Emergence of a multidrug-resistant Salmonella enterica serovar Amager lineage carrying the blaCTX-M-65-positive pESI megaplasmid

Miranda-Riveros, J.; Tichy-Navarro, D.; Navarrete, M. J.; Reyes-Jara, A.; Toro, M.; Ugalde, J. A.; Moreno-Switt, A. I.; Pina-Iturbe, A.

doi:10.64898/2026.03.02.708915

bioRxiv · 10.64898/2026.03.02.708915

Emergence of a multidrug-resistant Salmonella enterica serovar Amager lineage carrying the blaCTX-M-65-positive pESI megaplasmid

Miranda-Riveros, J.·Tichy-Navarro, D.·Navarrete, M. J.·Reyes-Jara, A.·Toro, M.·Ugalde, J. A.·Moreno-Switt, A. I.·Pina-Iturbe, A.

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Abstract

The spread of extended-spectrum {beta}-lactamase (ESBL)-producing and fluoroquinolone-resistant Salmonella pose a global public health challenge in addition to the high burden of infections associated with this foodborne pathogen. In this study we aimed to characterize a multidrug-resistant strain of Salmonella serovar Amager isolated from a Chilean river in October 2023. Antimicrobial susceptibility testing revealed a resistance phenotype against multiple antibiotic families, including fluoroquinolones and {beta}-lactams, showing ESBL production. Hybrid genome sequencing allowed the identification of a 311,303 bp plasmid carrying the aadA1, aph(4)-Ia, aac(3)-IVa, floR, sul1, tet(A), and blaCTX-M-65 genes, sharing 99.98% sequence identity with the Salmonella Infantis pESI-like megaplasmid. In addition, the qnrB19 gene was found in a {approx}2.7 kbp plasmid of widespread distribution. Population structure and temporal phylogenetic analysis at the global scale revealed the emergence of a Salmonella Amager lineage from the HC20_35565 cluster, carrying the Salmonella Infantis blaCTX-M-65-positive pESI-like megaplasmid and causing human infections in the United States and the United Kingdom. Our work describes the emergence of a Salmonella lineage with resistance against first-line antibiotics used for treating severe infections, underscoring the relevance of environmental surveillance as a means for detecting emergent pathogens and anticipating human infections.

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Miranda-Riveros, J., Tichy-Navarro, D., Navarrete, M. J., Reyes-Jara, A., Toro, M., Ugalde, J. A., Moreno-Switt, A. I., Pina-Iturbe, A.. 2026-03-02. Emergence of a multidrug-resistant Salmonella enterica serovar Amager lineage carrying the blaCTX-M-65-positive pESI megaplasmid. https://doi.org/10.64898/2026.03.02.708915

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