Molecular Characterization of Presumptive Klebsiella pneumoniae Isolates from Companion and Farm Animals in Germany Reveals Novel Sequence Types

TL;DR

This study identifies new genetic types of Klebsiella pneumoniae in animal isolates from Germany, highlighting their diversity and potential zoonotic risks.

Contribution

The study reports the discovery of novel sequence types of Klebsiella pneumoniae using whole-genome sequencing and MLST.

Findings

59 out of 64 isolates were identified as Klebsiella pneumoniae, with five classified as Klebsiella quasipneumoniae.

Eleven isolates contained novel alleles, leading to the designation of ST7681-ST7689 and ST7697-ST7698.

Most isolates had unique sequence types, indicating high genetic diversity among animal-derived K. pneumoniae strains.

Abstract

Klebsiella (K.) pneumoniae is a One Health pathogen that has been isolated from humans, animals, and environmental sources and is responsible for a diverse range of potentially life-threatening infections. In the present study, we analyzed the genomes of 64 presumptive K. pneumoniae strains isolated in 2023 from different companion and farm animals in Germany. Using whole-genome sequencing (WGS) data, 59 isolates (92.2%) were identified as K. pneumoniae and five (7.8%) as K. quasipneumoniae. Multilocus sequence typing (MLST) assigned 53 isolates to 46 distinct sequence types (STs). Eleven isolates could not be assigned to existing STs of the Pasteur classification scheme because they contained novel alleles not previously documented. Thus, these were considered novel and designated as ST7681-ST7689 and ST7697-ST7698. Almost all isolates in this study were assigned unique STs, and only five STs were shared among multiple isolates. This research highlights the genetic diversity among K. pneumoniae strains isolated from different companion and farm animals in Germany, provides information to help in surveillance strategies to mitigate zoonotic transmission risks, and demonstrates the value of WGS and MLST in identifying novel STs of K. pneumoniae.

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