Recent salmonella outbreaks that sickened at least 523 people and sent dozens to the hospital underscore “serious weaknesses” in the U.S. Department of Agriculture’s oversight of poultry plants, according to a study released Thursday by the Pew Charitable Trusts, which also criticized the government’s failure to push more aggressively for recalls of contaminated meat.

A separate investigation by Consumer Reports, also published Thursday, suggested that those lapses have contributed to the prevalence of potentially harmful bacteria that lurk in store-bought chicken. The magazine independently tested more than 300 raw chicken breasts purchased from stores across the country and found that every major brand contained “worrisome amounts” of pathogens such as salmonella and E.coli, including some strains resistant to treatment with antibiotics.

“When more than 500 people get sick from a food-borne illness outbreak, that means the system we have in place wasn’t working to protect public health,” said Sandra Eskin, director of Pew’s Food Safety Campaign. “This many people should not be getting sick.”

The USDA’s Food Safety Inspection Service said in a statement that the reports “confirm the need for measures already underway at FSIS to prevent food-borne illness,” including proposals to change how meat is inspected and another to help drive down salmonella rates.

National Chicken Council President Mike Brown said pathogen testing shows rates of both salmonella and E.coli declining over the past 10 years in poultry plants, adding in a statement, “Eliminating bacteria entirely is always the goal, but in reality, it’s simply not feasible.”

The Consumer Reports investigation, which was funded by Pew, found plenty of problematic bacteria in American grocery aisles. More than half the chicken breasts it tested were tainted with fecal contaminants, which can cause problems such as urinary tract infections in humans. Half the samples contained at least one multidrug-resistant bacterium. In addition, researchers found no significant difference in the presence of troublesome bacteria between conventional chicken breasts and those labeled “organic” or “no antibiotics.”

The Pew study was prompted by two salmonella outbreaks linked to chicken produced by California-based Foster Farms, which did not respond to calls and e-mails Wednesday. The Centers for Disease Control and Prevention has identified hundreds of victims across the country, but the agency said that because salmonella cases largely go undiagnosed, as many as 15,000 people could have been sickened by the contaminated meat.

The Pew study includes sharp criticisms of the response by the FSIS to the outbreaks, which it called “insufficient to protect public health.” In both cases, the department never asked Foster Farms to recall or stop shipping potentially contaminated chicken.

The study also faults the department for failing to issue a public health alert for the first outbreak, which lasted from June 2012 to April 2013. An alert was issued for the second outbreak, which began this March.

Both Pew and Consumer Reports called for USDA to be more aggressive in pushing for recalls and alerting the public to potential outbreaks. The groups said Congress should pass legislation to give the USDA mandatory recall authority. Currently, the department can put pressure on companies to recall products but, unlike the Food and Drug Administration, cannot force recalls.

The Pew study also said the outbreaks create a “new urgency” for the USDA to focus on prevention efforts, including strict requirements for plants to prevent contamination in the first place, particularly because many of the strains of salmonella tied to the outbreaks “have proven to be resistant to commonly prescribed antibiotics.”

If 7.5 percent or less of a plant’s chickens test positive for salmonella, the USDA considers that level acceptable. There is no such standard for chicken parts, such as thighs and breasts.

Pew also recommended that USDA abandon its practice of notifying plants of when it will perform pathogen testing and instead switch to conducting unannounced tests.

In addition, Consumer Reports called on the USDA to abandon plans to finalize a new poultry inspection system that would allow processing line speeds in plants to increase by about 25 percent, a proposal that also would replace about 40 percent of USDA’s inspectors with employees of the meat industry.

A USDA spokesman said the concerns raised by both groups offer further evidence that the new system should move forward as planned.

“The additional requirements in the modernization proposal, such as microbial testing, contamination prevention and stronger food safety inspection activities will allow FSIS to make significant progress in reducing illnesses,” a statement said. The USDA also pointed to its proposed Salmonella Action Plan that outlines ways for plants to reduce the prevalence of the pathogen.

However, Eskin and other food safety advocates have been critical of the plan because it does not give USDA inspectors clear authority to take aggressive action when plants fail to follow regulations.

“These studies draw a troubling conclusion: that the presence of antibiotic-resistant bacteria in meat is more widespread than we thought, and our federal regulatory agencies simply refuse to hold the industry accountable,” said Rep. Louise M. Slaughter (D-N.Y.), who has tried but failed to pass legislation curbing the use of antibiotics in farm animals.