endotracheal aspirate
performed in patients who are intubated. a catheter is passed through the endotracheal tube and aspirated. can be contaminated as it passes through the endotracheal tube.
71
Bronchial wash
bronchoscope doesn't go very far. takes sampling of fluid from the whole lung.
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bronchoalveolar lavage
bronchoscope is wedged into all lobes of the lungs
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bronchoalveolar lavage
bronchoscope is wedged into all lobes of the lungs
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Bacterial detection of pneumonia
common bacterial pathogens (eg. S.pneumoniae, H. influenzae, S. aureus) can be cultured routinely. legionella- respiratory culture or urine for legionella antigen.
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fungal culture for dx pneumonia
only 2 types in ontario that cause pneumonia; histoplasmosis, basromyces. travel, immunocompromised
76
TB specimens
- first morning sputum x3 days, bronchoscopy, spinal fluid, blood culture, tissue/aspirate, swabs not recommended
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fungal diagnostic methods
culture (mould detection requires longer incubation) | identification mainly based on microscopy, colonial features, growth at different temperatures, some reagents
78
Malaria
associated with travel in canada; specimens include blood by venipuncture, blood by capillary puncture. clinical info: country of travel, Sx
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Serology
used to diagnose acute or chronic infection. immune status is important.
80
Immunoassays
use antibodies directed at the analayte to detect a pathogen | enzyme immunoassay is the easiest method.
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molecular methods
nucleic acid is extracted from the specimen or isolate. can be applied to bacteria, viruses, parasitology, and fungi. different methods are used to amplify the RNA or DNA in the specimen.
Microbiology
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