TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory*

54

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Abscess (also
Lesion, Wound,
Pustule, Ulcer)
Superficial Aerobic swab Wipe area with sterile Swab along leading edge < 2 hrs 24 hrs/RT BA, CA, Mac, CNA Gram Add CNA if smear
moistened saline or 70% of wound optional suggests mixed
with Stuart’s alcohol gram- positive
or Amie’s and gram-
medium negative flora
Deep Anaerobic Wipe area with Aspirate material from < 2 hrs 24 hrs/RT BA, CA, Mac, Gram Wash any granules
transporter sterile saline or wall or excise tissue CNA Anaerobic and “emulsify” in
70% alcohol BBA, LKV, BBE saline
Blood or Bone
Marrow
Aspirate
Blood culture Disinfect Draw blood at time of Within 2 hrs/RT Must be Blood culture Direct gram Stain Other considerations:
PART II  General Principles in Clinical Microbiology

media set venipuncture site febrile episode; draw incubated at bottles may from positive brucellosis,
(aerobic and with 70% alcohol two sets from right 37° C on be used. BA, blood culture tularemia, cell
anaerobic and disinfectant and left arms; do not receipt in CA BBA- bottles wall–deficient
bottle) or such as Betadine draw more than three laboratory anaerobic bacteria,
Vacutainer sets in a 24-hr period; leptospirosis, or
tube with draw ≥20 ml/set AFB
SPS (adults) or 1-20 ml/set
(pediatric) depending
on patient’s weight
Body Fluids
Amniotic, Sterile, Disinfect skin before Needle aspiration < 15 min Plate as soon May use an Gram (vaginal fluid May need to
abdominal, screw-cap aspirating as received aerobic and is recommended) concentrate by
ascites tube or specimen Blood culture anaerobic centrifugation or
(peritoneal), anaerobic bottles blood culture filtration —stain
bile, joint transporter incubate at bottle set for and culture
(synovial), or direct 37° C on body fluids sediment
pericardial, inoculation receipt in BA, CA, thio
pleural into blood laboratory CNA, Mac
culture (Peritoneal)
bottles BBA, BBE, LKV
anaerobic
Bone
Sterile, Disinfect skin before Take sample from Immediately/RT Plate as soon BA, CA, Mac, Gram May need to
screw-cap surgical procedure affected area for as received thio homogenize
container biopsy


TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Cerebrospinal
Fluid
Sterile, Disinfect skin before Consider rapid testing < 15 min < 24 hrs BA, CA (Routine) Gram—best Add thio for CSF
screw-cap aspirating (e.g., Gram stain; Routine BA, CA, thio sensitivity by collected from
tube specimen cryptococcal antigen) Incubate at (shunt) cytocentrifugation shunt
37° C (may also want to
except for do AO if
viruses, cytocentrifuge not
which can available)
be held at
4° C for up
to 3 days
Ear
Inner Sterile, Clean ear canal with Aspirate material behind < 2 hrs 24 hrs/RT BA, CA, Mac Gram Add anaerobic
screw-cap mild soap solution drum with syringe if (add thio if culture plates for
tube or before ear drum intact; use prior tympanocentesis
anaerobic myringotomy swab to collect antimicrobial specimens
transporter (puncture of the material from ruptured therapy)
ear drum) ear drum BBA-(anaerobic)
Outer Aerobic swab Wipe away crust Firmly rotate swab in < 2 hrs/RT 24 hrs/RT BA, CA, Mac Gram
moistened with sterile saline outer canal
with Stuart’s
or Amie’s
medium
Eye
Conjunctiva Aerobic swab Sample both eyes; use < 2 hrs/RT 24 hrs/RT BA, CA, Mac Gram, AO, histologic Other considerations:
moistened swab premoistened stains (e.g., Chlamydia
with Stuart’s with sterile saline Giemsa) trachomatis,
or Amie’s viruses, and fungi
medium
Aqueous/ Sterile, screw < 15 min/RT Set up BA, Mac, Gram/AO
vitreous cap tube immediately 7H10, Ana
fluid on receipt
Corneal Bedside Clinician should < 15 min/RT Must be BA, CA, SDA, Gram/AO Other considerations:
scrapings inoculation instill local incubated at 7H10, Ana, The use of 10-mm Acanthamoeba
of BA, CA, anesthetic before 28° C (SDA) thio frosted ring slides spp., herpes
SDA, 7H10, collection or 37° C assists with simplex virus and
thio (everything location of other viruses,
Specimen Management  CHAPTER 5

else) on specimen due to Chlamydia

receipt in the size of the trachomatis, and
laboratory specimen fungi
55

Continued
 56

TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Foreign Bodies
IUD Sterile, Disinfect skin before < 15 min/RT Plate as soon Thio
screw-cap removal as received
container
IV catheters, Sterile, Disinfect skin before Do not culture Foley < 15 min/RT Plate as soon BA, Thio
pins, screw-cap removal catheters; IV catheters as received prosthetic
container are cultured if possible valves
quantitatively by store <
rolling the segment 2 hrs 4° C
back and forth across
agar with sterile
PART II  General Principles in Clinical Microbiology

forceps four times;

≥15 colonies are
associated with
clinical significance
GI Tract
Gastric Sterile, Collect in early AM Most gastric aspirates < 15 min/RT Must be BA, CA, Mac, HE, Gram/AO Other considerations:
aspirate screw-cap before patient are on infants or for neutralized CNA, EB AFB
tube eats or gets out of AFB with sodium
bed bicarbonate
within 1 hr
of collection
Gastric biopsy Sterile, Rapid urease test or < 1 hr/RT 24 hrs/4° C Skirrow’s, BA, H&E stain optional: Other considerations:
screw-cap culture for BBA Immunostaining urea breath test
tube (normal Helicobacter pylori Antigen test
saline < (H. pylori )
2 hrs
transport
medium
recomended)
Rectal swab Swab placed in Insert swab ~ 2.5 cm Within 24 hrs/RT < 48 hrs/RT or BA, Mac, XLD Methylene blue for Other considerations:
enteric past anal sphincter; store 4° C HE, Campy, fecal leukocytes Vibrio, Yersinia
transport feces should be visible EB enterocolitica,
medium on swab Escherichia coli
O157:H7


TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Stool culture Clean, Routine culture should Within 24 hrs/RT 72 hrs/4° C BA, Mac, XLD, Methylene blue for See considerations
leak-proof include Salmonella, Unpreserved HE, Campy, fecal leukocytes in previous rectal
container; Shigella, and < 1 hr/RT EB, optional: Optional: Shiga toxin swabs
transfer Campylobacter; Mac-S; testing Do not perform
feces to specify Vibrio, Chromogenic routine stool
enteric Aeromonas, agar cultures for
transport Plesiomonas, Yersinia, patients whose
medium Escherichia coli length of stay in
(Cary-Blair) if O157:H7, if needed the hospital
transport will Follow-up may include exceeds 3 days
exceed 1 hr Shiga toxin assay as and whose
recommened by CDC admitting
diagnosis was not
diarrhea; these
patients should be
tested for
Clostridium
difficile
O&P O&P Collect three Wait 7-10 days if patient Within 24 hrs/RT Indefinitely/RT Liquid specimen
transporters specimens every has received should be
(e.g., 10% other day at a antiparasitic examined for the
formalin and minimum for compounds, barium, presence of
PVA) outpatients; iron, Kaopectate, motile organisms
hospitalized metronidazole, Milk of
patients Magnesia, Pepto-
(inpatients) should Bismol, or tetracycline
have a daily
specimen
collected for 3
days; specimens
from inpatients
hospitalized more
than 3 days
should be
discouraged
Genital Tract
FEMALE
Bartholin cyst Anaerobic Disinfect skin before Aspirate fluid; consider < 2 hrs 24 hrs/RT BA, CA, Mac, Gram
transporter collection chlamydia and GC TM, Ana
Specimen Management  CHAPTER 5

culture

Continued
57
 58

TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Cervix Swab Remove mucus Do not use lubricant on < 2 hrs/RT 24 hrs/RT BA, CA, Mac, TM Gram
moistened before collection speculum; use viral/
with Stuart’s of specimen chlamydial transport
or Amie’s medium, if necessary;
medium swab deeply into
endocervical canal
Cul-de-sac Anaerobic Submit aspirate < 2 hrs/RT 24 hrs/RT BA, CA, Mac, Gram
transporter TM, Ana
Endometrium Anaerobic Surgical biopsy or < 2 hrs/RT 24 hrs/RT BA, CA, Mac, Gram
transporter transcervical aspirate TM, Ana
via sheathed catheter
Urethra Swab Remove exudate Collect discharge by < 2 hrs/RT 24 hrs/RT BA, CA, TM Gram Other considerations:
PART II  General Principles in Clinical Microbiology

moistened from urethral massaging urethra Chlamydia,

with Stuart’s opening against pubic Mycoplasma
or Amie’s symphysis or insert
medium flexible swab 2-4 cm
into urethra and rotate
swab for 2 seconds;
collect at least 1 hr
after patient has
urinated
Vagina Swab Remove exudate Swab secretions and < 2 hrs/RT 24 hrs/RT BA, TM Gram Examine Gram stain
moistened mucous membrane of Culture is not for bacterial
with Stuart’s vagina recommended vaginosis,
or Amie’s for the especially white
medium or diagnosis of blood cells, clue
JEMBEC bacterial cells, gram-
transport vaginosis; positive rods
system inoculate indicative of
selective Lactobacillus, and
medium for curved, gram-
group B negative rods
Streptococcus indicative of
(LIM broth) if Mobiluncus spp.
indicated on
pregnant
women


TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
MALE
Prostate Swab Clean glans with Collect secretions on < 2 hrs/RT for Swab: 24 hrs/ BA, CA, Mac, Gram
moistened soap and water swab or in tube swab; RT; tube: TM, CNA
with Stuart’s immediately if plate
or Amie’s in tube/RT secretions
medium or immediately
sterile,
screw-cap
tube

Urethra Swab Insert flexible swab < 2 hrs/RT for 24 hrs/RT for BA, CA, TM Gram Other considerations:
moistened 2-4 cm into urethra swab; within swab; put Chlamydia,
with Stuart’s and rotate for 2 2 hrs for JEMBEC at Mycoplasma
or Amie’s seconds or collect JEMBEC 37° C
medium or discharge on JEMBEC system immediately
JEMBEC transport system on receipt in
transport laboratory
system
Hair, Nails, or
Skin Scrapings
(for fungal
culture)
Clean, Nails or skin: wipe Hair: collect hairs with Within 24 hrs/RT Indefinitely/RT SDA, IMAcg, CW
screw-top with 70% alcohol intact shaft SDAcg
tube Nails: send clippings of
affected area
Skin: scrape skin at
leading edge of lesion
Respiratory
Tract
LOWER
BAL, BB, BW Sterile, Anaerobic culture < 2 hrs/RT 24 hrs/4° C BA, CA, Mac, Gram and other Other considerations:
screw-top appropriate only if CNA special stains as quantitative
container sheathed (protected) requested (e.g., culture for BAL,
catheter used Legionella DFA, AFB, Legionella,
acid-fast stain) Nocardia,
Mycoplasma,
Pneumocystis,
cytomegalovirus
Specimen Management  CHAPTER 5

Continued
59
 60

TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Sputum, Sterile, Sputum: have patient Sputum: have patient < 2 hrs/RT 24 hrs/4° C BA, CA, Mac Gram and other Other considerations:
tracheal screw-top brush teeth and collect from deep PC OFPBL-cystic special stains as AFB, Nocardia
aspirate container then rinse or cough; specimen fibrosis requested (e.g.,
(suction) gargle with water should be examined Legionella DFA,
before collection for suitability for acid-fast stain)
culture by Gram stain;
induced sputa on
pediatric or
uncooperative patients
may be watery
because of saline
nebulization
PART II  General Principles in Clinical Microbiology

UPPER
Nasopharynx Swab Insert flexible swab < 2 hrs/RT 24 hrs/RT BA, CA Other considerations:
Nose moistened through nose into BA, chromogenic add special
with Stuart’s posterior nasopharynx agar media for
or Amie’s and rotate for 5 Corynebacterium
medium seconds; specimen of diphtheriae,
choice for Bordetella pertussis,
pertussis Chlamydia, and
Mycoplasma
Pharynx Swab Swab posterior pharynx < 2 hrs/RT 24 hrs/RT BA or SSA Other considerations:
(throat) moistened and tonsils; routine add special media
with Stuart’s culture for group A for C. diphtheriae,
or Amie’s Streptococcus (S. Neisseria
medium pyogenes) only gonorrhoeae, and
epiglottis
(Haemophilus
influenzae)
Tissue
Anaerobic Disinfect skin Do not allow specimen to < 15 min/RT 24 hrs/RT BA, CA, Mac, Gram May need to
transporter dry out; moisten with CNA, Thio homogenize
or sterile, sterile, distilled water Anaerobic: BBA,
screw-cap if not bloody LKV, BBE
tube


TABLE 5-1  Collection, Transport, Storage, and Processing of Specimens Commonly Submitted to a Microbiology Laboratory—cont’d

Transportation Storage before Primary Plating

Specimen Container Patient Preparation Special Instructions to Laboratory Processing Media Direct Examination Comments
Urine
Clean-voided Sterile, Females: clean area Preserved within 24 hrs/4° C BA, Mac Check for pyuria, Plate quantitatively
midstream screw-cap with soap and 24 hrs/RT Optional: Gram stain not at 1 : 1000;
(CVS) container water, then rinse unpreserved Chromogenic recommended consider plating
Containers that with water; hold < 2 hrs/RT agar quantitatively at
include a labia apart and 1 : 100 if patient is
variety of begin voiding in female of
chemical commode; after childbearing age
urinalysis several mL have with white blood
preservatives passed, collect cells and possible
may also midstream acute urethral
be used Males: clean glans syndrome
with soap and
water, then rinse
with water; retract
foreskin; after
several mL have
passed, collect
midstream
Straight Sterile, Clean urethral area Insert catheter into < 2 hrs/RT 24 hrs/4° C BA, Mac Gram or check for Plate quantitatively
catheter (in screw-cap (soap and water) bladder; allow first preserved < pyuria at 1 : 100 and
and out) container and rinse (water) 15 mL to pass; then 24 hrs/RT 1 : 1000
collect remainder
Indwelling Sterile, Disinfect catheter Aspirate 5-10 mL of < 2 hrs/4° C 24 hrs/4° C BA, Mac Gram or check for Plate quantitatively
catheter screw-cap collection port urine with needle and (preserved < pyuria at 1 : 1000
(Foley) container syringe 24 hrs/RT)
Suprapubic Sterile, Disinfect skin Needle aspiration above Immediately/RT Plate as soon BA, Mac, Ana, Gram or check for Plate quantitatively
aspirate screw-cap the symphysis pubis as received Thio pyuria at 1 : 100 and
container or through the abdominal 1 : 1000
anaerobic wall into the full
transporter bladder

7H10, Middlebrook 7H10 agar; AFB, acid-fast bacilli; AM, morning; Ana, anaerobic agars as appropriate (see Chapter 41); AO, acridine orange stain; BA, blood agar; BAL, bronchial alveolar lavage; BB,
bronchial brush; BBA, brucella blood agar; BBE, Bacteroides bile esculin agar; BW, bronchial wash; CA, chocolate agar; Campy, selective Campylobacter agar; CNA, Columbia agar with colistin and
nalidixic acid; CW, calcofluor white stain; DFA, direct fluorescent antibody stain; EB, enrichment broth; GC, Neisseria gonorrhoeae; transport using JEMBEC system with modified Thayer-Martin; GI,
gastrointestinal; Gram, Gram stain; HBT, human blood-bilayer Tween agar; HE, Hektoen enteric agar; hrs, hours; IMAcg, inhibitory mold agar with chloramphenicol and gentamicin; IUD, intrauterine
device; LKV, laked blood agar with kanamycin and vancomycin; Mac, MacConkey agar; Mac-S, MacConkey-sorbitol; mL, milliliters; OFPBL, oxdative-fermentative polymixin B-bacitracin-lactose-agar;
O&P, ova and parasite examination; PC, Pseudomonas cepacia agar; PVA, polyvinyl alcohol; RT, room temperature; SDA, Sabouraud dextrose agar; SDAcg, Sabouraud; dextrose agar with cycloheximide
Specimen Management  CHAPTER 5

and gentamicin; SPS, sodium polyanethol sulfonate; SSA, group A streptococcus selective agar; thio, thioglycollate broth; TM, Thayer-Martin agar; XLD, xylose lysine deoxycholate agar.
*Specimens for viruses, chlamydia, and mycoplasma are usually submitted in appropriate transport media at 4° C to stabilize respective microorganisms.
61