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Organism

Klebsiella pneumoniae

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Sources cited
4 project reports and 1 cross-project digest, listed in the margin
Relations
supports 4refines 2
Linked from
11 pages5 topics

Identity

Canonical name: Klebsiella pneumoniae. 1

Known alias: K. pneumoniae. 1

Stable external identifier: No stable external identifier was reported in the source document. 1

Evidence across AMR studies

The environmental resistome study analyzed 13,637 Klebsiella pneumoniae genomes and identified 1,115 AMR gene clusters. 1 Of these clusters, 7 were classified as core and 1,108 as accessory, with accessory AMR accounting for 99% of the clusters. 1 The species was clinical-dominant at 80% in the study’s environmental representation analysis. 1 Only 7 of 1,115 clusters being core illustrates extensive accessory AMR variation in this clinically dominated species. 1

The pan-bacterial atlas supports this organism-level pattern: Klebsiella led all reported genera at 206 AMR clusters per species, placing it among the strongest AMR hotspots in the 27,690-species analysis. 2 The atlas therefore refines the earlier case study by showing that Klebsiella’s high and predominantly accessory AMR burden is also evident at broader pangenome scale, while the genus-level value is an average rather than a species-specific measurement. 2

The metabolic capability study supports and refines the pangenome interpretation: among well-sampled pathogens with more than 2,500 genomes, K. pneumoniae was reported as the most open pangenome, with 99.05% open genes and 0.95% core genes. 3 This is a species-level pangenome result distinct from the AMR-cluster measurements, but it is consistent with extensive accessory genomic variation. 3

The within-species strain-variation analysis further supports the interpretation of structured AMR heterogeneity: its K. pneumoniae case-study UMAP showed visible environmental structuring, although the broader environment–ecotype relationship was not established because the available tests were underpowered. 4 Because K. pneumoniae exceeded the 500-genome cap, it was excluded from that study’s ANI–AMR Mantel analysis, so no phylogenetic-signal estimate was reported for this species. 4

The discoveries synthesis supports the original cluster count and accessory-resistance interpretation, again reporting 1,115 AMR clusters across 13,637 K. pneumoniae genomes, with only 7 classified as core. 5 It also places this species within a broader finding that clinical species had 68% accessory AMR versus 43% in soil species, although that comparison is not a species-specific estimate. 5

The discoveries synthesis additionally reports that Klebsiella was the only PhageFoundry species with both SNIPE defense-system evidence and the ManX-family PTS domain: it had 1 DUF4041 annotation across 3 proteins and 4,619 PTS_EIIC annotations. 5 This is a defense/transport annotation result rather than evidence that these features explain the AMR burden.

These results provide an organism-level case study for environmental-resistome, supporting the conclusion that clinical representation is associated with high AMR diversity and predominantly accessory resistance. 1

The case study was assembled from the kbase-ke-pangenome collection using amrfinderplus-focused AMR annotation. 1

Sources cited

  1. Environmental Resistome at Pangenome Scaleamr_environmental_resistome · cited 14× · primary source
  2. Pan-Bacterial AMR Gene Landscapeamr_pangenome_atlas · cited 3× · supports · refines
  3. Metabolic Capability vs Metabolic Dependencymetabolic_capability_dependency · cited 3× · supports · refines
  4. Within-Species AMR Strain Variationamr_strain_variation · cited 3× · supports
  5. Discoveries Logdiscoveries · cited 5× · cross-project digest · supports