bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.09.05.556311

International and regional spread of carbapenem-resistant Klebsiella pneumoniae in Europe

Budia Silva, M.·Kostyanev, T.·Ayala Montano, S.·Bravo-Ferrer Acosta, J. M.·Garcia-Castillo, M.·Canton, R.·Goossens, H.·Rodriguez-Bano, J.·Grundmann, H.·Reuter, S.·EURECA/WP1B Group,
View original source ↗Export metadata ↓

Abstract

Klebsiella pneumoniae, an opportunistic pathogen able to cause hospital- and community-acquired infections, is of particular concern due to the active spread of antibiotic resistance genes associated with mobile genetic elements such as plasmids and transposons. Carbapenem-resistant K. pneumoniae (CRKP) exhibit a higher mortality rate than carbapenem-susceptible K. pneumoniae infections. In this COMBACTE-EURECA study, we present genomic data of 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018) and compared these with the previous EuSCAPE collection (2013-2014). All isolates were resistant (EUCAST criteria) to at least one carbapenem antibiotic. We identified 11 clonal complexes (CCs), with most isolates belonging to the high-risk clones CC258, CC101, CC11, and CC307. blaKPC-like was the most prevalent carbapenemase-encoding gene (45%), along with the dominance of the CC258 lineage. Equally, blaOXA-48 had a wide-ranging spread (39%), and blaNDM was present in half of the ST11 isolates representing a particular lineage circulating in Greece. Two carbapenemase genes were found in 38 isolates (5.5%). Through the combination of both EURECA and EuSCAPE collections, we elucidated the evolution of K. pneumoniae high-risk clones circulating in Europe. Dominating clones and their associated carbapenemase genes exhibit relevant regional differences, namely CC258 in Greece, Italy, and Spain, CC101 present in Serbia and Romania and CC14 in Turkiye. Due to the wide expansion of CRKP, genomic surveillance across Europe with projects such as EURECA provides crucial insights for risk mapping at geo-temporal scales and informs necessary adaptions to the local settings for implementation of control strategies.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Budia Silva, M., Kostyanev, T., Ayala Montano, S., Bravo-Ferrer Acosta, J. M., Garcia-Castillo, M., Canton, R., Goossens, H., Rodriguez-Bano, J., Grundmann, H., Reuter, S., EURECA/WP1B Group,. 2023-09-05. International and regional spread of carbapenem-resistant Klebsiella pneumoniae in Europe. https://doi.org/10.1101/2023.09.05.556311

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

Beta-lactam enhancement against methicillin-resistant Staphylococcus aureus by cell wall blockade is autolysis-dependent: a butyrolactone derivative as case in point

Methicillin-resistant Staphylococcus aureus (MRSA) is non-susceptible to beta-lactams. Blockade of cell wall biosynthesis is a potential target for beta-lactam enhancement but requires further investigation. A butyrolactone derivative enhanced beta-lactams against MRSA strains by reducing the availability of D-Ala-D-Ala. Unlike D-cycloserine, it did not inhibit D-Ala-D-Ala ligase (Ddl). Nor did it show an additive or synergistic effect when combined with cycloserine, indicating a unique mechanism for blocking cell wall precursor production that does not involve the traditional Lipid II pathway. Notably, beta-lactam potentiation by our chemical or D-cycloserine was highly dependent on the intrinsic autolytic ability of the tested MRSA strains. Strains that resisted lysis upon Triton X-100 exposure showed a minimal increase in beta-lactam susceptibility, whereas highly autolytic strains showed significant changes in their beta-lactam MICs. We have thus identified autolytic ability as the Achilles Heel in the strategy of targeting cell wall biosynthesis for beta-lactam potentiation.

microbiology↗
bioRxiv2026

Rapid and largely reversible shifts in the canine fecal metabolome during dietary change

Diet can rapidly change the fecal metabolome, but less is known about recovery after the original diet is restored. We used untargeted UPLC-MS metabolomics to analyze 72 fecal samples from nine Pumi dogs during an owner-managed switch from dry food to raw food and back to dry food. Diet phase accounted for a large proportion of variation in both ionization modes. More than 13,000 LC-MS features changed at the first sampling point after the switch to raw food, with a similarly large response after return to dry food. Among features significant in both comparisons, more than 99% changed in opposite directions. At the final sampling point, no positive-mode (ESI+) features and only 13 negative-mode (ESI-) features differed from the second dry-food baseline under the same threshold. BARF-associated patterns persisted in analyses excluding individual dogs and in pedigree-adjusted candidate models, although individual feature effects depended on normalization. Putative metabolites from several biochemical classes differed in their response and recovery. The fecal metabolome therefore changed rapidly and returned largely toward baseline, with differences among dogs.

microbiology↗