Scientists around the world are increasingly using Next-Generation Sequencing (NGS) to answer crucial microbiological questions across the fields of clinical diagnostics, public health, biodefense, and microbiome research. The... [ view full abstract ]
Scientists around the world are increasingly using Next-Generation Sequencing (NGS) to answer crucial microbiological questions across the fields of clinical diagnostics, public health, biodefense, and microbiome research. The depth of information provided by NGS for microbial analysis is immense, but a sophisticated data analysis platform is required to unlock its full potential. The One Codex Platform provides the analytical foundation needed for microbial genomics and metagenomics, with highly accurate analysis, complete analytical reproducibility, and HIPAA-level security. Using three use-cases, we describe how the One Codex platform enables NGS-backed assays for pathogen detection, outbreak surveillance, and antimicrobial resistance (AMR) profiling.
Whole-genome shotgun sequencing (WGS) provides a powerful source for detecting a broad range of human pathogens using metagenomics samples. However, the tools available for microbial detection vary widely in their ability to detect the organisms present with a high degree of sensitivity and precision. One Codex performs microbial detection by aligning every input sequence against the One Codex Database of ~45K complete microbial genomes, including bacteria, viruses, fungi, archaea, and protists. In addition to a first-pass k-mer based alignment, we also apply robust statistical analysis to remove false positives and predict genome-level abundance. We present the results of large-scale comparisons of computational methods for microbial detection from NGS data, showing that One Codex provides the highest degree of overall accuracy, including the prediction of organism abundance and detection of low-abundance pathogens.
Some of the most dangerous human pathogens require carefully designed detection modules to accurately identify them from complex environmental mixtures. One example is Bacillus anthracis, the causative agent of anthrax, which is closely related to the common non-pathogenic environmental organism B. thuringiensis. Working in collaboration with a group of academic researchers, we designed a detection tool for anthrax that takes the biology of the disease into account, specifically detecting the virulence plasmids as well as the core genome and a diagnostic SNP in the plcR gene. We applied this targeted detection technique to a range of environmental samples and found it was able to sensitively and precisely identify pathogenic B. anthracis without being confounded by near neighbors. This work highlights the ability to quickly and accurately detect difficult pathogens from complex environmental samples.
One of the greatest emerging threats to human health is the spread of antimicrobial resistance (AMR) among bacterial pathogens. One Codex is part of a collaborative effort to build new analytical methods for rapidly and sensitively identifying the genomic markers of AMR, with the goal of enabling clinicians to prescribe the appropriate antibiotic for every infection. Here, we present a targeted tool for detecting the genomic markers of antimicrobial resistance and reporting those efficiently to clinical practitioners. This work highlights the need to translate the vast complexity of NGS data into accurate, actionable guidance that can be used by a wide range of end-users.
One Codex is the leading bioinformatics platform for microbial genomics, supporting taxonomic and functional analysis of metagenomic (WGS), 16S, and other sequencing data and may be found at: www.onecodex.com
Analysis for metagenomics, antimicrobial resistance, and forensics , Bringing sequence to the clinic (i.e., diagnostics, cancer, inherited disorders) , Human, non-human, and infectious disease applications
