Identification of Salmonella for public health surveillance using whole genome sequencing
نویسندگان
چکیده
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.
منابع مشابه
Identification and typing of Salmonella for public health surveillance using whole genome sequencing
متن کامل
A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October
L Byrne ([email protected])1, I Fisher1, T Peters2, A Mather3, N Thomson3, B Rosner4, H Bernard4, P McKeown5, M Cormican6, J Cowden7, V Aiyedun1, C Lane1, on behalf of the International Outbreak Control Team8 1. Gastrointestinal, Emerging and Zoonotic Infections, Centre for Infectious Disease Surveillance and Control, Public Health England, Colindale, London, United Kingdom 2. Gastrointesti...
متن کاملRapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis
For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. There...
متن کاملConstruction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification
We built a pan-genome allele database with 395 genomes of Salmonella enterica serovar Enteritidis and developed computer tools for analysis of whole genome sequencing (WGS) data of bacterial isolates for disease cluster identification. A web server (http://wgmlst.imst.nsysu.edu.tw) was set up with the database and the tools, allowing users to upload WGS data to generate whole genome multilocus ...
متن کاملWhole-Genome Sequencing of a Clinically Isolated Antibiotic-Resistant Enterococcus faecium EntfacYE
Background and Objective: Enterococcal infections are considered the most common nosocomial infections. Nowadays, enterococci show high resistance to common antibiotics, especially vancomycin. Vancomycin-resistant Enterococcus faecium is one of the most common nosocomial infections, which is included in the World Health Organization priority pathogens list for research and development of new an...
متن کامل