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Bioinformatics Pipeline for Comprehensive Microbial Profiling from Tissue Biopsies Using RNA-Seq

Clinical Genetics and Therapeutics
  • Primary Categories:
    • Clinical Genetics
  • Secondary Categories:
    • Clinical Genetics
Introduction:
Persistent cutaneous infections (PCI) often involve complex interactions between host genetics and microbial pathogens, requiring advanced tools for comprehensive analysis. Here, we present HumMicroScan, a bioinformatics pipeline using whole-transcriptome RNA sequencing (RNA-Seq) to profile microbial content directly from tissue biopsies.

Methods:
HumMicroScan processes unaligned RNA-Seq reads to identify a wide range of microbial organisms, including bacteria, viruses, and fungi, associated with chronic skin infections. By analyzing both lesional and non-lesional biopsies, the pipeline provides a detailed microbial landscape, uncovering co-infections and potential pathogenic contributors.

Results:
Integrated microbial profiling enables the simultaneous detection of common pathogens such as Staphylococcus aureus, and Candida auris, and high-risk viruses like human papillomaviruses (HPV). In a case study of PCI patients, HumMicroScan identified clinically relevant microbial signatures, including co-occurrence of Mycobacterium tuberculosis with HPV5.

Conclusion:


Such insights facilitate improved understanding of pathogen-host interactions and inform tailored therapeutic strategies. HumMicroScan offers a robust and scalable tool for RNA-Seq-based microbial analysis, enhancing diagnostic precision and advancing the study of infection-related pathologies.

Availability: https://github.com/FPalizban/HumMicroScan

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