FDA’s New Interim NARMS Report: Bugs on Food. Some Good News on Salmonella, but Let's Wait for the Rest of It

In science, there’s a fine balance between timeliness and quality. With just about everyone demanding timelier data on the antibiotic resistance associated with livestock use, FDA clearly decided to jump the gun. Instead of a comprehensive report, they have published an interim report that analyzes the results from only one bacterium instead of four and is missing half of the most recent year’s data for 2015. With the data being incomplete, it is unclear to me that we should be drawing any early conclusions.

FDA’s NARMS or National Antimicrobial Resistance Monitoring System is a program that tracks four bacteria in retail meat: Salmonella, Campylobacter, Enterococcus, and E. coli, as well as their resistance traits. Yearly reports since 2002 have provided a good overview of resistance in all four bacteria found in turkey, chicken, pork, and beef taken from grocery shelves around the country.

Look at this week’s report and all you find is data on Salmonella. In fact, FDA tests for all four, but oddly decided to publish only on Salmonella. A Salmonella “teaser” on retail chicken provides only a very limited picture, especially in the absence of accompanying trends in humans and from slaughter plants. 

It’s important to include all four bacteria and hopefully that’s part of the full report.  Patterns of resistance in Salmonella and Campylobacter are important to track because both are foodborne pathogens, or bacteria from food that infect humans, that have been linked to outbreaks and CDC estimates that together they cause over 400,000 drug resistant infections per year. Enterococcus and E. coli are tested as “indicators” of resistance because they are generally found hanging out in animals and people and allow scientists to check for resistance patterns that are out in the environment, including in us or the animals around us. For example, the recent dramatic spread of resistance to the last resort drug, colistin, was detected mostly in E. coli in multiple countries.

On top of missing three of the four bacteria named above, this report includes only data from the first six months of 2015 in its analysis. Why? With literally half the year’s data missing, it isn’t appropriate to make conclusions about possible trends which include 2015.

Acknowledging the lack of any data on Campylobacter, E. coli, and Enterococcus, what does this report show?

Here’s the good:

• Levels of Salmonella have dropped in poultry and levels of multidrug resistant Salmonella seem to be dropping in poultry as well.
• Ciprofloxacin and ceftriaxone – two first line drugs for Salmonella (classes which were banned either entirely or for the most part in poultry) have shown good trends in Salmonella with no resistance observed for ciprofloxacin and dropping resistance for ceftriaxone.

Here’s the bad:

• Resistance to ciprofloxacin was detected in pork (notably, there’s no ban for use of this class in swine).
• Of the 13 Salmonella found in beef, 3 of them where highly multidrug resistant (resistant to 9-12 of the 14 drugs that were tested).

There is some good news, mostly around poultry, but part of that is associated with bans on the use of the antibiotic classes themselves.  FDA states that this is one of two reports that will be released this year, so perhaps the bulk of the analysis and other data will be published then? After reading this report, it’s hard to make heads or tails on progress of antibiotic resistance on retail meat and in livestock with so many pieces of the puzzle missing. As a scientist, I want to instead dive into their publically available dataset to figure out what the really story is. I may just do that – stay tuned.

What I do know is that the President’s National Action Plan has called for more and better data from FDA and USDA. Antibiotic use data at the farm level as well as resistance testing from bacteria on the farm are two major categories of data that, together with the data from NARMS, would provide a much clearer picture and would provide a strong basis for antibiotic use policy solutions. Unfortunately and despite the contribution of antibiotic use in livestock production to the antibiotic resistance crisis, FDA isn’t rushing to provide us with these data.