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<p><i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> are major contributors to antimicrobial resistance (AMR)-related mortality globally. The resistomes, mobilomes, clonalities, and phylogenies of 32 <i>E. coli</i> (15 clinical, 17 community) and 14 <i>K. pneumoniae</i> (6 clinical, 8 community) isolates from KwaZulu-Natal were compared to ascertain similarities and differences between healthcare-related pathogens and community commensals using whole genome sequencing and bioinformatic pipelines. Resistome analysis revealed that <i>bla</i><sub>CTX−M−15</sub> predominated in clinical isolates of both <i>E. coli</i> and <i>K. pneumoniae</i>, whereas <i>bla</i><sub>TEM−1B</sub> was more common in community <i>E. coli</i>. Two clinical <i>E. coli</i> harboured <i>bla</i><sub>OXA−181</sub>, and one <i>K. pneumoniae</i> carried <i>bla</i><sub>OXA−181</sub> and <i>bla</i><sub>NDM−5</sub>; none were detected in community isolates. IncF plasmid replicons were most frequent, and gene cassettes within class 1 integrons, insertion sequences, and transposons contributed to resistome mobilization across both settings. A broad range of sequence types (STs) were detected across both settings, with shared STs limited to ST131, ST10, and ST1193 in <i>E. coli</i>, and ST17 in <i>K. pneumoniae</i>. Phylogeny showed that clinical <i>E. coli</i> clustered with some community isolates, while <i>K. pneumoniae</i> showed limited clustering. The overlap of resistomes, mobilomes, STs and phylogenies suggests genomic relatedness between isolates from both settings, highlighting the importance of AMR surveillance in community settings.</p>

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Community and clinical resistomes and mobilomes: a comparative genomic snapshot of Escherichia coli and Klebsiella pneumoniae

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月28日

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  • Khanyisa Mahonisi,
  • Joshua Mbanga,
  • Arshad Ismail,
  • Sabiha Y. Essack

摘要

Escherichia coli and Klebsiella pneumoniae are major contributors to antimicrobial resistance (AMR)-related mortality globally. The resistomes, mobilomes, clonalities, and phylogenies of 32 E. coli (15 clinical, 17 community) and 14 K. pneumoniae (6 clinical, 8 community) isolates from KwaZulu-Natal were compared to ascertain similarities and differences between healthcare-related pathogens and community commensals using whole genome sequencing and bioinformatic pipelines. Resistome analysis revealed that blaCTX−M−15 predominated in clinical isolates of both E. coli and K. pneumoniae, whereas blaTEM−1B was more common in community E. coli. Two clinical E. coli harboured blaOXA−181, and one K. pneumoniae carried blaOXA−181 and blaNDM−5; none were detected in community isolates. IncF plasmid replicons were most frequent, and gene cassettes within class 1 integrons, insertion sequences, and transposons contributed to resistome mobilization across both settings. A broad range of sequence types (STs) were detected across both settings, with shared STs limited to ST131, ST10, and ST1193 in E. coli, and ST17 in K. pneumoniae. Phylogeny showed that clinical E. coli clustered with some community isolates, while K. pneumoniae showed limited clustering. The overlap of resistomes, mobilomes, STs and phylogenies suggests genomic relatedness between isolates from both settings, highlighting the importance of AMR surveillance in community settings.