SnapperDB: a database solution for routine sequencing analysis of bacterial isolates

Dallman, Timothy J.; Ashton, Philip; Schafer, Ulf; Jironkin, Aleksey; Painset, Anaïs; Shaaban, Sharif; Hartman, Hassan; Myers, Richard; Underwood, Anthony; Jenkins, Claire; Grant, Kathie

doi:10.1093/bioinformatics/bty212

Cited by 173 publications

(190 citation statements)

References 13 publications

Supporting

Mentioning

190

Contrasting

Order By: Relevance

“…Salmonella genomes have been assembled and stored in Enterobase (https://enterobase.warwick.ac.uk/). The availability of thousands of whole-genome sequences of S. Typhimurium has given epidemiological investigators an unprecedented ability to discover outbreaks, which involve S. Typhimurium isolates that vary by fewer than five core-genome SNPs [5]. However, Enterobase only contained four genome sequences of Colombian S. Typhimurium.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

Pulford

Díaz

et al. 2019

Preprint

View full text Add to dashboard Cite

Salmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar of Salmonella enterica, responsible for 32.5% of the Salmonella infections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology of Salmonella, but there has not yet been a WGS-based analysis of Salmonella associated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of Colombian S. Typhimurium and monophasic S. 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant of Salmonella in 2016, and resistance to nalidixic acid was associated with a plasmid-encoded qnrB19 gene. Our findings suggest multiple transfers of S. Typhimurium between Europe and Colombia.

show abstract

Section: Introductionmentioning

confidence: 99%

“…Since the 1990s, monophasic variants of S. Typhimurium, S. 4, [5],12:i:-(MVST) have arisen at high frequency across the world. MVST is a variant of S. Typhimurium that does not express the phase 2 H-antigen [6].…”

Section: Introductionmentioning

confidence: 99%

Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

Pulford

Díaz

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Upon the launch of the urgent inquiries from Scotland (18 January 2016) and the Netherlands (25 August 2016) in the Epidemic Intelligence Information System for Food-and Waterborne Diseases and Zoonoses (EPIS-FWD), an EU/EEA-level investigation into a multi-country outbreak of S. Enteritidis was initiated. For the EU outbreak case definition [1] whole genome sequencing (WGS)-based typing was used, applying the Public Health England's (PHE) single nucleotide polymorphism (SNP) calling pipeline PHEnix (https://github.com/phe-bioinformatics/PHEnix) and nomenclature implemented in PHE SnapperDB [2][3][4]. Two distinct SNP addresses at t5 level (≤5 SNP difference to at least one other case in the cluster, based on single linkage clustering) were selected to define an outbreakconfirmed case.…”

Section: Event Backgroundmentioning

confidence: 99%

Multi‐country outbreak of Salmonella Enteritidis infections linked to eggs, third update – 6 February 2020

2020

EFSA Supporting Publications

View full text Add to dashboard Cite

A multi‐country outbreak of Salmonella Enteritidis, delineated by whole genome sequencing (WGS), linked to eggs,has been ongoing in the EU/EEA for several years. From 1 February 2017 to 14 January 2020, 15 EU/EEA countries reported 656 confirmed cases and 202 probable cases. Before February 2017, 385 historical‐confirmed cases and 413 historical‐probable cases were identified, resulting in 18 affected countries. Due to differences in capacity for case confirmation, more countries are likely to be affected. This prolonged outbreak peaked during the summer months of 2016–2018. A notable decrease in the frequency of the cases reported to ECDC has been observed in 2019, which is a deviation from the three previous years. Epidemiological, microbiological and food tracing investigations have linked cases before 2018 to consumption of eggs originating from laying hen farms of a Polish consortium. A national investigation in 2018 in the UK identified epidemiological links between some cases and consumption of table eggs or egg products, with traceability possibly pointing to the Polish consortium. Despite the control measures implemented in 2016–2017, the farms of the Polish consortium were positive in 2018–2019 with outbreak strains, suggesting persistent contamination. Investigations focusing on the laying hen production and feed supply chains did not reveal any significant insights on the possible origin of the contamination. One of the outbreak strains was found in the period 2017‐2019 in primary production in Germany. In conclusion, the outbreak is still ongoing and since no evidence was provided that the source of contamination has been eliminated, it is expected that further infections will occur and that new cases will be reported in the coming months. Additional investigations are necessary to identify the source of contamination.

show abstract

“…Core genome positions that had a high-quality SNP (>90% consensus, minimum depth 10x, MQ >= 30) in at least one isolate were extracted and RaxML v8.2.8 [25] used to derive the maximum likelihood phylogeny of the isolates after first removing regions of the genome predicted to have undergone horizontal exchange using Gubbins v2.0.0 [26]. Hierarchical single linkage clustering was performed on the pairwise SNP difference between all isolates at various distance thresholds (Δ250, Δ100, Δ50, Δ25, Δ10, Δ5, Δ0) [27]. Genome-derived serotyping and AMR-conferring genes and SNPs was performed using the GeneFinder tool (https://github.com/phe-bioinformatics/gene_finder) [21,28].…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

Persistent transmission of shigellosis in England is associated with a recently emerged multi-drug resistant strain ofShigella sonnei

Jenkins

Bardsley

Mitchell

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Running title: Changing epidemiology of Shigella species in England SummaryShigella diagnoses in England are most prevalent amongst men who have sex with men. S. sonnei exhibiting resistance to both azithromycin and ciprofloxacin has replaced azithromycin-resistant S. flexneri as the most commonly isolated species in this setting. Abstract BackgroundWhole genome sequencing has enhanced surveillance and facilitated detailed monitoring of transmission of Shigella species in England. MethodsWe undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 to 2018 to explore recent strain characteristics and transmission dynamics of Shigella species. ResultsOf the 4950 confirmed cases of shigellosis identified during this period, the highest proportion of isolates were S. sonnei (54.4%), followed by S. flexneri (39.2%), S. boydii (4.1%) and S. dysenteriae (2.2%). Most cases were adults (82.9%) and male (59.5%), and 34.9% cases reported recent travel outside the UK. Throughout the study period diagnoses of S. flexneri and S. sonnei were most common in men with no history of recent travel abroad. Species prevalence was not static with cases of S. flexneri in men decreasing from 2015-2016, and the number of cases of S. sonnei increasing from 2017. Phylogenetic analysis showed this recent increase in S. sonnei was attributed to a novel clade exhibiting resistance to ciprofloxacin and azithromycin, which had emerged from a Central Asia sub-lineage. ConclusionsDespite changes in species prevalence, Shigella diagnoses in England are persistently the most common in adult males without reported travel history, consistent with sexual transmission amongst men who have sex with men. The trend in increasing ciprofloxacin resistance, in addition to plasmid-mediated azithromycin resistance, in S. sonnei is of significant public health concern with respect to transmission of multi-drug resistant gastrointestinal pathogens and the risk of treatment failures.

show abstract

SnapperDB: a database solution for routine sequencing analysis of bacterial isolates

Cited by 173 publications

References 13 publications

Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia

Multi‐country outbreak of Salmonella Enteritidis infections linked to eggs, third update – 6 February 2020

Persistent transmission of shigellosis in England is associated with a recently emerged multi-drug resistant strain ofShigella sonnei

Contact Info

Product

Resources

About