Biopsies may be from chronically infected tissues and so, in addition to investigation for bacterial infection, they will also require investigation for fungi, Mycobacterium species and parasites. Histological investigation will often inform the decision to investigate for particular classes of infection. For instance, the presence of caseating granulomata should raise the suspicion of tuberculous infection; similar appearances may be caused by deep fungal infection on occasion. Specific tissues Aortic aneurysm contents Aortic aneurysm contents may be sent for the exclusion of an infective cause1. Artificial materials Artificial materials may also be sent to the laboratory for investigation. Such materials include prosthetic cardiac valves, pacemakers, grafts, artificial joints and tissue implants. Brain biopsies Brain biopsies may sometimes be taken to differentiate non-infectious conditions from infection. Corneas Corneas should be examined in cases where deep eye infection is suspected. Donor heart valves or cornea rims Donor heart valves or cornea rims need to be screened for bacterial infection prior to implantation. Heart valves valves are submitted from patients with infective endocarditis undergoing valve replacement or at post mortem. Infected prosthetic valves may also be sent for culture. Where possible the results of these cultures should be correlated with blood cultures or serology. Lung biopsies (percutaneous, bronchoscopic, surgical or post mortem) 2 Lung biopsies are classified by the method of entry or the reason for biopsy. They may be useful for infections caused by bacteria including Actinomyces species, Norcardia species, Legionella species and Mycobacterium species and fungi, especially Aspergillus species, and Pneumocystis jirovecii. Pneumocystis pneumonia (PCP) occurs almost exclusively in patients who are immunocompromised. PCP may be diagnosed less invasively, but usually with reduced sensitivity, by processing induced sputum or bronchoalveolar lavage specimens. Lymph nodes
Clinical details/ conditions Specimen Supplementary media Incubation read Target organism(s) Temp. °C Atmos. Time If microscopy suggestive of infection Tissue Biopsy Selective anaerobic agar with metronidazole disc 5μg 35-37 Anaerobic 5d 40hr and at 5d Anaerobes Actinomycosis Tissue Biopsy Blood agar supplemented with metronidazole and nalidixic acid 35-37 Anaerobic 10d 40hr, at 7d and 10d Actinomyces species or suspected fungal infection Tissue Biopsy Sabouraud agar 35-37 and 25-30 Air 14d daily# Yeasts Moulds Mycetoma Tissue Biopsy slope / Blood agar 35-37 Air up to 28d every days Aerobic Actinomycetes species Nocardiosis Tissue Biopsy agar 35-37 Air Up to 7d 3d and 7d Nocardia species Suspected Legionellosis Tissue Biopsy BMPA or BCYEA or alternative Legionella agar 35-37 Atmos Up to 10d 3d, 7d and 10d Legionella species Optional When clinical details or when microscopy suggestive of infection or dependent on local policy Tissue Biopsy Staphylococci/ Streptococci selective agar or Manitol Salt Agar 35-37 Air daily S. aureus Streptococci organisms for consideration – Fungi (), H. pylori ()), Listeria species, Mycobacterium species () and parasites (). #Agents of exotic imported mycoses eg Histoplasma capsulatum may take up to 8 weeks to grow; adequate humidification of incubators will be necessary31,32. 4.6 Identification Refer to individual SMIs for organism identification. 4.6.1 Minimum level of identification in the laboratory Actinomycetes genus level Anaerobes "anaerobes"