Republic Airways Holdings filed a petition for Chapter 11 bankruptcy on Thursday in the Southern District of New York. The company flies regional routes under contracts with American, Delta and United.

In making the move, Republic cited difficulties caused by the nationwide pilot shortage that is plaguing regional airlines.

Republic Airlines and Shuttle Express, the two airlines that Republic Airways Holdings operates, are continuing to operate normal flight schedules, the company said.

"Over the last several months, we've attempted to restructure the obligations on our out-of-favor aircraft — made so by a nationwide pilot shortage — and to increase our revenues. It's become clear that this process has reached an impasse and that any further delay would unnecessarily waste valuable resources of the enterprise,” Republic CEO Bryan Bedford said in a statement.

Though he didn’t single out any network airlines, Bedford also hinted that the move was also a result of failed attempt to negotiate more generous contracts with the Big 3.

“Our negotiating effort with key stakeholders shows no apparent prospect of a near-term resolution," he said.

Republic Airways operates more than 1,300 daily flights on more than 250 aircraft. Delta Connection, United Express and American Eagle all fly contract flights with Republic. But last year, as Republic dealt with a protracted contract dispute with pilots, it experienced monthly cancellation rates as high as 9%, prompting Delta to accuse the company in an October lawsuit of not providing promised services.

Republic reached a new deal with its pilots in October, raising entry-level pay to a regional airline industry-leading $40 per hour. Nevertheless, the company reduced its flight capacity by 11% during 2015.

Bedford said the Chapter 11 filing would lead to a restoration of Republic.

"We filed with a strong core business and the liquidity resources necessary to carry out our restructuring plan,” he said.

The Chapter 11 filing was the second by a U.S. regional airline in February. Oregon-based SeaPort Airlines filed its reorganization petition on Feb. 5.

Analysts expect the pilot shortage to grow. An estimated 13,000 to 15,000 pilots at American, Delta, Southwest and United will retire between now and 2022 and their ranks will be filled to a significant degree by regional pilots.

Meanwhile, low pay at regional airlines, combined with a congressionally mandated 2013 rule that increased the minimum time a pilot must have in the cockpit in order to fly for a commercial airline from 250 hours to 1,500 hours, have made recruitment difficult.

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