A throat infection. Acute inflammation and infection of the pharynx can be caused by bacteria or viruses. Approximately 40%-60% of cases of pharyngitis are caused by a virus and about 15% are caused by the Streptococcus bacteria (strep throat). Other bacteria that can cause this infection include: Mycoplasma pneumoniae, Chlamydia pneumoniae, and Neisseria gonorrhoeae. Most infections that cause pharyngitis are contagious. Frequent hand washing and covering one's mouth when coughing can decrease the spread of the infection.