Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17

An outbreak surveillance system for Salmonella integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016-17 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal Salmonella 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs. In the remaining 22 unique clusters (126 weekly clusters) reported to HPTs, nine were known active outbreak investigations, seven were below locally agreed thresholds and six exceeded local thresholds. A common source or vehicle was identified in four of six clusters that exceeded locally agreed thresholds. This work demonstrates that a threshold-based surveillance system, taking into account time, place and genetic relatedness, is feasible and effective in directing the use of local public health resources for risk assessment and investigation of non-typhoidal Salmonella clusters.