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Introductory Microbiology > Specimen Collection & Laboratory Diagnosis > Flashcards

Specimen Collection & Laboratory Diagnosis Flashcards

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1
Q

In which phase of specimen collection and lab diagnosis is the error rate the highest?

A
  • most errors occur in the early “pre-analytical phase” (wrong test, order entry, patient-specimen misidentification, quality of sample collection poor, wrong container, inappropriate storage and transport)
  • very few errors in the performance of the lab test
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2
Q

Why is patient identification one of the most important process in specimen collection?

A
  • 50% of deaths from transfusion r/t errors in identification
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3
Q

What patient identifiers can be used by the HCP?

A
  • full name
  • hospital accession number
  • OHIP number
  • date of birth
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4
Q

What information is required on the laboratory requisition?

A
  • unique identification of the patient
  • gender, age, DOB
  • specimen type, anatomic site, clinical information
  • test ordered
  • date and time of collection
  • who requested the test (most responsible physician; must be uniquely identified; copy to physician)
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5
Q

What information should the specimen label include?

A
  • patient full name, hospital accession number, DOB
  • collection date and time, who collected it
  • type of test, source, and clinical info (ie. any antibiotics)
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6
Q

Where should specimen labelling take place?

A

At the bedside

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7
Q

What specimen labelling errors could occur?

A
  • unlabelled specimen
  • specimen label and specimen do not match
  • label information illegible
  • specimen covered up by label so quality cannot be assessed (need to relabel)
  • specimen label sideways, barcode horizontal (need to relabel)
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8
Q

How can we prevent specimen-patient mismatch?

A
  • verify correct patient selected for label

- verify patient identity on specimen label corresponds to patient

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9
Q

What are consequences of patient-specimen mismatch?

A
  • if the correct patient is not treated: potential side effects, increase length of stay, cost, etc.
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10
Q

What is transport media?

A
  • liquid, gel or charcoal designed to preserve the pathogen despite delay in transport to lab
  • specific to the bacteria/virus/parasite
  • some have resins, as with blood culture bottles, which bind to antibiotics to prevent them from affecting the pathogen
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11
Q

How can the HCP maximize the ability to isolate the pathogen during collection?

A
  • collect before patient is put on antibiotics
  • usually maximum volume of specimen
  • collect when organism will be most abundant (ex. first morning urine for UTI)
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12
Q

How can the HCP minimize specimen contamination with normal flora?

A
  • many specimens are in contact with non-sterile surfaces
  • blood culture collection requires disinfection of skin due to skin commensal flora: coagulase negative staphylococcus, viridans streptococci, propionibacterium
  • female genital tract: lactobacillus, streptococci, anaerobes
  • midstream urine minimizes contamination with genital tract flora
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13
Q

What errors can cause poor specimen quality?

A
  • hemolyzed specimen
  • delayed specimen transport
  • not a sufficient quantity of specimen
  • specimen leaked
  • incorrect specimen container
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14
Q

In what order should venous blood be drawn?

A

1) blood culture bottles
2) coagulation (light blue)
3) multi-purpose (red)
4) chemistry (green)
5) trace metals (royal blue)
6) transfusion medicine (pink)
7) hematology (lavender)
8) glucose (grey)
9) ACD (yellow)

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15
Q

What are causes of secondary bacteremia?

A
  • Endocarditis, pneumonia, urosepsis, meningitis, abscess
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16
Q

What are the most common organisms found in positive blood cultures?

A
  • E. coli, Coagulase negative staphylococcus, S. aureus and Enterococcus were the four most common organisms
  • Other pathogens: Klebsiella, Enterobacter, Pseudomonas, Candida spp
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17
Q

What volume of blood should be collected for blood cultures?

A
  • 8 - 10 mL for adults

- paediatric volumes vary by weight

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18
Q

How should skin be prepared to prevent blood culture contamination?

A
  • choose the right disinfectant: chlorhexidine, tincture of iodine
  • need contact time of the disinfectant on the skin
  • proviodine requires 1.5-2 minutes
  • tincture of iodine: 30 seconds
  • chlorhexidine: 30 seconds
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19
Q

How should the blood culture bottle be prepared to prevent contamination?

A
  • the rubber septum is not protected by the cap on the bottle
  • disinfecting the septum reduces contamination
  • in the summer or during construction, increase in Bacillus spp contamination occurs as it is commonly in the environment and survives as a spore
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20
Q

The HCP should only take blood culture from a catheter when…

A
  • line-related infection is suspected or if very difficult to draw
  • increase in false positive cultures with catheter draw
  • take from peripheral site instead
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21
Q

What are the most common breaks in technique that lead to blood culture contamination?

A
  • not allowing disinfectant to dry completely
  • not disinfecting BC bottle septum
  • palpating the site of puncture after cleaning with non-sterile finger
  • placing blood specimen on non-sterile surface
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22
Q

Why is the amount of blood drawn important for detecting the pathogen?

A
  • yield is proportional to the amount of blood
  • ratio of 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 patient is on antibiotics
  • both underfilled and overfilled bottles are an issue
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23
Q

When should urine cultures be collected?

A
  • only collected if the patient is symptomatic: dysuria, hematuria, urgency, fever, rigors, back pain
  • asymptomatic patients should only have urine cultures if: pregnant (routine screening at 16-18 weeks) or an invasive urologic procedure is scheduled
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24
Q

What is asymptomatic bacteriuria (ABU)?

A
  • positive urine culture without symptoms
  • common in catheterized patients, diabetics, elderly patients
  • positive urinalysis does not always indicate UTI
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25
Q

Are cloudy and foul smelling urine symptoms of UTI?

A

No

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26
Q

Why should ABU not be treated?

A

Increases:

  • antibiotic resistance
  • risk of subsequent UTIs
  • risk of C. difficile infection
  • side effects from antibiotics
  • only treat during pregnancy or prior to urologic procedures, even if aymptomatic
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27
Q

What are symptoms of UTI?

A

Includes new onset of any of the following:

  • dysuria
  • frequency, urgency
  • suprapubic pain
  • change in mental status/delirium
  • fevers/chills/diaphoresis
  • nausea and vomiting
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28
Q

What types of urine cultures exist?

A

Non-invasive:

1) clean-catch midstream specimens
2) catheter
- indwelling catheter
- in and out catheter
3) ileal conduit
4) bagged specimens in pediatrics

Invasive:

1) cystoscopic
2) ureteral
3) percutaneous nephrostomy
4) supra-pubic aspirate

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29
Q

How should midstream urine specimens be collected?

A
  • prone to contamination from bowel, vaginal, and urethral flora
  • advise men to clean glans
  • void first part into toilet, then without stopping collect midstream portion
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30
Q

What is the optimal specimen for a wound culture?

A
  • collection of fluid or tissue
  • if close abscess, MD can aspirate fluid with a needle
  • can collect tissue form biopsy or debridement
  • most wounds do not have enough fluid to aspirate, swab must be used
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31
Q

How are swabs taken from a wound?

A
  • open area usually contaminated, must be cleaned with sterile water or nonbacteriostatic saline with sponge or gauze
  • always sample advancing margin
  • pus itself may not grow anything; organism may be dead
32
Q

What are the most common multi-drug resistant organisms?

A
  • MRSA = Methicillin resistant Staphylococcus aureus
  • VRE = Vancomycin resistant Enterococcus
  • ESBL = Extended spectrum B-lactamase producing organisms (usually E. coli, Klebsiella)
  • CPO = Carbapenemase producing organism (E. coli, Klebsiella, Enterobacter, Pseudomonas)
33
Q

When should a surveillance swab for resistant organisms be ordered?

A
  • screening based on risk factors (ex. past hospitalization)
  • known exposure (ex. from high risk country or close contact)
  • previous colonization or infection
34
Q

What specimen types are required for MRSA, VRE, ESBL and CPO surveillance?

A

MRSA - screening of nares and rectal perineum (may pre-moisten swab for nares)
VRE - rectal swabs (must be fecally stained)
ESBL/CPO - rectal swabs

35
Q

What are the four types of specimens for stool collection?

A

1) Bacterial culture: Salmonella, Shigella, Campylobacter, E. coli 0157, Yersinia entercolitica - not rx if patient has been in hospital for over 72 hours and new onset of symptoms
2) C. difficile
3) Viral detection: norovirus, rotavirus, enterovirus
4) Parasites: eggs and larvae

36
Q

What is the most common cause of infectious diarrhea in hospitalized patients?

A

C. difficile

37
Q

In what container are stool specimens for C. difficile and viral detection placed in?

A

Sterile urine container

38
Q

What patient instructions should be given when collecting stool samples?

A
  • avoid sending rectal swab (except infants)
  • collect stool using plastic collection device that fits into toilet, saran wrap, or sterile bedpan
  • avoid laxatives and mixing with urine or water
  • amount of stool and preservative are indicated on the container
39
Q

What are nasopharyngeal swabs?

A
  • used to detect respiratory viruses such as influenza A and B, parainfluenza, RSV, rhinovirus, enterovirus, metapneumovirus, adenovirus
  • must go half way from base of nose to base of ear to go far enough
40
Q

How is a throat swab performed?

A
  • avoid touching tongue and cheeks

- only touch inflamed tonsil area at the back of the throat

41
Q

How is a sputum specimen taken?

A
  • taken in the morning to provide best sample
  • patient should rinse mouth, remove dentures and cough into the container
  • potential for contamination with mouth flora - avoid saliva
42
Q

What is an endotracheal aspirate?

A
  • respiratory specimen performed in intubated patients
  • catheter is passed through the endotracheal tube and aspirated
  • can be contaminated as it passes through the tube
43
Q

What are bronchoscopy specimens?

A
  • LRT specimens
  • bronchial wash: bronchoscope doesn’t go as far, takes sampling of fluid from the whole lung
  • bronchoalveolar lavage: bronchoscope is wedged into the RUL, RML, RLL, LUL, LLL
44
Q

How are spinal fluids collected?

A
  • obtained by physician
  • collected into sterile containers using aseptic technique
  • for spinal fluids, often 4 tubes are collected
  • order of tubes is very important, do not want blood in later tubes
45
Q

In what order should spinal fluid tubes be collected?

A
  • tube 1 for cell count
  • tube 2 for chemistry (glucose, protein)
  • tube 3 for microbiology (need large volumes of 10 mL if fungal or TB cultures requested)
  • tube 4 cell count (preferred if only 1 tube used for cell count)
46
Q

When is a vaginal swab taken?

A
  • suspected yeast infection, bacterial vaginosis and trichomonas
  • tested via wet mount and Gram stain
  • decreased sensitivity for trichomonas if delay >1 hour
47
Q

When is a vaginal-rectal swab taken?

A
  • group B streptococcus in pregnant women at 35-37 weeks

- culture or molecular method

48
Q

What specimens must be collected for molecular detection of Chlamydia and N. gonorrhoea?

A
  • cervical swab if female
  • urethral swab if male
  • first void urine
49
Q

What specimens must be collected for cultures of Chlamydia and N. gonorrhoea?

A
  • cervical swab if female
  • vaginal swab if pre-pubertal
  • urethral swab if male
  • extra-genital swab
50
Q

When is culture preferred for Chlamydia and Gonorrhoea?

A

Culture preferred if:

  • susceptibility testing required
  • sexual assault
  • test of cure (children, pregnancy, non-compliance)
51
Q

How is a specimen for malaria taken?

A
  • specimen taken based on country of travel and symptoms
  • blood by venipuncture
  • blood by capillary puncture - higher sensitivity from fingerprick capillary sample
52
Q

How is a specimen for TB taken?

A
  • sputum first morning for three days (do not rinse mouth with tap water as can lead to false positive stains)
  • bronchoscopy
  • spinal fluid
  • blood culture (requires special tube)
  • tissue/aspirate
  • swabs not rx due to hydrophobic nature of cell wall
  • gastric lavage in first morning for pediatric
53
Q

How are fungal specimens taken?

A
  • for yeast collect using regular BC bottles
  • fungus such as Histoplasmosis, Blastomyces, Coccidiodies and most moulds require special tube similar to mycobacteria blood culture
  • swabs NOT recommended except if yeast
  • use black paper to do skin scraping or collect nail specimen
54
Q

What specimens are considered STAT?

A
  • spinal fluid should be received in the laboratory within 1 hour of collection
  • tissue/wound culture if suspect necrotizing fasciitis
  • malaria
55
Q

All specimens should be transported to the lab within ____

A

2 hours

56
Q

Spinal fluids and STAT specimens should be transported within ____

A

1 hour

57
Q

Bacteria, such as N. gonorrhoeae decreases in viability after how many hours?

A

6-12 (will die if delay >24 hours)

58
Q

What specimens should never be refrigerated (2-8 ºC)?

A
  • spinal fluids
  • blood cultures
  • sterile fluids/aspirates except for sterile fluids for fungal culture
  • tissue/ biopsies/bone marrow
  • corneal/eye scrapings
59
Q

What specimens should be refrigerated?

A
  • urine
  • respiratory
  • feces (except parasitology)
  • virology samples in universal transport medium
  • blood for viral serology or viral PCR
  • spinal fluid for viral PCR
60
Q

What are the most common reasons a specimen is rejected?

A
  • wrong container or wrong swab
  • leaking specimen – urines, sputum
  • incorrectly labelled or misidentification
61
Q

What specimens are considered irretrievable?

A
  • specimen cannot be physically replaced without compromising the clinical condition of the patient
  • cardiac arrest or operating room gases
  • blood gases by arterial puncture & scalp blood gases
  • autopsy, surgical pathology & cytopathology specimens
  • sterile body fluid, aspirate or tissue (e.g. spinal fluid, pericardial fluid, paracentesis, pleural fluid)
  • blood cultures before antibiotics started
62
Q

What are some specific specimen rejections?

A
  • formed stool for C. difficile
  • delay in receipt of specimen
  • sputum contaminated with saliva (>10 epithelial cells per LPF)
  • swab or blood culture media is expired
63
Q

What is direct examination of a specimen?

A
  • portion of a specimen is put on a glass slide
  • the slide is fixed by heat or methabnol
  • gram stain is performed
  • the technologist reviews the slide and reports the type based on colour and shape
64
Q

How is the Gram stain performed?

A
  • primary crystal violet stain
  • decolorizer (alcohol) will remove primary stain from gram negative bacteria
  • secondary stain (safranin) is taken up by gram negatives
65
Q

How is media inoculated and incubated for a culture?

A
  • portion of sediment inoculated onto media, which is chosen to grow different types of bacteria
  • incubated usually at 35 °C in either 5% CO2 (N. gonorrhoeae), ambient air, or anaerobic environment (clostridium species)
66
Q

What is a critical call notification?

A
  • life threatening result which requires the RN or MD involved in the patient’s care to provide the name of the patient to the lab and read back the lab result
  • the RN or MD documents the critical result and must contact the MRP or physician on call
67
Q

What methods exist for bacterial identification?

A
  • colonial morphology on media
  • biochemical reactions and properties
  • automated instruments
  • antigen or antibody detection methods
  • molecular methods: PCR or sequencing
  • MALDI-TOF
68
Q

Which bacterium has a an “umbrella patten of spread”?

A

Listeria monocytogenes

69
Q

What is Vitek2 identification system?

A
  • rapid method involving biochemical and other reactions to identify a wide range of organisms
  • takes 6-18 hours
  • identifies bacteria and yeast
70
Q

What is MALDI-TOF?

A
  • system used now
  • 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 20 min compared to routine methods that can take up to 24-48 hours for identification
71
Q

How are blood cultures identified as aerobic or anaerobic?

A
  • placed in an instrument that incubates the bottle at 35 °C
  • as soon as an increase in CO2 or decreased O2 is detected signifying growth, an alarm sounds
  • BC bottles are incubated for 5 days
72
Q

What is an immunoassay?

A
  • use antibodies directed to the analyze to detect a pathogen
  • enzyme label to see if the sample reacted with the antibody or antigen
73
Q

What is immunofluorescent viral detection?

A

NPS swab for virus detection:

  • cells from the patient placed on a glass slide
  • fluorescent labelled antibody to the virus is added
  • if the virus is present, fluorescence is detected using a fluorescent microscope
74
Q

How are viruses detected with molecular methods?

A
  • very common nowadays
  • nucleic acid extracted from the specimen
  • can also be used for bacteria, parasitology or fungi
  • different methods to amplify the DNA or RNA in the specimen (PCR, strand displacement, transcription amplification, probe and signal amplification)
75
Q

What are advantages of molecular methods?

A
  • increased sensitivity compared to culture based method
  • can detect organisms when specimen is delayed in transit
  • detect organisms that cannot be cultured
  • detect new organisms more rapidly that traditional methods
  • provides quantitative result
76
Q

What are disadvantages of molecular methods?

A
  • contamination can occur in lab
  • if target site of organism mutates, the assay will not detect organism
  • susceptibility testing cannot be performed
  • extremely sensitive so picks up colonization and not necessarily disease
  • result can remain positive for a long time, even if organism is dead

Introductory Microbiology (11 decks)

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