Postpandemic Effects of COVID-19 Shelter-in-Place Orders on the Gastrointestinal Pathogen Landscape
Year: 2023
Type: article
Study design: Observational Study
Abstract: KEYWORDS gastrointestinal pathogen, gastroenteritis, COVID-19, shelter-in-place, community transmission I n 2020, California enforced several unprecedented stay-at-home orders to curb the spread of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).First, a strict shelter-inplace (SIP) order was issued in March 2020, followed by a gradual reopening of restaurants in May 2020 and then schools in September 2020.A winter surge of coronavirus disease 2019 (COVID-19) cases forced a conditional stay-at-home order in December 2020, which was lifted in January 2021, a month before mass COVID-19 vaccination sites opened.These government-mandated society-wide restrictions on human interaction outside the household, combined with increased use of masks and hand hygiene, had a major positive effect on stemming the spread of SARS-CoV-2 (1).These early pandemic countermeasures also had a profound and unintended impact on the spread of other community-acquired infections, as we and others have previously reported (2-6).Now, with the availability of 2 years of post-SIP data, we sought to determine the long-term impact of the pandemic and mitigation measures on the gastrointestinal pathogen landscape in Northern California.We hypothesized that SIP and associated behavioral changes altered the gastrointestinal pathogen landscape both during and after SIP, similar to what has recently been reported for respiratory syncytial virus (7,8).We examined test positivity rates for viral, bacterial, and parasitic gastrointestinal pathogens detected with the syndromic FilmArray GI panel (BioFire Diagnostics, Salt Lake City, UT) (9) at the Stanford Health Care clinical microbiology laboratory, serving adult and pediatric health systems, from 1 January 2018 to 31 December 2022.In total, 18,292 tests were performed during the study period (from 14,184 unique patients) and were included in the analysis.Of these, 8,634 were performed before SIP (1 January 2018 to 16 March 2020), 2,236 were performed during SIP (17 March 2020 to 25 January 2021), and 7,422 were performed after SIP (26 January 2021 to 31 December 2022).The SIP period was chosen to encompass the entire period in which government-mandated stay-at-home orders were in place in Santa Clara County and the intervening period which included various societal reopening stages.We calculated odds ratios and performed Fisher's exact tests to compare the test positivity rates between the pre-SIP, SIP, and post-SIP periods.We also compared pre-SIP and SIP rates with those from 2022 alone, to evaluate longer-term effects.The study was approved by the Stanford Institutional Review Board (protocol 59727).When comparing the pre-SIP, SIP, and post-SIP periods, several notable shifts in the gastrointestinal pathogen landscape are apparent (Fig. 1).Test positivity rates for enteric viruses (adenovirus F40/41, astrovirus, norovirus, rotavirus, and sapovirus), pathogenic Escherichia coli species, Shigella species, Cyclospora cayetanensis, and Giardia lamblia all declined significantly during and immediately after SIP.Enteric viruses, in particular, nearly vanished during
Source: Journal of Clinical Microbiology
DOI: 10.1128/jcm.00385-23
Institutions: Stanford Medicine, Stanford University
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W4384663238