Pope Francis had stabilised enough on Tuesday after two respiratory crises to be taken off non-invasive mechanical ventilation and resume receiving just high flows of supplemental oxygen via a nasal tube to help him breathe, a Vatican spokesperson said.

Francis woke up and was resuming respiratory physiotherapy after sleeping through the night, they added.

The Vatican said as of Tuesday morning, Francis no longer needed to wear the mechanical ventilation mask that covers his nose and mouth to pump oxygen into his lungs.

He had to resume using the mask on Monday after suffering two respiratory crises that required doctors to extract “copious” amounts of mucus from his lungs.

They performed two bronchoscopies, in which a camera-tipped tube was sent into his airways with a sucker at the tip to suction out fluid.

The 88-year-old pope, who has chronic lung disease and had part of one lung removed as a young man, was put back on non-invasive mechanical ventilation – a mask that covers his nose and mouth and pumps oxygen into the lungs.

Francis remained alert, oriented and co-operated with medical personnel, the Vatican said. The prognosis remained guarded, meaning he was not out of danger.

The crises were a new setback in what has become a more than two-week battle by the frail pope to overcome a complex respiratory infection.

The Vatican said the mucus that had accumulated in Francis’s lungs was his body’s reaction to the original pneumonia infection and not a new infection, given laboratory tests do not indicate any new bacteria.

Dr John Coleman, a pulmonary critical care doctor at Northwestern Medicine in Chicago, said the episodes were more concerning than the last one on Friday, in which Francis had a coughing fit, inhaled some vomit that needed to be extracted and then was put on the non-invasive mechanical ventilation for a day and then did not need it any more.

The use of bronchoscopies reflects a worrying level of mucus and phlegm in the lungs, Dr Coleman said.

“The fact that they had to go in there and remove it manually is concerning, because it means that he is not clearing the secretions on his own,” he said.

“He’s taking little steps forward and then steps back,” said Dr Coleman, who is not involved in Francis’s care.

Candles left outside the Agostino Gemelli Polyclinic, in Rome, where Pope Francis is being treated (Mosa’ab Elshamy/AP)

Francis, who is not physically active and uses a wheelchair, had been undergoing respiratory physiotherapy to try to improve his lung function. But the accumulation of the secretions in his lungs was a sign that he does not have the muscle tone to cough vigorously enough to expel the fluid.

Doctors often use non-invasive ventilation to stave off an intubation, or the use of invasive mechanical ventilation. Francis has not been intubated. It is not clear if he has provided any advance directives about the limits of his care if he declines or loses consciousness.

Catholic teaching holds that life must be defended from conception until natural death. It insists that chronically ill patients, including those in vegetative states, must receive “ordinary” care such as hydration and nutrition, but “extraordinary” or disproportionate care can be suspended if it is no longer beneficial or is only prolonging a precarious and painful life.

Francis articulated that in a 2017 speech to a meeting of the Vatican’s bioethics think tank, the Pontifical Academy for Life. He said there was “no obligation to have recourse in all circumstances to every possible remedy”.

He added: “It thus makes possible a decision that is morally qualified as withdrawal of ‘overzealous treatment’.”

Archbishop Vincenzo Paglia, who heads the academy which helps articulate the Catholic Church’s position on end-of-life care, said Francis is like any other Catholic and would follow church teaching if it came to that.

“Today the pope is giving us an extraordinary teaching on fragility,” he told reporters on Monday.

“Today the pope, not through words but with his body, is reminding all of us, we elderly people to begin with, that we are all fragile and therefore we need to take care of each other.”

Francis has been in hospital for 18 days. In 1981 John Paul II spent 55 days in hospital for a minor operation and then to be treated for a serious infection that followed.