Rapid Genomic Characterization and Global Surveillance of <i>Klebsiella</i> Using Pathogenwatch

Argimón, Silvia; David, Sophia; Underwood, Anthony; Abrudan, Monica; Wheeler, Nicole; Kekre, Mihir; Abudahab, Khalil; Yeats, Corin; Goater, Richard; Taylor, Ben; Harste, Harry; Muddyman, Dawn; Feil, Edward J.; Brisse, Sylvain; Holt, Kathryn E.; Donado-Godoy, Pilar; Ravikumar, K L; Okeke, Iruka N.; Carlos, Celia C.; Aanensen, David M.

doi:10.1093/cid/ciab784

Cited by 83 publications

(84 citation statements)

References 57 publications

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“…We investigated the prevalence of L3 insertions among a large collection of public KP genomes available in PathogenWatch ( https://pathogen.watch/genomes/all?genusId=570&speciesId=573 ; S1 Table ). This collection comprises 16,086 assembled genomes from 84 countries, belonging to a total of 1,177 STs [ 22 ]. We unambiguously identified the ompK36 gene in 94.4% (15,193/16,086) of the genomes; the gene was intact (i.e.…”

Section: Resultsmentioning

confidence: 99%

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

et al. 2022

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Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.

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Section: Resultsmentioning

confidence: 99%

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

et al. 2022

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“…We first investigated the prevalence of L3 insertions among a large collection of public KP genomes available in PathogenWatch (https://pathogen.watch/genomes/all?genusId=570&speciesId=573; S1 Table ). This collection comprises 16,086 assembled genomes from 84 countries, belonging to a total of 1,177 STs (17). We unambiguously identified the ompK36 gene in 94.4% (15,193/16,086) of the genomes; the gene was intact (i.e.…”

Section: Resultsmentioning

confidence: 99%

“…We used a public collection of 16,086 KP genomes available in Pathogenwatch (17) (https://pathogen.watch/genomes/all?genusId=570&speciesId=573; accessed September 2021) to characterise the diversity of ompK36 genes. The ompK36 gene was identified in the short-read assemblies using BLASTn v2.6.0 (37) with a query gene from the reference genome, ATCC43816 (accession CP009208).…”

Section: Methodsmentioning

confidence: 99%

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

David

Wong

Sanchez‐Garrido

et al. 2022

Preprint

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Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. In a murine pneumonia model, KP mutants harbouring L3 insertions have a competitive disadvantage relative to a strain expressing wild-type OmpK36 in the absence of antibiotics. This explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.

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“…A first automatic genome annotation was performed using RAST server [ 28 ]. Virulence factor search and pathogenic typing were performed using the Kleborate tool ( , accessed on 23 February 2022) [ 29 ] available on the Pathogenwatch platform ( , accessed on 21 February 2022) [ 30 ] and Resfinder ( , accessed on 3 March 2022) [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae

Laforêt

Antoine

Reuter³

et al. 2022

Viruses

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Antibiotic resistance represents a major public health concern requiring new alternatives including phage therapy. Klebsiella pneumoniae belongs to the ESKAPE bacteria and can cause urinary tract infections (UTIs). The aims of this study were to isolate and characterize new bacteriophages against a K. pneumoniae strain isolated from UTIs and to assess their efficacy in vitro and in vivo in a Galleria (G.) mellonella larvae model. For this purpose, two bacteriophages were newly isolated against an ST13 K. pneumoniae strain isolated from a UTI and identified as K3 capsular types by wzi gene PCR. Genomic analysis showed that these bacteriophages, named vB_KpnP_K3-ULINTkp1 and vB_KpnP_K3-ULINTkp2, belong to the Drulisvirus genus. Bacteriophage vB_KpnP_K3-ULINTkp1 had the narrowest host spectrum (targeting only K3), while vB_KpnP_K3-ULINTkp2 also infected other Klebsiella types. Short adsorption times and latent periods were observed for both bacteriophages. In vivo experiments showed their ability to replicate in G. mellonella larvae and to decrease host bacterial titers. Moreover, both bacteriophages improved the survival of the infected larvae. In conclusion, these two bacteriophages had different in vitro properties and showed in vivo efficacy in a G. mellonella model with a better efficiency for vB_KpnP_K3-ULINTkp2.

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Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

Cited by 83 publications

References 57 publications

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae

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