Clinical Metagenomics

What are virulence factors?

Virulence factors are molecules produced by pathogens that enhance their ability to cause disease. Identifying virulence factor genes in the detected bacteria can offer insights into their potential pathogenicity and inform treatment strategies.

What are antibiotic resistance genes?

Antibiotic resistance genes are genetic elements that provide bacteria with the ability to resist the effects of antibiotics. Identifying these genes helps healthcare professionals make informed decisions about appropriate antibiotic treatments.

What is the Q20 rate?

The Q20 rate is the percentage of bases with a Phred quality score of 20 or higher, indicating a 1% chance of an incorrect base call. A higher Q20 rate implies better sequencing quality.

What information is provided in the microorganisms report?

The microorganisms report includes statistics for input and preprocessed reads, the top three detected bacteria, viruses, and fungi, a full list of detected microorganisms (Appendix 1), antibiotic resistance genes associated with the top three bacteria, a full list of detected antibiotic resistance genes (Appendix 2), and virulence factor genes associated with the top three bacteria, as well as a full list of detected virulence factor genes (Appendix 3).

How does EzBioCloud Clinical Metagenomics detect and identify microorganisms?

EzBioCloud Clinical Metagenomics uses a proprietary algorithm to align the quality-processed sequencing reads to an extensive database of reference genomes for bacteria, viruses, and fungi. The algorithm enables accurate detection and identification of microorganisms in the sample.

What is the quality control (QC) process?

The QC process involves quality trimming, filtering, and adapter sequence removal using BBduk, followed by host sequence removal using Minimap2. This process ensures that only high-quality, non-human-derived sequences are retained for analysis, improving the accuracy and reliability of the results.

What types of sequencing data does EzBioCloud Clinical Metagenomics support?

EzBioCloud Clinical Metagenomics currently supports Illumina shotgun sequencing reads, with plans to support Nanopore reads in the near future. The service supports sequencing data from any clinical specimen and accepts data from DNA, RNA, or both. However, it does not support targeted or amplicon sequencing data.

What is the purpose of EzBioCloud Clinical Metagenomics?

EzBioCloud Clinical Metagenomics aims to provide healthcare professionals with comprehensive diagnostics reports, identifying and characterizing microorganisms present in a patient’s sample. This information helps clinicians make informed decisions about the diagnosis and treatment of infectious diseases.