Tonsillitis is most often caused by common viruses, but bacterial infections can also be the cause.The most common bacterium causing tonsillitis is Streptococcus pyogenes (group A streptococcus), the bacterium that causes strep throat. Other strains of strep and other bacteria also may cause tonsillitis.onsillitis is most often caused by common viruses, but bacterial infections can also be the cause.