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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.


ABSTRACT: Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

SUBMITTER: Holt KE 

PROVIDER: S-EPMC4500264 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

Holt Kathryn E KE   Wertheim Heiman H   Zadoks Ruth N RN   Baker Stephen S   Whitehouse Chris A CA   Dance David D   Jenney Adam A   Connor Thomas R TR   Hsu Li Yang LY   Severin Juliëtte J   Brisse Sylvain S   Cao Hanwei H   Wilksch Jonathan J   Gorrie Claire C   Schultz Mark B MB   Edwards David J DJ   Nguyen Kinh Van KV   Nguyen Trung Vu TV   Dao Trinh Tuyet TT   Mensink Martijn M   Minh Vien Le VL   Nhu Nguyen Thi Khanh NT   Schultsz Constance C   Kuntaman Kuntaman K   Newton Paul N PN   Moore Catrin E CE   Strugnell Richard A RA   Thomson Nicholas R NR  

Proceedings of the National Academy of Sciences of the United States of America 20150622 27


Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically impor  ...[more]

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