Genotypes and associated traits in Salmonella enterica Newport strains linked to fresh produce-associated outbreaks in the United States

Authors: Carter, Michelle; Carychao, Diana; Gorski, Lisa; LINDSEY, REBECCA - Centers For Disease Control And Prevention (CDC) - United States; Bono, James

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2025
Publication Date: 1/23/2026
Citation: Carter, M.Q., Carychao, D.K., Gorski, L.A., Lindsey, R.L., Bono, J.L. 2026. Genotypes and associated traits in Salmonella enterica Newport strains linked to fresh produce-associated outbreaks in the United States. Frontiers in Microbiology. 16. Article 1676706. https://doi.org/10.3389/fmicb.2025.1676706.
DOI: https://doi.org/10.3389/fmicb.2025.1676706

Interpretive Summary: Salmonella enterica is a leading cause of bacterial infection in humans and animals. Although over 2,600 serotypes have been identified, most human illness are caused by a subset of serotypes (~100). Serotype Newport is among the top five that cause most foodborne outbreaks overall and one of a few serotypes responsible for most of the human infections in the United States. Therefore, rapid detection and identification of Newport strains that can persist in food production systems and cause outbreaks would greatly benefit growers, food processing industry, and government regulatory agencies to timely assess health risks associated with Salmonella contamination. In this study, we identified a main genotype of Newport, ST118, linked to fresh produce-associated outbreaks that occurred between 2010-2018. Furthermore, several persistent SNP clusters were revealed. Strains within the persistent SNP clusters had been detected in the U.S. for a long period of time, e.g. > 20 years, and linked to multiple large outbreaks that were transmitted via different food products, from common ones like melons, tomatoes, and cucumbers to less common produce like onions, parsley, and peppers. Strains within the persistent SNP clusters appeared to carry a larger genome than the strains within transit SNP clusters, suggesting that accessory genes in the persistent strains likely encode functions contributing to their long-term survival in the environment. Such information will help develop targeted mitigation strategies to reduce Newport infections in humans.

Technical Abstract: Salmonella enterica is a leading cause of bacterial infection in humans and animals. Newport is among the most prevalent serotypes linked to fresh produce-associated salmonellosis outbreaks in the U.S. and among the top serotypes that cause most foodborne outbreaks overall. In this study, we performed comparative pathogenomic analyses and phenotypic assays to uncover genetic and phenotypic traits contributing to pathogenicity and epidemiological prevalence of Newport. Ten clinical strains were placed in four Sequence Types (ST5, ST31, ST45, and ST118) and ten SNP clusters using NCBI Pathogen Detection pipeline. Of the ten SNP clusters, several persistent SNP clusters were identified, including PDS000127718 and PDS000029636, and each contained more than 4,000 matched strains and had been detected over a long period of time (> 20 years). In contrast, some SNP clusters appeared to represent transient SNP clusters, such as PDS000002512 that contained less than 10 matched strains and had been detected within a short period of time (< five years). The core virulence determinants in Newport included SPI-1 and SPI-2 encoded T3SS, SPI-4 and SPI-9 encoded T1SS, SPI-6 encoded T6SS, and many fimbriae and nonfimbrial adhesins. Among the seven SPIs detected, SPI-6 exhibited great sequence divergence, including a large deletion that abolished both T6SS and Saf fimbriae simultaneously in two ST118 strains. Our study revealed common and lineage specific fimbriae: Peg and Ste fimbriae genes were only detected in the lineage II strains while Stc fimbriae genes were detected only in the lineage III strains. Our study also revealed vast strain variation in expression of curli fimbriae, biofilm formation, and adherence to cantaloupe rind. Expression of curli fimbriae appeared to be strain-specific and was not associated with ST or lineage. Under the condition tested, curli enhanced biofilm formation significantly but tempered adherence of Newport to cantaloupe rind, implying a role of other adhesins in the initial interaction between Newport cells and the surface of cantaloupe rind. More accessory genes were identified in strains with a persistent genotype than in strains with a transient genotype, suggesting a role of accessory genes in dissemination of the persistent Newport strains in the United States.