Dynamics of clinical Klebsiella pneumoniae strains over the COVID-19 pandemic in Qingdao, China

The dynamics of multidrug-resistant pathogens in response to large-scale societal and environmental disruptions remain poorly understood. Here, we investigated 528 Klebsiella pneumoniae clinical isolates collected from a tertiary hospital in Qingdao, China, spanning 2016 to 2023, with a primary focus on 2018–2023, across pre-, during-, and post-COVID-19 pandemic periods. All isolates underwent whole-genome sequencing. We identified SL258 and SL23 as dominant sequence lineages, with prevalent serotypes including K1 and O1. A wide range of resistance and virulence determinants were detected, particularly ybt genes, which showed strong lineage-specific associations. The COVID-19 pandemic coincided with a transient expansion of SL258 and an overall increase in antimicrobial resistance levels, followed by post-pandemic diversification of resistant clones. The structural complexity of the K. pneumoniae population decreased during the pandemic but rose significantly afterward, with the emergence and expansion of multiple previously rare multidrug-resistant (MDR) lineages. A serotype shift within SL258, from K25/O5 to K64/O2a, was also observed. These findings highlight the selective pressures exerted by hospital-based infection control strategies and antimicrobial usage patterns during the pandemic, which may have shaped the persistence and replacement of dominant MDR clones. Our study underscores the importance of genomic surveillance in tracking resistance evolution and pathogen adaptation in clinical environments under crisis conditions.