One important point made is that testing for pathogens is changing, where lab facilities are using more culture independent diagnotic tests or CIDTs. With CIDT's they look for markers and do not isolate the organism. According to the report - CIDTs complicate the interpretation of FoodNet surveillance data because pathogen detection could be affected by changes in health care provider behaviors or laboratory testing practices
- Health care providers might be more likely to order CIDTs because these tests are quicker and easier to use than traditional culture methods, a circumstance that could increase pathogen detection
- Pathogen detection could also be increasing as clinical laboratories adopt DNA-based syndromic panels, which include pathogens not often included in routine stool culture
- CIDTs do not yield isolates, which public health officials rely on to distinguish pathogen subtypes, determine antimicrobial resistance, monitor trends, and detect outbreaks.
So basically, year to year numbers may be more difficult to interpret because testing is easier, especially for pathogens that were more difficult to grow or were not normally considered. So while it looks like the incidence to certain pathogens are increasing, that is probably not the case.
CDC MMWR
https://www.cdc.gov/mmwr/volumes/66/wr/mm6615a1.htm?s_cid=mm6615a1_e
Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013–2016
Weekly / April 21, 2017 / 66(15);397–403
Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013–2016
Weekly / April 21, 2017 / 66(15);397–403