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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Toxicology & Mycotoxin Research » Research » Publications at this Location » Publication #430473
Research Project: Strategies to Reduce Mycotoxin Contamination in Animal Feed and its Effect in Poultry Production Systems

Location: Toxicology & Mycotoxin Research

Title: Gene expression analysis and whole genome sequencing reveal the potential mechanism of ciprofloxacin resistance in a salmonella dublin isolate

Author
item BENTUM, KINGSLEY - Tuskegee University
item LEESEMAKER-PALMER, AMY - Oregon State University
item NUSS, STEPHANIE - Oregon State University
item BALLARD, SOPHIA - Oregon State University
item MONTGOMERY, ALEXANDRA - Oregon State University
item ABEBE, WOUBIT - Tuskegee University
item TEMESGEN, SAMUEL - Tuskegee University
item Pokoo-Aikins, Anthony
item BEMUDEZ, LUIZ - Oregon State University

Submitted to: American Journal of Veterinary Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2026
Publication Date: 2/10/2026
Citation: Bentum, K.E., Leesemaker-Palmer, A., Nuss, S., Ballard, S., Montgomery, A., Abebe, W., Temesgen, S., Pokoo-Aikins, A., Bemudez, L. 2026. Gene expression analysis and whole genome sequencing reveal the potential mechanism of ciprofloxacin resistance in a salmonella dublin isolate. American Journal of Veterinary Research. Vet. Sci. 2026, 13, 177. https://doi.org/10.3390/vetsci13020177.
DOI: https://doi.org/10.3390/vetsci13020177

Interpretive Summary: This study shows how some bacteria become resistant to ciprofloxacin (CIP), an antibiotic. The study focused on a rare type of Salmonella called Salmonella Dublin, using samples collected between 1985 and 2023. The samples were tested to see how well CIP could stop them from growing. The scientists who worked on this also looked at the activity of certain genes that help bacteria resist antibiotics and checked for changes (mutations) in these genes. They searched for extra DNA pieces called plasmids and other resistance genes. One sample from 2023 was resistant to CIP, while another from 1985 was not. Both had genes linked to resistance, but only the older sample had a plasmid. The resistant sample showed higher activity in some genes and had a mutation in a protein called GyrA, which may help it resist CIP. The non-resistant sample didn’t have this mutation. This research helps explain how rare Salmonella strains become resistant and shows that certain genes and mutations play an important role.

Technical Abstract: There is a growing need to understand mutations and mechanisms linked to ciprofloxacin (CIP) resistance in less common isolates, such as Salmonella Dublin. This study, therefore, examined CIP resistance in biobanked Salmonella isolates collected from 1985 to 2023. Briefly, the susceptibilities and minimum inhibitory concentrations (MICs) of the isolates to CIP were determined by the Oregon Veterinary Diagnostic Laboratory on July 7th, 2023, using the broth dilution method. For each serovar, gene expression analysis of the acrAB efflux transporter genes and the regulator genes marA, ramA, and soxS was performed comparing CIP-resistant and CIP-sensitive isolates. Additionally, the isolates were sequenced using the Oxford Nanopore sequencing platform, and the sequences were analyzed for mutations. ABRicate was employed to search for plasmids and antimicrobial resistance genes in the sequences, while the SWISS-MODEL server was used for protein modeling and comparison. Our results showed that a Salmonella Dublin isolate recovered in 2023 and another in 1985 were the CIP-resistant (MIC 1.5µg/mL) and CIP-sensitive (MIC < 0.125µg/mL) isolates, respectively. Both isolates possessed the mdtK, emrR, emrA, and emrB genes, which are important in providing resistance against fluoroquinolones. No plasmids were found in the CIP-resistant isolate, although the CIP-sensitive isolate carried the IncFII(S) plasmid. The expression of the acrA, acrB, ramA, and soxS genes was significantly higher in the CIP-resistant isolate, which also harbored an Asparagine (N) to Serine (S) mutation at position 868 in the GyrA protein, unlike the sensitive isolate, which had no mutations. This study contributes to our understanding of mutations associated with CIP resistance, especially in less frequent isolates like Salmonella Dublin, and highlights the vital role of an efficient efflux system in contributing to CIP resistance within this serovar.