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. 2016 Apr 7:7:484.
doi: 10.3389/fmicb.2016.00484. eCollection 2016.

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology

Sarah K Hilton  1 , Eduardo Castro-Nallar  2 , Marcos Pérez-Losada  3 , Ian Toma  4 , Timothy A McCaffrey  5 , Eric P Hoffman  6 , Marc O Siegel  7 , Gary L Simon  7 , W Evan Johnson  8 , Keith A Crandall  1
Affiliations

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology

Sarah K Hilton et al. Front Microbiol. .

Abstract

Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs.

Keywords: drug resistance; high throughput sequencing; metagenomics; metataxonomics; microbiome; pathogen detection.

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Figures

Figure 1
Figure 1
The proportion of reads mapping to each identified taxonomic unit by results rank. The proportion of reads are highly skewed toward the top hits, more than 75% of the reads of each sample are represented by the first five results.
Figure 2
Figure 2
(A–D): Proportion of samples matching the clinical diagnosis at different taxonomic levels and results rank. The metagenomic analysis is more accurate than the 16S analysis in every scenario. The ideal combination, a match between the clinical diagnosis and the tophit at the species level, showed the largest discrepancy between the two sequencing types.
Figure 3
Figure 3
Twenty-seven metagenomic reads from sample s070 mapping to the mec-A (penicillin-binding protein CDS) region of the Staphylococcus aureus genome.
See this image and copyright information in PMC

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