# Genomic Characterization of NDM-1 Harboring Extensively-Drug Resistance Klebsiella pneumoniae Isolate From ICU-Admitted Patient With COVID-19

## TL;DR

This study reports a drug-resistant Klebsiella pneumoniae strain from a hospitalized COVID-19 patient, highlighting its genomic features and resistance profile.

## Contribution

The paper provides a genomic characterization of an NDM-1-producing XDR K. pneumoniae isolate from an ICU-admitted COVID-19 patient.

## Key findings

- The isolate CRKP-51 was identified as extensively drug-resistant, with resistance to all antibiotics except tigecycline.
- The strain belonged to sequence type 15 (ST15) and carried multiple resistance genes on the IncHI1B plasmid.
- High resistance was observed against sulfamethoxazole-trimethoprim, nitrofurantoin, and piperacillin-tazobactam.

## Abstract

Currently, carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains, particularly those producing New Delhi metallo-beta-lactamase (NDM), are increasingly recognized as a significant threat to global health. The present study aimed to conduct a genomic analysis of an NDM-1-producing CR-KP strain isolated from patients with coronavirus disease of 2019 (COVID-19) admitted to the intensive care unit (ICU). The K. pneumoniae isolate was obtained from the bronchoalveolar lavage fluid of a 68 year-old male patient hospitalized in the ICU with COVID-19 at Besat Hospital in Sanandaj, Iran. The minimum inhibitory concentrations (MICs) for 15 antibiotics were determined using the VITEK 2 system. Genomic analysis of the isolate was performed using whole genome sequencing. The CRKP-51 strain was identified as an extensively drug-resistant (XDR) strain, exhibiting resistance to all tested antibiotics except tigecycline (MIC = 2 μg/mL). The highest resistance values were recorded against sulfamethoxazole-trimethoprim (SXT), nitrofurantoin (NIT), and piperacillin-tazobactam (TZP), with MICs of ≥ 320, 256 μg/mL, and ≥ 128 μg/mL, respectively. Multilocus sequence typing revealed that CRKP-51 belonged to sequence type 15 (ST15). The IncHI1B replicon type associated with this strain harbored several resistance genes, including blaNDM−1, armA, msrE, mphE, BRP (MBL), blaOXA−1, aadA2, dfrA12, qnrB1, blaCTX−M−15, and cat1. High-risk K. pneumoniae clones, such as ST15, are increasingly associated with antimicrobial resistance and the emergence of XDR strains in ICUs. Additionally, the global dissemination of the NDM enzyme occurs through various plasmid replicon types. Therefore, monitoring local epidemiology is essential for the effectiveness of antimicrobial stewardship programs.