Miranda-Riveros, J. | Search bioRxiv

bioRxiv2026

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

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.

genomics↗

bioRxiv2025

Emergent Salmonella enterica serovar Infantis forms a monophyletic lineage shaped by geographic structuring

Multidrug-resistant Salmonella Infantis carrying pESI-like megaplasmids have disseminated worldwide representing a serious threat to public health. Previous studies have investigated its population structure and temporal dynamics above the continental level. However, their conclusions were constrained by limited datasets and sampling biases. To address these issues, we analyzed all publicly available Salmonella Infantis genomes to characterize its global population structure and phylogeographic dispersal. We selected a non-redundant dataset of 14,012 genomes representing the temporal, geographic, isolation source, and genomic diversity of Salmonella Infantis from 78 countries across five continents, collected between 1910 to 2024. Phylogenomic analyses showed that emergent megaplasmid-positive Salmonella Infantis forms a monophyletic lineage with significant geographic structuring. The megaplasmid-positive lineage was inferred to be originated in West Asia around 1990, followed by multiple introductions into Europe and a single transmission to South America which resulted in the dissemination of this pathogen to Northern America, and from there to the rest of the continent. Multiple recent transmission events of the American lineage to all continents were observed, driving the dispersal of the blaCTX-M-65 gene encoding extended-spectrum {beta}-lactamases. Moreover, genomic evidence also suggests that the emergence of ESBL-producing strains in parts of Asia and Africa may be associated to poultry trading from the Americas. Our findings underscore the urgent need for integrating global human, animal, and environmental surveillance data with population genomic analyses to contain the threats posed by ESBL-producing Salmonella Infantis.

genomics↗