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Genomic Characterization of Klebsiella quasipneumoniae from Clinical Specimens in Singapore.

ABSTRACT: A total of 1,281 specimens from 1,024 patients were screened. Phylogenetic analysis classified 44 of these isolates as Klebsiella quasipneumoniae subsp. similipneumoniae (44/1,281 [3.4%]) and the remaining three as K. quasipneumoniae subsp. quasipneumoniae. The most common specimen source was urine (21/47 [44.7%]) followed by blood (14/47 [29.8%]). K. quasipneumoniae isolates were nonclonal. Carbapenemase-encoding genes (bla_NDM and bla_OXA-181) were detected in only two isolates (2/47 [4.3%]). K. quasipneumoniae appears to cause a spectrum of infections similar to those of K. pneumoniae, although higher rates of susceptibility to many commonly tested antimicrobials and low prevalence of virulence genes were demonstrated.

SUBMITTER: Chew KL

PROVIDER: S-EPMC8284435 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Genomic Characterization of Klebsiella quasipneumoniae from Clinical Specimens in Singapore.

Chew Ka Lip KL Octavia Sophie S Lai Deborah D Lin Raymond T P RTP Teo Jeanette W P JWP

Antimicrobial agents and chemotherapy 20210716 8

A total of 1,281 specimens from 1,024 patients were screened. Phylogenetic analysis classified 44 of these isolates as Klebsiella quasipneumoniae subsp. similipneumoniae (44/1,281 [3.4%]) and the remaining three as K. quasipneumoniae subsp. quasipneumoniae. The most common specimen source was urine (21/47 [44.7%]) followed by blood (14/47 [29.8%]). K. quasipneumoniae isolates were nonclonal. Carbapenemase-encoding genes (blaNDM and blaOXA ...[more]

PMID: 34060897

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Project description:BackgroundKlebsiella pneumoniae has emerged as a significant pathogen that causes community and hospital infections due to its high resistance rate and transmissibility. Klebsiella pneumoniae complex is classified into three phylogroups: Klebsiella pneumoniae (KpI), Klebsiella quasipneumoniae (KpII), and Klebsiella variicola (KpIII) in classical taxonomy, but KpII and KpIII are infrequently isolated clinically. Although pathogenic KpII has been reported worldwide, the understanding of this pathogen remains limited.MethodsWhole-genome sequencing (WGS) of K. quasipneumoniae subsp. similipneumoniae ACESH00366hy was performed. Plasmid characterization was demonstrated using S1-PFGE, Southern blotting, and conjugation assays. Antimicrobial susceptibility testing was performed and interpreted according to CLSI, EUCAST, and FDA standards. The virulence of the strain was assessed using the Galleria mellonella infection assay, serum-killing assay, and biofilm formation assay. A phylogenetic tree was constructed to explore its biological evolution.ResultsThe K. quasipneumoniae subsp. similipneumoniae isolate ACESH00366hy, belonging to ST2012 and KL139, contains several resistance genes including blaNDM-1, blaSHV-12, blaOKP-B-2, and oqxAB, as well as various virulence genes including iroE, iutA, mrkABCDFHIJ, entABCDEFS, and fepABCDG. The blaNDM-1 and blaSHV-12 genes were present on the 53,624 bp IncX3 plasmid. Virulence assays showed that the virulence of ACESH00366hy was greater than that of the low-toxicity strain ATCC 700,603. Phylogenetic analysis demonstrated the emergence of ST2012 KpII-B in Asia and revealed the spread of K. quasipneumoniae subsp. similipneumoniae in humans, animals, and the environment.ConclusionThis study highlights the emergence of clinical ST2012 KpII strains harbouring blaNDM-1 via the IncX3 plasmid in China. We evaluated its resistance and virulence characteristics and performed phylogenetic analysis, thereby enhancing our understanding of its resistance and pathogenicity and contributing to the clinical surveillance of K. quasipneumoniae.

Project description:Klebsiella pneumoniae 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 Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as K. pneumoniae, 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 Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella. IMPORTANCEKlebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae 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 K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola 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 Klebsiella is cause for additional concern.

Project description:Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.

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Genomic Characterization of Klebsiella quasipneumoniae from Clinical Specimens in Singapore.

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Genomic Characterization of Klebsiella quasipneumoniae from Clinical Specimens in Singapore.

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