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

TL;DR

This study analyzes the genomes of Bacteroides bacteria from hospital patients in southern Thailand to understand their resistance to antibiotics and potential for causing disease.

Contribution

The study provides new insights into the genomic diversity and antimicrobial resistance patterns of clinical Bacteroides isolates in a specific geographic region.

Findings

Genomic analysis identified two distinct clusters of Bacteroides isolates with different resistance profiles.

All isolates showed resistance to ampicillin, cephalothin, and penicillin, with some B. fragilis strains resistant to all tested antibiotics.

Phylogenomic analysis revealed underrecognized lineages and confirmed species-level classifications.

Abstract

Background/Objectives: Bacteroides species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical Bacteroides isolates from southern Thailand. Methods: 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. Results: ANI and SNP analysis revealed two clusters: one comprising B. ovatus, B. intestinigallinarum, and B. thetaiotaomicron, and another mainly B. fragilis with one B. hominis isolate. All isolates were resistant to ampicillin, cephalothin, and penicillin; six B. fragilis strains were resistant to all tested antibiotics. The β-lactamase gene cepA was detected in all B. fragilis 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. Conclusions: Clinical Bacteroides isolates display diverse resistance and virulence profiles, highlighting the importance of strain-level genomic surveillance.

Figures