Dataset Information

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

ABSTRACT:

Background

Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration.

Results

GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings.

Conclusions

GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .

SUBMITTER: Permana B

PROVIDER: S-EPMC10199467 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Publications

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

Permana Budi B Beatson Scott A SA Forde Brian M BM

BMC bioinformatics 20230519 1

<h4>Background</h4>Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration.<h4>Results</h4>GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related o ...[more]

PMID: 37208588

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Project description:BackgroundNoroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission.Here, we present a combined molecular and statistical method for assessing:1) whether observed clusters provide evidence of local transmission and2) the probability that anecdotally|linked outbreaks truly shared a transmission event.Methods76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1) and capsid (ORF 2) regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns.ResultsTwo out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population.ConclusionThe evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while others were refuted. The combined molecular/epidemiologic approach presented here could be applied to other viral populations and potentially to other pathogens for a more thorough view of transmission.

Dataset Information

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

Background

Results

Conclusions

Publications

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

Similar Datasets

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