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Background <p><i>Aerococcus urinaeequi</i>, as a zoonotic opportunistic pathogen, has seen its issue of multidrug resistance become increasingly prominent in the fields of animal husbandry and public health. However, systematic whole-genome studies on this bacterium are still lacking, which has limited the in-depth understanding of its resistance transmission patterns and evolutionary mechanisms.</p> Objective <p>Whole-genome sequencing and comparative genomic analysis were performed on three swine-origin multidrug-resistant <i>Aerococcus urinaeequi</i> strains to provide genomic insights into their genetic features, phylogenetic relationships, and predicted antibiotic resistance and virulence-associated genes.</p> Methods <p>Antimicrobial susceptibility was determined using the disk diffusion method, and biofilm formation ability was assessed via crystal violet assay. Whole-genome sequencing was performed using high-throughput sequencing technology. Phylogenetic analysis, pan-genome analysis, and prediction of mobile genetic elements (MGEs), resistance genes, and virulence genes were performed using genome data from 20 publicly available <i>Aerococcus urinaeequi</i> strains of diverse hosts.</p> Results <p>Antimicrobial susceptibility testing confirmed that all three strains were multidrug-resistant, exhibiting resistance to penicillin, tetracycline, linezolid, and other antimicrobial agents. Phylogenetic tree and average nucleotide identity analysis indicated that the three strains clustered with swine-origin reference strains. Pan-genome analysis suggested that <i>Aerococcus urinaeequi</i> has an open pan-genome with a large accessory gene pool, implying considerable genetic diversity and potential for environmental adaptation. Prediction of mobile genetic elements revealed differences among the strains: the copy numbers of insertion sequences (ISs) varied, and all three strains carried a predicted repUS43-type plasmid replicon; however, no prophage regions were predicted in any of the three strains. Resistance gene prediction indicated that all three strains commonly harbored <i>tetM</i> and <i>optrA</i>; among the 23 strains analyzed in this dataset, the detection rate of <i>optrA</i> was 39%. A total of 19 putative virulence-associated genes were predicted, with annotated functions including adhesion, stress survival, and immune evasion. Phenotypic testing of the three newly isolated strains showed that only AU3 formed detectable biofilms under the assay conditions.</p> Conclusions <p>This study describes the resistance phenotypes and genomic features of these three swine-origin <i>Aerococcus urinaeequi</i> isolates, providing baseline genomic data that may inform future surveillance efforts for this species in pig farms.</p>

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Whole genome sequencing and comparative genomic characteristics analysis of three strains of Aerococcus urinaeequi from swine

  • 期刊论文

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  • 发表日期：

    2026年7月31日

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  • Hailong Wang,
  • Jiamin Ma,
  • Yangyang Li,
  • Wenchao Li,
  • Weina Guo

摘要

Background

Aerococcus urinaeequi, as a zoonotic opportunistic pathogen, has seen its issue of multidrug resistance become increasingly prominent in the fields of animal husbandry and public health. However, systematic whole-genome studies on this bacterium are still lacking, which has limited the in-depth understanding of its resistance transmission patterns and evolutionary mechanisms.

Objective

Whole-genome sequencing and comparative genomic analysis were performed on three swine-origin multidrug-resistant Aerococcus urinaeequi strains to provide genomic insights into their genetic features, phylogenetic relationships, and predicted antibiotic resistance and virulence-associated genes.

Methods

Antimicrobial susceptibility was determined using the disk diffusion method, and biofilm formation ability was assessed via crystal violet assay. Whole-genome sequencing was performed using high-throughput sequencing technology. Phylogenetic analysis, pan-genome analysis, and prediction of mobile genetic elements (MGEs), resistance genes, and virulence genes were performed using genome data from 20 publicly available Aerococcus urinaeequi strains of diverse hosts.

Results

Antimicrobial susceptibility testing confirmed that all three strains were multidrug-resistant, exhibiting resistance to penicillin, tetracycline, linezolid, and other antimicrobial agents. Phylogenetic tree and average nucleotide identity analysis indicated that the three strains clustered with swine-origin reference strains. Pan-genome analysis suggested that Aerococcus urinaeequi has an open pan-genome with a large accessory gene pool, implying considerable genetic diversity and potential for environmental adaptation. Prediction of mobile genetic elements revealed differences among the strains: the copy numbers of insertion sequences (ISs) varied, and all three strains carried a predicted repUS43-type plasmid replicon; however, no prophage regions were predicted in any of the three strains. Resistance gene prediction indicated that all three strains commonly harbored tetM and optrA; among the 23 strains analyzed in this dataset, the detection rate of optrA was 39%. A total of 19 putative virulence-associated genes were predicted, with annotated functions including adhesion, stress survival, and immune evasion. Phenotypic testing of the three newly isolated strains showed that only AU3 formed detectable biofilms under the assay conditions.

Conclusions

This study describes the resistance phenotypes and genomic features of these three swine-origin Aerococcus urinaeequi isolates, providing baseline genomic data that may inform future surveillance efforts for this species in pig farms.