Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples

Area of Science:

• Genomics
• Microbiology
• Clinical Diagnostics

Background:

• Next-generation sequencing (NGS) provides accurate quantification of genetic material.
• NGS has significant potential for pathogen discovery and diagnosis in human diseases.
• Existing human RNA-seq datasets often contain substantial bacterial contamination from environmental sources.

Purpose of the Study:

• To highlight the potential of NGS for pathogen discovery.
• To address the issue of bacterial contamination in human RNA-seq data.
• To emphasize the need for stringent protocols in clinical sample analysis.

Main Methods:

• Review of existing human-derived RNA-seq datasets.
• Analysis of bacterial contamination sources.
• Assessment of NGS accuracy and sensitivity.

Main Results:

• NGS demonstrates high accuracy and sensitivity in quantifying genetic material.
• Significant bacterial contamination is a common issue in human RNA-seq datasets.
• Environmental sources are likely contributors to this contamination.

Conclusions:

• Stringent sequencing and analysis protocols are crucial for studies involving clinical samples.
• Addressing bacterial contamination is essential for accurate sequence-based microbial signature investigations.
• The potential of NGS for pathogen discovery requires careful data handling to ensure reliability.