Epidemiology and Monitoring of Antimicrobial-Resistant Zoonotic Pathogens
We conduct comprehensive epidemiological and genomic studies to track the emergence and dissemination of antimicrobial-resistant (AMR) zoonotic pathogens. Using high-throughput whole genome sequencing, our lab identifies and characterizes resistance genes, mobile genetic elements, and virulence factors in isolates collected from animals, food sources, environmental reservoirs, and clinical settings. We monitor trends in resistance among pathogens of concern, including Salmonella, Campylobacter, Klebsiella pneumoniae, Rhodococcus equi, Listeria monocytogenes, E. coli, Clostridium perfringens, Clostridium difficile, and Staphylococcus aureus, and assess how resistance is transmitted across species and environments. Our One Health surveillance approach integrates molecular tools and spatial mapping to uncover reservoirs and transmission routes. By collaborating with state and federal partners, we contribute to antimicrobial resistance (AMR) surveillance systems and provide actionable data to inform policy, outbreak response, and risk mitigation strategies.
Here are some of our publications:
Kabir , Kelley WG., Glover C., Erol E., and Helmy Y.A. (2025). Phenotypic and genotypic characterization of antimicrobial resistance and virulence profiles of Salmonella enterica serotypes isolated from necropsied horses in Kentucky. Microbiology Spectrum e02501-24. https://doi.org/10.1128/spectrum.02501-24
Helmy Y.A., Kabir A, Salah M, Kennedy LA, Burns L, and Johnson B (2024). Draft Genome Sequence Analysis of Multidrug-Resistant Salmonella enterica subsp. enterica serovar Mbandaka Harboring Colistin Resistance Gene mcr-9.1 Isolated from Foals in Kentucky, USA. Microbiology Resource Announcements 7:e0073724. PMID: 39373480; https://doi.org/10.1128/mra.00737-24.
Kabir A, Lamichhane B, Habib T, Adams A, El-Sheikh Ali H, Slovis NM, Troedsson MHT, Helmy Y.A. (2024). Antimicrobial Resistance in Equines: A Growing Threat to Horse Health and Beyond- A Comprehensive Review. Antibiotics 13(8), 713. PMID: 39200013; PMCID: PMC11350719; https://doi.org/10.3390/antibiotics13080713.
Lamichhane B, Mawad AMM., Saleh M., Kelley WG, Harrington PJ, Lovestad CW, Amezcua J, Sarhan MM, El Zowalaty ME, Ramadan H, Morgan M, Helmy Y.A. (2024). Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate Antimicrobial Resistant Infections. Antibiotics 13 (1): 76. PMID: 38247636; PMCID: PMC10812683; https://doi.org/10.3390/antibiotics13010076.
El Zowalaty M., Falgenhauer L., Ashour H., Zishiri O., Forsythe S, and Helmy Y.A. (2024). Draft genome sequences of Bacillus licheniformis strains MEZBL63 and MEZBL64 harboring the lichenysin toxin operon isolated from livestock in South Africa. Microbiology Resource Announcements 13(3):e0096723. PMID: 38323846; PMCID: PMC10927698; https://doi.org/10.1128/mra.00967-23.
El Zowalaty ME, Lamichhane B., Falgenhauer L., Mowlaboccus S., Zishiri O., Forsythe S., Helmy Y.A.* (2023). Antimicrobial Resistance and Whole Genome Sequencing of Novel Sequence Types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans Isolated from Livestock. Scientific Reports 13 (1). PMID: 37903806; PMCID: PMC10616195; https://doi.org/10.1038/s41598-023-42838-z.
El ZowalatyE., Falgenhauer L., Forsythe, S. and Helmy Y.A.* (2023). Draft Genome Sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance mcr-9 gene isolated from wastewater in South Africa. Journal of Global Antimicrobial Resistance 33 (231-237). PMID: 36948496; https://doi.org/10.1016/j.jgar.2023.03.007.