Emerging Role of whole-genome sequencing in the Diagnosis of biofilm-associated infection

Sanjay Kapoor; V. Iyer; K. Mehta

doi:10.5281/zenodo.22812813

Authors

Sanjay Kapoor Department of Clinical Medical Microbiology, Indus Academy of Medical Microbiology Author https://orcid.org/9295-2964-2431-9519
V. Iyer Division of Clinical Bacteriology, Tigris Academy of Medical Microbiology Author https://orcid.org/3687-8553-1245-3005
K. Mehta Department of Medical Microbiology, Murray Research Center for Medical Microbiology Author https://orcid.org/0256-3618-1718-0621

DOI:

https://doi.org/10.5281/zenodo.22812813

Keywords:

biofilm, whole-genome sequencing, metagenomics, diagnosis, prosthetic joint infection

Abstract

Graphical abstract

Background: Biofilm-associated infection, seen in prosthetic joint and cardiac-device infection, chronic wounds, and chronic rhinosinusitis, is frequently missed or mischaracterized by standard culture because embedded organisms are often slow-growing, polymicrobial, and resistant to efficient dispersal into culture medium.

Objective: This review synthesizes the evidence for whole-genome and metagenomic sequencing as culture-independent diagnostic tools in biofilm-associated infection, focusing on pathogen detection, polymicrobial resolution, resistance prediction, and strain-level discrimination.

Methods: We conducted a narrative synthesis of clinical validation studies applying shotgun metagenomic, whole-genome, and 16S rRNA sequencing to sonication fluid, synovial fluid, and tissue specimens from suspected device-related and biofilm-associated infection, alongside methodological reviews of genomic diagnostic workflows.

Results: Direct sequencing of clinical specimens identified causative organisms in a substantial proportion of culture-negative but clinically infected cases, resolved polymicrobial infections that culture reported as monomicrobial, and returned genotypic resistance and strain-relatedness data within the same assay, typically within a single working day.

Conclusions: Whole-genome and metagenomic sequencing address a specific diagnostic blind spot of culture in biofilm-associated infection, and their routine adoption will depend on standardizing contamination control, bioinformatic interpretation, and integration with existing diagnostic criteria.

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