WGS Results

The scientific evaluation demonstrated that WGS provided information that could not be obtained with the same discriminatory resolution through conventional microbiological testing alone. During the period from September 2025 to the reporting period, 2500 CPE isolates were detected and characterised by WGS.

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The distribution of the principal organisms was: K.pneumoniae 67% , E. coli  21% and other Enterobacterales 12%.  

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​​The predominance of K. pneumoniae within the dataset is particularly relevant to national AMR surveillance, given its recognised role as an important reservoir and disseminator of carbapenem resistance.

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Genomic analysis identified clinically and epidemiologically relevant high-risk lineages, including K. pneumoniae ST147 and ST307.  In the case of E. coli, MLST, the predominant sequence type was ST127 followed by ST167.

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The WGS workflow also identified ST23 K. pneumoniae isolates carrying both antimicrobial resistance and virulence-associated determinants. Such findings demonstrate the added value of genomic surveillance in identifying organisms with potentially important combinations of resistance and virulence characteristics.

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The genomic analysis further demonstrated the importance of carbapenemase-mediated resistance, including OXA-48-like carbapenemases among the characterised K. pneumoniae and E. coli isolates.

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The project therefore generated a national genomic dataset capable of supporting surveillance of both the distribution of resistance mechanisms and the genetic backgrounds in which these mechanisms occur.

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Carbapenemases are most often located on genetic elements such as plasmids, which are mobile and can be easily shared among Enterobacteriaceae. Plasmids harbouring carbapenemase genes were identified in 97 % of K. pneumoniae isolates and 98% of E.coli isolates.