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

## TL;DR

This study shows that certain non-SE/STm Salmonella strains persist in Swiss broiler farms over time, despite disinfection, highlighting the need for improved biosecurity.

## Contribution

The study provides evidence of clonal persistence of non-SE/STm Salmonella serovars in commercial broiler farms using whole-genome sequencing.

## Key findings

- S. Infantis and S. Livingston isolates showed clonal persistence in broiler houses.
- S. 13,23:i:- isolates from integration B were clonal over 11 years, indicating long-term persistence.
- S. Welikade isolates showed genetic diversity, suggesting possible reintroduction or evolution.

## 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. enterica 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.

Identical clones of non‐Enteritidis/Typhimurium Salmonella serovars (non SE/STm), repeatedly isolated from the same broiler houses over months and years, suggesting their persistence in the farm environment, despite disinfection after each production cycle. This study stresses the utmost importance of on‐farm biosafety measures as fundamental elements to protect public health.