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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

ABSTRACT: Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencingCulture and Nanopore

PROVIDER: PRJEB60525 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR11001110.fastq.gz	Fastqsanger.gz
	ERR11001111.fastq.gz	Fastqsanger.gz
	ERR11001112.fastq.gz	Fastqsanger.gz
	ERR11001113.fastq.gz	Fastqsanger.gz

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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.

Project description:Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.

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