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Background <p>The global rise of multidrug-resistant Enterobacterales, particularly extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i>, poses a critical threat to intensive care unit (ICU) patients. Despite the clinical importance of these pathogens in sub-Saharan Africa, studies on their molecular characterization remains scarce.</p> Methods <p>We performed antibiotic susceptibility testing and whole-genome sequencing (WGS) on 22 multidrug-resistant isolates (<i>15 E. coli</i> and 7 <i>K. pneumoniae</i>) recovered from ICU patients at Kenya’s public referral hospital between January and June 2021. Isolates were obtained from blood, tracheal aspirates, urine, and pus swabs. We characterized antimicrobial resistance genes, virulence determinants, plasmid replicons, and genetic lineages, and assessed phenotype-genotype concordance.</p> Results <p>All isolates exhibited resistance to third-generation cephalosporins, with resistance rates exceeding 80% for at least 10 antibiotics. The ESBL gene <i>bla</i><sub>CTX−M−15</sub> was detected in 93% of <i>E. coli</i> and 100% of <i>K. pneumoniae</i> isolates. The concordance between phenotypic resistance and genotypic determinants was highest for β-lactams and lowest for aminoglycosides, trimethoprim-sulfamethoxazole and carbapenems. MLST revealed considerable genetic diversity among <i>E. coli</i>, including high-risk clones STc131 and ST648. Virulence genes (e.g., <i>fimH</i>, <i>chuA</i>, <i>fyuA</i>) were more prevalent in <i>E. coli</i>, particularly among isolates from urine and tracheal aspirate samples. Plasmid profiling revealed greater replicon diversity in <i>E. coli</i>, with frequent detection of IncFII and IncFIB plasmids, suggesting a stronger capacity for horizontal gene transfer.</p> Conclusion <p>These findings underscore the complexity of multidrug-resistant pathogen dynamics in ICU environments. They emphasize the need for species-specific surveillance, rapid diagnostics, and context-informed stewardship strategies to guide infection control and therapeutic interventions. While limited in scale, this study adds to the genomic landscape of multidrug-resistant pathogens in African ICUs and highlights critical targets for infection control and therapeutic interventions.</p>

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Phenotypic and genomic profiling of multidrug-resistant Escherichia coli and Klebsiella pneumoniae isolated from Intensive Care Unit patients in Kenya

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月23日

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  • Beatrice Oduor,
  • Anne Maina,
  • Job Mwale,
  • Brian Ogoti,
  • Leon Otieno,
  • Moureen Jepleting,
  • Charchil Ayodo,
  • Robert Mugoh,
  • Teresa Ita,
  • Josiah Kuja,
  • Sylvia Omulo

摘要

Background

The global rise of multidrug-resistant Enterobacterales, particularly extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae, poses a critical threat to intensive care unit (ICU) patients. Despite the clinical importance of these pathogens in sub-Saharan Africa, studies on their molecular characterization remains scarce.

Methods

We performed antibiotic susceptibility testing and whole-genome sequencing (WGS) on 22 multidrug-resistant isolates (15 E. coli and 7 K. pneumoniae) recovered from ICU patients at Kenya’s public referral hospital between January and June 2021. Isolates were obtained from blood, tracheal aspirates, urine, and pus swabs. We characterized antimicrobial resistance genes, virulence determinants, plasmid replicons, and genetic lineages, and assessed phenotype-genotype concordance.

Results

All isolates exhibited resistance to third-generation cephalosporins, with resistance rates exceeding 80% for at least 10 antibiotics. The ESBL gene blaCTX−M−15 was detected in 93% of E. coli and 100% of K. pneumoniae isolates. The concordance between phenotypic resistance and genotypic determinants was highest for β-lactams and lowest for aminoglycosides, trimethoprim-sulfamethoxazole and carbapenems. MLST revealed considerable genetic diversity among E. coli, including high-risk clones STc131 and ST648. Virulence genes (e.g., fimH, chuA, fyuA) were more prevalent in E. coli, particularly among isolates from urine and tracheal aspirate samples. Plasmid profiling revealed greater replicon diversity in E. coli, with frequent detection of IncFII and IncFIB plasmids, suggesting a stronger capacity for horizontal gene transfer.

Conclusion

These findings underscore the complexity of multidrug-resistant pathogen dynamics in ICU environments. They emphasize the need for species-specific surveillance, rapid diagnostics, and context-informed stewardship strategies to guide infection control and therapeutic interventions. While limited in scale, this study adds to the genomic landscape of multidrug-resistant pathogens in African ICUs and highlights critical targets for infection control and therapeutic interventions.