| Commonly cultured organisms | | Gram-negative bacteria | | Escherichia coli | | Klebsiella spp | | Enterobacter spp | | Pseudomonas aeruginosa | | Citrobacter spp | | Acinetobacter spp | | Stenotrophomonas maltophila | | Gram-positive bacteria | | Coagulase-negative staphylococci | | Staphylococcus aureus | | Enterococcus spp | | Viridans group streptococci | | Streptococcus pneumoniae | | Streptococcus pyogenes | | Other bacteria | | Clostridioides difficile | | Anaerobes | | Mycobacteria | | Fungi | | Aspergillus spp | | Candida spp | | | Less commonly cultured organisms | | Gram-negative bacteria | | Proteus spp | | Haemophilus spp | | Serratia spp | | Neisseria meningitidis | | Capnocytophaga canimorsus | | Legionella spp | | Moraxella spp | | Gram-positive bacteria | | Bacillus spp | | Listeria monocytogenes | | Stomatococcus spp | | Corynebacterium jeikeium | | | Additional organisms | | Fungi | | Cryptococcus spp | | Histoplasma capsulatum | | Coccidioides spp | | Mucorales | | Pneumocystis jirovecii (formerly P. carinii) | | Viruses | | Herpes simplex virus 1,2 | | Varicella-zoster virus | | Cytomegalovirus | | Epstein-Barr virus | | Human herpesvirus 6 | | Enteroviruses | | Respiratory syncytial virus | | Influenza virus | | Parainfluenza virus | | Other | | Babesia spp | | Plasmodium spp (the cause of malaria) | | Toxoplasma spp | | Strongyloides stercoralis | | Nocardia spp | |
