The Pope will be undergoing a tracheotomy
Some are speculating that he is suffering from secondary bacterial pneumonia related to influenza. Streptococcus pneumoniae and Staphylococcus aureus are the two most common bacteria implicated. More from UptoDate:

The hallmark of the clinical presentation in patients with secondary bacterial pneumonia is the exacerbation of fever and respiratory symptoms after initial improvement in the symptoms of acute influenza. Fever may abate for one day or more after two to three days of acute influenza, but, instead of continuing to improve, the patient with secondary bacterial pneumonia relapses with higher fevers, cough, production of purulent sputum, and radiographic evidence of pulmonary infiltrates.

More was previously written here.

Update:
Dr. Sanjay Gupta of CNN comments.

Prev
Next