Genomic Analysis of the First S. Enteritidis Outbreak in the New Zealand Poultry Sector
A new study published in Microbial Genomics investigates the first documented outbreak of Salmonella Enteritidis (specifically sequence type ST11) in New Zealand's poultry sector, which was linked to both human illness and poultry production environments. Prior to 2021, this pathogen had not been detected in local poultry flocks, with human cases historically attributed to international travel. The researchers analyzed 231 S. Enteritidis genomes from human cases and poultry sources, revealing that the outbreak strain emerged around February 2019. Genomic data indicated significant amplification and spread within the poultry industry, with transmission events occurring across various points in the production chain. Phylodynamic analysis identified a specific hatchery as the most probable origin of the infection.
The outbreak evolved into three distinct genetic clades, indicating a shift in transmission pathways over time. Early transmission (Clade 1) was primarily associated with egg producers and a specific restaurant outbreak in 2019. Later stages of the outbreak (Clades 2 and 3) demonstrated a shift toward broiler production systems. Formal interventions initiated by the Ministry for Primary Industries (MPI) and the Ministry of Health in April 2021 proved effective. These control measures coincided with a sharp decline in the effective population size of the bacteria and a significant reduction in notified human cases.
The specific outbreak strain (SE-19C01) clustered independently and was genetically distinct from all other international S. Enteritidis ST11 genomes analyzed, reinforcing the conclusion that this was a unique, localized introduction. The study suggests that while the hatchery was the primary source, other cryptic transmission routes, such as feed, equipment, or staff, likely contributed to the dissemination.
