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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
Q

Peripheral blood culture vs draw from a line

A

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.

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26
Q

Blood culture instruments

A

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.

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27
Q

Gram Stain

A

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.

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28
Q

Vitek-2 identification system

A

rapid method involving biochemical and other reactions to identify a wide range of organisms. identification usually 6-8hrs

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29
Q

MALDI-TOF

A

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

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30
Q

Urine cultures

A

one of the most common lab specimens. cultures should only be done if pt is symptomatic with dysuria, hematuria, urgency, fever, rigors, back pain.

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31
Q

asymptomatic bacteruria

A

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.

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32
Q

Non-Invasive urine specimens

A

clean catch midstream specimens, catheter, ileal conduit, bagged specimen (peds)

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33
Q

Invasive urine specimens

A

cytoscopic, ureteral, percutaneous nephrostomy, supra-pubic aspirate

34
Q

Midstream urine culture

A

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
Q

Foley catheter specimen

A

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
Q

Urine sample contamination

A

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
Q

Swabs from superficial ulcers for culture?

A

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
Q

Best specimen for wound cultures

A

fluid or tissue

39
Q

taking a swab from a wound

A

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
Q

Antimicrobial resistance

A

occurs when microbes develop resistance to antibiotics.

41
Q

MRSA

A

methicillin-resistant staphylococcus aureus

screened via nares and rectum/peritoneum

42
Q

VRE

A

vancomycin resistant enterococcus

rectal swab

43
Q

ESBL

A

extended spectrum beta-lactamase

44
Q

CPE

A

Carbapenemase-producing Enterobacteriaceae
rectal swab
resistant to almost all Abx and include resistance to all penicillins, cephalosporins, carbapenems, and all other antibiotic classes.

45
Q

MDR

A

pseudomonas

46
Q

Candida auris

A

yeast

nares, groin, axilla, rectum

47
Q

Surveillance swabs

A

ordered based on risk factors, known exposure, previous colonization/infection

48
Q

Lab detection of antibiotic resistance

A

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
Q

Bacterial causes of infectious diarrhea

A

salmonella, shigella, campylobacter, yersinia entercolitica, shigatoxin producing E.Coli, C. diff, vibrio cholera, aeromonas, plesiomonas

50
Q

Viral causes of infectious diarrhea

A

norovirus, adenovirus, astrovirus, enterovirus

51
Q

Parasitic causes of infectious diarrhea

A

giardia, entamoebahistolytica, dientamoeba fragilis, tapeworms, nematodes, cryptosporium, cyclospora

52
Q

Green Lidded Stool Container

A

bacteria

53
Q

Yellow lidded stool container

A

parasitology

54
Q

Orange lidded stool container

A

C. diff, virus detection

55
Q

Positive stool culture rejection criteria

A

C.diff: formed stool from a patient <1y/o
incorrect transport media
in a hospitalized pt admitted for >72hrs

56
Q

Diagnosis of enteric pathogens

A

routine stool culture still performed at most hospitals.

57
Q

Molecular Assay

A

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
Q

Sterile fluids

A

collected by a physician. considered irretrievable specimens (eg. CSF, pleural fluid, joint aspirate, pericardial fluid, vitreous fluid)

59
Q

Inoculation of media

A

portion of the sediment is inoculated onto media. media is chosen to help grow different types of bacteria.

60
Q

Incubation of media

A

media is incubated at 35 degrees in different atmospheres (eg. 5% CO2, anaerobic, etc)

61
Q

Invasive Meningococcal Disease

A

thrombosis and gangrene of fingers, hemorrhage of adrenals, macular and non-blanching petechial rash

62
Q

critical call notification

A

life-threatening results are called to the nurse/physician involved in the care of the patient by the lab.

63
Q

Diagnosis with sterile fluids

A
  • gram stain of CSF, culture
  • molecular detection using PCR in CSF
  • aspiration or biopsy of skin lesion for IMD
64
Q

listeria monocytogenes

A

cause of meningitis in older and immunocompromised patients.

detected with MALDI-TOF

65
Q

nasopharyngeal swabs

A

used to detect influenza A & B, parainfluenza, respiratory syncitial virus, rhinovirus, enterovirus, metapneumovirus, and adenovirus

66
Q

Respiratory Viral Detection

A

involves viral culture, antigen detection, immunofluorescent methods, and molecular assays.

67
Q

Immunofluorescence

A

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
Q

throat swabs

A

sample the inflamed area of the back of the throat and the tonsils, avoiding other areas.

69
Q

Sputum

A

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
Q

Endotracheal aspirate

A

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
Q

Bronchial wash

A

bronchoscope doesn’t go very far. takes sampling of fluid from the whole lung.

72
Q

bronchoalveolar lavage

A

bronchoscope is wedged into all lobes of the lungs

73
Q

bronchoalveolar lavage

A

bronchoscope is wedged into all lobes of the lungs

74
Q

Bacterial detection of pneumonia

A

common bacterial pathogens (eg. S.pneumoniae, H. influenzae, S. aureus) can be cultured routinely. legionella- respiratory culture or urine for legionella antigen.

75
Q

fungal culture for dx pneumonia

A

only 2 types in ontario that cause pneumonia; histoplasmosis, basromyces. travel, immunocompromised

76
Q

TB specimens

A
  • first morning sputum x3 days, bronchoscopy, spinal fluid, blood culture, tissue/aspirate, swabs not recommended
77
Q

fungal diagnostic methods

A

culture (mould detection requires longer incubation)

identification mainly based on microscopy, colonial features, growth at different temperatures, some reagents

78
Q

Malaria

A

associated with travel in canada; specimens include blood by venipuncture, blood by capillary puncture.
clinical info: country of travel, Sx

79
Q

Serology

A

used to diagnose acute or chronic infection. immune status is important.

80
Q

Immunoassays

A

use antibodies directed at the analayte to detect a pathogen

enzyme immunoassay is the easiest method.

81
Q

molecular methods

A

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 (7 decks)

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