Dataset Information

Core genome multi locus sequence typing (cgMLST) of Clostridioides difficile to investigate nosocomial transmission

ABSTRACT: Clostridioides difficile cgMLST to investigate nosocomial transmission

PROVIDER: PRJEB56399 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	ERR10483900_1.fastq.gz	Fastqsanger.gz
	ERR10483900_2.fastq.gz	Fastqsanger.gz
	ERR10483901_1.fastq.gz	Fastqsanger.gz
	ERR10483901_2.fastq.gz	Fastqsanger.gz
	ERR10483902_1.fastq.gz	Fastqsanger.gz

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Project description:Background: Healthcare-associated infections represent a major threat to patient, staff and visitor safety. Identification of episodes that are likely to have resulted from nosocomial transmission has important implications for infection control. Routinely collected data on ward admissions and sample dates, combined with pathogen genomic information could provide useful insights. We describe a novel, open-source, application for visualising these data, and demonstrate its utility for investigating nosocomial transmission using a case study of a large outbreak of norovirus infection. Methods: We developed the application using Shiny, a web application framework for R. For the norovirus case study, cases were defined as patients who had a faecal sample collected at the hospital in a winter season that tested positive for norovirus. Patient demographics and ward admission dates were extracted from hospital systems. Detected norovirus strains were genotyped and further characterised through sequencing of the hypervariable P2 domain. The most commonly detected sub-strain was visualised using the interactive application. Results: There were 156 norovirus-positive specimens collected from 107 patients. The most commonly detected sub-strain affected 30 patients in five wards. We used the interactive application to produce three visualisations: a bar chart, a timeline, and a schematic ward plan highlighting plausible transmission links. Visualisations showed credible links between cases on the elderly care ward. Conclusions: Use of the interactive application provided insights into transmission in this large nosocomial outbreak of norovirus, highlighting where infection control practices worked well or could be improved. This is a flexible tool that could be used for investigation of any infection in any hospital by interactively changing parameters. Challenges include integration with hospital systems for extracting data. Prospective use of this application could inform better infection control in real time.

Dataset Information

Core genome multi locus sequence typing (cgMLST) of Clostridioides difficile to investigate nosocomial transmission

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