Uncertainty over Obamacare's future is causing consternation and instability in American healthcare markets.

President Donald Trump's decision to go his own way on healthcare after Congressional Republicans failed to repeal and replace the Affordable Care Act has caused unease among insurers, hospitals and patients. The president last week signed an executive order that could potentially split up insurance pools, causing some premiums to skyrocket, and he has given mixed signals on a bipartisan fix to a key insurance subsidy program he abruptly scrapped.

Both maneuvers have insurance companies and hospitals on edge.

Hospitals such as Community Health Systems Inc. CYH, HCA Holdings Inc. (HCA) - Get Report , LifePoint Health Inc. (LPNT) , Quorum Health Corp. (QHC) - Get Report and Tenet Healthcare Corp. (THC) - Get Report stand to lose if the end of Obamacare's cost-sharing reduction payments leads to fewer insured patients and an uptick in patients who can't pay their bills. The scenario could become even worse if Trump's executive order results in a rise of skimpy health plans that have low premiums, high deductibles and cover less.

"Net-net, hospitals will be the losers in all this," said Jeffrey Loo, analyst at CFRA Research, in an interview with TheStreet.

Investors thus far appear to be taking a cautious view of the implications of Trump's actions on the healthcare industry as a whole. Insurance stocks opened higher on Wednesday, and hospital stocks were mixed. The Healthcare SPDR ETF (XLV) - Get Report was up 0.16% in late-morning trading.

"Investors are being pragmatic here," Loo said. "They realize there are going to be some lawsuits that may delay the implementation of [Trump's decisions], and keep in mind there's been bipartisan support to continue the CSR payments."

Insurance stocks edged higher on Tuesday when Senators Lamar Alexander (R-TN) and Patty Murray (D-WA) announced a tentative two-year agreement to fund the CSRs that make health insurance more affordable for low-income individuals and families. Stocks dipped last week when the president announced late Thursday he would be stopping the payments, a move he celebrated on Twitter over the weekend.

Many Wall Street analysts, business leaders and lawmakers applauded the Alexander-Murray agreement and expressed optimism about its prospects on Capitol Hill, despite headwinds.

Height Securities analyst Stefanie Miller in a note on Wednesday said she sees "enough favorable signs" that she gives the agreement 70% odds of passage.

Senate Minority Leader Chuck Schumer (D-NY) said the deal has "broad support" among Senate Democrats, and Representative Mark Meadows (R-NC), head of the conservative House Freedom Caucus, called it a "good start."

"We view the deal as positive for the individual insurance market and providers," wrote Evercore ISI director Michael Newshel in a note on Tuesday. "It remains to be seen if such a deal can pass both houses of Congress, but we think the risk of destabilizing the individual market could be enough to build sufficient support among most Democrats and enough moderate Republicans if a bill can get to the floor."

The Alexandar-Murray agreement has a "long way to go," said Patrick Pilch, national co-leader of BDO's Center for Healthcare Excellence & Innovation.

House Speaker Paul Ryan's (R-WI) press secretary told Axios on Wednesday that the Wisconsin Republican "does not see anything that changes his view that the Senate should keep its focus on repeal and replace of Obamacare."

President Trump initially expressed support for the deal but appears to have since walked it back. At a speech at the Heritage Foundation on Tuesday he said while he commends the deal he still believes Congress "must find a solution to the Obamacare mess instead of providing bailouts to insurance companies." He hit the agreement again Wednesday morning on Twitter.

Ending CSR payments would affect different insurers to a varying degree depending on their exposure to the Obamacare markets. Anthem Inc. (ANTM) - Get Report is among the insurers with the most exposure, while Cigna Corporation (CI) - Get Report , Aetna Inc. (AET) , Humana Inc. (HUM) - Get Report and UnitedHealth Group Inc. (UNH) - Get Report have less.

To be sure, there is more to the healthcare industry and markets than the constant push-and-pull over Obamacare, said David Friend, managing director at BDO's Center for Healthcare Excellence & Innovation.

Most Americans have health insurance through their employers, Medicare or Medicaid or choose to go uninsured, meaning about 10% of the country, or 30 million Americans, will be affected by the current debate over subsidies and association health plans.

"Those 10% of the people in this country, because they're the political football, are wagging this whole dog and taking up all the oxygen [in the healthcare conversation]," Friend said. "This is almost a side-show on some level."

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