The Collection

KlebPhaCol consists of 52 barrier-free, open-source Klebsiella spp. targeting phages and 61 Klebsiella spp. clinical strains.

See here how you could use the collection in your research.

The original collection is currently being prepared for submission to a peer-reviewed journal, as such the data contained here is a work in progress and there will be more to come. Stay tuned!

To keep the collection up-to-date, we are committed to reviewing additions every 5 years to result in a follow-up publication.

If you are using any information or data from our website, please remember to cite us.

Last updated: August 4th 2023

The Roth phages

The Roth phages were isolated between 2021-2023 using sewage filtrate (UMC, Utrecht) as the phage source, enriched with 32 Klebsiella spp. clinical isolates.

TEM images for 47/52 phages (more to come!)

Morphologies of 47/52 phages

The Roth phages:

Roth01

Roth04

Roth08

Roth09

Roth10

Roth16

Roth17

Roth19

Roth20

Roth21

Roth22

Roth23

Roth24

Roth26

Roth27

Roth30

Roth32

Roth34

Roth71

Roth72

Roth74

Roth75

Roth76

Roth77

Roth37

Roth39

Roth41

Roth42

Roth44

Roth47

Roth51

Roth61

Roth66

Roth67

Roth68

Roth71

ST323-targeting phages (read more below):

RothC

RothD

RothG

RothI

RothJ

Roth78

Roth79

Roth80

Roth83

Roth84

Roth85

Roth87

Roth88

Roth90

Roth93

Roth96

Roth98

Genomic analyses

We currently have genomic data for 32/52 phages - stay tuned for the rest.

These 32 phages belong to the Caudoviricetes class and expand across four different phage families:

and across five different phage genera:

Slopekvirus

Jiaodavirus

Sugarlandvirus

Webervirus

Gajwadongvirus

Roth32 is the only podophage currently in KlebPhaCol

Do you have a Klebsiella podophage you would like to share to KlebPhaCol? Let us know!

Phylogeny of 32/52 phages

Tree displayed is made from whole genome alignments of the phage genomes.

Host range

The phages target 32/61 (52.5%) strains of the collection.

Currently displaying the host range of 58/61 strains. Stay tuned for the complete one!

Klebsiella spp. clinical strains

The 61 Klebsiella clinical strains come from different geographical locations and different tissue infections.

Strains covered by the collection:

K. pneumoniae

K. variicola

54 strains

2 strains

K. similipneumoniae

The strain collection currently covers 29 known* sequence types (ST) and 24 known* capsular types (K).

*some strains were unable to be classified by the genomic typing tools used.

Sequence types (ST) covered by the collection:

ST11

ST14

ST15

ST17

ST23

ST35

ST37

ST38

ST45

ST86

ST91

ST101

ST190

ST199

ST258

ST268

ST323

ST353

ST458

ST489

ST1411

ST1875

ST1958

ST2459

ST848

ST635

ST873

ST896

Capsular types (K) covered by the collection:

K10

K13

K17

K20

K21

K22

K24

K28

K29

K46

K52

K53

K54

K61

K68

K79

K. aerogenes

1 strain

K. oxytoca

1 strain

K. pneumoniae subspecies ozaenae

2 strains

1 strain

Unknown

ST5392

4 isolates have an unknown ST type

K129

K81

K104

K154

Unknown

KL24

KL116

KL124

19 isolates have an unknown K type

The strains

Complete list of strains coming soon…

We are currently preparing MTAs for them, stay tuned!

Klebsiella pneumoniae subsp. ozaenae
K4, ST91
Targeted by 4 phages
Klebsiella oxytoca
K29, ST199
Targeted by 0 phages
Klebsiella similipneumoniae
K53, ST489
Targeted by 17 phages
Klebsiella pneumoniae
K-type unknown, ST258
Targeted by 16 phages
Klebsiella pneumoniae
K2, ST14
Targeted by 6 phages
Klebsiella pneumoniae
K2, ST86
Targeted by 32 phages
Klebsiella pneumoniae
K20, ST268
Targeted by 4 phages
Klebsiella pneumoniae
K46, ST5392
Targeted by 4 phages
Klebsiella pneumoniae
K-type unknown, ST1958
Targeted by 0 phages
Klebsiella pneumoniae
K61, ST1411
Targeted by 6 phages
Klebsiella pneumoniae
K21, ST635
Targeted by 4 phages
Klebsiella pneumoniae
K3, ST896
Targeted by 16 phages
Klebsiella pneumoniae
K-type unknown, ST353
Targeted by 0 phages
Klebsiella pneumoniae
K52, ST45
Targeted by 0 phages
Klebsiella pneumoniae
K10, ST unknown
Targeted by 0 phages
Klebsiella pneumoniae
K-type unknown, ST-type unknown
Targeted by 0 phages
Klebsiella pneumoniae
K-type unknown, ST2459
Targeted by 0 phages
Klebsiella pneumoniae
K-type unknown, ST17
Targeted by 4 phages
Klebsiella pneumoniae
K-type unknown, ST-type unknown
Targeted by 7 phages
Klebsiella variicola
K13, ST848
Targeted by 0 phages
Klebsiella pneumoniae
K28, ST1221
Targeted by 0 phages
Klebsiella pneumoniae
K22, ST35
Targeted by 35 phages
Klebsiella pneumoniae
KL116 , ST133
Targeted by 8 phages
Klebsiella variicola
K53, ST1875 (novel tonB, nearest ST)
Targeted by 17 phages
Klebsiella pneumoniae
K24, ST458
Targeted by 0 phages
Klebsiella aerogenes
K68, ST190
Targeted by 0 phages
Klebsiella pneumoniae
K52, ST873
0
Klebsiella oxytoca
K68, ST37
Targeted by 20 phages
Klebsiella pneumoniae
K81, ST type unknown
Targeted by 0 phages
Klebsiella pneumoniae
KL124 , ST48
Targeted by 4 phages

Characterization

Strains have been genomically and phenotypically characterised.

Phylogeny was created by building a custom model on Poppunk. Stress and virulence genes are predicted from NCBI AMR database, virulence and AMR were additionally predicted with Abricate. Defense systems were predicted using both Padloc and DefenseFinder. Lastly prophage identification was done with Phigaro.

Applications beyond Phage Therapy

Klebsiella pneumoniae is a pathogen most commonly associated with nosocomial (hospital-acquired) infections leading to pneumonia, urinary tract, and soft tissue infections, as well as to more severe conditions such as septicemia, liver abscess, and sepsis, particularly for the hypervirulent strains. However, K. pneumoniae is also a gut colonizer and pathobiont. In fact, it has been associated with several gut-related diseases. Federici et al demonstrated that K. pneumoniae was significantly enriched in patients with inflammatory bowel disease (IBD), including both Crohn’s disease and ulcerative colitis patients (Federici et al, 2022). A similar observation was seen in patients with primary sclerosing cholangitis (Ichikawa et al 2023).

The IBD study identified a specific clade of K. pneumoniae associated with the condition: ST323

In both studies, phages were considered as a therapeutic option in rodent models, with promising results. Phage modulation of the gut microbiome was tolerated and successful, providing evidence that phages can be a therapeutic alternative beyond classical bacterial infections.

KlebPhaCol contains two ST323 strains targeted by 5 of the phages in the collection (RothC, RothD, RothG, RothI, RothJ).

This only showcases the potential of utilizing this collection outside of what is classically known as Phage Therapy.

Use the collection for your research!

Request collection

You can request the collection as a whole or partially, depending on your research focus and needs!