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Background <p>Reliable genotyping tools are essential for understanding genomic diversity and tracking strain variation in <i>Escherichia coli</i>. Traditional typing approaches, including SNP and MLST based methods, focus mainly on conserved regions of the genome and may overlook potential changes in the unconserved gene content. To address this gap, this study proposed a new genotyping approach that combines diversity profiles observed from repeat-rich protein sequence and genomic neighborhood structural organization.</p> Results <p>Comparative genomic analysis was conducted on 83 publicly available <i>E. coli</i> genomes. Sequence comparison identified a repeat hotspot within the RSXC protein, while gene neighborhood (synteny) analysis revealed three variable genomic regions (hotspots A–C). Differences in RSXC repeat copy number and terminal motifs allowed the strains to be classified into seven repeat types (R7a, R7b, R6a, R6b, R5a, R5b, and R4a). Structural variation within genomic hotspots A, B, and C was characterized by the presence, absence, and arrangement of intermediate genes and classified into 7, 8, and 4 structure types, respectively. Integration of RSXC repeat profiles with genomic hotspot patterns generated 14 distinct sequence types (ST1–ST14). RSXC repeat patterns and the combined genotyping scheme both showed good discriminatory power (Simpson’s diversity index of 0.726), which is comparable to MLST typing (0.723) among the 83 <i>E. coli</i> strains analysed. Virulence and antimicrobial resistance (AMR) profiling of the examined strains further supported biological relevance of the proposed method. Strains with higher RSXC repeat numbers (R7 and R6) positively linked with virulence genes presence and negatively associated with AMR gene counts as supported by a significant positive correlation with virulence genes (ρ = 0.323, <i>p</i> = 0.0026) and a negative correlation with AMR genes (ρ = −0.276, <i>p</i> = 0.0105).</p> Conclusions <p>This repeat–synteny based genotyping approach captures genomic diversity in the 83 <i>E. coli</i> strains that is often overlooked by conventional typing approaches and provides a practical framework for discriminating <i>E. coli</i> strains. The strong association with MLST, combined with meaningful relationships to virulence and AMR profiles, suggests that this approach may serve as a useful marker for epidemiological identifications.</p>

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New genotyping method for Escherichia coli using RSXC repeat polymorphism and gene-neighborhood architecture

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月14日

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  • Ravi Jothi,
  • Kyung Min Park,
  • Soobin Yim ,
  • Kwang-Kyo Oh,
  • Injun Hwang,
  • Myeong-In Jeong,
  • Dong Suk Park

摘要

Background

Reliable genotyping tools are essential for understanding genomic diversity and tracking strain variation in Escherichia coli. Traditional typing approaches, including SNP and MLST based methods, focus mainly on conserved regions of the genome and may overlook potential changes in the unconserved gene content. To address this gap, this study proposed a new genotyping approach that combines diversity profiles observed from repeat-rich protein sequence and genomic neighborhood structural organization.

Results

Comparative genomic analysis was conducted on 83 publicly available E. coli genomes. Sequence comparison identified a repeat hotspot within the RSXC protein, while gene neighborhood (synteny) analysis revealed three variable genomic regions (hotspots A–C). Differences in RSXC repeat copy number and terminal motifs allowed the strains to be classified into seven repeat types (R7a, R7b, R6a, R6b, R5a, R5b, and R4a). Structural variation within genomic hotspots A, B, and C was characterized by the presence, absence, and arrangement of intermediate genes and classified into 7, 8, and 4 structure types, respectively. Integration of RSXC repeat profiles with genomic hotspot patterns generated 14 distinct sequence types (ST1–ST14). RSXC repeat patterns and the combined genotyping scheme both showed good discriminatory power (Simpson’s diversity index of 0.726), which is comparable to MLST typing (0.723) among the 83 E. coli strains analysed. Virulence and antimicrobial resistance (AMR) profiling of the examined strains further supported biological relevance of the proposed method. Strains with higher RSXC repeat numbers (R7 and R6) positively linked with virulence genes presence and negatively associated with AMR gene counts as supported by a significant positive correlation with virulence genes (ρ = 0.323, p = 0.0026) and a negative correlation with AMR genes (ρ = −0.276, p = 0.0105).

Conclusions

This repeat–synteny based genotyping approach captures genomic diversity in the 83 E. coli strains that is often overlooked by conventional typing approaches and provides a practical framework for discriminating E. coli strains. The strong association with MLST, combined with meaningful relationships to virulence and AMR profiles, suggests that this approach may serve as a useful marker for epidemiological identifications.