ICU environment as a reservoir of KPC-ST307-Klebsiella pneumoniae high-risk clone resistant to ceftazidime-avibactam

TL;DR

The ICU environment was found to be a source of antibiotic-resistant Klebsiella pneumoniae, which spread among patients and sinks during the pandemic.

Contribution

The study identifies the ICU environment as a reservoir for a high-risk antibiotic-resistant Klebsiella pneumoniae clone.

Findings

Ten patients and two ICU sinks were found to be colonized with ceftazidime-avibactam-resistant KPC-ST307-Klebsiella pneumoniae.

The same resistant clone was found in both patients and sinks, suggesting environmental transmission.

The resistant bacteria showed reduced susceptibility to multiple last-line antibiotics.

Abstract

We characterized all ceftazidime-avibactam-resistant KPC-producing K. pneumoniae (KPC-Kp) isolates recovered from both patients and environmental samples at the ICU of our hospital in 2020, during the COVID-19 pandemic initiation. Antimicrobial susceptibility testing (Sensititre-EUMDROXF; disk-diffusion) and WGS analysis (Illumina-Novaseq/Miseq; Oxford Nanopore®-MinION) were performed. Ten patients (16% of ICU patients) were colonized/infected by a ceftazidime-avibactam-resistant KPC-Kp isolate (March-December), six of them during/after treatment with ceftazidime-avibactam. Two ceftazidime-avibactam-resistant KPC-Kp were also recovered from two ICU sinks (July-September). All isolates belonged to ST307 clone and had identical resistance gene content. Six KPC-variants were detected in patient isolates (KPC-62, KPC-92, KPC-150, KPC-66, KPC-53, KPC-46). KPC-92 and KPC-66 variants were also detected in sink isolates. Regardless of the origin (patients or sinks), KPC-92-, KPC-150 and KPC-62-Kp isolates combining altered porin proteins also exhibited increased/resistant MIC values to cefiderocol, cefepime-taniborbactam, aztreonam-avibactam, meropenem-vaborbactam and/or imipenem-relebactam. A cgMLST analysis demonstrated the clonal spread of KPC-ST307-Kp within the ICU, between patients and the hospital environment. Clustering was observed mainly by KPC variants (KPC-92, KPC-62). A variant calling analysis and plasmid characterization showed possible transmission between patients and sinks. Our results suggest that the patient care environment likely contributed to persistence and spread of last-line antibiotics-resistant KPC-Kp within the ICU during the COVID-19 pandemic.

The online version contains supplementary material available at 10.1038/s41598-025-14987-w.

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