Whole genome sequencing and comparative genomic characteristics analysis of three strains of Aerococcus urinaeequi from swine
- 1College of Animal Science, Anhui Science and Technology University, Chuzhou, 233100 China
- 2Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Anhui Science and Technology University, Chuzhou, 233100 China
- 3Anhui Engineering Research Center of Pork Quality Control and Enhancement, Anhui Science and Technology University, Chuzhou, 233100 China
Abstract
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.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05466-x.
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BibTeX
@article{wang2026whole,
title = {{Whole genome sequencing and comparative genomic characteristics analysis of three strains of Aerococcus urinaeequi from swine}},
author = {Hailong Wang and Jiamin Ma and Yangyang Li and Wenchao Li and Weina Guo},
journal = {BMC Microbiology},
year = {2026},
month = jul,
doi = {10.1186/s12866-026-05466-x},
url = {https://doi.org/10.1186/s12866-026-05466-x},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Whole genome sequencing and comparative genomic characteristics analysis of three strains of Aerococcus urinaeequi from swine
AU - Hailong Wang
AU - Jiamin Ma
AU - Yangyang Li
AU - Wenchao Li
AU - Weina Guo
PY - 2026
DA - 2026/07/31
JO - BMC Microbiology
DO - 10.1186/s12866-026-05466-x
UR - https://doi.org/10.1186/s12866-026-05466-x
AB - 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. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05466-x.
SN - 1471-2180
ER -