Federal disease detectives say they’ve seen a significant decline in rates of E. coli infections because of better testing of the meat supply, but they’re making slow progress against contamination by drug-resistant strains of salmonella.

Robert Tauxe, chief of the foodborne-disease unit at the CDC, said he’s also concerned by increasing rates of contamination of shellfish – mainly raw oysters – from a bacterium called vibrio that can be lethal to people with chronic liver problems.

Tauxe said the industry is responding to the problem, and he noted that this year, California’s Almond Board is requiring that all nuts harvested be pasteurized after sporadic cases of salmonella were traced to raw almonds. Some 95 percent of the almond crop was already being treated through roasting or heating to kill the pathogen.

Tauxe said CDC disease detectives are also improving their ability to use genetic fingerprints to track the source of outbreaks.

He said fingerprinting was responsible for last year’s breakthrough that allowed the CDC to match several outbreaks at Mexican and Italian restaurants in Pennsylvania to Roma tomatoes shipped from a Florida distributor.

Tauxe said government surveillance data shows that the meat industry has made improvements in averting outbreaks of E. coli O157:H7, a particularly virulent strain of the common pathogen that can attack the kidneys of young children and has killed some.