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Sinai Department of Pathology
Pathology Lab Users Guide
Microbiology
Microbiology 10
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 LifeBridge Health - Department of Pathology
Microbiology
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Table 8 Collection considerations for respiratory specimens
| Culture |
Vol. (ml)
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Comments
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| Bacteria |
NA
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Contact lab if Legionella is suspected. Submit sputum only; saliva is unacceptable. |
| Fungi |
3-5
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Collect three early morning fresh specimens resulting from deep cough or sputum induction. Lung biopsy or lung aspirates are also appropriate. |
| Anaerobes |
1
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Sinus aspirate, tympanocentesis fluid, transtracheal aspirate, and lung aspirates or biopsy specimens are appropriate. |
| Mycobacteria |
5-10
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Collect three early morning fresh specimens resulting from deep cough or sputum induction. Lung biopsy or lung aspirates are also appropriate. |
| Pneumocystis |
2
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Use induced sputum, bronchoalveolar lavage, or lung biopsy specimen. |
| Parasites |
3-5
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Can be examined for amoebae, helminth eggs (Paragonimus westermanii), hooklets of Echinococcus spp., larvae of hookworm, and Ascaris and Strongyloides spp. |
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Table 9 Collection considerations for sterile body fluids
| Culture |
Vol. (ml)
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Comments
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| Bacteria |
Bacteria
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If gonococcal arthritis is suspected, notify lab to add modified TM or GC lect. |
| Fungi |
3-5
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Blood for Histoplasma capsulatum (AIDS), Cryptococcus spp., Candida albicans, and Candida tropicalis. |
| Anaerobes |
1
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Use anaerobic transport system |
| Mycobacteria |
5-10
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Table 10 Collection considerations for subcutaneous tissue and skin specimens
| Culture |
Comments
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| Bacteria |
Syringe aspirates or biopsy specimens are preferable to swab specimens. |
| Anaerobes |
Uncommon in burn, ulcer, nodules, or superficial skin infections; useful following bites and trauma. |
| Fungi |
Useful in diagnosing dermatophytes, yeast. filamentous fungi, and dimorphic fungi. |
| Mycobacteria |
Useful in diagnosing Mycobacterium marinum, Mycobacterium fortuitum, and M. chelonei. |
| Virus |
Useful in diagnosing HSV and varicella-zoster virus
Rate of recovery of HVS and varicella-zoster virus is highest from the youngest lesions, then from pustules, ulcers, and crusted lesions, in that order.
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Table 11 Collection considerations for deep wound, aspirate, and tissue specimens
| Culture |
Comments
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| Bacteria |
Biopsy specimens or aspirates are better than swab specimens. |
| Anaerobes |
Useful in diagnosing actinomycosis; send in anaerobic transport system. |
| Fungi |
Useful in diagnosing Pseudallescheria boydii, bipolaris spp., Exophiala spp., and Fusarium spp. |
| Mycobacteria |
Useful in diagnosing M. tuberculosis, M. bovis, and M. kansasii. |
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Table 12 Collection considerations for urine
| Culture |
Vol (ml)
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Comments
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| Bacteria |
0.5-1
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Do not collect 24 hr specimen. After proper cleansing, use first morning midstream. |
| Fungi |
>20
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Do not collect 24 hr specimen. First morning void is recommended. |
| Mycobacteria |
>20
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Do not collect 24 hr specimen. First morning three consecutive urine specimens are recommended. |
| Anaerobes |
1
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Use suprapubic aspirate. Send in anaerobic transport system. |
| Virus |
10-50
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Do not collect 24 h specimen. First morning void is recommended. Useful for adenovirus, mumps, and CMV detection. Send on ice, and transport to lab ASAP. |
| Parasites |
24h col.
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Shistosoma haematobium eggs, Trichomonas vaginalis trophozoites in males, and Onchoecerca volvulus microfilariae. |
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