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His own record as the head of the Jesuit order in Argentina at the time has been tarnished as well.
NPR: Argentine Jorge Bergoglio Elected Pope Francis
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Francis, the first pope from the Jesuit order, which is known for its missionary zeal, praised the Colombian saint for "instilling hope" in the indigenous people.
NPR: Pope Francis Gives Church Hundreds Of New Saints
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It was the understated beginning of a papacy that church observers might expect from his Jesuit order, which is known for promoting education and working closely with the poor.
WSJ: New Argentine Pope Faces Church Splits
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Argentina's northern province of Misiones, named for the settlements established during Spanish colonial times by the Catholic Church's Jesuit order, juts like a finger far into Brazil and Paraguay.
WSJ: Bird Watching in Misiones Province, Argentina
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There had been speculation that Pope Francis - who was a member of the Jesuit order - had chosen his name in honour of St Francis Xavier, a 16th Century Jesuit missionary in Asia.
BBC: Pope Francis wants 'poor Church for the poor'
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One of the 16th century founders of the Jesuit order, Francis Xavier was a legendary missionary who spread the faith as far as India and Japan giving the new pope's name selection possibly further symbolic resonance in an age when the church is struggling to maintain its numbers.
NPR: Argentine Jorge Bergoglio Elected Pope Francis
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Instead the cardinals chose this 76-year-old Jesuit whose order is headed by a priest called the superior general, in homage to the military origin of its founder.
BBC: Pope Francis' first moves hint at break with past
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Pope Francis is also the first Jesuit Pope - from an ancient and fiercely independent Catholic order that has not always enjoyed the best relationship with Rome.
BBC: Humble Francis brings both change and continuity
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One unexpected factor is that the new Pope is a Jesuit, a member of perhaps the most powerful and experienced religious order of the Catholic Church.
BBC: Pope Francis quick to stamp his style on papacy
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As a Jesuit, he also carries the strong missionary and educational traditions of that muscular order of priests.
WSJ: Review & Outlook: A Pope From the People
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Yet this Jesuit takes the name Francis from the humble servant of medieval Assisi who began the Franciscan order 300 years before Ignatius.
CNN: Pope Francis, humble, authentic and credible