Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

Abstract

<i>Klebsiella pneumoniae</i> is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of <i>Klebsiella pneumoniae</i> into three distinct phylogenetic groups: <i>Klebsiella pneumoniae</i>, <i>Klebsiella variicola</i>, and <i>Klebsiella quasipneumoniae</i>. <i>K. variicola</i> and <i>K. quasipneumoniae</i> have often been described as opportunistic pathogens that have less virulence in humans than <i>K. pneumoniae</i> does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing <i>K. pneumoniae</i> isolates recovered from human infections and discovered that 28 strains were phylogenetically related to <i>K</i>. <i>variicola</i> and <i>K. quasipneumoniae</i>. Whole-genome sequencing of 95 additional non-ESBL-producing <i>K. pneumoniae</i> isolates recovered from patients found 12 <i>K. quasipneumoniae</i> strains. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as <i>K. pneumoniae</i>, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among the <i>Klebsiella</i> species. For the first time, strains of both <i>K. variicola</i> and <i>K. quasipneumoniae</i> were found to carry the <i>Klebsiella pneumoniae</i> carbapenemase (KPC) gene, while another <i>K. variicola</i> strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. <i>K. variicola</i> and <i>K. quasipneumoniae</i> infections were not less virulent than <i>K</i>. <i>pneumoniae</i> infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one <i>K. variicola</i> strain, as well as one strain from a novel <i>Klebsiella</i> species, which challenge the current understanding of interrelationships between clades of <i>Klebsiella</i>. <b>IMPORTANCE</b><i>Klebsiella pneumoniae</i> is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. <i>K. variicola</i> and <i>K. quasipneumoniae</i> are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that <i>K. variicola</i> and <i>K. quasipneumoniae</i> isolates are often misidentified as <i>K. pneumoniae</i> by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to <i>K. pneumoniae</i>. The presence of KPC in <i>K. variicola</i> and <i>K. quasipneumoniae</i> strains as well as NDM-1 metallo-beta-lactamase in one <i>K. variicola</i> strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of <i>Klebsiella</i> is cause for additional concern.