Washington (CNN) The Pentagon believes that the US-led anti-ISIS coalition has seized the offensive and made significant progress in taking back key territory from ISIS, US defense officials told CNN Monday.

Officials are pointing to the recent declaration that a coalition of US-backed Syrian fighters has been able to free the ISIS stronghold of Manbij, Syria. That comes as the US military now estimates some 45,000 ISIS personnel have been killed by the coalition since operations began in mid-2014, 25,000 since last September.

Yet last week a Republican congressional investigation concluded that CENTCOM intelligence painted an overly optimistic picture of the anti-ISIS campaign at least from mid 2014 to 2015.

Outside of Iraq and Syria, the self-proclaimed Islamic State has conducted or inspired more than 140 terrorist attacks in 29 countries since declaring its caliphate in June 2014. CNN has calculated those attacks have killed at least 2,043 people and injured thousands more.

But that doesn't mean there haven't been gains.

In the fight for Manbij, a US defense official told CNN that the US-supported Syrian Democratic Forces, or SDF, are still clearing the city of explosives and perhaps some final fighters. Meanwhile the US -- using overhead surveillance aircraft -- has seen a convoy of up to 500 vehicles headed out of the city toward the northern city of Jarabulus near the Turkish border.

That convoy is largely full of civilians, but the SDF and the US believe perhaps 200 or more ISIS fighters may have blended into that group. For now, it is not being struck from the air because of the civilian presence.

Defense Secretary Ash Carter congratulated the SDF and people of Manbij in a statement Monday.

"Their success, enabled by critical Coalition support, is another significant milestone in the campaign to deal ISIL a lasting defeat," he said, using another term for ISIS. "Manbij city was a key transit point for ISIL fighters going into both Syria and Iraq, and for its external operators plotting attacks against our allies, our partners, and our homeland."

He also pointed to the development as helping cut off Raqqa, Syria. The US believes that the key city is where ISIS is largely being administered out of, although there had been reports some operatives were traveling back-and-forth to Mosul, Iraq, in recent months.

With Manbij now largely out of ISIS hands, ISIS is also reinforcing Raqqa with explosives, berms and even trenches filled with tires to burn for potential smoke screens, according to US defense officials.

CNN has learned the US military's secret special operations unit known as the Expeditionary Targeting Force has also picked up the pace of its operations in recent weeks because of increased intelligence on key ISIS individuals it is trying to target and capture.

One of the goals of the ETF to a large extent is to capture mid-level operatives it can turn over the Kurds in Syria and Iraq, and then interrogate for further intelligence that could lead them to key leaders and even operational plots, a defense official said.

Several US officials told CNN that with the increased pressure of US military and local on Raqqa, and Iraqi forces building pressure around Mosul, ISIS is reacting in various ways, including digging into city centers and allowing fighters to flee and try to blend into local populations.

That is a strategy increasingly evident with a key ISIS affiliate branch in Libya. The US has now conducted 46 airstrikes around the ISIS stronghold of Sirte, Libya, since August 1, at the request of the Libyan Government of National Accord.

The current 30-day authorization by President Barack Obama for strikes can be extended. But in Libya as well, US officials say they are seeing ISIS fighters try to rapidly move out of Sirte into other areas to blend in with the local population.

At the same time, the US is significantly rethinking its estimate of the strength of the ISIS presence in Libya.

The group is still considered highly dangerous there because of its ability to use Libya as a safe haven.

But the latest US estimates calculate there may only be about 1,000 ISIS operatives in Libya, significantly down from earlier estimates of 5,000 or more. Some may have been killed, while others may have blended into the local population or fled to different pars or Libya

US officials said those estimates proved to be high once US forces were better able to communicate with GNA operatives on the ground to see what was happening.