A Chicago psychiatric hospital that treats hundreds of children in state care is under federal and state investigation over safety concerns and alleged sexual assaults, and it may be forced to close if it can’t correct deficiencies.

The Illinois Department of Children and Family Services has investigated 16 allegations of abuse and neglect this year at the Aurora Chicago Lakeshore Hospital in the city’s Uptown community, including allegations that children were raped and sexually abused by staff and other patients, physically assaulted and inadequately supervised, a ProPublica Illinois investigation found.

Among those reportedly abused or hurt in the incidents were children who were cleared for discharge from the hospital weeks or months earlier. DCFS, however, had failed to find them a place to go — a persistent issue for the troubled agency that ProPublica Illinois documented this year.

In addition to child welfare investigations, the Illinois Department of Public Health has conducted a series of inspections on behalf of federal authorities since July that found the hospital had failed to ensure the safety of suicidal patients, obtain consent before giving patients — including children — powerful medications and sufficiently monitor patients.

Federal authorities have said they will cut off funding that is crucial to the hospital’s operations by the end of November if officials there do not implement immediate changes, according to federal records and court documents.

Hospital officials declined to answer specific questions from ProPublica Illinois, but the CEO, David Fletcher-Janzen, said in a statement that they have been working with state and federal authorities to fix deficiencies. He said the hospital strives to provide a safe, therapeutic environment for patients.

“Chicago Lakeshore Hospital takes every allegation of impropriety very seriously and files reports immediately. All allegations, regardless of probability, are reported to maintain a high level of caution and transparency,” Fletcher-Janzen said. “Our goal is to improve the lives of these young patients so they can grow to be healthy adults both physically and mentally.”

The hospital has come under fire before. State inspection reports in recent years found that an employee, who was later terminated, repeatedly punched a 26-year-old patient who had hit him; that the hospital failed to ensure a safe setting for a 15-year-old girl who received 18 stitches after cutting herself by breaking off part of a toilet; and that proper precautions were not taken with a patient with a history inappropriate sexual behavior, according to records obtained through a Freedom of Information Act request.

In 2010, DCFS hired consultants from the University of Illinois at Chicago to conduct a review of Lakeshore and found a host of problems, from patients reporting sexual assaults by peers to “lax or inconsistent supervision by staff.” Lakeshore officials disputed the findings at the time, saying the report was “highly subjective” and contained findings “unsupported by the facts.”

The Chicago Tribune revealed in 2010 that children at the hospital had been sexually assaulted.

Neil Skene, the special assistant to DCFS Acting Director Beverly “B.J.” Walker, said the agency is focused on making sure children are properly cared for and addressing the issues federal officials have identified.

“We are fulfilling our responsibility to oversee the care of youth who are our responsibility,” he said. “We believe that the current monitoring bodies will let us know if their concerns rise to a level where we need to stop using the hospital.”

Many of the new allegations echo those of the past. In September, a 7-year-old girl was taken to the emergency room at UIC after she reported that a 12-year-old boy pulled down her pants, sexually assaulted her with his finger and “made her bleed,” according to confidential reports obtained by ProPublica Illinois.

While at the emergency room, she also reported that a Lakeshore employee had kissed her on the mouth and sexually assaulted her with his finger, and said she was “afraid to go back” to Lakeshore. A UIC social worker, records show, expressed concerns about delays in Lakeshore’s reporting and seeking medical care for the girl.

That same Lakeshore employee was at the center of another investigation in August. A 12-year-old girl reported that the man had locked her door, grabbed her by the shirt and touched her breasts. When she tried to pull away, she said that he pulled her down onto his lap, squeezed her buttocks and made her sit on his lap and touch his penis.

Both girls are in DCFS care. The agency said it continues to investigate the alleged assaults and the employee is not currently working at the hospital. Chicago police have also opened an investigation.

DCFS found sufficient evidence to support four other complaints this year, including one report in June that an 11-year-old girl sexually acted out toward four girls on her unit, according to agency records.

In yet another case, a 17-year-old boy diagnosed with bipolar disorder was left with a bloody mouth and bruising in April after he said two male employees dragged him to his room, where they pinned him down while holding his arms over the bedrail, according to DCFS records. The boy said one of the workers threatened to break his arm.

He had been admitted to the hospital that day after a suicide attempt, his mother said.

“It’s never easy sending your child to the hospital, but the thing that helps you sleep at night is at least you know they’re safe,” the mother said in an interview. “But he was far from safe. He was hurt and scared.”

When she arrived at the hospital to visit her son, she said she was horrified at the sight of blood on his lips and mouth and bruises on his face and arm. She began looking for another hospital to transfer him to immediately.

“I knew I could rescue him from there,” the mother said. “But most of the kids there are wards of the state. There is no one to rescue them.”

Hospital officials did not respond to allegations about individual cases. Fletcher-Janzen said employees who are subjects of allegations are either suspended or moved to a different building while Lakeshore and DCFS investigate.

The child welfare agency continues to send children to the hospital, which serves children and adults in two buildings a few blocks apart. Nearly half of the 16 investigations have not been substantiated, and the other cases reflect individual incidents rather than a systemic problem, Skene said.

“The question for DCFS is whether children are safe there,” Skene said. “Nothing that we are seeing gives us concern for their safety.”

As of late September, after officials with the Centers for Medicare and Medicaid Services notified the hospital it planned to stop making its Medicare payments, 18 children in DCFS care were patients there, including a 4-year-old boy who had been at the hospital for nearly three weeks, according to documents.

At least three of those children had already been cleared for discharge but DCFS had not found them other placements, records show. ProPublica Illinois revealed in June that hundreds of children have spent weeks and even months trapped in psychiatric hospitals as the agency searched for residential treatment centers, foster homes and other placements.

DCFS acknowledged the problem and said it was working to find more appropriate homes.

The number of DCFS patients at Lakeshore remained at 18 earlier this month; some children, including the 4-year-old, had been released, but others were admitted as federal and state officials continued their inquiries.

The investigations alarmed Meryl Paniak, DCFS’ acting inspector general, who in a confidential memo urged Walker to take action. Paniak wrote that she had “significant concerns for the care and safety of the children” at Lakeshore, according to a copy of the memo obtained by ProPublica Illinois.

Paniak listed steps the agency could take, ranging from immediately planning for alternative placements for the children to sending an official to Lakeshore each day to evaluate the hospital’s progress resolving its problems.

DCFS officials complied with nearly all of the recommendations, including the daily inspections and making plans to move children. But they have not agreed to one of Paniak’s most sweeping recommendations: bringing in an independent expert to do a comprehensive review of the treatment and mental health services at the hospital.

In an interview, Paniak said an independent voice could provide expertise and objectivity. She said she was disappointed by the agency’s decision not to seek an independent review.

“I don’t think that the department has done enough to ensure the safety of the kids there,” Paniak said.

DCFS relies on Lakeshore to treat children in need of psychiatric hospitalization. Last year, of the approximately 1,100 children and adolescent patients treated at the hospital, 41 percent were in state care, according to court filings from the hospital. The majority of the hospital’s revenue comes from Medicaid payments.

Lakeshore typically sees more children from DCFS than other area hospitals because it accepts children with the “highest needs and most volatile behaviors (that) other hospitals won’t,” Skene said.

The majority of the cases that DCFS substantiated or continues to investigate involve sexual abuse or assault.

A 12-year-old boy reported in January that he was fondled by a 17-year-old. Five other patients reported the teen tried to touch them inappropriately when employees were not looking, records show. The 17-year-old was on probation and was sent to juvenile detention following the incidents, according to DCFS documents.

In that case, DCFS cited hospital staff for inadequate supervision and wrote that it was unclear “where responsible staff were” when the abuse happened and why a 12-year-old was on the same unit with older teens.

Another investigation into allegations of inadequate supervision involved a 16-year-old from Honduras who had come to the U.S. unaccompanied. The girl, who is transgender and in the custody of the federal government, reported she had sex with another patient at the hospital this summer. That investigation is ongoing.

DCFS also is investigating an allegation by an 8-year-old boy who said one of his roommates climbed on top of him and started “to hump” him and another stood next to his bed while masturbating, records show.

One complication in investigating these cases is the lack of video evidence. While the hallways contain cameras, the hospital has not provided footage to DCFS investigators on several occasions when asked for it, ProPublica Illinois found.

Skene said the agency has discussed the issue with the hospital, and the hospital is in the process of replacing its surveillance system. The installation of the new system in the children’s building is expected to be completed this week, a hospital representative said.

“It’s just an awful lot of very serious red flags in a very short period of time,” Charles Golbert, Cook County acting public guardian, said in an interview. He said children would be better served by an independent review of the hospital instead of separate investigations done by state and federal agencies.

He added it’s difficult for DCFS to be objective because it depends on Lakeshore to care for so many of its children. Without Lakeshore, he said, the agency has few options for psychiatric treatment.

“That’s a conflict of interest,” he said.

Last month, Michael Jones, a DCFS senior deputy director, said in court records that “significant challenges and harm” would follow if Lakeshore lost its federal funding and was unable to treat DCFS children, reducing the number of available beds for them by 25 percent. He called the hospital a “community partner and a necessary ally for DCFS and the children we serve.”

Jones also said the three other hospitals in Chicago that DCFS primarily uses do not always accept children in the agency’s care and may not be geographically convenient for some patients.

But Golbert said there’s another reason other hospitals are reluctant to take some children from DCFS. Those children, he said, sometimes end up staying weeks or months past their release dates because the agency can’t find homes for them. Children who remain locked in psychiatric hospitals for long periods of time may suffer additional emotional harm and sometimes begin mimicking the negative behaviors they are exposed to, including sexual and physical misconduct.

The 12-year-old boy who allegedly sexually assaulted the 7-year-old girl at Lakeshore last month had been admitted to the hospital in June and was cleared for discharge three weeks later. But he remained at the hospital for nearly four more months because DCFS could not find him an appropriate placement.

The alleged assault occurred during that time. The girl he allegedly assaulted was cleared for release at the end of August but did not leave until September, a week after the reported incident.

In addition, one of four girls targeted for sexual acts by an 11-year-old girl in June was cleared for discharge in May. She remained unnecessarily hospitalized for more than three months. And records show the 12-year-old girl who an employee allegedly sexually abused in August had been on a waiting list to go to a residential treatment center for two months.

Lakeshore’s most recent regulatory troubles began this summer at its adult building, though documented concerns there go back several years. In the last 12 months, at least two people have filed lawsuits in Cook County Circuit Court against the hospital alleging sexual assaults at the adult building, including a woman who said an employee followed her into a bathroom and raped her. Both lawsuits are pending.

This year alone, state regulators conducted inspections three times at the hospital, in July, August and this month. During the July inspection, public health inspectors faulted the hospital for having doors that posed a suicide risk. They also found that the hospital did not collect samples for a rape kit after a patient alleged she was sexually assaulted, failed to complete required safety checks and did not obtain informed consent from patients before administering psychotropic medications, according to a July 27 report obtained through an open records request.

“IDPH is always concerned about the health and safety of patients and when deficiencies are found, we follow-up to make sure they are corrected,” department spokeswoman Melaney Arnold said in an email. “In situations where the health and safety of patients are in immediate jeopardy, the hospital is required to eliminate the immediate jeopardy and surveyors stay in the hospital until it does.”

When state inspectors returned the next month, they found the hospital had replaced the doors, but they identified additional suicide risks: 15 phones with long metal cords hanging from walls in hallways and dayrooms.

“This failure potentially put all 54 patients on suicide precautions, at risk for serious harm,” public health investigators wrote in the August report.

About three weeks later, federal authorities issued the notice to terminate Lakeshore’s Medicare participation, effective Sept. 28.

One day before the deadline, Lakeshore attorneys filed an emergency motion in federal court to halt the move. The attorneys said the hospital serves a unique role as one of the largest behavioral health providers in Illinois, treating more than 5,000 patients a year and routinely accepting children in state custody.

The attorneys said the hospital would be forced to close and lay off hundreds of employees if its Medicare and Medicaid payments were ended. Attorneys argued the hospital is doing its best to comply with suicide prevention guidelines that are vague and often change. Safer doors had been on back order when inspectors arrived in July. The day after the inspection, an employee drove to Wyoming to pick up the doors from the manufacturer. In addition, they said the phone cords were removed while the inspectors were on site.

The hospital already spent hundreds of thousands of dollars before the inspections to remove and replace equipment that posed suicide risks throughout the buildings, according to the hospital’s filings.

Hospital officials also took issue with some of the state regulators’ other findings, saying many were related to documentation rather than actual patient harm. Still, they submitted a total of three correction plans — the most recent one just days ago — they said would “ensure patients are able to receive care in a safe setting,” according to records.

Federal regulators have twice extended the termination deadline, but a threat still looms. While the hospital addressed many of the violations, more emerged in an October inspection. Patients as young as 14 in the children’s building were given powerful psychotropic medications without informed consent, records show.

With Lakeshore still out of compliance, federal authorities have notified hospital officials they are setting a new termination date of Nov. 30. On that date, the government will stop reimbursing the hospital for patients on Medicare. It is unclear if Medicaid payments would be affected. More than 80 percent of the hospital’s patients this year were insured through Medicare or Medicaid, according to court records.

The American Civil Liberties Union of Illinois, which monitors DCFS as part of a federal consent decree, has requested additional information from the agency about the conditions at Lakeshore in light of the ongoing investigations.

Claire Stewart, an ACLU attorney, said the group also wants an independent review of the hospital. The organization is considering legal intervention, she added.

“We will do what we need to do to protect the youth in care,” Stewart said. “This is an immediate safety concern and priority.”