In the midst of all of the Republican debt ceiling/government shutdown lunacy, one of the casualties has been the CDC’s inability to respond to a Salmonella outbreak that has currently sickened hundreds of people in twenty states and territories throughout the U.S. (Scary Disease Woman, aka ‘Maryn McKenna’, has done some really good reporting on this story). While much of the coverage–correctly–has focused on the inability of the CDC to monitor and coordinate data collection and other responses due to the worker furlough, that’s not the most disturbing part. This is (boldface mine):
To date, seven strains of Salmonella Heidelberg have been included in this investigation based on epidemiologic, laboratory and traceback information. The information collected for cases associated with each strain indicates that each of the strains is linked to this outbreak of multidrug-resistant Salmonella Heidelberg infections and that Foster Farms brand chicken is the likely source.
CDC’s NARMS laboratory conducted antibiotic-resistance testing on clinical isolates collected from ten ill persons infected with three of the seven outbreak strains. Nine of these isolates exhibited drug resistance to one or more commonly prescribed antibiotics. Of those, three were multidrug resistant. One isolate was susceptible to all antibiotics tested. To date, isolates collected from ill persons were resistant to combinations of the following antibiotics: ampicillin, chloramphenicol, gentamicin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Antimicrobial resistance may increase the risk of hospitalization or possible treatment failure in infected individuals
According to McKenna, there are four different antibiotic resistance profiles. So what’s bad (other than all of the sick people)? Well, this is an incredible amount of diversity. While there are some caveats that need to be attached here*, this doesn’t look like a single contamination event (e.g., a bird craps in the meat grinder, and everyone gets sick). The high amounts of diversity (seven strains with different antibiotic resistance patterns) suggests there were multiple, ongoing contamination events. In other words, basic food safety procedures brokedown–and not just once (accidents do happen).
That’s a far more serious problem, though not have the CDC fully staffed means learning the lessons of this outbreak will either be delayed–or never happen since the evidence couldn’t be collected.
Added: A lawyer suing Foster Farms claims the contamination has been happening for a year. Consider the source (pun intended), but that is in line with the genetic data.
*The typing method used is pulse field electrophoresis (PFGE). PFGE patterns can be changed by gains and losses of resistance plasmids (mini-chromosomes that confer resistance and that can move from strain to strain). So it’s not entirely clear how much chromosomal diversity is involved here. That said, even if all of the observed changes in PFGE patterns were solely due to plasmid gain and loss, that kind of variation would also suggest multiple contamination events (plasmids move, but that variation would require multiple events into a single background. Not impossible, but not that probable). WE CAN HAZ GENOMIK SEQUENCEZ? Seriously, it’s 2013…