P1323 Akkermansia and Gut Microbial SNP Signatures as Determinants of Ustekinumab Treatment Outcomes in Crohn’s Disease

Abstract Background Gut microbiota plays a key role in CD and may shape therapeutic outcomes; however, whether biologics can truly correct dysbiosis and whether baseline microbial signatures predict response is still unclear. This study attempted to understand the effect of Ustekinumab (UST) on the gut microbiome in CD patients. Methods Consecutive moderate–severe CD patients (CDAI>150) were enrolled for this study. Those on recent/ongoing NSAIDs, probiotic supplements, antibiotics, ATT, on special diets or diabetic were excluded. In patients exposed to prior biologics, only those who had discontinued atleast 2 months before initiation of UST were included. Patients provided fecal sample at Week-0 and 24. Demographics, clinical data, fecal calprotectin (FCal), and CDAI scores were recorded at both timepoints. Clinical response was assessed by improvement in symptoms and inflammatory markers. Patients were stratified by week-24 CDAI for endoscopic remission into responders (R; CDAI < 150) and non-responders (NR;CDAI ≥150). Fecal DNA samples were subjected to whole-genome shotgun metagenomics. Taxonomy was assigned using MetaPhlAn4 (CHOCOPhlAnSGB_202503), Shannon diversity by vegan package, differential analysis by MaAsLin, strain resolution using StrainPhlAn, and bacterial SNP detection using SNIPPY. Results Of 34 patients screened, 18 were included. Clinical response was noted in 77% & endoscopic remission in 61% (11R,7NR). At baseline, α-diversity in CD (median 2.7) was significantly lower than healthy (3.5). Metagenomic analyses revealed increase in α-diversity at Week-24 (3.0) and significant increase in Lactococcus,Agathobacter, Blautia & Coprococcus. The following features were observed to relate to treatment outcomes: Akkermansia muciniphila & Bifidobacterium were high at baseline for those who achieved clinical response and remission at Week-24. On the contrary, at Week-24, NR had significantly high abundance of pro-inflammatory Klebsiella species. SNP analysis identified 920666 synonymous, 257386 missense & 695 nonsense mutations. Bifidobacterium_longum showed higher missense mutations in NR compared to R,while Escherichia coli showed the inverse. Variant calling and annotations for the identified strains from R and NR patients highlighted variations in 7 genes involved with nucleotide & carbohydrate metabolism that were significantly associated with NR. Conclusion Metagenomic analyses following UST treatment showed significant taxonomical distinctions with increase in microbial diversity and beneficial SCFA-producing bacteria. Akkermansia and Bifidobacterium stand out as possible biomarkers to predict UST response. Strain-level profiling and identification of functionally relevant SNPs seem to influence immunotherapy efficacy. Conflict of interest: Raghunathan, Nalini: No conflict of interest Gunala, Nikhil: No conflict of interest Thakur, Manisha: No conflict of interest Mekala, Dhanush: No conflict of interest Patel, Rajendra: No conflict of interest Neelam, Pardhu Bharath: No conflict of interest Gavate, Rutuja: No conflict of interest Thangalla, Vishistitha: No conflict of interest Munagala, Sharvani: No conflict of interest Dr. Banerjee, Rupa: RB has received grants/research support from Asian Healthcare Foundation, and the Leona M and Harry B Helmsley Charitable Trust Advisory board fees from Abbott, AstraZeneca, Abbvie, Cadila, Cipla, Dr Reddy Labs, Eli Lilly, Emcure, Ferring Pharma, Hetero Drugs, Janssen, MSN Labs, Mankind Pharma, Menarini, Micro Labs, Pfizer, Sun Pharmaceuticals, Takeda Pharmaceuticals, Torrent, Waterley, and Zydus.