Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis

Abstract

Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All of the tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all of the tools performed well overall, there were some differences, particularly in their predilection for identifying low-abundance or contaminant organisms as present.

Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection

“…The results observed from real-world applications have difficulty reaching the level claimed by method validation because they are easily affected by various variation factors associated with samples, laboratory environment, reagents, consumables and human operation [7] . Increasing studies have made efforts to enhance the detection sensitivity of mNGS for different specimen types by optimizing the procedures of sample preparation [17] , nucleic acid extraction and purification [33] , library preparation [34] , sequencing amount/depth [35] and bioinformatics tools [20] , [21] , [36] . The interference of host DNA in clinical samples and the different efficiency of nucleic acid extraction kits to different microbial DNA are considered to be two critical obstacles that affect the sequencing results.…”

“…Laboratories adopt highly customized strategies based on their own experiences for reducing inter-sample/laboratory/reagent contamination, removing host DNA interference, improving the efficiency of microbial nucleic acid extraction methods, increasing the integrity of the reference database and enhancing the accuracy of bioinformatics algorithms [17] , [18] . These nonstandardized processing strategies greatly affect the interlaboratory reproducibility of metagenomic sequencing, leading to uncertainty in the results [19] , [20] , [21] . As reported, the sensitivity and specificity of mNGS platforms developed in different laboratories for diagnosing infectious disease vary widely, ranging from 50.7% to 96.6% and 41.7% to 85.7%, respectively [10] , [22] , [23] .…”

A gut-restricted glutamate carboxypeptidase II inhibitor reduces monocytic inflammation and improves preclinical colitis

“…Fecal specimens were collected before euthanasia and submitted to CosmosID for whole-genome shotgun sequencing as detailed elsewhere (51,52). Comparative taxonomic analysis was performed using the CosmosID-HUB bioinformatics platform (53)(54)(55). No differences in alpha diversity (Chao1, Shannon and Simpson indices) (fig.…”

Mass Spectrometry-Based Proteomic Profiling of Sonicate Fluid DifferentiatesStaphylococcus aureusPeriprosthetic Joint Infection from Non-Infectious Failure: A pilot study

“…The copyright holder for this this version posted December 30, 2022. ; https://doi.org/10.1101/2022.12.28.22284010 doi: medRxiv preprint Multi-omics approaches have recently been investigated as potential alternatives to overcome limitations of currently used diagnostic tools [26,29,[37][38][39][40] . Previous studies have shown that liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based profiling may be able to differentiate synovial fluid samples from PJI and NIAF patients [31,41] .…”