Commuters struggle with severe service disruptions at McPherson Square after a train derails near the Smithsonian Metro station during the early morning commute on Aug. 6, 2015. (Astrid Riecken/For The Washington Post)

Metro’s No. 2 official resigned Thursday in the first big personnel shake-up at the beleaguered transit agency since Paul J. Wiedefeld became general manager in late November.

Rob Troup, who had been Metro’s deputy general manager and top engineer, becomes the first senior official to depart the agency under Wiedefeld, who said in a brief interview Thursday night that Troup’s departure was “a mutual decision” between the two men.

“He’s resigning, he’s moving on,” Wiedefeld said. He said he was not dissatisfied with Troup’s job performance but wants to “put my own team together.”

In a letter to Metro’s board of directors, made public shortly before 7 p.m. Thursday, Wiedefeld praised Troup, who began working at the agency in August 2010 as chief of infrastructure services under then-General Manager Richard ­Sarles.

“During his tenure and applying three decades of rail and transit design, construction and maintenance expertise, Rob played an invaluable role in the rebuilding and expansion of Metrorail,” Wiedefeld said in the letter.

General Manager Paul Wiedefeld stated in a memo Thursday that he accepted the resignation of Deputy General Manager of Operations Rob Troup, thanking him for his "24-7 leadership." (WUSA9)

“Under his leadership, Metro launched the Silver Line, introduced new rail cars, and began the tough work of rebuilding the Metrorail system, including the rail infrastructure itself as well as the stations, elevators and escalators and facilities that our customers rely on each day.”

But Troup also was Metro’s second-ranking official during one of the most tumultuous periods in the system’s 40-year history — a sometimes calamitous stretch that began with the Jan. 12, 2015, smoke crisis in a subway tunnel.

In that incident, an electrical malfunction on tracks near the L’Enfant Plaza station enveloped a stalled train in smoke, killing one passenger and sickening scores of others. In the months since, amid numerous operational breakdowns, an array of safety and financial problems have come to light at the agency.

Wiedefeld, in succeeding Sarles, has said that his top priority is to instill a strong safety culture within Metro and restore public confidence in the transit agency. Thursday’s announcement makes it clear that Wiedefeld did not envision Troup as being part of that effort.

Like Sarles, Troup arrived at Metro as part of a management shake-up months after the worst disaster in the agency’s history — the June 22, 2009, crash of two Red Line trains near Fort Totten, which killed nine people. Troup had previously worked at Amtrak for 15 years and as an international consultant in the transit industry.

Hours before his resignation was announced, Troup offered no public hint that he was leaving Metro, as he spent much of Thursday at the agency’s headquarters, briefing board members about Metro issues in a series of routine meetings.

After serving as chief of infrastructure under Sarles, Troup became assistant general manager for engineering and later Sarles’s top deputy, the job he continued to hold under Wiedefeld until Thursday.

“Effective immediately, I have assigned Assistant General Manager of Transit Infrastructure and Engineering Services Andy Off to focus on the day-to-day delivery of rail service by overseeing Rail Transportation, Track and Structures and Car Maintenance,” Wiedefeld told the board.

“All other offices and parts” of Metro that formerly reported to Troup will temporarily be overseen by Jack Requa, who is Metro’s executive managing officer, Wiedefeld said, “until a new rail organization is announced in the near future.”