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Microorganisms
Volume 13
Issue 12
10.3390/microorganisms13122723
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Article

Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance

by
Yaqian Liang
1,†,
Wenjing Wang
1,†,
Yuling Guo
1,
Meihui Tian
1,
Junkai Wang
1 and
Haihong Hao
1,2,*
1
College of Animal Science and Technology, Shihezi University, Shihezi 832000, China
2
National Key Laboratory of Agricultural Microbiology Resources Exploration and Utilization, Huazhong Agricultural University, Wuhan 430070, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2025, 13(12), 2723; https://doi.org/10.3390/microorganisms13122723 (registering DOI)
Submission received: 2 November 2025 / Revised: 25 November 2025 / Accepted: 26 November 2025 / Published: 28 November 2025
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates)
Review Reports Versions Notes

Abstract

Staphylococcus aureus is the core pathogen causing bovine mastitis, and its antimicrobial resistance evolution is closely linked to prophage-mediated genetic material transfer, but their systematic association remains unclear. This study focused on 101 bovine-derived S. aureus strains isolated from large-scale dairy farms in Shihezi, Xinjiang, from September 2024 to January 2025, to explore their genomic diversity, prophage distribution characteristics, and intrinsic links to resistance. Results showed that the strains had resistance rates of 0.00–80.20% to 18 antibiotics across 12 classes, with ceftiofur having the highest resistance rate (80.20%) and 10 antibiotics including amoxicillin showing 0.00% resistance. Multidrug-resistant (MDR) strains accounted for 9.9% (10 strains), among which 2 had a resistance spectrum covering 7 antibiotic classes. The average genome size was 2.57 Mb with a GC content of 33.44%, cloud genes accounted for 85.00% of the pan-genome, and MLST identified 14 ST types, with ST5404 as the dominant type (36.6%). A total of 398 prophages were detected: 82.18% of strains carried resistance genes via prophages (Type I), while this proportion was 50.00% in MDR strains (Type II). This study confirms that prophages synergize with the ST5404 clonal group to promote clustered resistance gene transmission, providing a scientific basis for regional control of mastitis-causing drug-resistant strains and precise drug use.
Keywords: dairy cows; Staphylococcus aureus; genome; prophage; antimicrobial resistance dairy cows; Staphylococcus aureus; genome; prophage; antimicrobial resistance

Share and Cite

MDPI and ACS Style

Liang, Y.; Wang, W.; Guo, Y.; Tian, M.; Wang, J.; Hao, H. Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance. Microorganisms 2025, 13, 2723. https://doi.org/10.3390/microorganisms13122723

AMA Style

Liang Y, Wang W, Guo Y, Tian M, Wang J, Hao H. Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance. Microorganisms. 2025; 13(12):2723. https://doi.org/10.3390/microorganisms13122723

Chicago/Turabian Style

Liang, Yaqian, Wenjing Wang, Yuling Guo, Meihui Tian, Junkai Wang, and Haihong Hao. 2025. "Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance" Microorganisms 13, no. 12: 2723. https://doi.org/10.3390/microorganisms13122723

APA Style

Liang, Y., Wang, W., Guo, Y., Tian, M., Wang, J., & Hao, H. (2025). Study on Genomic Diversity, Prophage Distribution of Bovine-Derived Staphylococcus aureus and Their Association with Antimicrobial Resistance. Microorganisms, 13(12), 2723. https://doi.org/10.3390/microorganisms13122723

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