Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-01-22

AUTHORS

Jeremiah J. Minich, Farhana Ali, Clarisse Marotz, Pedro Belda-Ferre, Leslie Chiang, Justin P. Shaffer, Carolina S. Carpenter, Daniel McDonald, Jack Gilbert, Sarah M. Allard, Eric E. Allen, Rob Knight, Daniel A. Sweeney, Austin D. Swafford

ABSTRACT

BACKGROUND: Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical-grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients including COVID-19+ patients. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. RESULTS: Compared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4× higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic (SYN) swab. The limit of detection (LoD) of SARS-CoV-2 from floor samples collected using the consumer-grade plastic (CGp) or research-grade plastic The Microsetta Initiative (TMI) swabs was similar or better than the SYN swab, further suggesting that swab type does not impact RNA recovery as measured by the abundance of SARS-CoV-2. The LoD for TMI was between 0 and 362.5 viral particles, while SYN and CGp were both between 725 and 1450 particles. Lastly microbiome analyses (16S rRNA gene sequencing) of paired samples (nasal and floor from same patient room) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type, but instead driven by the patient and sample type. CONCLUSIONS: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer-grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity and lack of antibiotics in these samples makes it possible to perform concomitant microbiome analyses. Video abstract. More... »

PAGES

25

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s40168-020-00960-4

DOI

http://dx.doi.org/10.1186/s40168-020-00960-4

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1134800839

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/33482920


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386 Division of Gastroenterology, Department of Pediatrics, University of California San Diego, La Jolla, CA USA
387 Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA USA
388 Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA USA
389 schema:name Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
390 Department of Bioengineering, University of California San Diego, La Jolla, CA USA
391 Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
392 Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA USA
393 Division of Biological Sciences, University of California San Diego, La Jolla, CA USA
394 Division of Gastroenterology, Department of Pediatrics, University of California San Diego, La Jolla, CA USA
395 Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA USA
396 Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA USA
397 Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA USA
398 rdf:type schema:Organization
 




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