Intratumoral presence of the genotoxic gut bacteria pks + E. coli , Enterotoxigenic Bacteroides fragilis , and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer

Background This study aimed to investigate clinicopathological and molecular tumour features associated with intratumoral pks + Escherichia coli ( pks + E.coli + ), pks + E.coli - (non- E.coli bacteria harbouring the pks island), Enterotoxigenic Bacteroides fragilis (ETBF) and Fusobacterium nucleatum ( F. nucleatum ). Methods We screened 1697 tumour-derived DNA samples from the Australasian Colorectal Cancer Family Registry, Melbourne Collaborative Cohort Study and the ANGELS study using targeted PCR. Results Pks + E.coli + was associated with male sex ( P < 0.01) and APC :c.835-8 A > G somatic mutation ( P = 0.03). The association between pks + E.coli + and APC :c.835-8 A > G was specific to early-onset CRCs (diagnosed<45years, P = 0.02). The APC :c.835-A > G was not associated with pks + E.coli - ( P = 0.36). F. nucleatum was associated with DNA mismatch repair deficiency (MMRd), BRAF: c.1799T>A p.V600E mutation, CpG island methylator phenotype, proximal tumour location, and high levels of tumour infiltrating lymphocytes ( P s < 0.01). In the stratified analysis by MMRd subgroups, F. nucleatum was associated with Lynch syndrome, MLH1 methylated and double MMR somatic mutated MMRd subgroups ( Ps < 0.01). Conclusion Intratumoral pks + E.coli + but not pks + E.coli - are associated with CRCs harbouring the APC :c.835-8 A > G somatic mutation, suggesting that this mutation is specifically related to DNA damage from colibactin-producing E.coli exposures . F. nucleatum was associated with both hereditary and sporadic MMRd subtypes, suggesting the MMRd tumour microenvironment is important for F. nucleatum colonisation irrespective of its cause.