Impact of COVID-19 shelter-in-place order on transmission of gastrointestinal pathogens in Northern California

Abstract Society-wide cessation of human interaction outside the household due to the COVID-19 shelter-in-place created a unique opportunity in modern history to reexamine the transmission of communicable gastrointestinal pathogens. We conducted a quasi-experimental study from January 1, 2018 to Sept 30, 2020 to investigate the effect of California’s COVID-19 shelter-in-place order on the community transmission of viral, bacterial, and parasitic gastrointestinal pathogens detected with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT). The incidence of viral causes of gastroenteritis, enteroaggregative/enteropathogenic/enterotoxigenic Escherichia coli, Shigella, and Cyclospora cayetanensis decreased sharply after shelter-in place took effsect, whilst Salmonella, Campylobacter, shiga toxin-producing E. coli (O157 and non-O157) and other bacterial and parasitic causes of gastroenteritis were largely unaffected. Findings suggest community spread of viral gastroenteritis, pathogenic E. coli (except for shiga toxin-producing E. coli), Shigella, and Cyclospora is more susceptible to changes associated with shelter-in-place than other gastrointestinal pathogens.