Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing
Authors: Luo Lijuan , Payne Michael , Kaur Sandeep , Hu Dalong , Cheney Liam , Octavia Sophie , Wang Qinning , Tanaka Mark M. , Sintchenko Vitali , Lan Ruiting 
Published: July 2020

Salmonella entericaserovar Enteritidis is a major cause of foodborneSalmonellainfections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels forS.Enteritidis and characterised the genomic epidemiology ofS.Enteritidis in detail. We examined 26,670 publicly availableS. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA were identified; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018, revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified MDR associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the globalS. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance ofS. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool forS. Enteritidis surveillance and outbreak detection.

Impact statement

Salmonella entericaserovar Enteritidis is a common foodborne pathogen that can cause large outbreaks. Surveillance and high-resolution typing are essential for outbreak prevention and control. Genome sequencing offers unprecedented power for these purposes and a standardised method or platform for the interpretation, comparison and communication of genomic typing data is highly desirable. In this work, we developed a genomic typing scheme called Multilevel Genome Typing (MGT) forS. Enteritidis. We analysed 26,670 publicly available genomes ofS.Enteritidis using MGT. We characterised the geographic and temporal distribution of S. Enteritidis MGT types as well as their association with multidrug resistance (MDR) and virulence genes. A publicly available MGT database forS. Enteritidis was established, which has the potential facilitate the unified global public health surveillance for this pathogen.

Data Summary

The MGT database forS.Enteritidis is available athttps://mgtdb.unsw.edu.au/enteritidis/.

All accession numbers of the public available genomes were available in the MGT database and Data Set S1, Tab 1. And there were no newly sequenced data in this study.

Supplementary material: Supplementary Fig. S1 to S7, supplementary methods and supporting results about the evaluation of potential repeat sequencing bias.

Data Set S1: Supporting tables of the main results.

Data Set S2. Supporting tables of the repeat sequencing bias evaluation by removing the potential repeat sequencing isolates. Note outbreak isolates may also be removed.