Specimen collection and Handling Flashcards
1
Q
Specimen Collection Timing
A
Collect during ACUTE/EARLY PHASE OF ILLNESS (2-3 days for viral infection). Collect before administration of antibiotic, antifungal, or antiviral.
2
Q
Specimen Storage
A
Collect and store specimen in STERILE SCREW-CAP CONTAINER except for STOOL
3
Q
Swab Use - General
A
POOR specimen if aspirate or biopsy can be obtained
4
Q
Swab Use - Appropriate
A
nasal/nasopharyngeal, oropharyngeal, eyes, ears, or genitals
5
Q
Swab Use - Not Appropriate
A
NOT FOR ANAEROBES AND FUNGI
6
Q
Swab Shaft - Toxic to Chlamydia and Mycoplasma
A
Wooden
7
Q
Swab Shaft - Used usually in a calcium alginate-tipped swab
A
Aluminum
8
Q
Swab Shaft - General purpose shaft for bacteria and viruses
A
Plastic
9
Q
Swab Tip - General use for bacteria and viruses
A
Dacron
10
Q
Swab Tip - Excellent collection and release of samples
A
Rayon
11
Q
Swab Tip - Toxic to Neisseria (unless with charcoal)
A
Cotton
12
Q
Swab Tip - Toxic to enveloped virus & Neisseria, interferes with PCR methods
A
Calcium alginate
13
Q
Swab Design - Can trap organisms, leading to decreased recovery/sensitivity
A
Woven/Traditional
14
Q
Swab Design - Uses Nylon fibers for enhanced uptake and release of microbes
A
Flocked
15
Q
Enhancing Microbe Recovery
A
Place swab in 0.5-1.0 mL of sterile broth/saline and vortex it
16
Q
Specimen Transport - Container
A
Leak-proof plastic bag with separation for paperwork; has BIOHAZARD label
17
Q
Specimen Transport - Time Frame
A
Transport within 2 hours to the lab, except sterile specimens (within 15 minutes)
18
Q
SARS-CoV-2 Transport Medium
A
3mL of viral transport medium (VTM), Amies transport medium, phosphate buffered saline, or sterile saline
19
Q
Bacteria Susceptible to Air Exposure
A
Anaerobes
20
Q
Bacteria Susceptible to Temperature Changes
A
Neisseria meningitidis
21
Q
Bacteria Susceptible to pH Changes
A
Shigella
22
Q
Bacteria Susceptible to Glycerol
A
Vibrio
23
Q
Shipment - Arrangement of Container
A
Sample > Primary container > Absorbent > Secondary container > Dry ice/Liq. nitrogen > Outer/Tertiary container
24
Q
Shipment - Category A
A
Substances/microbes capable of permanent disability or life-threatening
25
Shipment - Category B
Substances/microbe incapable of permanent disability or life-threatening on its current form
26
Preservation - Urine
Use BORIC ACID (bacteriostatic for 3 days)
27
Preservation - For Parasites
Don’t use formalin or Polyvinyl alcohol (PVA)
28
Preservation - Stuart/Amies Medium
Contains charcoal to neutralize fatty acid toxic to bacteria with pili
29
Preservation - Anticoagulants
Prevent clotting in blood, bone marrow, synovial fluid
30
Preservation - SPS (Sodium Polyanethol Sulfonate)
0.025-0.050% concentration, anticoagulant, anticomplement, antiphagocytic
31
Preservation - SPS - Function
Neutralizes aminoglycoside, neutralize with 1% gelatin
32
Preservation - SPS - Anaerobe Sensitivity
0.025% concentration preferred for some anaerobes and Neisseria
33
Preservation - Heparin
Can be used for viral culture and Mycobacterium culture, inhibits some gram-positive bacteria and yeasts
34
Preservation - Unused Anticoagulants
Citrate, EDTA, and others – should never be used
35
Preparation - Plating
Sterile specimens are plated directly into the culture media
36
Preparation - Centrifuge
>1 mL of fluid samples centrifuged at 3000 g for 20 minutes
37
Preparation - Tissue Homogenization
Tissues may be homogenized using a tissue grinder (disadvantages: destroys fungi)
38
Specimen for Abscess, Lesion, Wound, Ulcer container
Swab in Amie's or Stuart's medium
39
Common Isolates Abscess, Lesion, Wound, Ulcer - Macule
Dermatophytes, T. pallidum
40
Common Isolates -Abscess, Lesion, Wound, Ulcer Papule
HPV, S. aureus, Pox
41
Common Isolates -Abscess, Lesion, Wound, Ulcer Nodule
C. diphtheriae, Sporothrix, M. marinum
42
Common Isolates - Abscess, Lesion, Wound, Ulcer Pustule
Candida, Herpes, N. gonorrhoeae, S. aureus, VZV
43
Common Isolates - Abscess, Lesion, Wound, Ulcer Bulla
C. perfringens, HSV, S. aureus, V. vulnificus
44
Common Isolates - Abscess, Lesion, Wound, Ulcer Ulcer
B. anthracis, H. ducreyi, T. pallidum
45
Blood - Adult Volume
≥ 20mL/set
46
Blood - Pediatric Volume
1-20mL/set
47
Blood - Culture Bottle
Both aerobic and anaerobic
48
Blood - When to Draw
During febrile episodes, 2-3 sets per 24 hours, Do not draw >4 sets in 24 hours
49
ARD (Antimicrobial Removal Device) - Manual
1:10 blood to broth ratio, Growth detected in pellicle/turbidity/hemolysis/bubbles
50
ARD - Automated
1:5 blood to broth ratio, Growth detected by BacT/Alert (5 days TAT)
51
Common Blood Isolates
Staphylococcus aureus, E. coli, Staphylococcus epidermidis, Enterococcus, B-hemolytic streptococci, Candida albicans, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterobacter cloacae, Proteus, Bacteroides, Clostridium
52
Bone Marrow - Culture Bottle
May use blood culture bottle if volume is sufficient
53
Common Bone Marrow Isolates
Brucella, Histoplasma
54
Amniotic, Peritoneal, Pericardial, Pleural Fluids container
Sterile screw cap or blood culture bottle, Transport within 15 minutes at room temperature
55
Common Fluid Isolates - Pericardial
Coxsackie, Adenovirus, Influenza
56
Common Fluid Isolates - Arthritis
S. aureus, Streptococci, H. influenzae, Bacteroides, N. gonorrhoeae, Candida, Cryptococcus
57
CSF/Spinal Fluid - Transport Temperature
22-25°C, delayed testing at 20-24°C or 35°C
58
CSF/Spinal Fluid - Viral Studies
Transport at 4°C, Transport within 15 minutes at room temperature
59
CSF/Spinal Fluid - Direct Examination
India ink and Gram stain
60
CSF Collection - Number of Bottles
3 or more bottles collected: 2nd bottle → Micro, if only 1 bottle collected: Micro (1st) → Hema (2nd) → Chem/Serology (3rd)
61
CSF - Cytocentrifugation
Use acridine orange for best sensitivity and organism recovery
62
Meningitis - Newborn
S. agalactiae, E. coli
63
Meningitis - Children
H. influenzae
64
Meningitis - Adult
N. meningitidis
65
Meningitis - Geriatric
S. pneumoniae
66
Meningitis - Immunocompromised
L. monocytogenes
67
Meningitis/Encephalitis - Additional Causes
P. cantonensis, N. fowleri, Acanthamoeba, Coxsackie, HIV, T. solium, Toxoplasma
68
Ear Specimen - Transport Container
Sterile screw cap container
69
Ear Specimen - Anaerobic Transporter
Inner ear aspirate
70
Otitis Externa - Acute
S. aureus, S. pyogenes, P. aeruginosa (Swimmer’s ear/Acute diffuse otitis externa)
71
Otitis Externa - Chronic
P. aeruginosa, Anaerobes
72
Otitis Media - Acute
S. pneumoniae, H. influenzae, M. catarrhalis, S. pyogenes, RSV, Influenza virus, coronavirus, enterovirus, rhinovirus
73
Otitis Media - Chronic
Anaerobes (Bacteroides, Fusobacterium, Prevotella, Porphyromonas, Peptostreptococcus)
74
Eye Conjunctiva or Corneal Scraping - Transport Method
Direct inoculation to BAP and CAP
75
Eye Conjunctiva or Corneal Scraping - Transport Time
Transport within 15 mins at room temperature
76
Corneal Scraping - Incubation
28°C in SDA
77
Common Eye Isolates
Chlamydia trachomatis, Acanthamoeba, Herpes simplex virus
78
Gastric Wash or Lavage - Transport Time
Transport within 15 mins at room temperature
79
Gastric Aspirates - Indications
Infants or AFB, process within 4 hours or neutralize with 10% sodium carbonate
80
Common Gastric Isolates
Campylobacter jejuni, Helicobacter pylori, Mycobacterium tuberculosis, Ascaris larvae
81
Rectal Swab - Transport Medium
Enteric transport medium
82
Rectal Swab - Inoculation Method
Insert 1-1.5 cm deep, feces visible on swab, inoculate in enteric media
83
Common Rectal Swab Isolates
Pathogenic Enterobacteria, Vibrio, Campylobacter, Helicobacter, Parasites (stool sample), Norwalk, Rotavirus, C. difficile
84
Urine - Best Collection Method
Mid-stream clean catch (Ambulatory/Outpatient/Non-invasive)
85
Urine - Catheterized Collection Method
Non-Ambulatory/In-Patient/Invasive, Clean urethra with soap and water, collect remainder after first 15mL
86
Urine - Suprapubic Aspiration
For Anaerobic culture, disinfect skin first
87
Common Urine Isolates
Escherichia coli (UPEC), Klebsiella, Staphylococcus saprophyticus, Enterococci, Proteus, Pseudomonas, Candida, Acinetobacter
88
Urine - Quantitative Counting
1 µL Loop (1 colony x 1000 = CFU/mL), 10 µL Loop (1 colony x 100 = CFU/mL)
89
Urethra - Collection Method
Swab in Amie's or Stuart's medium, collect 1 hour after patient has urinated
90
Urethra - Direct Smear
Gram stain
91
Urethra - Collection Time
Do not refrigerate, collect if >1 hour after urination
92
Common Urethral Isolates
N. gonorrhoeae, Chlamydia trachomatis, Ureaplasma, Mycoplasma
93
Cervix - Collection Method
Swab in Amie's or Stuart’s medium, Remove mucus before collection
94
Cervix - Collection Instructions
Do NOT use lubricant on speculum, Swab deeply into endocervical canal
95
Cervix - Swab Material
Do NOT use wooden shaft or Calcium alginate swab
96
Common Cervix Isolates
N. gonorrhoeae, C. trachomatis, Ureaplasma
97
Vagina - Collection Method
Swab in Amie's or Stuart’s medium, Remove exudate
98
Vagina - Collection Instructions
Swab secretions and mucous membrane
99
Vagina - Bacterial Vaginosis Diagnosis
Culture is not recommended
100
Vagina - Group B Streptococcus Screening
Use LIM broth
101
Common Vagina Isolates
Lactobacillus, G. vaginalis, Mobiluncus, S. agalactiae
102
Prostate - Collection Method
Swab in Amie's or Stuart’s medium, Clean urethral meatus with soap and water
103
Prostate - Collection Instructions
Massage prostate through rectum and swab the secretions, Plate immediately
104
Common Prostate Isolates
E. coli, other enteric organisms, P. aeruginosa, Mycoplasma genitalium
105
IUD - Collection Method
Sterile screw cap container, Disinfect skin before removal
106
IUD - Transport Instructions
Transport within 15 mins at room temperature, Plate immediately
107
Common IUD Isolates
Actinomyces infections
108
IV Catheter - Collection Method
Sterile screw cap container, Disinfect skin with alcohol before removal
109
IV Catheter - Collection Instructions
Do not accept foley catheters, Roll segment back and forth for 4x using sterile forceps
110
IV Catheter - Quantitative Culture
≥ 15 colonies are significant
111
Common IV Catheter Isolates
S. epidermidis, S. aureus, other CONS, Enterobacteria, P. aeruginosa, Candida, Corynebacterium
112
Nasopharyngeal Swab - Collection Method
Swab in Amie's or Stuart’s medium, Rotate the swab for 5 seconds
113
Nasopharyngeal Swab - Transport Instructions
Transport within 15 mins if no transport media, or within 2 hours at 20-24°C
114
Common Nasopharyngeal Isolates
B. pertussis, SARS-CoV, H. influenzae, N. meningitidis, Rhinovirus, Coronavirus, Adenovirus, Influenza, Klebsiella ozaenae
115
Nasal Swab - Collection Method
Swab in Amie’s/Stuart’s, Premoisten with sterile saline, insert 1-2 cm into nares and rotate
116
Common Nasal Isolate
MRSA screening
117
Throat Swab - Collection Method
Sterile screw cap, Clean genitals with soap and water
118
Common Throat Isolates
S. pyogenes (Grp A Streptococcus), Pharyngitis – S. pyogenes, Group C/G streptococcus, Arcanobacterium, Fusobacterium, N. gonorrhoeae, Corynebacterium ulceran
119
Sputum - Collection Method
Sterile screw cap, Brush teeth then rinse or gargle with water
120
Sputum - Aerosol-induced Sample
Use 15% NaCl or 10% glycerin
121
Common Sputum Isolates
M. tuberculosis, Corynebacterium, Mycoplasma pneumoniae, Chlamydia trachomatis, Chlamydia pneumoniae, Bordetella pertussis, Legionella, Pneumocystis, Nocardia, Histoplasma, Coccidioides, RSV, Coronavirus, Influenza/Parainfluenza
122
Tissue - Collection Method
Anaerobic transporter, Disinfect skin, Do not allow the specimen to dry, May need to be homogenized
123
Common Tissue Isolates
Anaerobes, Gram-negative bacilli, Gram-positive organisms, Fungi
124
Specimen Transport for Viruses, Chlamydia, Mycoplasma
Transport in appropriate media at 4°C (ice pack or liquid nitrogen)
125
Transport Time for Majority of Samples
Transport within 2 hours at room temperature
126
Exceptions to Transport Time
Normally sterile samples (within 15 minutes), gastric biopsy (within 1 hour)
127
Specimen Storage at Room Temperature (20-24°C)
Hair, Nails, Skin scraping for fungi (<2 hrs)
128
Specimen Storage Up to 24 Hours at Room Temperature
Abscess, lesion, wound, pustule, ulcer, Nasopharyngeal swab, Oropharyngeal swab, Sterile body fluids (Peritoneal, Pleural, Pericardial), Inner ear sample, Eye samples (Conjunctiva, Cornea, Vitreous fluid), Rectal swab, Genital samples (cervix, vagina, cul-de-sac, prostate, Urethral swab), Bone marrow, Tissues, Preserved stool (in holding media), Preserved urine (in holding media), CSF (or at 35°C)
129
Specimen Storage at 4°C (Refrigerator Temperature) Up to 48 Hours
Feces for Clostridium difficile (culture or molecular)
130
Specimen Storage at 4°C (Refrigerator Temperature) Up to 24 Hours
Feces for E. coli O157:H7, Outer ear sample, Gastric aspirate/biopsy, Respiratory samples (BAL, Bronchial washing, Sputum), Unpreserved/Fresh urine, Unpreserved/Fresh stool
131
Specimen Storage at 4°C (Refrigerator Temperature) Up to 2 Hours
IV catheters, Pins
132
Specimen Storage at 35°C (Incubator Temperature) Within 6 Hours
CSF
133
Specimen Storage Upon Receipt at the Lab
Blood, Sterile body fluids in blood culture bottle
134
Level 1 Immediate Critical/Invasive Specimen
Amniotic fluid, Blood, Heart valve, Brain, CSF
135
Level 2 Unpreserved Specimen
Body fluids (not listed in Level 1), Bone, Wound Drainage, Feces, Sputum, Tissue
136
Level 3 Quantitation Required Specimen
Catheter tip, Urine (midstream/suprapubic/catheterized)
137
Level 4 Preserved Specimen
Preserved Urine, Preserved Stool, Swabs in holding/transport medium
138
Rejected Samples - Criteria
Non-matching label and requisition, Specimen transported at wrong temperature or wrong media, QNS, Leaking sample, Exceeds 2-hour transport, Preserved with fixative (formalin), Swabs for anaerobic culture, Calcium alginate swab for molecular assay, Dried sample/swab, Foley catheter tip
