Phylogenomics and Antimicrobial Resistance of Clinical Bacteroides Isolates from a Tertiary Hospital in Southern Thailand

<b>Background/Objectives</b>: <i>Bacteroides</i> species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical <i>Bacteroides</i> isolates from southern Thailand. <b>Methods</b>: Sixteen isolates were collected from body fluids, tissues, and pus at Songklanagarind Hospital (2022-2024). Whole-genome sequencing was performed on the BGI platform, followed by genome assembly, annotation, average nucleotide identity (ANI), pairwise single-nucleotide polymorphism (SNP) analysis, antimicrobial resistance (AMR) gene profiling, plasmid prediction, virulence screening, and phylogenetic analysis. <b>Results</b>: ANI and SNP analysis revealed two clusters: one comprising <i>B. ovatus</i>, <i>B. intestinigallinarum</i>, and <i>B. thetaiotaomicron</i>, and another mainly <i>B. fragilis</i> with one <i>B. hominis</i> isolate. All isolates were resistant to ampicillin, cephalothin, and penicillin; six <i>B. fragilis</i> strains were resistant to all tested antibiotics. The β-lactamase gene <i>cepA</i> was detected in all <i>B. fragilis</i> isolates, and plasmids were predicted in two genomes. Three virulence types (capsule formation, lipopolysaccharide modification, and stress response) were identified. Phylogenomic analysis confirmed species-level assignments and revealed underrecognized lineages, emphasizing the value of genome-based approaches for accurate classification. <b>Conclusions</b>: Clinical <i>Bacteroides</i> isolates display diverse resistance and virulence profiles, highlighting the importance of strain-level genomic surveillance.