Biology subjects

Tichy-Navarro, D.

Publications and source records attributed to Tichy-Navarro, D..

3 recordsLinked to original sources

bioRxiv2026

Prophage {Phi}ESI promotes competitive dominance in the emergent Salmonella serovar Infantis lineage

The global spread of multidrug-resistant Salmonella enterica serovar Infantis has been largely attributed to the pESI megaplasmid, yet additional factors underlying the ecological success of this lineage remain unclear. Here, we characterize {Phi}ESI (phage of emergent Salmonella Infantis), a temperate bacteriophage discovered during coculture of an emergent pESI-positive strain (PM57) and a non-emergent strain (DR006). Phage {Phi}ESI shows a siphovirus morphotype with a long tail and an elongated head, with a genome of 46,490 bp, which is integrated as a prophage in the 3-end of an Arg-tRNA gene in PM57, but is absent in DR006, which is susceptible to the {Phi}ESI-mediated lysis. The screening of {Phi}ESI genes across 20,429 global Salmonella Infantis genomes revealed an almost exclusive association of {Phi}ESI and {Phi}ESI-like phages with the emergent pESI-positive Salmonella Infantis lineage. Further bioinformatic analyses of complete chromosomes revealed diverse {Phi}ESI insertion profiles showing geographic clustering, and the presence of large-scale chromosomal inversions flanked by {Phi}ESI genes. Competition assays showed that PM57 outcompeted DR006 in coculture, coinciding with high viral loads that selectively targeted DR006, and susceptibility assays showed that strains lacking {Phi}ESI/{Phi}ESI-like prophages were susceptible to {Phi}ESI-mediated lysis. Together, our findings identify {Phi}ESI as a competitive factor associated with emergent Salmonella Infantis, able to selectively eliminate susceptible competitors. Our findings suggest that {Phi}ESI/{Phi}ESI-like prophages contributed to the persistence and global dissemination of the emergent Salmonella Infantis lineage. ImportanceEmergent multidrug-resistant Salmonella enterica serovar Infantis strains carrying pESI megaplasmids have spread worldwide, posing a global public health threat and a significant economic burden. Nevertheless, the factors contributing to the success of this foodborne pathogen, beyond pESI, remain poorly understood. Here, we describe {Phi}ESI, a novel temperate bacteriophage carried by the emergent lineage as a chromosomally integrated prophage. We show that {Phi}ESI provides a competitive advantage to emergent strains by selectively killing non-emergent competitors while protecting lysogens from reinfection. Our findings uncover the contribution of {Phi}ESI/{Phi}ESI-like bacteriophages to the success of emergent Salmonella Infantis, highlighting how lineage-associated prophages can shape the ecological success of pathogenic bacteria.

microbiology↗

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↗