Dataset Information

Whole genome based characterization of ESBL producing Salmonella enterica in Germany, 2017-19

ABSTRACT: Whole genome based characterization of clinical Salmonella enterica producing extended-spectrum beta-lactamses (ESBLs) in Germany, 2017-19

PROVIDER: PRJEB41165 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4832790_1.fastq.gz	Fastqsanger.gz
	ERR4832790_2.fastq.gz	Fastqsanger.gz
	ERR4832800_1.fastq.gz	Fastqsanger.gz
	ERR4832800_2.fastq.gz	Fastqsanger.gz
	ERR4832810_1.fastq.gz	Fastqsanger.gz

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Project description:Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.

Dataset Information

Whole genome based characterization of ESBL producing Salmonella enterica in Germany, 2017-19

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