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.
Highlights
The Salmonellae are major human pathogens and represent a significant global public health issue causing morbidity and mortality resulting in a high social and economic burden worldwide (Majowicz et al, 2010)
Achtman et al (2012) described the population structure of Salmonella enterica as monophyletic lineages of sequence type (ST) that have evolved from a single founder node and termed these discrete clusters e-Burst Groups (eBGs)
There were 249 cultures submitted to Salmonella Reference Service (SRS) by the local hospital and regional laboratories for Salmonella typing that were a mix of Salmonella and non-Salmonella species. These were identified by the k-mer identification step and included 138 Escherichia coli, 40 Morganella morganii, 11 Citrobacter species and four Escherichia albertii. In their seminal 2012 paper Achtman and colleagues (2012) argued convincingly for replacing serotyping with a multilocus sequence typing (MLST) approach based on genetic population groupings for typing S. enterica
Summary
The Salmonellae are major human pathogens and represent a significant global public health issue causing morbidity and mortality resulting in a high social and economic burden worldwide (Majowicz et al, 2010). There are six subspecies of S. enterica differentiated by biochemical. Enterica cause 99% of human and animal infections. The two main pathologies associated with S. enterica are gastroenteritis and typhoidal disease. They are host restricted, monophyletic, rarely undergo recombination events and exhibit convergent evolution driven by genome degradation (Wain et al, 2015). The majority of gastroenteritis in the UK is caused by the host generalist serovars, such as S. Enteritidis, and host adapted serovars that are adapted to a specific animal reservoir but can infect man and include S. Bovismorbificans (Langridge et al, 2015)
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