Project deliverable Open Access

Deliverables of Codes4strains project (Part2)

Hennart Melanie; Brisse Sylvain

Background

One of the main objectives of the PhD project is to develop a novel nomenclature system, potentially applicable to all bacterial pathogens. Here we first focus is on a highly antibiotic resistant bacterial pathogen, K. pneumoniae (Kp), and on a foodborne bacterial pathogen, Escherichia coli (Ec). The aim is to combine two main microbial strain nomenclatures approaches that are currently being used separately.

(further details: https://onehealthejp.eu/codes4strains/)

Deliverables

D-PhD16-3.2: cgLINcodes algorithm defined and implemented on full dataset

D-PhD16-4.2: Preprint publication on the cgLIN codes concept and comparison with multi-level single-linkage classifications

D-PhD16-4.3: A novel tool to define the population structure of species, called MSTclust

D-PhD16-4.4: An inheritance algorithm to provide backwards compatibility of MLSL groups with 7-gene MLST identifiers

D-PhD16-4.5: Comparison of the ANI metric with the cgMLST metric

D-PhD16-4.6: A novel method to identify recombination in cgMLST profiles

D-PhD16-4.7: Integration of MLSL identifiers into the BIGSdb platform to make them publicly available

 

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  • https://doi.org/10.1101/2021.07.26.453808

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Publication date:
August 27, 2021
DOI:
10.5281/zenodo.5284876

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10.5281/zenodo.5284876

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Keyword(s):
Klebsiella pneumoniae genomic classification strain nomenclature
Grants:
European Commission:
  • One Health EJP - Promoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards. (773830)
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License (for files):
Creative Commons Attribution 4.0 International

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