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Background <p><i>Klebsiella pneumoniae</i> is a major opportunistic pathogen and a recognized contributor to the global burden of antimicrobial resistance (AMR). Although traditionally associated with healthcare settings, it is increasingly detected in environmental compartments influenced by anthropogenic activities. Aquatic ecosystems may act as reservoirs and dissemination hubs for multidrug-resistant (MDR) lineages and resistance genes. However, genomic data on environmental <i>K. pneumoniae</i> in Morocco remain scarce. This pilot study aimed to characterize a targeted subset of MDR <i>K</i>. <i>pneumoniae</i> isolates recovered from Moroccan rivers using whole-genome sequencing (WGS), with a focus on resistance determinants, virulence-associated loci, plasmid content, and phylogenetic relationships.</p> Results <p>The main findings revealed marked genetic heterogeneity among the environmental <i>K. pneumoniae</i> isolates. Of the 44 isolates recovered from six Moroccan rivers, 11 MDR isolates were selected for WGS and belonged to nine distinct sequence types, including the high-risk clones ST147 and ST307. Resistance to extended-spectrum β-lactams was mainly associated with ESBL genes, particularly <i>bla</i><sub>CTX−M−15</sub>, whereas carbapenem resistance was linked to <i>bla</i><sub>OXA−48</sub> and <i>bla</i><sub>NDM−14</sub> in a subset of isolates. The genomes also carried multiple determinants associated with resistance to other major antimicrobial classes. In addition, the isolates showed diverse plasmid backgrounds, heterogeneous virulence-associated loci, and substantial capsular diversity. Phylogenetic and pangenome analyses further indicated high intraspecific variability and extensive genome plasticity across the collection.</p> Conclusions <p>This pilot study provides the first whole-genome-based characterization of river-derived MDR <i>K. pneumoniae</i> in Morocco. It demonstrates that aquatic ecosystems harbor genetically diverse lineages carrying clinically relevant resistance and virulence determinants. These findings underscore the imperative of integrating environmental surveillance into national AMR monitoring strategies within a One Health framework.</p>

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Whole-genome sequencing of MDR K. pneumoniae circulating in Moroccan river ecosystems: a comprehensive genomic analysis of environmental isolates

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月1日

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  • Amine Aiddi ,
  • Ilham Zerdani ,
  • Aboubakr Khazaz ,
  • Hafsa Mguild ,
  • Adil El Hamouchi,
  • Kaotar Nayme

摘要

Background

Klebsiella pneumoniae is a major opportunistic pathogen and a recognized contributor to the global burden of antimicrobial resistance (AMR). Although traditionally associated with healthcare settings, it is increasingly detected in environmental compartments influenced by anthropogenic activities. Aquatic ecosystems may act as reservoirs and dissemination hubs for multidrug-resistant (MDR) lineages and resistance genes. However, genomic data on environmental K. pneumoniae in Morocco remain scarce. This pilot study aimed to characterize a targeted subset of MDR K. pneumoniae isolates recovered from Moroccan rivers using whole-genome sequencing (WGS), with a focus on resistance determinants, virulence-associated loci, plasmid content, and phylogenetic relationships.

Results

The main findings revealed marked genetic heterogeneity among the environmental K. pneumoniae isolates. Of the 44 isolates recovered from six Moroccan rivers, 11 MDR isolates were selected for WGS and belonged to nine distinct sequence types, including the high-risk clones ST147 and ST307. Resistance to extended-spectrum β-lactams was mainly associated with ESBL genes, particularly blaCTX−M−15, whereas carbapenem resistance was linked to blaOXA−48 and blaNDM−14 in a subset of isolates. The genomes also carried multiple determinants associated with resistance to other major antimicrobial classes. In addition, the isolates showed diverse plasmid backgrounds, heterogeneous virulence-associated loci, and substantial capsular diversity. Phylogenetic and pangenome analyses further indicated high intraspecific variability and extensive genome plasticity across the collection.

Conclusions

This pilot study provides the first whole-genome-based characterization of river-derived MDR K. pneumoniae in Morocco. It demonstrates that aquatic ecosystems harbor genetically diverse lineages carrying clinically relevant resistance and virulence determinants. These findings underscore the imperative of integrating environmental surveillance into national AMR monitoring strategies within a One Health framework.