# Genomic Characterization of Carbapenem-Resistant Klebsiella pneumoniae ST1440 and Serratia marcescens Isolates from a COVID-19 ICU Outbreak in Ecuador

## TL;DR

This study analyzes carbapenem-resistant bacteria from a hospital in Ecuador, revealing plasmid-mediated resistance genes that suggest strong co-selection during the pandemic.

## Contribution

The study provides novel genomic insights into carbapenem-resistant Klebsiella pneumoniae and Serratia marcescens isolates from Ecuador, highlighting plasmid-mediated resistance and co-selection.

## Key findings

- Nineteen plasmids carrying 70 resistance-related genes were identified in carbapenem-resistant isolates.
- Six distinct gene clusters showed co-localization of antimicrobial and disinfectant resistance genes.
- Conjugative plasmids with high-risk elements like blaKPC-2 were found in multiple isolates, indicating interspecies spread.

## Abstract

The global rise of antimicrobial resistance (AMR), exacerbated by the COVID-19 pandemic, has led to a surge in infections caused by multidrug-resistant (MDR) bacteria. A key driver of this phenomenon is co-selection, where exposure to one antimicrobial promotes resistance to others via horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs). Carbapenem-resistant Enterobacteriaceae, known for their genomic plasticity, are particularly worrisome; yet genomic data from Latin America—especially Ecuador—remain scarce. This study investigated four carbapenem-resistant clinical isolates (two Klebsiella pneumoniae ST1440 and two Serratia marcescens) from tracheal aspirates of three ICU patients during a COVID-19 outbreak at Hospital IESS Quito Sur, Ecuador. Phenotypic profiling and whole-genome sequencing were performed, followed by bioinformatic reconstruction of plasmid content. Nineteen plasmids were identified, carrying 70 resistance-related genes, including antimicrobial resistance genes (ARGs), metal resistance genes (MRGs), integrons, transposons, and insertion sequences. Hierarchical clustering revealed six distinct gene clusters, with several co-localizing ARGs and genes for resistance to disinfectants and heavy metals—suggesting strong co-selective pressure. Conjugative plasmids harboring high-risk elements such as blaKPC-2, qacE, and Tn4401 were found in multiple isolates, indicating potential interspecies dissemination. These findings emphasize the importance of plasmid-mediated resistance during the pandemic and highlight the urgent need to enhance genomic surveillance and infection control, particularly in resource-limited healthcare settings.