Whole genome sequencing to decipher the virulence phenotype of hypervirulent Klebsiella pneumoniae responsible for liver abscess, Marseille, France

Baron, Sophie Alexandra; Pascale, L. De; Million, Matthieu; Briantais, Antoine; Durand, Jean-Marc; Hadjadj, Linda; Rolain, Jean‐Marc

doi:10.1007/s10096-020-04080-7

Cited by 7 publications

(6 citation statements)

References 16 publications

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“…It was reported previously that overexpression of rmpA could enhance the virulence of K. pneumoniae isolates in the mouse model [ 31 ]. Virulence genes iroN and iroD associated with utilization of trivalent iron were detected in K. pneumoniae of ST23, ST218, ST76, ST86, and ST268 (isolates associated with severe bloodstream infections) which agrees with reports from other countries [ 22 , 23 , 29 ]. It is known that the majority of pathogenic bacteria including K. pneumoniae possess the iron-acquisition system with a higher affinity for iron than the host, which serves as one of the strategies for increasing bacterial virulence [ 32 ].…”

Section: Discussionsupporting

confidence: 88%

“…Nine STs in our study (ST14, ST23, ST39, ST76, ST86, ST218, ST219, ST268, and ST2674) were identified only for the isolates that caused severe bloodstream infections. Previously K. pneumoniae of ST23, ST86, ST76, and ST218 were described as a hypervirulent pathogen causing bacteremia, sepsis, and liver abscess in India, France, China, Taiwan, and Russia [ 21 , 22 , 23 , 24 , 25 ]. Three STs (ST14, ST39, and ST268) in our study were associated with fatal outcomes.…”

Section: Discussionmentioning

confidence: 99%

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Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

et al. 2021

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The purpose of this study was the identification of genetic lineages and antimicrobial resistance (AMR) and virulence genes in Klebsiella pneumoniae isolates associated with severe infections in the neuro-ICU. Susceptibility to antimicrobials was determined using the Vitek-2 instrument. AMR and virulence genes, sequence types (STs), and capsular types were identified by PCR. Whole-genome sequencing was conducted on the Illumina MiSeq platform. It was shown that K. pneumoniae isolates of ST14K2, ST23K57, ST39K23, ST76K23, ST86K2, ST218K57, ST219KL125/114, ST268K20, and ST2674K47 caused severe systemic infections, including ST14K2, ST39K23, and ST268K20 that were associated with fatal incomes. Moreover, eight isolates of ST395K2 and ST307KL102/149/155 were associated with manifestations of vasculitis and microcirculation disorders. Another 12 K. pneumoniae isolates of ST395K2,KL39, ST307KL102/149/155, and ST147K14/64 were collected from patients without severe systemic infections. Major isolates (n = 38) were XDR and MDR. Beta-lactamase genes were identified: blaSHV (n = 41), blaCTX-M (n = 28), blaTEM (n = 21), blaOXA-48 (n = 21), blaNDM (n = 1), and blaKPC (n = 1). The prevalent virulence genes were wabG (n = 41), fimH (n = 41), allS (n = 41), and uge (n = 34), and rarer, detected only in the genomes of the isolates causing severe systemic infections—rmpA (n = 8), kfu (n = 6), iroN (n = 5), and iroD (n = 5) indicating high potential of the isolates for hypervirulence.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

et al. 2021

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“…PLA caused by multidrug-resistant hvKp has rarely been reported (Table 4). [19][20][21][22][23][24][25][26] The strain in our case showed a trend of multidrug resistance. There needs to be awareness of infection caused by hypervirulent strains with drug resistance.…”

Section: Discussionmentioning

confidence: 99%

Pyogenic liver abscess caused by extended-spectrum β-lactamase-producing hypervirulent Klebsiella pneumoniae diagnosed by third-generation sequencing: a case report and literature review

Zhang,

Huang,

et al. 2023

J Int Med Res

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We report a case of a woman with diabetes mellitus and choledocholithiasis who had a low fever with chills and severe weakness for 7 days. The patient’s abdominal tenderness was positive. Computed tomography and magnetic resonance imaging showed a giant abscess in the liver. The production of extended-spectrum β-lactamases by hypervirulent Klebsiella pneumoniae was found in the purulent fluid of the liver by nanopore-based metagenomic third-generation sequencing combined with an antibiotic susceptibility test. The patient recovered after intravenous antibiotic therapy and percutaneous drainage. Patients with a history of diabetes mellitus and choledocholithiasis should be aware of the possibility of pyogenic liver abscesses caused by hypervirulent Klebsiella pneumoniae. To rapidly control the development of this disease, nanopore-based metagenomic third-generation sequencing plays an important role not only in rapidly identifying pathogens, but also in guiding the use of antibiotics.

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“…Non-carbapenem-resistant hvKp can also cause severe invasive infections, and carbapenemase-producing K. pneumoniae can acquire hypervirulence-associated genes by plasmid transfer and the formation of hybrid plasmids combining both characteristics on a single transferable unit [ 1 , 3 , 12 ]. This suggests that the diagnostic focus needs to shift from the detection of antimicrobial resistance alone to a broader strategy that includes the identification of virulence factors in order to limit the spread of high-risk K. pneumoniae clones and to improve timely clinical decision-making within antibiotic stewardship programmes [ 13 , 14 , 15 ].…”

Section: Discussionmentioning

confidence: 99%

Screening of Klebsiella pneumoniae Isolates for Carbapenemase and Hypervirulence-Associated Genes by Combining the Eazyplex® Superbug CRE and hvKp Assays

et al. 2023

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The acquisition of hypervirulence-associated genes by carbapenemase-producing Klebsiella pneumoniae is being increasingly observed, and easy-to-use diagnostic tests are needed for the surveillance of the hypervirulent K. pneumoniae (hvKp). In this pilot study, 87 K. pneumoniae isolates from invasive infections collected in 2022 and 2023 were analysed using the LAMP-based eazyplex® Superbug CRE and hvKp assays for the simultaneous identification of carbapenemases and virulence genes (rmpA/A2, iuC, iroC, ybt, clb). Nine isolates showed a Kleborate virulence score of 4 or 5 (10.3%). The time for the results of the eazyplex® assays ranged from 6.5 to 13 min, and the total turnaround time, including sample preparation, was less than 30 min. Five isolates, three of which produced New Delhi metallo-beta lactamase (NDM), were subjected to whole-genome sequencing (WGS) analysis for further characterisation. The eazyplex® test results for beta-lactamase and virulence genes were confirmed. The eazyplex® hvKp, currently only available as a Research Use Only assay, may be a useful tool for the rapid identification of hvKp without significant additional workload when combined with the eazyplex® Superbug CRE assay for the detection of carbapenemases.

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Whole genome sequencing to decipher the virulence phenotype of hypervirulent Klebsiella pneumoniae responsible for liver abscess, Marseille, France

Cited by 7 publications

References 16 publications

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

Pyogenic liver abscess caused by extended-spectrum β-lactamase-producing hypervirulent Klebsiella pneumoniae diagnosed by third-generation sequencing: a case report and literature review

Screening of Klebsiella pneumoniae Isolates for Carbapenemase and Hypervirulence-Associated Genes by Combining the Eazyplex® Superbug CRE and hvKp Assays

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