Retrospective Analysis of Persistent Clonal Salmonella enterica Strains of Various Serovars in Commercial Swiss Broiler Farms

ABSTRACT Detection of Salmonella Enteritidis (SE) and S . Typhimurium (STm) in broiler holdings is regulated by European and Swiss law to ensure public health. Persistence of Salmonella in broiler houses may jeopardize this goal. The aim of this study was to analyze whether non‐SE/STm isolated from boot socks were of clonal origin. Four Salmonella serovars from 11 broiler houses from 10 Swiss farms were selected: S . Infantis, S . Livingston and S . Welikade (meat integration A) and S. enterica subsp. e nterica 13,23:i:‐ (integration B). The genetic relationship was evaluated by whole‐genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST)‐based tree analysis, with a cluster being defined as < 8 cg alleles differences. The isolates of S . Infantis and S . Livingston, respectively, were shown to belong to the same serovar‐specific clusters (range: 1–7 cg alleles differences), suggesting that the Salmonella strains persisted in the respective broiler houses. S . Welikade, however, showed 8–11 cg alleles differences among isolates, indicating either a reintroduction of similar but not clonal strains into the houses due to insufficient biosecurity, or the evolution of a persistent strain. Remarkably, all isolates of S . 13,23:i:‐ from integration B from 2013 to 2024 were clonal, suggesting dispersal and persistence in the broiler integration. The clonality of analyzed strains suggests that Salmonella can persist on farms or integration level despite disinfection after each production cycle. Hence, improved farm and vehicle cleaning and disinfection practices are essential to ensure that the next flock is not exposed to non‐SE/STm Salmonella serovars.