By Antonia Mortensen, Christopher Lamb and Hira Humayun, CNN

(CNN) — Pope Francis experienced “two episodes of acute respiratory failure,” the Vatican said Monday, marking the latest in a series of medical crises the 88-year-old pontiff has endured since he was first hospitalized last month.

Monday’s episodes were caused by “significant accumulation of endobronchial mucus” and a consequent narrowing of the airways, the Vatican said.

Earlier in the day, the pope underwent two bronchoscopies and doctors removed a buildup of secretions.

In the afternoon, Francis was given oxygen through a mask to help with his breathing, according to the Vatican.

Throughout, the pontiff remained alert and cooperative, the Vatican said.

“It was a complicated afternoon,” Vatican sources said Monday evening, adding that the acute respiratory crisis, which lasted for part of the afternoon, is over, and that the pope was resting.

“The accumulation of the mucus is a result of the pneumonia and that causes coughing and spasm as the bronchi try to expel the mucus as it irritates them,” the sources said.

Dr. Theodore Iwashyna, professor of pulmonary and critical care medicine at Johns Hopkins University told CNN that a bronchoscopy is a moderately invasive procedure, and that “it is not good” to need two bronchoscopies within a short period of time to manage secretions.

“In a person that’s quite ill and requiring non-invasive ventilatory support, you would usually need to have a good reason to do it,” Iwashyna said, adding that mucus buildup is not a positive sign in a patient with pneumonia.

“As your pneumonia gets better you’ll produce less mucus. Sometimes as your pneumonia gets better you finally get strong enough to cough it up,” he said.

The Vaticansources said Monday that Francis’ blood tests remain the same and his prognosis remains “reserved.”

Dr. Jeremy Faust, a Boston-based emergency physician told CNN the “non-invasive mechanical ventilation” that Vatican sources said was an oxygen mask, is meant to help deliver oxygen with a little bit of pressure.

“Non-invasive ventilation would be the step you would take before putting a patient on a mechanical ventilator with sedation and a breathing tube in their windpipe,” Faust said.

Such non-invasive treatment, Faust said, could be because a patient does not need or want to be intubated.

“The two reasons to use noninvasive ventilation is either that you’re not yet at the point where intubation and sedation are needed, or you are, but the patient has made it clear that they would not want that – which is a very reasonable thing to do if you’re an older person with a lot of medical problems and you don’t want to die on machines.”

In a previous update on Monday morning, Vatican said the pope “rested well” throughout the night and sources said he was receiving high flows of oxygen through nose cannulas.

Pope Francis has been hospitalized at Rome’s Gemelli Hospital since mid-February, where he has been battling double pneumonia. On Friday, he had a sudden respiratory episode, which required him to receive an oxygen mask. His current hospitalization is his fourth – and now longest – stay since he became pope in 2013.

The Vatican has been releasing twice daily updates on the pope’s health.

The pontiff has suffered from lung-related issues for much of his life. As a young man, he suffered from severe pneumonia and had part of one lung removed.

On Sunday, Vatican sources said the “picture is still complex” and that the “risk of crisis” remains.

Francis’ cousin Carla Rabezzana told CNN Monday that the family is worried about him.

Rabezzana said the family has not been in touch with Francis but receives updates through the news. The last phone call the family had with the pope was on Christmas, she said.

“Knowing him, he faces everything with great courage and serenity,” she said, adding: “He’s a calm and wise man.”

On Monday night, Cardinal Robert Prevost led a rosary for the pontiff at St. Peter’s Square, in Vatican City. Bishops, nuns and hundreds of people have been gathering there each evening to say prayers for the pope’s recovery.

Francis’ schedule has been cleared to accommodate his intensive medical treatment. He did not lead the Angelus prayer on Sunday, for the third week in a row.

He also will not lead the Ash Wednesday service, which marks the start of Lent, a 40-day period of prayer, repentance and fasting for many Christians, for only the second time in his papacy, according to the Vatican. A cardinal is expected to lead the service instead.

Antonia Lehnert contributed to this report.