Dataset Information

Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences.

ABSTRACT: Carbapenem-resistant bacteria have quickly become a worldwide concern in nosocomial infections. Of the seven known carbapenemases, four have been shown to be particularly problematic: KPC, NDM, IMP, and VIM. To date, many local and species- or carbapenemase-specific epidemiological studies have been performed, which often focus on the organism itself. This report attempts to perform an inclusive (encompass both species and carbapenemase) epidemiologic study using publicly available plasmid sequences from NCBI. In this report, the gene content of these various plasmids has been characterized, replicon types of the plasmids identified, and the global spread and species promiscuity of the plasmids analyzed. Additionally, support to several groups targeting plasmid maintenance and transfer mechanisms to slow the spread of resistance plasmids is given.

SUBMITTER: Card GE

PROVIDER: S-EPMC9221968 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences.

Card Galen E GE Pickett Brandon D BD Ridge Perry G PG Robison Richard A RA

Genome 20190906 12

Carbapenem-resistant bacteria have quickly become a worldwide concern in nosocomial infections. Of the seven known carbapenemases, four have been shown to be particularly problematic: KPC, NDM, IMP, and VIM. To date, many local and species- or carbapenemase-specific epidemiological studies have been performed, which often focus on the organism itself. This report attempts to perform an inclusive (encompass both species and carbapenemase) epidemiologic study using publicly available plasmid seque ...[more]

PMID: 31491336

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Project description:Background: Antibiotics are often prescribed empirically to treat infection syndromes before causative bacteria and their susceptibility to antibiotics are identified. Guidelines on empiric antibiotic prescribing are key to effective treatment of infection syndromes, and need to be informed by likely bacterial aetiology and antibiotic resistance patterns. We aimed to create a clinically-relevant composite index of antibiotic resistance for common infection syndromes to inform recommendations at the national level. Methods: To create our index, we used open-access antimicrobial resistance (AMR) surveillance datasets, including the ECDC Surveillance Atlas, CDDEP ResistanceMap, WHO GLASS and the newly-available Pfizer ATLAS dataset. We integrated these with data on aetiology of common infection syndromes, existing empiric prescribing guidelines, and pricing and availability of antibiotics. Results: The ATLAS dataset covered many more bacterial species (287) and antibiotics (52) than other datasets (ranges = 8-11 and 16-32 respectively), but had a similar number of samples per country per year. Using these data, we were able to make empiric prescribing recommendations for bloodstream infection, pneumonia and cellulitis/skin abscess in up to 44 countries. There was insufficient data to make national-level recommendations for the other six syndromes investigated. Results are presented in an interactive web app, where users can visualise underlying resistance proportions to first-line empiric antibiotics for infection syndromes and countries of interest. Conclusions: We found that whilst the creation of a composite resistance index for empiric antibiotic therapy was technically feasible, the ATLAS dataset in its current form can only inform on a limited number of infection syndromes. Other open-access AMR surveillance datasets are largely limited to bloodstream infection specimens and cannot directly inform treatment of other syndromes. With improving availability of international AMR data and better understanding of infection aetiology, this approach may prove useful for informing empiric prescribing decisions in settings with limited local AMR surveillance data.

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Dataset Information

Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences.

Publications

Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences.

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