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Federal agencies to hold October meeting on whole genome sequencing

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Federal food safety agencies will host a public meeting Oct. 26 and 27 at the USDA headquarters in Washington, D.C. to discuss their practices and plans for collecting and analyzing whole genome sequence (WGS) data, as well the state of the science and other issues surrounding this technology, USDA’s Food Safety and Inspection Service (FSIS) announced Thursday (Sept. 21).

Food trade groups asked federal food safety agencies to hold a meeting on the government’s use of WGS in November 2016 to help stakeholders better understand how this technology can be reliably used for regulatory purposes.

FSIS plans to expand its use of WGS analysis to bacteria isolated from FSIS sampling projects to aid in accurately identifying and responding to outbreaks, conducting efficient traceback, and studying the environmental harborage and movement of pathogens in regulated establishments, the agency said in the Sept. 21 Federal Register notice.

Though a final agenda has yet to be posted on the agency’s website, general topics at the meeting, which is being co-hosted by FSIS, FDA, the Centers for Disease Control and Prevention (CDC), and the National Center for Biotechnology Information (NCBI), include:

  • WGS technology: the global and local perspective and advantages and limitations;
  • Collaboration and data sharing among federal and non-federal entities;
  • Information on the GenomeTrakr and PulseNet databases;
  • International standards for WGS;
  • Information on the equivalency of methods used by different agencies and stakeholders;
  • Communicating WGS results to stakeholders; and
  • Transitioning from pulsed-field gel electrophoresis (PFGE) to WGS in PulseNet.

Food companies have been apprehensive of WGS after a 2015 FDA investigation of a Listeria outbreak tied to Blue Bell Creameries’ ice cream products used the technology to link the outbreak back to patients in 2010.

Whether private companies should be encouraged to use WGS methodology to conduct internal investigations, or if this could place them in regulatory jeopardy, remains one of the open questions about WGS.

The Grocery Manufacturers Association (GMA) believes WGS "is an important new technology that, when used correctly, has the potential to help public health officials and the producers of all food products (manufactured, restaurant and all others) to identify, track, trace, and prevent bacterial contamination and thereby limit the adverse effects associated with foodborne illness outbreaks," a spokesman told IEG Policy.

"And, like any new diagnostic tool, WGS has certain limitations that need to be understood and addressed to ensure that the results are reliable for use in making public health decisions," he added. "The upcoming meeting will provide input on the benefits and limits of the technology to help FSIS implement it effectively.”

FSIS said Thursday it will continue to upload all WGS data to a publicly accessible federal database, and that it will analyze WGS data from FSIS samples and other food, environmental, and clinical samples contributed by other sources and organizations.

Expanded use of WGS may help FSIS and other public health partners to identify genes associated with virulence, antimicrobial resistance (AMR), and newly emerging pathogen sub-types that were previously indistinguishable from routinely isolated bacteria, FSIS said.

FSIS has started to analyze WGS data to identify specific genes associated with emerging antibiotic resistance threats, the agency said. In collaboration with federal partners, FSIS uses an AMR gene database to identify genes associated with emerging resistance to beta-lactamase, colistin, linezolid and other critically important antibiotics. In partnership with the National Antimicrobial Resistance Monitoring System (NARMS), FSIS is searching for additional genes linked to AMR within the genomes of bacteria recovered from FSIS-regulated and other product samples.

FSIS noted that together with USDA’s Agricultural Research Service (ARS), it reported in June 2016 WGS analysis of an E. coli isolate from the cecal contents of swine, which contained a recently discovered resistance gene to the last-resort antibiotic colistin. While colistin is not used in animals in this country, the finding reinvigorated calls to restrict the use of drugs important to human medicine in food producing animals.

FSIS also pointed to a 2013 pilot study on Listeria monocytogenes (Lm) isolates, which shows how much more effective WGS analysis is compared with PFGE analyses.

In the 2013 pilot study, FSIS, FDA, CDC and NCBI collaborated with local, state, and international partners to use WGS to analyze Lm isolates from patients, food, and domestic food processing environments. Results from the study were routinely made available to CDC epidemiologists and other public health and regulatory partners.

“The availability of WGS analyses transformed outbreak surveillance and response: more illness clusters were detected (14 clusters detected in the year before the pilot versus 19 and 21 clusters detected in the two years after implementing WGS),” FSIS said. “In addition, illness clusters were detected sooner, median cluster size was markedly reduced, and more outbreaks were resolved by linking Lm illness and food sources.”

Based on its Lm WGS pilot experience, FSIS said it expects expanding the use of WGS analyses will lead to greater efficiencies by consolidating laboratory workflows into a single step for bacterial characterization. Also, by using WGS together with epidemiologic and traceback evidence, federal food safety agencies will be able to identify the sources of outbreaks more quickly and potentially put preventive actions in place to reduce the chance of outbreaks, FSIS said.

FSIS said that it and other federal agencies expect to phase out PFGE and other sub-typing methods as they expand their use of WGS. Noting that “consequently it will be important to build WGS capacity to perform sequencing and develop analyses to adequately support the respective regulatory frameworks,” federal agencies hosting the meeting are asking stakeholders to weigh in on how best to address this.

FSIS noted that on Oct. 24 and 25 – the same week as the WGS meeting – federal food safety agencies will hold a separate meeting on NARMS at USDA headquarters, and that FDA will publish a Federal Register notice to announce this meeting.


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