NDM-1 plasmid clustering reflects clonal transmission of Klebsiella pneumoniae ST147 in four hospitals in Berlin, Germany.

Abstract

Background: In recent years, the detection of Klebsiella pneumoniae (KLPN) producing New Delhi metallo-β-lactamase (NDM), particularly NDM-1, has increased in Germany. Plasmids play a crucial role in the dissemination of NDM-1, facilitating its persistence in both clinical and environmental reservoirs. Between 2021 and 2024, a substantial number of NDM-1-producing KLPN isolates were detected across multiple hospital sites in Berlin. This study aimed to investigate a potential multi-site outbreak involving NDM-1-producing KLPN, and to assess the role of clonal versus plasmid-mediated dissemination.

Methods: We performed short-read sequencing for all isolates, complemented by long-read sequencing for a subset (Illumina and Oxford Nanopore Technologies). Core genome multi locus sequence typing (cgMLST) was conducted using SeqSphere+. NDM-1 plasmids were characterized with the MOB-suite tools. Reference plasmids were reconstructed from hybrid assemblies using TaDReP. Short-read sequences from all isolates were aligned against these reference plasmids to assess genetic relatedness.

Results: Analysis of 57 NDM-1 plasmid carrying KLPN isolates at the clonal level revealed three distinct outbreak clusters (O1-O3). These corresponded to three unique NDM-1 reference plasmids: p1 (54.0 kb IncFIB(pQil)), p2 (54.3 kb IncR), and p3 (355.5 kb; no Inc type specified). Plasmid clustering from short-reads was consistent with the clonal clusters.

Conclusions: Both plasmid-level analysis and cgMLST yielded congruent results, effectively ruling out the possibility of multi-site, plasmid-mediated NDM-1 transmission. The detection of a globally disseminated NDM-1 plasmid within one of the clonal clusters highlights its potential role in the spread of resistance during the recent surge of NDM-1 carrying KLPN isolates in Germany.