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The researchers estimate a 40% increase in the annual incidence of resistant Salmonella.
Officials have traced 43 cases in multiple states to hedgehogs and bearded dragons.
The CDC confirmed 356 cases in 2018 and 2019, but illnesses continue to be noted.
Officials are tracking a 17-case E coli outbreak tied to salads and an 11-case Salmonella outbreak linked to beef.
Conventionally raised poultry harbored nearly twice as much multidrug-resistant Salmonella as meat from antibiotic-free poultry.
"The antibiotic resistance pattern of this strain is alarming," a CDC expert says.
Officials have confirmed 127 cases in 33 states, and 26 people have been hospitalized.
Almost 500 cases are tied to backyard poultry, and nearly 100 infections are linked to dog treats.
Other high-priority diseases include West Nile, plague, rabies, and brucellosis.
One of the notable developments for 2018 was a spike in Cyclospora cases, likely the result of multiple factors, the CDC said.
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