The Collection

KlebPhaCol consists of 53 barrier-free, open-source Klebsiella spp. targeting phages and 74 Klebsiella spp. clinical strains.

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

To keep the collection up-to-date, we are committed to reviewing additions on a regular basis.

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

Last updated: November 4th 2024

Search through the collection

To make your KlebPhaCol experience better, we’ve created a searchable domain were you can search for the characteristics you are interested in, for either the phages or the strains.

The Roth phages

The Roth phages were isolated between 2021-2023 using wastewater (from Utrecht Medical Centre in the Netherlands and from Portswood, Southampton in the UK) as the phage source, enriched with 32 Klebsiella spp. clinical isolates.

TEM images for all phages!

They span the three classic morphotypes

The Roth phages:

Roth01

Roth04

Roth08

Roth09

Roth10

Roth16

Roth17

Roth19

Roth20

Roth21

Roth22

Roth23

Roth24

Roth26

Roth27

Roth30

Roth32

Roth34

Roth37

Roth39

Roth41

Roth42

Roth44

Roth47

Roth49

Roth50

Roth51

Roth61

Roth66

Roth67

Roth68

Roth71

Roth72

Roth74

Roth75

Roth76

ST323-targeting phages (read more below):

RothC

RothD

RothG

RothI

RothJ

Roth77

Roth78

Roth79

Roth80

Roth83

Roth84

Roth85

Roth87

Roth88

Roth90

Roth93

Roth96

Genomic analyses

These 53 phages belong to the Caudoviricetes class and expand across five different phage families:

NEW!

and across seven different phage genera:

Drulisvirus

Webervirus

Sugarlandvirus

NEW!

Slopekvirus

Jiaodavirus

Nakavirus

Gajwadongvirus

Host range

The phages target 46/74 (62%) strains of the collection.

See the phage taxonomic clustering network here!

Search through the KlebPhaCol phages

Klebsiella spp. clinical strains

The 74 Klebsiella clinical strains come from different geographical locations and different tissue infections.

The strain collection currently covers 40 known* sequence types (ST) 32 known* capsular locus types (KL), and 10 O-antigens.

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

Strains covered by the collection:

K. pneumoniae

K. variicola

67 strains

2 strains

K. similipneumoniae

K. oxytoca

1 strain

2 strains

Sequence types (ST) covered by the collection:

ST11

ST14

ST15

ST17

ST23

ST26

ST35

ST37

ST38

ST45

ST86

ST91

ST101

ST133

ST190

ST199

ST635

ST716

ST848

ST873

ST896

ST1221

ST1254

ST1411

ST1875

ST1958

ST2459

ST2559

ST5392

ST48

ST485

ST1774

Unknown

5 isolates have an unknown ST type

O1

O2afg

O2a

O2ac

O3/O3a

O3b

O4

O5

KL112

KL107

KL110

KL113

ST353

ST258

ST268

ST323

Capsular locus types (KL) covered by the collection:

KL1

KL2

KL3

KL4

KL17

KL20

KL21

KL22

KL24

KL27

KL28

KL29

KL54

KL61

KL68

KL79

KL81

KL104

KL105

KL106

KL116

KL124

KL127

KL129

KL154

Unknown

K. pneumoniae subspecies ozaenae

1 strain

K. aerogenes

1 strain

KL46

KL38

KL52

KL53

1 isolate has an unknown K type

O-antigen types covered by the collection:

O13

O12

Unknown

ST528

ST458

ST489

ST661

KL12

KL5

KL10

KL13

8 isolates have an unknown O-antigen

Strain 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.

Antibiotic susceptibility was also experimentally verified for 13 commonly used antibiotics. Kleborate was used to assign virulence and resistance scores.

Find our K. pneumoniae strains in a Pathogenwatch public collection

With Pathogenwatch, you can compare your K. pneumoniae strains to those of the collection, and see additional metadata from the strains.

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). Gut colonization of K. pneumoniae can also lead to subsequent serious infections such as liver abcess and septicemia, particularly in immunocompromised individuals.

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.

Search through the KlebPhaCol strains

Use the collection for your research!

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