Evolutionary genomics of KPC-2-producing Serratia marcescens and characterization of a novel bla_KPC-2-harboring...

Serratia marcescens is a common opportunistic pathogen in hospitals. Its carbapenem-resistant strains, especially those carrying the bla_KPC-2 gene, pose a serious challenge to clinical infection treatment.

In this study, we identified 14 strains that were positive for bla_KPC-2 from tertiary hospitals in Zhejiang Province, China, through phenotypic tests and sequencing. We also incorporated data from the GenBank public database, resulting in a total of 2005 Serratia strains included for bioinformatic analysis.

A total of 121 strains (6.03%) were found to carry bla_KPC-2. These positive isolates predominantly originated from China (76.86%) and the United States (14.88%), with the vast majority (94.21%) identified as clinical isolates. The period from 2018 to 2019 was relatively active for global data collection, particularly for samples from the Yangtze River Delta region in China. Phylogenetic analysis classified the 121 strains carrying bla_KPC-2 into six evolutionary clusters (Cluster I-VI), with most strains grouped in Cluster V and Cluster VI. Cluster VI, largely consisting of ST595, was predominantly composed of Chinese isolates. In contrast, Cluster V displayed coexistence of diverse sequence types and geographic origins. Resistance gene profiling identified 52 antimicrobial resistance genes. Besides bla_KPC-2, three strains were also positive for bla_NDM-1. Additionally, a novel plasmid lineage was identified and designated as pK17-KPC/pK1030-KPC (approximately 87 kb). Its replication initiator gene, repA1, showed low homology (≤ 93.25%) to known plasmids. This plasmid has a complex structure and carries a bla_KPC-2 resistance module mediated by unit transposon ΔTn6296.

This study systematically describes the global transmission patterns and molecular genetic features of Serratia marcescens strains carrying bla_KPC-2. It reveals the structural characteristics of a novel plasmid harboring bla_KPC-2 and provides key scientific evidence for clinical prevention and control of antimicrobial resistance.