Scientific article
OA Policy
English

Genomic surveillance reveals long-term endemicity and outbreak potential of Klebsiella pneumoniae sequence type 48 in a German hospital and its global context

Published inMicrobial genomics, vol. 12, no. 7, 001707
Publication date2026-07
Abstract

Klebsiella pneumoniae sequence type 48 (Kp-ST48) is a globally distributed clone linked to antimicrobial resistance (AMR) yet lacks a comprehensive genomic analysis. Here, we investigated the persistence, transmission dynamics and global context of ST48 in a large tertiary hospital in Berlin, Germany. Between 2014 and 2022, 48 surveillance and 15 putative outbreak Kp-ST48 isolates were isolated in a tertiary care, multi-site hospital in Berlin, Germany. Genomic diversity was analysed by short- and long-read sequencing. Additionally, we included 223 publicly available Kp-ST48 genomes from five continents over 40 years (1982-2022) in the phylodynamic analysis. We identified two genetically distinct clades (A and B) within the global Kp-ST48 population. The global spread of Kp-ST48 was driven by clade B, which included all the genomes from the Berlin hospital. Two hospital-specific lineages (1 and 2) were identified with distinct population dynamics. Lineage 2 was transient and linked to a putative outbreak in 2019. Meanwhile, lineage 1 was first detected in 2014 and persisted for over 8 years until 2022, with multiple putative patient-to-patient and indirect transmission events identified. Carbapenem resistance determinants (ompK35/36 mutations, bla KPC , bla NDM , bla OXA-48 , bla VIM ) were present in 57% (n =163/286) of genomes, and up to three bla CTX-M-15 copies were found integrated into chromosomes. Although Kp-ST48 generally did not contain a high number of virulence genes, 19 genomes showed potential for AMR-hypervirulence convergence. This study reveals the endemic persistence with outbreak potentials of Kp-ST48 in a hospital over 8 years, characterized by high genome plasticity. Our results highlight the global distribution of this clone, which warrants continuous surveillance.

Keywords
  • Klebsiella pneumoniae
  • Antimicrobial resistance
  • International clone
  • Phylogenomics
  • Sequence type ST48
  • Klebsiella pneumoniae / genetics
  • Klebsiella pneumoniae / classification
  • Klebsiella pneumoniae / isolation & purification
  • Klebsiella pneumoniae / drug effects
  • Klebsiella pneumoniae / pathogenicity
  • Klebsiella Infections / epidemiology
  • Klebsiella Infections / microbiology
  • Germany / epidemiology
  • Disease Outbreaks
  • Humans
  • Genome, Bacterial
  • Phylogeny
  • Drug Resistance, Multiple, Bacterial / genetics
  • Beta-Lactamases / genetics
  • Anti-Bacterial Agents / pharmacology
  • Cross Infection / epidemiology
  • Cross Infection / microbiology
  • Genomics
Funding
  • European Commission - Resistance in Gram-Negative Organisms: Studying Intervention Strategies [282512]
Citation (ISO format)
NGUYEN, Ngoc Minh et al. Genomic surveillance reveals long-term endemicity and outbreak potential of Klebsiella pneumoniae sequence type 48 in a German hospital and its global context. In: Microbial genomics, 2026, vol. 12, n° 7, p. 001707. doi: 10.1099/mgen.0.001707
Main files (1)
Article (Published version)
Identifiers
Journal ISSN2057-5858
1views
0downloads

Technical informations

Creation26/08/2026 06:34:43
First validation07/09/2026 14:43:23
Update07/09/2026 14:43:23
Status update07/09/2026 14:43:23
Last indexation07/09/2026 14:43:24
All rights reserved by Archive ouverte UNIGE and the University of GenevaunigeBlack