…we run into a problem. From Morbidity and Mortality Weekly Report (what you don’t read it? Loser. Boldface mine):

To evaluate progress toward prevention of enteric and foodborne illnesses in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) monitors the incidence of laboratory-confirmed infections caused by nine pathogens transmitted commonly through food in 10 U.S. sites.* This report summarizes preliminary 2015 data and describes trends since 2012. In 2015, FoodNet reported 20,107 confirmed cases (defined as culture-confirmed bacterial infections and laboratory-confirmed parasitic infections), 4,531 hospitalizations, and 77 deaths. FoodNet also received reports of 3,112 positive culture-independent diagnostic tests (CIDTs) without culture-confirmation, a number that has markedly increased since 2012 (1). Diagnostic testing practices for enteric pathogens are rapidly moving away from culture-based methods. The continued shift from culture-based methods to CIDTs that do not produce the isolates needed to distinguish between strains and subtypes affects the interpretation of public health surveillance data and ability to monitor progress toward prevention efforts. Expanded case definitions and strategies for obtaining bacterial isolates are crucial during this transition period….

Diagnostic testing practices for enteric pathogens are rapidly moving away from culture-based methods, and the impact of this change varies by pathogen. Although CIDTs are still most commonly being used for Campylobacter and STEC [Shiga-toxin producing E. coli], the highest percentage increase in use compared with the previous 3-year average was observed for Shigella and Salmonella, most likely due to laboratories using the newly available DNA-based syndrome panels (FoodNet, unpublished data)

In English, more and more food-borne illnesses are being diagnosed using methods where we don’t grow the bacterium. While these have advantages, in that they are often cheaper and faster, without the bacterium in hand, we lose the ability to learn about the pathogen: is this Salmonella infection caused by the same Salmonella someone else observed in Oregon (meaning you might be facing a national outbreak), or what antibiotic resistance genes does this organism carry? We are essentially back to the bad old days in terms of what these tests can tell us about the infectious organism.

So just as we are making genome-based microbial surveillance feasible, we stop collecting the bacterial isolates we need to make this useful. Not sure this is a good thing in the long run.