Predictions of Sampling Site Based on Microbial Compositions Using a Decision Tree-based Method

Incheol Seo

doi:10.4167/jbv.2020.50.4.257

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2020 Vol.50, Issue 4 Preview Page Next Page

Original Article

Predictions of Sampling Site Based on Microbial Compositions Using a Decision Tree-based Method

31 December 2020. pp. 257-262

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Abstract

The nose and throat are sites commonly used to obtain swab specimens to diagnose upper respiratory tract infections, and some studies have shown differences between the diagnostic accuracies of nose and throat swabs for upper respiratory infections. However, current sampling methods for the diagnosis of upper respiratory tract infections do not differentiate between nose and throat samples. The present study was undertaken to devise a means of determining whether samples were obtained from the nose or throat. Microbiome abundance data of 576 upper respiratory swab samples were obtained from the human microbiome project website. Predictive models were generated to determine sampling sites based on microbiomes using the random forest and regression tree with recursive partitioning methods. The final prediction model showed a near-perfect prediction for sampling sites using only the abundances of Staphylococcaceae and Streptococcaceae. The devised model can be used to predict sampling sites for upper respiratory specimens.

Keywords

Sampling site

Microbiome

Supervised learning

Decision tree

References

Centers for Disease Control and Prevention. Specimen collection and handling. 2020. https://www.cdc.gov/urdo/specimen.html.

Korea Disease Control and Prevention Agency. Respiratory infection control guidelines. 2020. http://www.kdca.go.kr/ board/board.es?mid=a20507020000&bid=0019.

World Health Organization. Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: interim guidance. 2020. https://apps.who.int/iris/handle/10665/331501.

Kim C, Ahmed JA, Eidex RB, Nyoka R, Waiboci LW, Erdman D, et al. Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays. PLoS One 2011;6:e21610.

10.1371/journal.pone.002161021738731PMC3128075

Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med 2020;382:1177-9.

10.1056/NEJMc200173732074444PMC7121626

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-14.

10.1038/nature1123422699609PMC3564958

Foster ZS, Sharpton TJ, Grünwald NJ. Metacoder: an R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 2017;13:e1005404.

10.1371/journal.pcbi.100540428222096PMC5340466

Liaw A, Wiener M. Classification and regression by randomForest. R News 2002:18-22.

Kuhn M. Building predictive models in R using the caret package. J Stat Softw 2008;28:1-26.

10.18637/jss.v028.i05

Therneau T, Atkinson B, Ripley B. Rpart: recursive partitioning and regression trees, 2015. R Package Version 4 2016.

R Core Team. R: A language and environment for statistical computing. 2020. https://www.r-project.org/.

Biau G, Scornet E. A random forest guided tour. Test 2016;25:197-227.

10.1007/s11749-016-0481-7

Mertz D, Frei R, Jaussi B, Tietz A, Stebler C, Flückiger U, et al. Throat swabs are necessary to reliably detect carriers of Staphylococcus aureus. Clin Infect Dis 2007;45:475-7.

10.1086/52001617638197

Margolis E, Yates A, Levin BR. The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus: the role of competition and interactions with host’s immune response, BMC Microbiol 2010;10:59.

10.1186/1471-2180-10-5920178591PMC2844402

Information

Publisher :The Korean Society for Microbiology and The Korean Society of Virology
Publisher(Ko) :대한미생물학회‧대한바이러스학회
Journal Title :JOURNAL OF BACTERIOLOGY AND VIROLOGY
Volume : 50
No :4
Pages :257-262
Received Date : 2020-08-15
Revised Date : 2020-12-21
Accepted Date : 2020-12-22
DOI :https://doi.org/10.4167/jbv.2020.50.4.257

JOURNAL OF BACTERIOLOGY AND VIROLOGY ISSN:1598-2467(Print) 2093-0429(Online)

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