The hum of US drones is becoming more familiar over African skies.

From Nigeria to Somalia, US military presence on the continent is a creeping reality. US troops may be thin on the ground, with the Pentagon preferring to rely on training and financial support to allied forces, but special forces are now operating at any given moment.

The trend has its most recent roots in the aftermath of the September 2001 attacks on the US, when US officials scoured the globe for “ungoverned spaces” with the potential, like Afghanistan, to foster anti-American extremists. Several African countries cropped up on the radar, notably Somalia. In the semi-desert underbelly of the Sahara, Mali was identified among other weak states vulnerable to jihadi influence spreading south from the Maghreb. Nigeria, too, soon featured in assessments of threats.

These were either prescient musings by US spies or a self-fulfilling prophecy coaxed partly into reality by US meddling – there are subscribers to both camps. Either way, Islamist extremism in Africa has metastasised just as the Pentagon and the CIA assessments predicted.

As President Barack Obama on Tuesday opens the first summit between the US and Africa, combating Islamist militant groups is perhaps Washington’s biggest priority in the region.

“We are concerned about efforts by terrorist groups to gain a foothold in Africa,” says Ben Rhodes, US deputy national security adviser. “International terrorist networks sometimes seek to take advantage of ungoverned spaces [in Africa] so that they can get a safe haven.”

Once isolated, locally formed militias with a medley of grievances have in recent years morphed into jihadi insurgencies along the faultlines where Muslim and Christian traditions meet, from Somalia in the Horn of Africa across the Sahel to west Africa. These pose an increasingly pronounced and connected threat to regional stability and the economic resurgence of pivotal states such as Kenya and Nigeria.

US military strategy in Africa is co-ordinated out of Stuttgart, Germany. African states resisted Pentagon efforts to centre on the continent the new Africa command, which was created in 2006 in recognition of the specific military challenges that the region posed. But as Linda Thomas-Greenfield, US assistant secretary of state for Africa, suggests, African leaders threatened by extremism are now more ready to seek US assistance and asked Washington to put security on the agenda this week.

“This was an issue that was brought to our attention by African leaders . . . equally concerned about the rise in terrorism,” she says.

The escalating nature of the problem points to a long-term and priority role for US forces in Africa. But the US response has been no more successful in Africa in helping to stem the extremist tide than it has been in other parts of the world.

In the view of security officials across the region, one of the biggest recent boosts to the extremist cause came in 2011 when Muammer Gaddafi was overthrown in Libya by a US-backed rebellion. Apart from in Libya itself, the blowback has been felt keenly south of the Sahara, with parts of Gaddafi’s arsenal ending up in the hands of jihadi groups such as Nigeria’s Boko Haram.

Jeremy Keenan, a professor at the School of Oriental and African Studies in London and author of several books on the US response to African terrorism, says Libya was a defining moment. “From having exaggerated a problem, suddenly the US got a serious problem with terrorism in Africa,” he says.

Arguably, in Somalia too, extremists posed no more than a marginal threat until the US-backed Ethiopian invasion in 2006. This fuelled the radicalisation of Islamist factions, and ultimately the spread of al-Shabaab militants, the group which in 2012 aligned itself with al-Qaeda and is now threatening neighbouring Kenya.

There have been other embarrassing policy boomerangs. To the dismay of Washington, junior Malian officers trained as part of a $620m pan-Sahelian counter terrorism initiative took part in a coup in March 2012.

Choosing which of the continent’s myriad armies to ally with is a regular Pentagon dilemma.

Comfort Ero, Africa programme director at International Crisis Group, a non-governmental organisation, says the US is “still looking for surrogate useful partners who can work with them on counterterrorism”.

Johnnie Carson, a veteran US diplomat in Africa and assistant secretary of state for the continent until last year, says the US “can be helpful to African countries in dealing with these insurgencies” but insists that it needs to be “very careful in the kind of help we provide”.

US officials acknowledge that its record is mixed and calibrating the extent to which they get involved will remain a delicate balancing act.

“We should not take ownership of another country’s problems. We don’t need to put boots on the ground in response to every extremist threat that emerges. We also have to be careful not to identify and attach an international element to every extremist threat that emerges,” says Mr Carson.

“Some threats are indigenous and grow out of issues of political and economic marginalisation and are not linked to the international network of jihadis. If we start linking all of these things it will become a self-fulfilling prophecy,” he says.