New Genomic Analysis of Global REP Salmonella Strain May Help Inform Interventions
A recent study sought to better understand the genomic characteristics associated with an important reoccurring, emerging, and persistent (REP) Salmonella strain in comparison to closely related S. Infantis isolates, which may help with the identification of new intervention and/or control strategies that can reduce the pathogen’s spread.
S. Infantis REPJFX01 has been designated a REP strain by the U.S. Centers for Disease Control and Prevention (CDC) due to its association with foodborne illness outbreaks, contaminated poultry, and international travel. This multidrug-resistant (MDR) strain is increasingly implicated in human salmonellosis cases across North and South America.
Key findings of the research that may inform targeted interventions include:
- S. Infantis REPJFX01 isolates from both the U.S. and South America may belong to a single, emerging strain
- Chicken is the primary source of S. Infantis REPJFX01
- Water is a notable reservoir of S. Infantis REPJFX01, suggesting that agricultural runoff may facilitate the dissemination of REPJFX01 and its resistance genes
- Antimicrobial resistance (AMR) genes co-located with arsenic resistance genes suggest potential co-selection driven by environmental arsenic exposure/arsenic-containing compounds used in the poultry industry.
The study was conducted by researchers from Cornell University’s Department of Food Science. Authors include Anna Schuman, Ph.D. student; Martin Wiedmann, Ph.D., Gellert Family Professor in Food Safety; and Renato H Orsi, Ph.D., Senior Research Associate.
Genomic Characterization of Salmonella Infantis REPJFX01
A genome-wide association study comparing REPJFX01 isolates from the U.S. and South America with non-REP S. Infantis strains revealed 135 genes significantly associated with REPJFX01. Metadata for the isolates were downloaded from the National Center for Biotechnology Information Pathogen Detection (NCBI PD) database.
Notably, 50 of the 135 genes were located on the plasmid of emerging S. Infantis (pESI), a mosaic megaplasmid known to harbor AMR genes. Among the 135 REP-associated genes, 29 were functionally annotated, including genes involved in transcription, recombination, arsenic resistance, and AMR—suggesting that mobile genetic elements may drive the strain’s persistence and spread.
International Distribution and Poultry Reservoirs
Phylogenetic analysis confirmed that U.S. and South American REP isolates belong to the same single nucleotide polymorphism cluster, supporting the hypothesis that REPJFX01 represents a single international strain. Epidemiological data link its spread to travel in South America, particularly Ecuador and Peru, and to contaminated chicken meat—a primary reservoir for S. Infantis.
Between 2015 and 2020, the prevalence of S. Infantis in retail chicken meat in the U.S. rose from 2.8 percent to 39.7 percent, underscoring its growing public health relevance.
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Environmental Persistence and Plasmid Evolution
While S. Infantis has not traditionally been linked to water contamination, 19 percent of South American REP isolates were recovered from water sources, aligning with global findings that MDR Salmonella can persist in environmental reservoirs. Agricultural runoff may facilitate the dissemination of REPJFX01 and its resistance genes, including the pESI plasmid, which has been detected in other Salmonella serovars such as S. Senftenberg and S. Alachua.
The REPJFX01 strain appears to carry a newer, pESI-like plasmid formed through the insertion of gene cassettes like blaCTX-M-65. A total of seven transposases were associated with U.S. REP isolates, reinforcing the plasmid’s plasticity and its role in the evolution of REPJFX01.
Resistance Profile and Co-Selection with Heavy Metals
Among 300 analyzed isolates, 89 percent were MDR. Key AMR genes associated with U.S. REP isolates included blaCTX-M-65 (indicating β-lactam resistance), aph(4)-Ia and aacC(3)-Iva (aminoglycoside resistance), and floR (amphenicol resistance). These genes were primarily plasmid-located and often co-located with arsenic resistance operons, suggesting potential co-selection driven by environmental arsenic exposure.
Arsenic-containing compounds, historically used in poultry production and other industries, may contribute to the persistence and spread of REPJFX01.
Implications for Food Safety and Public Health
The international distribution of REPJFX01 and its strong association with poultry highlight the need for coordinated global surveillance and intervention strategies. Controlling its spread in chicken production, limiting environmental dispersal through farm runoff management, and curbing the use of antibiotics and heavy metals in agriculture are critical steps. Continued genomic monitoring of pESI plasmids will be essential to track the evolution and potential cross-serovar transmission of REPJFX01.
