With Food Pathogens on the Rise, FDA to Employ Smart Digital Technologies

Some of last year’s increase may be due to greater use by the reporting laboratories of culture-independent diagnostic tests (CIDTs), CDC says. But produce itself was a major culprit, with romaine lettuce linked to two multistate outbreaks of E. coli O157 infections. CDC specifically tied the jump in Cyclospora infections to outbreaks associated with produce.

“More targeted prevention measures are needed on produce farms, food animal farms, and in meat and poultry processing establishments to make food safer and decrease human illness,” the CDC report said.

FDA this year began routine inspections of large farms for compliance with FSMA’s produce safety rule. While this will hopefully mitigate some of the contamination problems, more needs to be done. For example, in December 2018, USDA reported that 22 percent of establishments that produce chicken parts failed to meet the Salmonella performance standard.

Despite all the increased attention and effort on improving food safety, there seems to be no reduction in problems. During the first few months of this year alone CDC has been tracking Salmonella in turkey and in pre-cut melons, and E. coli in ground beef, among many others.

Limits of Diagnostics Tests

The public health labs that contribute data to FoodNet are increasingly using CIDTs, such as immunoassays and nucleic-acid amplified tests. CIDTs are faster and easier to perform than traditional culture-based methods, which require use of trained personnel. CIDTs can identify a general bacteria type within hours without having to culture or grow the pure bacteria strain (or isolate) in a laboratory, a process that typically takes days. But without the isolate, public health scientists are unable to determine the DNA subtype (“fingerprint”), its resistance pattern, or other characteristics necessary to detect outbreaks, track antibiotic resistance, monitor disease trends, and ultimately prevent outbreaks.

For example, PulseNet, the CDC-run network that connects public health and food regulatory agency laboratories, relies on the collection of DNA fingerprints of bacteria taken from sick patients to identify local and multistate outbreaks. The growing use of CIDTs is endangering PulseNet’s effectiveness.

“Without a DNA fingerprint of the bacteria, CDC and public health labs will not be able to find, monitor, and prevent foodborne disease outbreaks, track antibiotic resistance, or follow trends to know if prevention policies are working,” CDC says. Even in FoodNet, CIDTs “complicate data interpretation,” CDC says.

This is where advances in technology, such as whole genome sequencing (WGS) for pathogen detection and blockchain for product traceability are expected to yield big dividends for food safety.

WGS can map the genetic sequence of pathogens and other organisms with such precision that researchers can distinguish between different strains of a bacterium or even slight variations by geography within the same strain. Prior to WGS, scientists used such tools as polymerase chain reaction and pulsed-field electrophoresis (PFGE) to genotype microorganisms for diagnostic subtyping.

Last year, WGS replaced PFGE in PulseNet as the primary method for detecting and investigating Listeria outbreaks and is increasingly being used for Salmonella, E. coli, and Campylobacter.

“The more widespread use of WGS has also increased the number of detected outbreaks and subsequent investigations,” said then-FDA Commissioner Scott Gottlieb, MD, and Yiannas in a recent joint statement. But, they added, this has also increased FDA’s workload to identify and mitigate potential food safety concerns. “As part of the president’s 2020 budget, we’re also requesting additional resources to support the use of WGS and expand our ability to respond when we identify food contamination,” they explained.

Updating Technology Use

When it comes to food traceability, most companies keep records of one step back to identify the source and one step forward to where the food has gone, as required by federal law. And many companies keep these records on paper, not electronically. Investigators found this especially frustrating last year as they sought to determine the source of E. coli-tainted romaine lettuce. Had growers and shippers used electronic records and blockchain technology, tracing the origin might have taken minutes or even seconds, instead of weeks.