Installation#

Dependencies#

Kleborate requires the following software and libraries to be installed and available in your path:

Install Kleborate#

Create a conda environment containing Kleborate dependencies:

conda create -n klebsiella_analysis --solver=libmamba \
    -c conda-forge \
    -c bioconda \
    python=3.11 \
    biopython=1.81 \
    beautifulsoup4 \
    numba \
    minimap2 \
    mash \
    mist_typing \
    ezclermont \
    ectyper \
    ncbi-stxtyper \
    shigapass \
    ncbi-amrfinderplus -y

Activate the environment and install kleborate (and Kaptive) using pip:

conda activate klebsiella_analysis
pip install kleborate==3.3.0b1

Quick installation check#

Download K. pneumoniae genome and run kpsc__mlst module

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz
kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -m kpsc__mlst --trim_headers

Database set up#

Before running Kleborate, set up the reference databases required

KpSC cgMLST database (MiST)#

NOTE: KpSC cgMLST is only used by the module -m kpsc__cgmlst and preset -p kpsc, so if you are not analysing K. pneumoniae species complex you don’t need to do this step.

The kpsc__cgmlst module performs core-genome MLST (cgMLST) allele calling using MiST and uses the scgMLST629_S scheme hosted on the Institut Pasteur BIGSdb instance.

This requires a local, indexed copy of the cgMLST scheme to be stored in kleborate/modules/kpsc__cgmlst/data. As the scheme is under license, we cannot distribute it with Kleborate, and you will need to download the latest version yourself. To simplify this, we have supplied the Python script setup_cgmlst.py download and index the scheme database:

python setup_cgmlst.py

Note

Downloading profiles can take a long time due to the large number of entries.

Prerequisites#

Before running the setup_cgmlst.py script, ensure the following tools are installed and available in your PATH:

  • MiST (mist)

  • bigsdb-downloader (Required for authenticated Pasteur downloads: pip install bigsdb-downloader)

What the script does#

  1. Verifies Dependencies: Confirms mist is accessible in your environment

  2. Installs bigsdb-downloader

  3. Locates Kleborate data path (kleborate/modules/kpsc__cgmlst/data)

  4. Downloads the scgMLST629_S scheme from the Institut Pasteur BIGSdb instance

Download modes#

When running setup_cgmlst.py, you will be prompted to select one of two download modes:

  1. Standard download (Public) Pulls public scheme data (frozen on 2024-12-31) without requiring login credentials.

  2. Latest Pasteur database (Authenticated) Pulls the most up-to-date scheme data directly from Institut Pasteur and requires OAuth authentication. Uses the bigsdb_auth downloader with credentials stored in .bigsdb_tokens/.

Pasteur credential setup (Mode 2)#

If you select Mode 2 and valid tokens are not found in .bigsdb_tokens/access_tokens, the script initiates the OAuth setup:

  1. Obtain API Client Credentials: Register for database access via the Institut Pasteur BIGSdb Portal.

    • Request an OAuth Client Key and Secret by emailing bigsdb@pasteur.fr.

  2. Run Authentication via the Setup Script and input API Keys: Enter your Client ID and Client Secret at the terminal prompts.

  3. Authorize in Browser: Open the generated URL in your browser, log in to your Pasteur account, and copy the verification code.

  4. Complete Verification: Paste the verification code into the terminal. Access tokens will be saved to .bigsdb_tokens/, and subsequent runs will skip re-authentication.

Output files#

Upon completion, the following files will be downloaded inside the target folder:

  • kleb_scgmlst_s/ — Raw scheme FASTA alleles and profiles.tsv.

  • kleb_scgmlst_s-index/ — Indexed binary database used by mist during Kleborate runs.

Test kpSC cgMLST module#

kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test_cgmlst -m kpsc__cgmlst --trim_headers

AMRFinderPlus database#

NOTE: AMRFinderPlus is only used by the module -m escherichia__amr and preset -p escherichia, so if you are not analysing E. coli/Shigella you don’t need to do this step.

Download the latest AMRFinderPlus database:

amrfinder -u

Verify the installation and database#

# Check the software and database versions
amrfinder --version
amrfinder -l

E. coli cgMLST database (MiST)#

NOTE: E. coli cgMLST is only used by the module -m escherichia__cgmlst and preset -p escherichia, so if you are not analysing E. coli/Shigella you don’t need to do this step.

Note

In this beta release, E. coli cgMLST is provided as an optional module and is not included in the default -p escherichia preset. To run it, specify -m escherichia__cgmlst.

The escherichia__cgmlst module performs core-genome MLST (cgMLST) allele uses the Escherichia.cgMLSTv1 scheme hosted on EnteroBase.

Run the setup_ecoli_cgmlst.py script to download and index the scheme:

python setup_ecoli_cgmlst.py

Output files#

The following files will be created inside the kleborate/modules/ecoli__cgmlst/data folder:

  • ecoli_cgmlst_v1/ — Raw scheme FASTA alleles and profiles.tsv.

  • ecoli_cgmlst_v1-index/ — Indexed binary database used by mist during allele calling.

EnteroBase API token (required for E. coli LIN codes)#

EnteroBase schemes do not include LIN codes in the downloaded profiles file. To retrieve the LIN code for a matched cgST, this module queries EnteroBase’s API token

Please request API access to the EnteroBase E. coli database at https://enterobase.warwick.ac.uk/ Once, you have obtained the token run;

echo 'YOUR_TOKEN' > ./enterobase_token
chmod 600 ./enterobase_token

When running the module pass the --ecoli_entero_token path

kleborate \
-a *.fasta \
-o kleborate_results \
-m escherichia__cgmlst \
--trim_headers \
--ecoli_entero_token ./enterobase_token

Test E. coli cgMLST module#

Download E. coli genome and test cgMLST module

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/559/655/GCA_001559655.1_ASM155965v1/GCA_001559655.1_ASM155965v1_genomic.fna.gz
kleborate -a GCA_001559655.1_ASM155965v1_genomic.fna.gz -o escherichia_test -m escherichia__cgmlst --trim_headers

Validation tests#

kpsc preset test#

To test that Kleborate is installed and working correctly, download the example genome assembly and run Kleborate using the -p kpsc:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz
kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc --trim_headers

If the installation is successful, the analysis should complete without errors and generate the expected output files.

Additional tests#

Additional K. pneumoniae test datasets are provided to further validate your installation:

kleborate -a test/kpsc_test/data/*.fasta.gz -o kleborate_kpsc_test -p kpsc --trim_headers

The generated output should match the corresponding reference files located in test/kpsc_test/example_output/:

test/kpsc_test/example_output/klebsiella_pneumo_complex_output.txt:

strain

species

species_match

contig_count

N50

largest_contig

total_size

GC_content

ambiguous_bases

QC_warnings

ST

gapA

infB

mdh

pgi

phoE

rpoB

tonB

YbST

Yersiniabactin

ybtS

ybtX

ybtQ

ybtP

ybtA

irp2

irp1

ybtU

ybtT

ybtE

fyuA

spurious_YbST

CbST

Colibactin

clbA

clbB

clbC

clbD

clbE

clbF

clbG

clbH

clbI

clbL

clbM

clbN

clbO

clbP

clbQ

spurious_CbST

AbST

Aerobactin

iucA

iucB

iucC

iucD

iutA

spurious_AbST

SmST

Salmochelin

iroB

iroC

iroD

iroN

spurious_SmST

RmST

RmpADC

RmpADC_status

rmpA

rmpD

rmpC

rmpA_promoter

argR

spurious_RmST

virulence_score

rmpA2

peg-344

AGly_acquired

Col_acquired

Fcyn_acquired

Flq_acquired

Gly_acquired

MLS_acquired

Phe_acquired

Rif_acquired

Sul_acquired

Tet_acquired

Tgc_acquired

Tmt_acquired

Bla_acquired

Bla_inhR_acquired

Bla_ESBL_acquired

Bla_ESBL_inhR_acquired

Bla_Carb_acquired

Bla_chr

SHV_mutations

Omp_mutations

Col_mutations

Flq_mutations

truncated_resistance_hits

spurious_resistance_hits

resistance_score

num_resistance_classes

num_resistance_genes

Ciprofloxacin_prediction

Ciprofloxacin_profile_support

Ciprofloxacin_profile

Ciprofloxacin_MIC_prediction

wzi

K_locus

K_type

K_locus_confidence

K_locus_problems

K_locus_identity

K_Missing_expected_genes

O_locus

O_type

O_locus_confidence

O_locus_problems

O_locus_identity

O_Missing_expected_genes

cgST

LIN code

Sublineage

Clonal group

mrkST

mrkA

mrkB

mrkC

mrkD

mrkF

mrkH

mrkI

mrkJ

007_S09

Klebsiella pneumoniae

strong

274

56676

199420

5902084

56.66

no

N50

ST11-1LV

3

3

1

1

1

4

346-4LV

ybt 0; ICEKp10 (truncated)

48

15

5

94

60

181

200*-8%

50*-78%

11*-43%

4

84*

17-3LV

clb 3 (truncated)

2

10*-24%

2

2

2

2

2

8

2

2*-40%

2

2

2*

2

2

0

0

0

present

2

aac(6’)-Ib3^

catA1^

dfrA30*

TEM-1^;OXA-1;OXA-2

CTX-M-2

NDM-1

SHV-11

SHV:p.L35Q

ompK36:p.134_135insGD;ompK35:p.R115VfsTer30

mgrB:c.T72del;pmrB:p.R94AfsTer32

gyrA:p.S83I;parC:p.S80I

sul1.v2?-76%;aac(3)-IIa.v1?-0%;aac(3)-IId*?-0%;catB3.v1?-70%

3

8

8

nonwildtype R

99.21% R (N=2147/2167)

>1 QRDR, 0 PMQR, * aac(6`)-Ib-cr

2 mg/L [2-4]

wzi64

KL64

Capsule null

Typeable

!

99.76%

OL2α.1

O2α

Typeable

98.73%

cgST766

0_0_105_0_0_0_9_0_0_0

SL258

Cannot be determined

0

2024187392

Klebsiella pneumoniae

strong

132

174550

459900

5682502

56.66

yes (20)

ambiguous_bases

ST383

2

6

1

3

8

1

18

183

ybt 9; ICEKp3

5

11

6

5

1

25

37

9

5

5

11

0

63

iuc 1

1

15

1

1

1

0

147

rmp 1; KpVP-1

ON

27

2

2

11T

present

4

rmpA2_6*-47%

present

strB.v1;aph(3’)-Ia.v1^;aph(3’’)-Ib.v1*;aadA1.v2;aph(3’)-VI;armA;aac(6’)-Ib-AKT

qnrS1

msrE;mrx;mphA;mphE.v2

sul1;sul2

tet(A).v1

dfrA5

CTX-M-15;CTX-M-14^

NDM-5;OXA-48

SHV-1

ompK36:p.135_136insD;ompK35:c.T106del

mgrB:c.T50del

gyrA:p.S83F;gyrA:p.D87N;parC:p.S80I

OXA-9.v1*-42%;TEM-135.v1*?-0%

catA1*?-0%

3

9

20

nonwildtype R

99.22% R (N=2424/2443)

>0 QRDR, >0 PMQR, * aac(6`)-Ib-cr

4 mg/L [4-4]

KL30

K30

Typeable

!

97.84%

OL2α.2

O2β

Typeable

99.21%

cgST19975; cgST20666; cgST52869; cgST63343

0_0_87_5_0_3_1_0_0_0

SL383

CG383

ST2977

22

147

352

231

71

256

143

140

SRR33580217

Klebsiella pneumoniae

strong

76

272064

1055808

5520554

57.3

no

ST23

2

1

1

1

9

4

12

47-2LV

ybt 1; ICEKp10

2

2

2

2*

2

6*

6

2

2

2

2

29-1LV

clb 2

2

2

2

2

2

2

2

3*

2

2

2

2

2

2

2

1

iuc 1

1

1

1

1

1

2

iro 1

1

4

1

1

26

rmp 1; KpVP-1

ON

2

2

2

11T

present

5

rmpA2_5-54%

present

SHV-11^

SHV:p.L35Q

0

0

0

wildtype S

90.99% S (N=5168/5680)

0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr

0.25 mg/L [0.25-0.25]

wzi1

KL1

K1

Typeable

99.83%

OL2α.2

O2β

Typeable

99.45%

cgST65856

0_0_429_0_44_1_19_0_0_0

SL23

CG23

ST9549

985

1

1

1

1

1

2

1

SRR33580216

Klebsiella pneumoniae

strong

98

215497

539719

5596385

57.23

no

ST23

2

1

1

1

9

4

12

46-1LV

ybt 1; ICEKp10

2

2

2

2

2

36

6*

2

2

2

2

29-1LV

clb 2

2

2*

2

2

2

2

2

3

2

2

2

2

2

2

2

1

iuc 1

1

1

1

1

1

2

iro 1

1

4

1

1

40

rmp 1; KpVP-1

ON

2

3

2

11T

present

5

rmpA2_5-54%

present

SHV-11^

SHV:p.L35Q

0

0

0

wildtype S

90.99% S (N=5168/5680)

0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr

0.25 mg/L [0.25-0.25]

wzi1

KL1

K1

Typeable

99.81%

OL2α.2

O2β

Typeable

99.45%

cgST65857

0_0_429_0_4_0_35_0_0_0

SL23

CG23

ST1

1

1

1

1

1

1

2

1

SRR5386028

Klebsiella pneumoniae

strong

312

104936

348607

5604201

57.03

no

ST13

2

3

1

1

10

1

19

267-1LV

ybt 17; ICEKp10

6*

15

5

13

11

28

26

2

11

4

2

19-1LV

clb 3

2

10

2

2

2

4

2

8

2

2

2

2*

2

2

2

0

0

0

present

2

aph(3’)-Ia.v1^;aadA2.v1;aac(6’)-Ib-cr5^

aac(6’)-Ib-cr5^

mrx;mphA

sul1

tet(D)

dfrA12

TEM-1^;OXA-1

CTX-M-15;SHV-5

KPC-2

SHV:p.G238S;SHV:p.E240K

ompK36:c.25C>T

mgrB:p.K43Ter

gyrA:p.S83F;gyrA:p.D87N;parC:p.S80I

OXA-9.v1*-42%

catB3.v1?-70%

3

10

14

nonwildtype R

99.21% R (N=2147/2167)

>1 QRDR, 0 PMQR, * aac(6`)-Ib-cr

2 mg/L [2-4]

wzi40

KL3

K3

Typeable

?

99.89%

OL2α.2

O2β

Typeable

99.13%

cgST32525

0_0_98_0_11_2_0_1_1_0

SL13

CG13

ST633-1LV

5

143

659

229

1

116

1

ERR14097885

Klebsiella pneumoniae

strong

140

245450

558119

5866622

56.56

no

ST147

3

4

6

1

7

4

38

584-2LV

ybt 9; ICEKp?

5

11

6

5

1

293

318

9

5

142

11

0

63

iuc 1

1

15

1

1

1

0

147

rmp 1; KpVP-1

ON

27

2

2

11T

present

4

rmpA2_6*-47%

present

aph(3’)-Ia.v1^;aadA1.v2;aph(3’)-VI;armA

qnrS1

msrE;mrx*;mphA;mphE.v2

catB3.v2

arr-3

sul1;sul2

dfrA5;dfrA50*

OXA-9.v1;OXA-1

CTX-M-15

NDM-5

SHV-11^

SHV:p.L35Q

ompK36:p.134_135insGD;ompK35:p.R60LfsTer31

pmrB:c.G445del

gyrA:p.S83I;parC:p.S80I

TEM-150*?-0%;aac(6’)-Ib-AKT.v3?-89%

3

11

19

nonwildtype R

99.22% R (N=2424/2443)

>0 QRDR, >0 PMQR, * aac(6`)-Ib-cr

4 mg/L [4-4]

wzi64

KL64

K64

Typeable

99.89%

OL2α.1

O2α

Typeable

98.73%

cgST10000; cgST11351; cgST35980; cgST65374

0_0_197_0_4_1_0_7_15_0

SL147

CG147

ST8-1LV

6

3

2

12

8

7

15

test/kpsc_test/example_output/klebsiella_pneumo_complex_hAMRonization_output.txt:

Input File Name

Gene Symbol

Gene Name

Nucleotide mutation

Amino acid mutation

Genetic Variation Type

Drug Class

Input Sequence ID

Input Gene Length

Input Gene Start

Input Gene Stop

Reference Gene Length

Reference Gene Start

Reference Gene Stop

Sequence Identity

Coverage

Reference Accession

Strand Orientation

Analysis Software Name

Analysis Software Version

Reference Database Name

Reference Database Version

Input Protein Length

Reference Protein Length

Input Protein Start

Input Protein Stop

Reference Protein Start

Reference Protein Stop

007_S09

aac(6)-Ib3

aac(6)-Ib3

Gene presence detected

aminoglycoside antibiotic

assembly_contig_237

654

67

621

555

1

555

99.64

100.00

NG_051438.1:20-574

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

catA1

catA1

Gene presence detected

phenicol antibiotic

assembly_contig_211

1493

223

882

660

1

660

99.85

100.00

NG_047582.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

dfrA30

dfrA30

Gene presence detected

trimethoprim antibiotic

assembly_contig_224

940

212

685

474

1

474

99.58

100.00

NG_047727.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

TEM-1

TEM-1

Gene presence detected

penicillin beta-lactam

assembly_contig_202

1745

37

897

861

1

861

99.88

100.00

AY263331.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

OXA-1

OXA-1

Gene presence detected

penicillin beta-lactam

assembly_contig_213

1474

65

895

831

1

831

100.00

100.00

NG_049392.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

OXA-2

OXA-2

Gene presence detected

penicillin beta-lactam

assembly_contig_223

940

98

925

828

1

828

100.00

100.00

NG_049496.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

CTX-M-2

CTX-M-2

Gene presence detected

third-generation cephalosporin

assembly_contig_166

4341

1046

1921

876

1

876

100.00

100.00

NG_048968.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

NDM-1

NDM-1

Gene presence detected

carbapenem

assembly_contig_156

5363

4188

5000

813

1

813

100.00

100.00

NG_049326.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

SHV-11

SHV-11

Gene presence detected

penicillin beta-lactam

assembly_contig_33

56676

27911

28771

861

1

861

100.00

100.00

CP168408.1:2797577-2798437

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

sul1.v2

sul1.v2

Gene presence detected

sulfonamide antibiotic

assembly_contig_233

694

1

635

840

1

635

100.00

75.60

NG_048081.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

aac(3)-IIa.v1

aac(3)-IIa.v1

Gene presence detected

aminoglycoside antibiotic

assembly_contig_225

913

1

639

861

223

861

100.00

74.22

NG_047244.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

aac(3)-IId

aac(3)-IId

Gene presence detected

aminoglycoside antibiotic

assembly_contig_205

1685

1

639

861

223

861

99.84

74.22

EU022314.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

catB3.v1

catB3.v1

Gene presence detected

phenicol antibiotic

assembly_contig_213

1474

1033

1474

633

1

442

100.00

69.83

NG_047605.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

blaSHV

blaSHV

p.L35Q

Protein variant detected

penicillin beta-lactam

assembly_contig_33

56676

27911

28771

861

1

861

100.00

100.00

CP067381.1:82914-84074

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

ompK36

ompK36

p.134_135insGD

Inactivating mutation detected

assembly_contig_11

96727

33833

34942

1104

1

1104

99.46

100.54

NC_016845.1:3727882-3728985

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

ompK35

ompK35

p.R115VfsTer30

Inactivating mutation detected

assembly_contig_14

91113

88694

89772

1080

1

1080

99.91

40.11

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

mgrB

mgrB

c.T72del

Inactivating mutation detected

peptide antibiotic

assembly_contig_101

18945

18872

18945

144

1

74

100.00

51.06

NC_016845.1:3337154-3337297

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

pmrB

pmrB

p.R94AfsTer32

Inactivating mutation detected

peptide antibiotic

assembly_contig_19

78336

67548

68644

1098

1

1098

99.54

34.25

NC_016845.1:1694393-1695491

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

007_S09

gyrA

gyrA

p.S83I

Protein variant detected

fluoroquinolone antibiotic

assembly_contig_11

96727

44326

44686

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

007_S09

parC

parC

p.S80I

Protein variant detected

fluoroquinolone antibiotic

assembly_contig_10

96805

29927

30287

360

1

360

99.72

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

2024187392

strB.v1

strB.v1

Gene presence detected

aminoglycoside antibiotic

45_pilon

15773

13554

14390

837

1

837

100.00

100.00

NG_047464.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

aph(3)-Ia.v1

aph(3)-Ia.v1

Gene presence detected

aminoglycoside antibiotic

94_pilon

1056

67

882

816

1

816

99.75

100.00

CP157740.1:12584-13348

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

aph(3)-Ib.v1

aph(3)-Ib.v1

Gene presence detected

aminoglycoside antibiotic

45_pilon

15773

14390

15193

804

1

804

99.88

100.00

NG_047413.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

aadA1.v2

aadA1.v2

Gene presence detected

aminoglycoside antibiotic

74_pilon

2416

659

1447

789

1

789

100.00

100.00

NG_047327.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

aph(3)-VI

aph(3)-VI

Gene presence detected

aminoglycoside antibiotic

48_pilon

12362

5950

6729

780

1

780

100.00

100.00

NG_051730.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

armA

armA

Gene presence detected

aminoglycoside antibiotic

57_pilon

7423

6437

7210

774

1

774

100.00

100.00

NG_047476.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

aac(6)-Ib-AKT

aac(6)-Ib-AKT

Gene presence detected

aminoglycoside antibiotic

74_pilon

2416

35

589

555

1

555

100.00

100.00

NG_056043.1:5-559

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

qnrS1

qnrS1

Gene presence detected

Fluoroquinolone antibiotic

48_pilon

12362

1416

2072

657

1

657

100.00

100.00

NG_050543.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

msrE

msrE

Gene presence detected

macrolide antibiotic

57_pilon

7423

2663

4138

1476

1

1476

100.00

100.00

NG_048007.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

mrx

mrx

Gene presence detected

macrolide antibiotic

66_pilon

4017

973

2211

1239

1

1239

100.00

100.00

LC613143.1:28805-30043

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

mphA

mphA

Gene presence detected

macrolide antibiotic

66_pilon

4017

71

976

906

1

906

100.00

100.00

NG_047985.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

mphE.v2

mphE.v2

Gene presence detected

macrolide antibiotic

57_pilon

7423

1723

2607

885

1

885

100.00

100.00

NG_064660.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

sul1

sul1

Gene presence detected

sulfonamide antibiotic

85_pilon

1489

312

1151

840

1

840

100.00

100.00

NG_048082.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

sul2

sul2

Gene presence detected

sulfonamide antibiotic

60_pilon

5091

3808

4623

816

1

816

100.00

100.00

NG_051852.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

tet(A).v1

tet(A).v1

Gene presence detected

tetracycline antibiotic

64_pilon

4106

901

2100

1200

1

1200

100.00

100.00

NG_048154.1:101-1300

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

dfrA5

dfrA5

Gene presence detected

trimethoprim antibiotic

81_pilon

1897

1351

1824

474

1

474

100.00

100.00

NG_051699.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

CTX-M-15

CTX-M-15

Gene presence detected

third-generation cephalosporin

80_pilon

1902

981

1856

876

1

876

100.00

100.00

NG_048935.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

CTX-M-14

CTX-M-14

Gene presence detected

third-generation cephalosporin

88_pilon

1256

341

1216

876

1

876

99.89

100.00

NG_048929.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

NDM-5

NDM-5

Gene presence detected

carbapenem

48_pilon

12362

9162

9974

813

1

813

100.00

100.00

NG_049337.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

OXA-48

OXA-48

Gene presence detected

carbapenem

84_pilon

1610

26

823

798

1

798

100.00

100.00

NG_049762.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

SHV-1

SHV-1

Gene presence detected

penicillin beta-lactam

14_pilon

148667

119862

120722

861

1

861

100.00

100.00

CP165807.1:2737916-2738776

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

OXA-9.v1

OXA-9.v1

Gene presence detected

penicillin beta-lactam

74_pilon

2416

1492

2331

840

1

840

99.88

100.00

CP067618.1:18845-19684

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

TEM-135.v1

TEM-135.v1

Gene presence detected

penicillin beta-lactam

96_pilon

991

2

844

861

19

861

99.88

97.91

CP117718.1:71328-72188

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

catA1

catA1

Gene presence detected

phenicol antibiotic

93_pilon

1119

670

1119

660

211

660

99.78

68.18

NG_047582.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

ompK36

ompK36

p.135_136insD

Inactivating mutation detected

2_pilon

438666

240738

241859

1104

1

1104

92.38

101.63

NC_016845.1:3727882-3728985

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

ompK35

ompK35

c.T106del

Inactivating mutation detected

22_pilon

93665

2

106

1080

1

105

100.00

9.75

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

mgrB

mgrB

c.T50del

Inactivating mutation detected

peptide antibiotic

11_pilon

174550

2

50

144

1

49

100.00

34.04

NC_016845.1:3337154-3337297

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

2024187392

gyrA

gyrA

p.S83F

Protein variant detected

fluoroquinolone antibiotic

2_pilon

438666

230990

231350

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

2024187392

gyrA

gyrA

p.D87N

Protein variant detected

fluoroquinolone antibiotic

2_pilon

438666

230990

231350

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

2024187392

parC

parC

p.S80I

Protein variant detected

fluoroquinolone antibiotic

24_pilon

87413

57118

57478

360

1

360

99.72

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

SRR33580217

SHV-11

SHV-11

Gene presence detected

penicillin beta-lactam

1

1055808

375169

376029

861

1

861

99.88

100.00

CP168408.1:2797577-2798437

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR33580217

blaSHV

blaSHV

p.L35Q

Protein variant detected

penicillin beta-lactam

1

1055808

375169

376029

861

1

861

99.88

100.00

CP067381.1:82914-84074

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR33580216

SHV-11

SHV-11

Gene presence detected

penicillin beta-lactam

1

539719

246594

247454

861

1

861

99.88

100.00

CP168408.1:2797577-2798437

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR33580216

blaSHV

blaSHV

p.L35Q

Protein variant detected

penicillin beta-lactam

1

539719

246594

247454

861

1

861

99.88

100.00

CP067381.1:82914-84074

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

aph(3)-Ia.v1

aph(3)-Ia.v1

Gene presence detected

aminoglycoside antibiotic

139

1042

88

903

816

1

816

99.88

100.00

CP157740.1:12584-13348

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

aadA2.v1

aadA2.v1

Gene presence detected

aminoglycoside antibiotic

89

4753

2301

3092

792

1

792

100.00

100.00

NG_047343.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

aac(6)-Ib-cr5

aac(6)-Ib-cr5

Gene presence detected

aminoglycoside antibiotic

113

2188

1541

2095

555

1

555

99.82

100.00

NG_051711.1:101-655

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

aac(6)-Ib-cr5

aac(6)-Ib-cr5

Gene presence detected

Fluoroquinolone antibiotic

113

2188

1541

2095

555

1

555

99.82

100.00

NG_051711.1:101-655

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

mrx

mrx

Gene presence detected

macrolide antibiotic

83

5960

3749

4987

1239

1

1239

100.00

100.00

LC613143.1:28805-30043

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

mphA

mphA

Gene presence detected

macrolide antibiotic

83

5960

4984

5889

906

1

906

100.00

100.00

NG_047985.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

sul1

sul1

Gene presence detected

sulfonamide antibiotic

89

4753

3597

4436

840

1

840

100.00

100.00

NG_048082.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

tet(D)

tet(D)

Gene presence detected

tetracycline antibiotic

97

3526

1642

2826

1185

1

1185

100.00

100.00

NG_051690.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

dfrA12

dfrA12

Gene presence detected

trimethoprim antibiotic

89

4753

1396

1893

498

1

498

100.00

100.00

NG_047689.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

TEM-1

TEM-1

Gene presence detected

penicillin beta-lactam

101

2693

148

1008

861

1

861

99.77

100.00

AY263331.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

OXA-1

OXA-1

Gene presence detected

penicillin beta-lactam

113

2188

580

1410

831

1

831

100.00

100.00

NG_049392.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

CTX-M-15

CTX-M-15

Gene presence detected

third-generation cephalosporin

92

4288

1701

2576

876

1

876

100.00

100.00

NG_048935.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

SHV-5

SHV-5

Gene presence detected

third-generation cephalosporin

3

232195

203475

204335

861

1

861

100.00

100.00

NG_050087.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

KPC-2

KPC-2

Gene presence detected

carbapenem

62

17724

11109

11990

882

1

882

100.00

100.00

NG_049253.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

OXA-9.v1

OXA-9.v1

Gene presence detected

penicillin beta-lactam

101

2693

1708

2547

840

1

840

99.88

100.00

CP067618.1:18845-19684

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

catB3.v1

catB3.v1

Gene presence detected

phenicol antibiotic

113

2188

1

442

633

1

442

100.00

69.83

NG_047605.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

blaSHV

blaSHV

p.G238S

Gene presence detected

third-generation cephalosporin

3

232195

203475

204335

861

1

861

100.00

100.00

NG_050087.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

blaSHV

blaSHV

p.E240K

Gene presence detected

third-generation cephalosporin

3

232195

203475

204335

861

1

861

100.00

100.00

NG_050087.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

ompK36

ompK36

c.25C>T

Nucleotide variant detected

2

276505

127569

128687

1104

1

1104

92.44

101.36

NC_016845.1:3727882-3728985

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

mgrB

mgrB

p.K43Ter

Inactivating mutation detected

peptide antibiotic

5

193631

83176

83319

144

1

144

99.31

89.36

NC_016845.1:3337154-3337297

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

SRR5386028

gyrA

gyrA

p.S83F

Protein variant detected

fluoroquinolone antibiotic

2

276505

117822

118182

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

SRR5386028

gyrA

gyrA

p.D87N

Protein variant detected

fluoroquinolone antibiotic

2

276505

117822

118182

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

SRR5386028

parC

parC

p.S80I

Protein variant detected

fluoroquinolone antibiotic

7

156589

145285

145645

360

1

360

99.72

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

ERR14097885

aph(3)-Ia.v1

aph(3)-Ia.v1

Gene presence detected

aminoglycoside antibiotic

76

1051

67

882

816

1

816

99.75

100.00

CP157740.1:12584-13348

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

aadA1.v2

aadA1.v2

Gene presence detected

aminoglycoside antibiotic

62

2006

136

924

789

1

789

100.00

100.00

NG_047327.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

aph(3)-VI

aph(3)-VI

Gene presence detected

aminoglycoside antibiotic

44

7811

1083

1862

780

1

780

100.00

100.00

NG_051730.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

armA

armA

Gene presence detected

aminoglycoside antibiotic

45

7423

6437

7210

774

1

774

100.00

100.00

NG_047476.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

qnrS1

qnrS1

Gene presence detected

Fluoroquinolone antibiotic

44

7811

5740

6396

657

1

657

100.00

100.00

NG_050543.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

msrE

msrE

Gene presence detected

macrolide antibiotic

45

7423

2663

4138

1476

1

1476

100.00

100.00

NG_048007.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

mrx

mrx

Gene presence detected

macrolide antibiotic

46

5939

3731

4969

1239

1

1239

99.92

100.00

LC613143.1:28805-30043

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

mphA

mphA

Gene presence detected

macrolide antibiotic

46

5939

4966

5871

906

1

906

100.00

100.00

NG_047985.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

mphE.v2

mphE.v2

Gene presence detected

macrolide antibiotic

45

7423

1723

2607

885

1

885

100.00

100.00

NG_064660.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

catB3.v2

catB3.v2

Gene presence detected

phenicol antibiotic

57

2443

1165

1797

633

1

633

100.00

100.00

NG_047604.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

arr-3

arr-3

Gene presence detected

rifamycin antibiotic

57

2443

1882

2334

453

1

453

100.00

100.00

NG_048581.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

sul1

sul1

Gene presence detected

sulfonamide antibiotic

67

1611

318

1157

840

1

840

100.00

100.00

NG_048082.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

sul2

sul2

Gene presence detected

sulfonamide antibiotic

48

5101

3806

4621

816

1

816

100.00

100.00

NG_051852.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

dfrA5

dfrA5

Gene presence detected

trimethoprim antibiotic

85

560

71

544

474

1

474

100.00

100.00

NG_051699.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

dfrA50

dfrA50

Gene presence detected

trimethoprim antibiotic

17

112548

12768

13244

477

1

477

98.95

100.00

NG_242637.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

OXA-9.v1

OXA-9.v1

Gene presence detected

penicillin beta-lactam

62

2006

969

1808

840

1

840

100.00

100.00

CP067618.1:18845-19684

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

OXA-1

OXA-1

Gene presence detected

penicillin beta-lactam

57

2443

197

1027

831

1

831

100.00

100.00

NG_049392.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

CTX-M-15

CTX-M-15

Gene presence detected

third-generation cephalosporin

59

2170

981

1856

876

1

876

100.00

100.00

NG_048935.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

NDM-5

NDM-5

Gene presence detected

carbapenem

54

3392

192

1004

813

1

813

100.00

100.00

NG_049337.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

SHV-11

SHV-11

Gene presence detected

penicillin beta-lactam

3

391795

276306

277166

861

1

861

99.88

100.00

CP168408.1:2797577-2798437

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

TEM-150

TEM-150

Gene presence detected

penicillin beta-lactam

43

8581

1

842

861

20

861

99.88

97.79

NG_050194.1

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

aac(6)-Ib-AKT.v3

aac(6)-Ib-AKT.v3

Gene presence detected

aminoglycoside antibiotic

87

521

1

489

555

1

489

100.00

88.11

NG_052418.1:101-655

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

blaSHV

blaSHV

p.L35Q

Protein variant detected

penicillin beta-lactam

3

391795

276306

277166

861

1

861

99.88

100.00

CP067381.1:82914-84074

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

ompK36

ompK36

p.134_135insGD

Inactivating mutation detected

11

198590

122632

123741

1104

1

1104

98.83

100.54

NC_016845.1:3727882-3728985

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

ompK35

ompK35

p.R60LfsTer31

Inactivating mutation detected

6

348123

178574

179660

1080

1

1080

99.26

25.07

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

pmrB

pmrB

c.G445del

Inactivating mutation detected

peptide antibiotic

6

348123

91

534

1098

1

444

99.55

40.55

NC_016845.1:1694393-1695491

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

ERR14097885

gyrA

gyrA

p.S83I

Protein variant detected

fluoroquinolone antibiotic

11

198590

112885

113245

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

ERR14097885

parC

parC

p.S80I

Protein variant detected

fluoroquinolone antibiotic

19

103230

72931

73291

360

1

360

99.44

100.00

HM560971.1:119269-119072

Kleborate

3.2.4

Kleborate_AMRdb

3.3.0

120

120

1

120

1

120

test/kpsc_test/example_output/klebsiella_pneumo_complex_genotype_spec.txt:

sample

genotyping_method

genotyping_schema_taxon

genotyping_database_name

genotyping_database_version

genotyping_schema_name

genotyping_software_name

genotyping_software_version

genotype

genotype_confidence_value

genotype_predicted_phenotype

007_S09

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

007_S09

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST11-1LV

007_S09

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL64

Typeable

Capsule null

007_S09

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.1

Typeable

O2α

007_S09

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST766

007_S09

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_105_0_0_0_9_0_0_0

007_S09

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL258

007_S09

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

Cannot be determined

2024187392

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

2024187392

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST383

2024187392

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL30

Typeable

K30

2024187392

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.2

Typeable

O2β

2024187392

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST19975; cgST20666; cgST52869; cgST63343

2024187392

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_87_5_0_3_1_0_0_0

2024187392

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL383

2024187392

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

CG383

SRR33580217

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

SRR33580217

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST23

SRR33580217

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL1

Typeable

K1

SRR33580217

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.2

Typeable

O2β

SRR33580217

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST65856

SRR33580217

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_429_0_44_1_19_0_0_0

SRR33580217

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL23

SRR33580217

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

CG23

SRR33580216

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

SRR33580216

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST23

SRR33580216

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL1

Typeable

K1

SRR33580216

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.2

Typeable

O2β

SRR33580216

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST65857

SRR33580216

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_429_0_4_0_35_0_0_0

SRR33580216

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL23

SRR33580216

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

CG23

SRR5386028

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

SRR5386028

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST13

SRR5386028

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL3

Typeable

K3

SRR5386028

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.2

Typeable

O2β

SRR5386028

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST32525

SRR5386028

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_98_0_11_2_0_1_1_0

SRR5386028

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL13

SRR5386028

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

CG13

ERR14097885

In silico species detection

Enterobacterales [NCBITaxon:91347]

kleborate_enterobacterales__species

3.2.4

enterobacterales__species

Kleborate

3.2.4

Klebsiella pneumoniae

strong

ERR14097885

MLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2024-12-31

MLST

Kleborate

3.2.4

ST147

ERR14097885

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_K

3.2.2

Kaptive

3.3.1

KL64

Typeable

K64

ERR14097885

In silico serotyping

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

Klebsiella_pneumoniae_Species_Complex_O

3.2.0

Kaptive

3.3.1

OL2α.1

Typeable

O2α

ERR14097885

cgMLST

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

cgST10000; cgST11351; cgST35980; cgST65374

ERR14097885

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

0_0_197_0_4_1_0_7_15_0

ERR14097885

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

SL147

ERR14097885

LIN code

Klebsiella pneumoniae species complex [NCBITaxon:3390273]

pubmlst_klebsiella_seqdef

2026-04-29

scgMLST629_S

MiST

1.4.0

CG147

See also#