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A Burkina Faso protestor holds a loaded slingshot as others gesture, in the city of Ouagadougou, Burkina Faso, Thursday, Sept. 17, 2015.Theo Renaut/The Associated Press

When the Pentagon organized its annual counterterrorism training exercises in West Africa, one of the most prominent beneficiaries was a powerful Burkina Faso military officer named Gilbert Diendéré, who said he wanted to learn how to "work together more effectively in fighting terrorism."

Today, the general has a new job: putsch leader. For the second time in three years, a U.S.-trained military officer has led a coup against a democratic government in West Africa, raising new questions about whether Western support for African armies can inadvertently threaten democracy.

Gen. Diendéré, the long-time spymaster and chief military aide to Burkina Faso's former authoritarian president, Blaise Compaoré, is the head of a military junta called the National Council for Democracy, which announced that it had seized power on Thursday morning, a day after soldiers burst into a cabinet meeting and arrested the interim president and prime minister.

In a similar move in Mali in 2012, a military coup was led by U.S.-trained army captain Amadou Sanogo, who had graduated from a Pentagon counterterrorism program. The $500-million training program, which Canada also assists, is an ambitious high-profile effort to fight the growing terrorism threat in West Africa, but even U.S. commanders have admitted that it was badly flawed.

Gen. Carter Ham, former chief of the U.S. military command for Africa, criticized the U.S. training program for focusing too much on tactics and equipment, while neglecting the crucial values of democracy. "We didn't spend, probably, the requisite time focusing on values, ethics and military ethos," he said in a 2013 speech. "When you put on the uniform of your nation, then you accept the responsibility to defend and protect that nation, to abide by the legitimate civilian authority."

Gen. Ham acknowledged that the Mali coup was led by a graduate of the U.S. counterterrorism program, and he called this "very worrisome for us."

He added: "Did we miss the signs that this was happening? And was there anything that we did in our training that could have been done differently, perhaps, and have caused a different outcome?" The answer, he said, was "a little bit of both."

The Pentagon may be asking similar questions in the aftermath of the coup in Burkina Faso, which took place less than a month before the scheduled date of elections that were meant to restore democracy.

The United States, along with former colonial power France, has been preoccupied by the rise of Islamist radical groups in West Africa, including Boko Haram in northern Nigeria and a collection of Islamist extremist militias in northern Mali, Algeria and Libya, which roam across borders in the Sahara and Sahel regions.

To fight these threats, the United States has been willing to work with authoritarian leaders and regional armies in countries such as Chad and Burkina Faso, despite their poor records on human rights.

Gen. Diendéré, for example, has been a key participant in the annual U.S. counterterrorism training exercises, according to media reports at the time of the 2010 and 2015 exercises, known as "Flintlock." In these exercises, hundreds of U.S. troops travel to Africa help train soldiers in small-unit tactics, desert patrols, airborne operations, cross-border co-operation and intelligence-sharing.

Gen. Diendéré, reportedly a close ally of U.S. intelligence agencies, has orchestrated a shadowy intelligence network across West Africa and served as right-hand man to Mr. Compaore throughout his 27-year rule after seizing power in a 1987 coup.

Mr. Compaoré was finally toppled in a popular uprising last year, but there is speculation that he might be linked to the latest coup. The putsch on Thursday was led by Burkina Faso's presidential guard, an elite military unit that has been heavily involved as the power behind the throne since the 1987 coup.

Several days ago, a government committee called for the disbanding of the presidential guard, but the unit was unwilling to accept the loss of its power. It denounced the government as a "deviant regime," and it criticized an electoral law that would have prevented Mr. Compaoré's associates from running as candidates in next month's election.

The U.S. State Department has issued a statement criticizing the coup, but it has said nothing so far on its role in providing training to the coup leader.

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