Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012-2019

Logan C Ray; Patricia M Griffin; Katie Wymore; Elisha Wilson; Sharon Hurd; Bethany LaClair; Sophia Wozny; Dana Eikmeier; Cyndy Nicholson; Kari Burzlaff; Julie Hatch; Melissa Fankhauser; Kristy Kubota; Jennifer Y Huang; Aimee Geissler; Daniel C Payne; Danielle M Tack

doi:10.1093/ofid/ofac344

Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012-2019

Open Forum Infect Dis. 2022 Jul 25;9(8):ofac344. doi: 10.1093/ofid/ofac344. eCollection 2022 Aug.

Authors

Logan C Ray¹, Patricia M Griffin¹, Katie Wymore², Elisha Wilson³, Sharon Hurd⁴, Bethany LaClair⁵, Sophia Wozny⁶, Dana Eikmeier⁷, Cyndy Nicholson⁸, Kari Burzlaff⁹, Julie Hatch¹⁰, Melissa Fankhauser¹¹, Kristy Kubota¹², Jennifer Y Huang¹, Aimee Geissler¹, Daniel C Payne¹, Danielle M Tack¹

Affiliations

¹ Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
² California Department of Public Health, Sacramento, California, USA.
³ Colorado Department of Public Health and Environment, Denver, Colorado, USA.
⁴ Connecticut Emerging Infections Program, New Haven, Connecticut, USA.
⁵ Georgia Department of Public Health, Atlanta, Georgia, USA.
⁶ Maryland Department of Health, Baltimore, Maryland, USA.
⁷ Minnesota Department of Health, St. Paul, Minnesota, USA.
⁸ New Mexico Emerging Infections Program, Albuquerque, New Mexico, USA.
⁹ New York State Department of Health, Buffalo, New York, USA.
¹⁰ Oregon Health Authority, Salem, Oregon, USA.
¹¹ Tennessee Department of Health, Nashville, Tennessee, USA.
¹² Association of Public Health Laboratories, Silver Spring, Maryland, USA.

Abstract

Background: Pathogen detection has changed with increased use of culture-independent diagnostic tests (CIDTs). CIDTs do not yield isolates, which are necessary to detect outbreaks using whole-genome sequencing. The Foodborne Diseases Active Surveillance Network (FoodNet) monitors clinical laboratory testing practices to improve interpretation of surveillance data and assess availability of isolates. We describe changes in practices over 8 years.

Methods: During 2012-2019, 10 FoodNet sites collected standardized data about practices in clinical laboratories (range, 664-723 laboratories) for select enteric pathogens. We assessed changes in practices.

Results: During 2012-2019, the percentage of laboratories that used only culture methods decreased, with the largest declines for Vibrio (99%-57%) and Yersinia (99%-60%). During 2019, the percentage of laboratories using only CIDTs was highest for Shiga toxin-producing Escherichia coli (43%), Campylobacter (34%), and Vibrio (34%). From 2015 to 2019, the percentage of laboratories that performed reflex culture after a positive CIDT decreased, with the largest declines for Shigella (75%-42%) and Salmonella (70%-38%). The percentage of laboratories that routinely submitted isolates to a public health laboratory decreased for all bacterial pathogens examined from 2015 to 2019.

Conclusions: By increasing use of CIDTs and decreasing reflex culture, clinical laboratories have transferred the burden of isolate recovery to public health laboratories. Until technologies allow for molecular subtyping directly from a patient specimen, state public health laboratories should consider updating enteric disease reporting requirements to include submission of isolates or specimens. Public health laboratories need resources for isolate recovery.

Keywords: Foodborne Diseases Active Surveillance Network (FoodNet); clinical laboratory testing practices; culture-independent diagnostic test; foodborne illness; reflex culture.

Published by Oxford University Press on behalf of Infectious Diseases Society of America 2022.