Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Abstract

BackgroundFoodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response. We initially investigated this outbreak by whole-genome sequencing using a novel rapid protocol on the Illumina MiSeq; we then integrated these data with whole-genome data from surveillance sequencing, thereby placing the outbreak in a national context. Additionally, we investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella.ResultsWe demonstrate that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results. We show, for the first time, that the MinION can acquire clinically relevant information in real time and within minutes of a DNA library being loaded. MinION sequencing permits confident assignment to species level within 20 min. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 min and determined to be part of the outbreak in less than 2 h.ConclusionsBoth approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

“…Furthermore, recent updates in nanopore sequencing technology that became commercially available in late 2016 made it possible to obtain gigabases of sequence data from a single flowcell. Prior to this, due to relatively low output, the nanopore sequencing technology was mainly used to analyze and assemble microbial samples (Loman et al, 2015;Quick et al, 2015;Jain et al, 2016;Kranz et al, 2017). Notably, early reports of Oxford nanopore reads indicate that they are exceptionally long (Weirather et al, 2017) but have a high (Judge et al, 2015), and nonrandom, error rate (Deschamps et al, 2016).…”

Considerations in centralizing whole genome sequencing for microbiology in a public health setting

“…It is clear that only WGS has the capability to fulfill all of these features and has already been used, or shown to be potentially useful, for epidemiological (and potentially diagnostic) investigation [4][5][6][7][8][9][10][11][12]. In what is a transformation in microbiology, Public Health England (PHE) has sequenced a total of approximately 50,000 bacterial and viral genomes with resulting improved surveillance and outbreak investigations and intends to harness its full potential in supporting the NHS to deliver the best care for patients [13].…”

From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks

“…Its portability and capacity to perform real-time analysis during sequencing has made it an attractive companion for outbreak investigations in remote regions, as was the case with the ZIBRA project 29 . Clinically, MinION sequencing has been used to retrospectively analyse S. enterica isolates in relation to a European-wide outbreak 30 , which showed that the outbreak strain could be identified from less than 2 hours of sequencing, despite not having the resolution to elucidate transmission pathways. Viral pathogens have also been identified from clinical metagenomic samples, with a projected turn-around time of less than 6 hours 31 .…”