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<p><i>Klebsiella pneumoniae</i> is a global public health concern, recognized by the World Health Organization’s Global Antimicrobial Resistance Surveillance System for its ability to develop resistance to multiple antibiotics and facilitate the spread of antibiotic resistance genes. Despite its potential to cause severe and high-mortality hospital-associated infections, genomic and epidemiological data on <i>K. pneumoniae</i> remain limited in sub-Saharan Africa (SSA), including Ghana. In this study, 201 isolates from diverse clinical sources were whole genome sequenced and characterized through bioinformatic analysis as part of the UK Aid Fleming Fund Regional Grant SeqAfrica project. Among the 201&#xa0;<i>K</i><i>. pneumoniae</i> genomes from six Ghanaian regions, urine was the dominant specimen (50.25%). The population was highly diverse, with ST17, ST15, ST39, and ST22 predominating, and K2:O1 identified as the leading serotype. Resistance determinants were widespread. <i>bla</i><sub>CTX-M-15</sub> was the dominant beta-lactamase gene (57.21%), while carbapenemase genes occurred in nine genomes, mainly <i>bla</i><sub>NDM-1</sub> in ST147. 80.43% of the genomes concurrently haboured chromosomal and acquired fluoroquinolone resistance determinants, with 62.16% of these isolates originating from urine samples.&#xa0;A wound-associated O3/O3a-ST1263 genome carried the colistin resistance gene <i>mcr-10</i>. Virulence determinants were detected in 57.71% of genomes, dominated by yersiniabactin, while six genomes carried <i>rmpADC</i>-associated hypervirulence markers. Plasmid replicon analysis identified 27 types in 97.01% of genomes, predominantly IncFIB(K), IncFII(K), and Col(pHAD28), with distribution varying by specimen and geographic region. Carbapenemases and the <i>mcr-10</i> gene were linked to mobile genetic elements. Core SNP analysis identified closely related genomic clusters within several hospitals suggesting missed potential outbreaks. This study enhances our understanding of antibiotic-resistant <i>K. pneumoniae</i> in Ghana, including their clonal diversity, antimicrobial resistance burden, and other genetic factors influencing their success.</p>

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Genomic landscape of resistance and virulence in clinical Klebsiella pneumoniae from Ghana

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月29日

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  • Beverly Egyir,
  • William Boateng,
  • Christian Owusu-Nyantakyi,
  • Grebstad Rabbi Amuasi,
  • Alfred Bortey,
  • Felicia Owusu,
  • Quaneeta Mohktar,
  • Justice Danso,
  • Agnes Oclu,
  • Hawawu Ahmed,
  • Francis Kwame Morgan Tetteh,
  • Abass Inusah,
  • Oliver Nangkuu Deberu,
  • Kennedy Mensah Osei,
  • Esther Gyinae,
  • Harold Kwadzo Amegbletor,
  • Joana Twasam,
  • James Sampah,
  • Sarkodie Kodom,
  • Georgina Tetteh-Ocloo,
  • Solomon Asante Sefa,
  • Nicholas T.K.D Dayie,
  • Appiah-Korang Labi,
  • Noah Obeng-Nkrumah,
  • William Addo Mills-Pappoe,
  • Gifty Boateng,
  • Pernille Nilsson,
  • Natasia Rebekka Thornval,
  • Bright Adu,
  • Rene S. Hendriksen

摘要

Klebsiella pneumoniae is a global public health concern, recognized by the World Health Organization’s Global Antimicrobial Resistance Surveillance System for its ability to develop resistance to multiple antibiotics and facilitate the spread of antibiotic resistance genes. Despite its potential to cause severe and high-mortality hospital-associated infections, genomic and epidemiological data on K. pneumoniae remain limited in sub-Saharan Africa (SSA), including Ghana. In this study, 201 isolates from diverse clinical sources were whole genome sequenced and characterized through bioinformatic analysis as part of the UK Aid Fleming Fund Regional Grant SeqAfrica project. Among the 201 K. pneumoniae genomes from six Ghanaian regions, urine was the dominant specimen (50.25%). The population was highly diverse, with ST17, ST15, ST39, and ST22 predominating, and K2:O1 identified as the leading serotype. Resistance determinants were widespread. blaCTX-M-15 was the dominant beta-lactamase gene (57.21%), while carbapenemase genes occurred in nine genomes, mainly blaNDM-1 in ST147. 80.43% of the genomes concurrently haboured chromosomal and acquired fluoroquinolone resistance determinants, with 62.16% of these isolates originating from urine samples. A wound-associated O3/O3a-ST1263 genome carried the colistin resistance gene mcr-10. Virulence determinants were detected in 57.71% of genomes, dominated by yersiniabactin, while six genomes carried rmpADC-associated hypervirulence markers. Plasmid replicon analysis identified 27 types in 97.01% of genomes, predominantly IncFIB(K), IncFII(K), and Col(pHAD28), with distribution varying by specimen and geographic region. Carbapenemases and the mcr-10 gene were linked to mobile genetic elements. Core SNP analysis identified closely related genomic clusters within several hospitals suggesting missed potential outbreaks. This study enhances our understanding of antibiotic-resistant K. pneumoniae in Ghana, including their clonal diversity, antimicrobial resistance burden, and other genetic factors influencing their success.