Whole-Genome Sequencing-Based Monitoring of Cronobacter sakazakiiST4 Persistence in an Irish Dairy Powder Facility

Cronobacter sakazakii, an emerging foodborne pathogen linked to neonatal infections, poses significant risks in dairy powder processing facilities, particularly those supplying ingredients for powdered infant formula (PIF). This case study employed whole-genome sequencing (WGS) to monitor C. sakazakii persistence in a large-scale Irish high-protein milk powder plant over a 12-month period, focusing on ultrafiltration, evaporation, spray-drying, and packaging zones. Environmental swab samples of 240 in total from 20 fixed locations were collected monthly and analyzed using the ISO 22964 method, followed by real-time PCR confirmation and Illumina-based WGS for isolate characterization. Eighty-eight Cronobacter spp positive samples were isolated out. Multilocus sequence typing identified four sequence types, with 10 isolates of ST4 associated with clinical meningitis. Phylogenetic analysis revealed two distinct ST4 clades: one persistent but spatially limited (isolates K08 and C19), detected sporadically across months, and another clonal group exhibiting temporal proliferation, peaking in the final month across multiple dryer levels. These findings indicate recurrent contamination events and long-term persistence, underscoring WGS's superior resolution over traditional typing methods for tracking pathogen dynamics. The method of WGS, as the new gold standard, offers the highest resolution, the greatest amount of information, permanent traceability, lower cost, and faster speed in bacterial analysis-advantages that MLST (Multilocus sequence typing) cannot match. The study demonstrates WGS as a powerful tool for enhancing surveillance in dairy facilities, enabling early detection of colonization risks and informing targeted hygiene interventions to safeguard PIF supply chains. Therefore, the rational and widespread adoption of WGS in food safety surveillance can markedly simplify and accelerate the precise identification and source tracking of contaminants, thereby providing robust technical support for the early prevention and rapid response to food safety incidents.