Widespread dissemination of ESBL-producingSalmonella entericaserovar Infantis exhibiting intermediate fluoroquinolone resistance and harboringbla_CTX-M-65-positive pESI-like megaplasmids in Chile

Abstract

Background: Multidrug-resistant (MDR)SalmonellaInfantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases ofSalmonellaInfantis infections have substantially increased in recent years, a better understanding of its molecular epidemiology and antimicrobial-resistance profiles are required to inform effective surveillance and control measures. Methods: We sequenced 396SalmonellaInfantis genomes and analyzed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and AMR profiles ofSalmonellaInfantis in the country. Findings: The genomic and phylogenetic analyses showed thatSalmonellaInfantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. The latter was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343SalmonellaInfantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity. Interpretation: Our findings show a widespread dissemination of MDRSalmonellaInfantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producingSalmonellaInfantis with intermediate fluoroquinolone resistance in the continent. Funding: Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID - Millennium Science Initiative Program - ICN2021_044.

ECOPHAGE: Combating Antimicrobial Resistance Using Bacteriophages for Eco-Sustainable Agriculture and Food Systems

“…A collection of more than 2000 isolates from humans, animals, food, and water determined that multidrug-resistant Salmonella Infantis is the main strain to target for a phage intervention. Genomic analysis of 440 genomes of S. Infantis isolates found two clades of S. Infantis circulating in Chile since 2009 [4,5]. Overall, 92% of its strains clustered together and presented multiple antimicrobial resistance genes.…”