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. 2016 Apr 5:4:e1752.
doi: 10.7717/peerj.1752. eCollection 2016.

Identification of Salmonella for public health surveillance using whole genome sequencing

Philip M Ashton  1 , Satheesh Nair  1 , Tansy M Peters  1 , Janet A Bale  1 , David G Powell  1 , Anaïs Painset  1 , Rediat Tewolde  2 , Ulf Schaefer  2 , Claire Jenkins  1 , Timothy J Dallman  1 , Elizabeth M de Pinna  1 , Kathie A Grant  3 ; Salmonella Whole Genome Sequencing Implementation Group
Affiliations

Identification of Salmonella for public health surveillance using whole genome sequencing

Philip M Ashton et al. PeerJ. .

Abstract

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6,887 isolates of S. enterica subspecies I, and of these, 6,616 (96%) were concordant. Of the 4% (n = 271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II-IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I-IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates.

Keywords: Bioinformatics; Multi-locus sequence typing; Public health; Salmonella; Whole genome sequencing.

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Conflict of interest statement

The authors declare there are no competing interests

Figures

Figure 1
Figure 1
Population structure of all Salmonella enterica isolates submitted to PHE from local and regional hospital laboratories in England and Wales between April 2014 and March 2015 (see Table S1 for details).
Figure 2
Figure 2. Trends in preliminary sequence types.
(A) Novel, preliminary STs (PST) and the modal number of isolates identified per PST. (B) The rate at which PSTs were identified throughout the time frame of the study.
Figure 3
Figure 3. Phylogenetic relationship within two sequence types containing multiple serotypes.
(A) Phylogenetic relationship of S. Richmond and S. Bareilly (ST909). (B) Phylogenetic relationship of S. Saintpaul and S. Haifa (ST49).
Figure 4
Figure 4. Salmonella lineage 3 population structure.
Serovars in lineage 3 mainly consist of multiple eBGs and are polyphyletic by nature.
See this image and copyright information in PMC

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