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Objectives <p>Carbapenemase-producing <i>Klebsiella pneumoniae</i> remains a major driver of multidrug resistance, traditionally linked to healthcare-associated infections but its detection in community-acquired infections represents a worrying shift. We aimed to characterize community-origin KPC- or NDM-producing <i>K. pneumoniae</i> isolates from two cities in São Paulo State, Brazil.</p> Methods <p>A laboratory-based surveillance was conducted, including 111 non-duplicate <i>K. pneumoniae</i> isolates from urine of non-hospitalized patients. Polymyxin B MICs were determined by broth microdilution. All isolates underwent Illumina WGS. In silico analyses used Kleborate and Roary were used for bioinformatics analyses.</p> Results <p>76% of the isolates were susceptible to polymyxin. The most frequent carbapenemase gene detected was KPC-2 (94.5%), but KPC-3, NDM-1 and NDM-5 were detected. MLST showed high clonal diversity (14 STs), dominated by ST11 (n = 34) and ST437 (n = 20), followed by ST16 (n = 12), ST6386 (n = 10), ST258 (n = 9), ST147 (n = 6), ST307 (n = 5), among others. Core-genome phylogeny revealed a polyclonal structure with multiple subclusters, consistent with community dissemination, grouped by ST. No classic hvKp plasmid markers were detected by Kleborate. Resistome were diverse.</p> Conclusions <p>The predominance of CC11-related lineages (including ST11, ST437, and ST6386) indicates the persistence of the pandemic <i>K. pneumoniae</i> clone historically associated with <i>bla</i><sub>KPC-2</sub>. The detection of secondary complexes such as CC16, CC147, and CC307, and the identification of NDM-producing isolates, highlight the polyclonal nature of dissemination and suggest ongoing genomic adaptation in community settings. The genomic diversity observed here reinforces the potential of environmental and community as non-obvious reservoirs contributing to KPC and NDM spread beyond hospital boundaries.</p>

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Hidden in the community: poly-clonal spread of KPC- or NDM-producing Klebsiella pneumoniae revealed by whole-genome sequencing in Southeastern Brazil

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月20日

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  • Carlos H. Camargo,
  • Taise C. D. M. Barbosa,
  • Amanda Y. Yamada,
  • Ana Beatriz N. Costa,
  • Daniel S. Miranda,
  • Pedro S. P. Ferraro,
  • Karoline R. Campos,
  • Claudio T. Sacchi,
  • Monique R. Tiba-Casas

摘要

Objectives

Carbapenemase-producing Klebsiella pneumoniae remains a major driver of multidrug resistance, traditionally linked to healthcare-associated infections but its detection in community-acquired infections represents a worrying shift. We aimed to characterize community-origin KPC- or NDM-producing K. pneumoniae isolates from two cities in São Paulo State, Brazil.

Methods

A laboratory-based surveillance was conducted, including 111 non-duplicate K. pneumoniae isolates from urine of non-hospitalized patients. Polymyxin B MICs were determined by broth microdilution. All isolates underwent Illumina WGS. In silico analyses used Kleborate and Roary were used for bioinformatics analyses.

Results

76% of the isolates were susceptible to polymyxin. The most frequent carbapenemase gene detected was KPC-2 (94.5%), but KPC-3, NDM-1 and NDM-5 were detected. MLST showed high clonal diversity (14 STs), dominated by ST11 (n = 34) and ST437 (n = 20), followed by ST16 (n = 12), ST6386 (n = 10), ST258 (n = 9), ST147 (n = 6), ST307 (n = 5), among others. Core-genome phylogeny revealed a polyclonal structure with multiple subclusters, consistent with community dissemination, grouped by ST. No classic hvKp plasmid markers were detected by Kleborate. Resistome were diverse.

Conclusions

The predominance of CC11-related lineages (including ST11, ST437, and ST6386) indicates the persistence of the pandemic K. pneumoniae clone historically associated with blaKPC-2. The detection of secondary complexes such as CC16, CC147, and CC307, and the identification of NDM-producing isolates, highlight the polyclonal nature of dissemination and suggest ongoing genomic adaptation in community settings. The genomic diversity observed here reinforces the potential of environmental and community as non-obvious reservoirs contributing to KPC and NDM spread beyond hospital boundaries.