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<p><i>Proteus mirabilis</i> is a foodborne and environmental pathogen causing catheter-associated urinary tract infections (CAUTIs) with antimicrobial resistance (AMR) and virulence. As the potential of Indian strains remains underexplored, whole-genome sequence (WGS) data of 18 strains were analyzed for AMR, virulence, and genetic relatedness. The disc diffusion method assessed phenotypic AMR. Genomic DNA sequencing was performed on Illumina MiSeq platform, followed by quality control, read assembly, gap closure, and annotation using software tools. Various tools were used to predict antimicrobial resistance genes (ARGs), resistome, virulence, mobile genetic elements (MGEs), pathogenicity, single nucleotide polymorphisms (SNPs), and plasmids. Phylogenetic analysis based on SNPs was performed using maximum likelihood (ML) and neighbor-joining (NJ) methods. All isolates showed resistance to tetracycline but were sensitive to gentamicin, amoxicillin/clavulanic acid, and streptomycin. Genome sizes ranged from 3,824 to 4,296&#xa0;kb (average 3691.6 ± 164.3) and 5–26 ARGs per isolate. Common intrinsic resistance genes, including <i>tetJ</i>, <i>tet(D)</i>, <i>K. pneumoniae KpnF</i>, and amphenicol resistance genes (<i>cat</i> and <i>catA4</i>) were present in all but one isolate. Predominant ARGs were linked to tetracycline, quinolone, cephalosporin, cephamycin, penam, quaternary ammonium compounds, and glycopeptide groups present in MGEs. Isolates contained numerous virulence genes (<i>n</i> = 4785) across 10 categories. The average SNP count was 4114.27 ± 3216.91, with four isolates showing no SNPs. Phylogenetic analysis revealed diversity (D= -1.6910, <i>P</i> = 0.0047) among 86 reference strains. Ongoing monitoring through WGS analysis is essential for understanding and managing infections caused by this pathogen.</p> Graphical Abstract <p></p>

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Genomic Constellation of Foodborne Proteus Mirabilis Isolates Harboring AMR, Virulence Genes and Comparative WGS Analysis

  • 期刊论文

  • 发表日期：

    2025年12月1日

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  • Swati Singh,
  • Zunjar Baburao Dubal,
  • G. Ravi Kumar,
  • Shikha Tamta,
  • Shubham Saini,
  • Shivangi Dosar,
  • Jitha KR,
  • Vinodhkumar Obli Rajendran,
  • Kiran Narayan Bhilegaonkar,
  • Mark Holmes,
  • Bibek Rhanjan Shome,
  • Shivaraman GK

摘要

Proteus mirabilis is a foodborne and environmental pathogen causing catheter-associated urinary tract infections (CAUTIs) with antimicrobial resistance (AMR) and virulence. As the potential of Indian strains remains underexplored, whole-genome sequence (WGS) data of 18 strains were analyzed for AMR, virulence, and genetic relatedness. The disc diffusion method assessed phenotypic AMR. Genomic DNA sequencing was performed on Illumina MiSeq platform, followed by quality control, read assembly, gap closure, and annotation using software tools. Various tools were used to predict antimicrobial resistance genes (ARGs), resistome, virulence, mobile genetic elements (MGEs), pathogenicity, single nucleotide polymorphisms (SNPs), and plasmids. Phylogenetic analysis based on SNPs was performed using maximum likelihood (ML) and neighbor-joining (NJ) methods. All isolates showed resistance to tetracycline but were sensitive to gentamicin, amoxicillin/clavulanic acid, and streptomycin. Genome sizes ranged from 3,824 to 4,296 kb (average 3691.6 ± 164.3) and 5–26 ARGs per isolate. Common intrinsic resistance genes, including tetJ, tet(D), K. pneumoniae KpnF, and amphenicol resistance genes (cat and catA4) were present in all but one isolate. Predominant ARGs were linked to tetracycline, quinolone, cephalosporin, cephamycin, penam, quaternary ammonium compounds, and glycopeptide groups present in MGEs. Isolates contained numerous virulence genes (n = 4785) across 10 categories. The average SNP count was 4114.27 ± 3216.91, with four isolates showing no SNPs. Phylogenetic analysis revealed diversity (D= -1.6910, P = 0.0047) among 86 reference strains. Ongoing monitoring through WGS analysis is essential for understanding and managing infections caused by this pathogen.

Graphical Abstract