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Category: Clinical Microbiology
Specimen Management Summary Tables, Page 1 of 2
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This section presents tables that summarize and document the salient features of the common specimens that arrive in a microbiology laboratory. Table 15 lists bacteriology and mycology specimen collection guidelines. Specimen types include abscess, bite wound, blood cultures, bone marrow, burn, vaginal, cervical and decubitus ulcer. Table 16 includes specimen management for infrequently encountered organisms. Table 17 presents specimen guide for virus isolation. Table 18 offers virology specimen collection guidelines. Table 19 is on parasitology: anatomic sites containing diagnostic stages. The literature supporting these guidelines is included in case further study is warranted.
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Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Bacteriology and mycology specimen collection guidelines a
a EtOH, ethanol; RT, room temperature; i.v., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative.
b All specimens should be transported in leakproof plastic bags having a separate compartment for the requisition.
Specimen management for infrequently encountered organisms (4, 25) a
a SPS, sodium polyanethol sulfonate; AO, acridine orange; FA, fluorescent antibody stain; CSF, cerebrospinal fluid; IFA, indirect fluorescent antibody stain.
b Laboratory safety hazard.
Specimen management for infrequently encountered organisms (4, 25) a
a SPS, sodium polyanethol sulfonate; AO, acridine orange; FA, fluorescent antibody stain; CSF, cerebrospinal fluid; IFA, indirect fluorescent antibody stain.
b Laboratory safety hazard.
Specimen guide for virus isolation a
a CNS, central nervous system; HIV, human immunodeficiency virus; CMV, cytomegalovirus; DFA, direct fluorescent antibody; EBV, Epstein-Barr virus; THR, throat; LES, lesion; URN, urine; CSF, cerebrospinal fluid; FEC, feces.
b Virus isolation: method of choice for diagnosis. ‘‘Enterovirus’’ includes the historical designation of echovirus and coxsackie A and B viruses.
c Serology: method of choice for diagnosis.
d Includes western equine, eastern equine, St. Louis, and California encephalitis viruses.
e Antigen / nucleic acid detection methods available
Specimen guide for virus isolation a
a CNS, central nervous system; HIV, human immunodeficiency virus; CMV, cytomegalovirus; DFA, direct fluorescent antibody; EBV, Epstein-Barr virus; THR, throat; LES, lesion; URN, urine; CSF, cerebrospinal fluid; FEC, feces.
b Virus isolation: method of choice for diagnosis. ‘‘Enterovirus’’ includes the historical designation of echovirus and coxsackie A and B viruses.
c Serology: method of choice for diagnosis.
d Includes western equine, eastern equine, St. Louis, and California encephalitis viruses.
e Antigen / nucleic acid detection methods available
Virology specimen collection guidelines a
a BAL, bronchoalveolar lavage; CSF, cerebral spinal fluid; VTM, viral transport medium; RT, room temperature; CMV, cytomegalovirus; HSV, herpes simplex virus; EBV, Epstein-Barr virus; HIV-1, human immunodeficiency virus type 1; LCMV, lymphocytic choriomeningitis virus; EIA, enzyme immunoassay; RSV, respiratory synctial virus; ELISA, enzyme-linked immunosorbent assay; VZV, varicella-zoster virus.
b Dacron-, rayon-, or cotton-tipped swabs with plastic or aluminum shafts are acceptable; calcium alginate swabs or swabs with wooden shafts are not acceptable.
Virology specimen collection guidelines a
a BAL, bronchoalveolar lavage; CSF, cerebral spinal fluid; VTM, viral transport medium; RT, room temperature; CMV, cytomegalovirus; HSV, herpes simplex virus; EBV, Epstein-Barr virus; HIV-1, human immunodeficiency virus type 1; LCMV, lymphocytic choriomeningitis virus; EIA, enzyme immunoassay; RSV, respiratory synctial virus; ELISA, enzyme-linked immunosorbent assay; VZV, varicella-zoster virus.
b Dacron-, rayon-, or cotton-tipped swabs with plastic or aluminum shafts are acceptable; calcium alginate swabs or swabs with wooden shafts are not acceptable.
Parasitology: anatomic sites containing diagnostic stages a
a BLD, blood; CNS, central nervous system; GI, gastrointestinal; L/ S, liver / spleen; LN, lymph node; MUS, muscle; RBC, red blood cell; WBC, white blood cell.
b Includes L. tropica, L. mexicana complex, and L. braziliensis complex.
c Wuchereria brancrofti and Brugia malayi.
d Skin snips for M. streptocerca and O. volvulus.
e Naegleria fowleri.
f Clonorchis sinensis.
g Cysticerci.
h IncludesTrypanosoma brucei gambiense and T. brucei rhodesiense.
Parasitology: anatomic sites containing diagnostic stages a
a BLD, blood; CNS, central nervous system; GI, gastrointestinal; L/ S, liver / spleen; LN, lymph node; MUS, muscle; RBC, red blood cell; WBC, white blood cell.
b Includes L. tropica, L. mexicana complex, and L. braziliensis complex.
c Wuchereria brancrofti and Brugia malayi.
d Skin snips for M. streptocerca and O. volvulus.
e Naegleria fowleri.
f Clonorchis sinensis.
g Cysticerci.
h IncludesTrypanosoma brucei gambiense and T. brucei rhodesiense.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.
Parasitology specimen collection guidelines a
a RT, room temperature; CSF, cerebrospinal fluid; CNS, central nervous system; FOR, 10% formalin; MIF, merthiolate–iodine-formalin; SAF, sodium acetate-formalin; PVA, polyvinyl alcohol.
b Collect 10 ml of heparinized blood for buffy coat concentration.
c Additional smears obtained 6, 12, or 24 h after admission may be necessary.
d CSF is specimen of choice for patients infected >6 months.