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Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and

Nicholas C Bank1, Vaidhvi Singh1, Alex Rodriguez-Palacios1,2,3

  • 1Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States.

Gut Microbes
|January 29, 2022
PubMed

Insights

This study developed a novel rfbA gene-based classification system to distinguish pathogenic Parabacteroides distasonis strains from probiotic ones. The rfbA-Typing method effectively differentiates bacterial lineages, aiding in understanding strain variability and pathogenicity.

Area of Science:

  • Microbiology
  • Genomics
  • Bacterial Pathogenesis

Background:

  • Parabacteroides distasonis (Pdis), a gut commensal, is increasingly misidentified as probiotic despite its opportunistic pathogen status.
  • Lack of methods to classify Bacteroidetes strains hinders pathogenicity assessment.
  • Strain-specific virulence variability in Pdis requires urgent characterization.

Purpose of the Study:

  • To develop a virulence gene-based classification system for Pdis and Bacteroidetes.
  • To differentiate pathogenic Pdis strains from potentially probiotic ones.
  • To facilitate pathogenicity characterization of Pdis and other Bacteroidetes.

Main Methods:

  • Developed an in silico classification system based on the rfbA O-antigen synthesis gene.
  • Performed phylogenetic analysis of rfbA from complete Pdis genomes and related bacteria.
  • Proposed a PCR-based Restriction-Fragment Length Polymorphism (RFLP) method for laboratory implementation.
  • Designed specific PCR primers for Pdis rfbA amplification and MboII-RFLP analysis.

Main Results:

  • Classified Pdis into four lineages (rfbA-Types I-IV) based on rfbA gene variations.
  • Identified 14 additional rfbA-types across Bacteroidetes and Enterobacteriaceae, forming three major rfbA-superclusters.
  • Confirmed rfbA as a highly discriminant marker, validated by comparative analysis of the lpxK gene.
  • Most pathogenic Pdis strains were identified as single-copy rfbA-Type I.

Conclusions:

  • rfbA-Typing provides a robust method to classify Bacteroidetes and Pdis based on rfbA sequence and copy number variability.
  • The classification system aids in distinguishing potentially pathogenic Pdis strains.
  • Strain variability in rfbA may influence interactions with host immune receptors, impacting disease relevance.
Keywords:
AlistipesBacteroidesBacteroidetesEscherichia coliGenomic based classificationMboII enzymeO-antigen serotypingPrevotellaRFLPSalmonellasuperclusters

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