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There are many potential pathogenic bacteria in the mouth, nose and throat. The bacteria most commonly responsible for infections in these area are nontypable Haemophilus influenza, Streptococcus pneumoniae, and Moraxella (Brahmanella) catarrhalis. These three bacteria cause the vast majority of ear infections and sinusitis that have a bacterial cause. The most common cause of all infections of the ears, nose and throat are viruses. Another important pharyngeal pathogen is Streptococcus pyogenes, the bacterium that causes Strep throat. Again, however, the most common cause of a sore throat is a viral infection, including the Epstein-Barr virus, which is the causative agent for Mono - a disease very commonly misdiagnosed as Strep throat.

Other, more serious infections are possible and usually involve one or more of the bacteria listed above, but can also include others that are normal flora of the oral cavity. Diabetics, specifically, can have strange infections caused by fungi, including a rapidly fatal fungal infection of the nasal cavity and sinuses caused by fungi in the genera of Mucor or Rhizopus. Other immunosuppressed patients can also have strange infections.

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