Genomic Signatures and Functional Pathways Underlying 5-Fluorouracil Resistance in Head and Neck Cancer associated Streptococci

The chemotherapeutic agent 5-fluorouracil (5-FU), widely used in the treatment of head and neck cancer (HNC), also exhibits broad antimicrobial activity, yet fluoropyrimidine resistance within HNC-associated microbiota remains poorly characterised. We assessed 5-FU susceptibility and resistance-associated genomic features in 101 Streptococcus isolates obtained from tumour tissue and oral swabs of 31 HNC patients using minimum inhibitory concentration assays integrated with whole-genome sequencing and pangenome analysis. Resistance to 5-FU was prevalent across multiple Streptococcus species and was primarily associated with species identity rather than resistance phenotype or anatomical niche. Resistant isolates showed functional convergence in pathways related to multidrug efflux, stress response, DNA repair, cell-envelope biosynthesis, and virulence, whereas sensitive isolates were enriched for genes involved in core metabolism, nutrient acquisition, and colonisation. Species-resolved analyses revealed heterogeneous, polygenic resistance architectures rather than conserved resistance determinants. Together, these findings suggest that 5-FU exposure may act as an ecological selective pressure shaping microbial functional potential within tumour- and oral communities in HNC.