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Old 04-17-2018, 05:28 AM   #1
SK-N-BE
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Default Correct species identification impossible?

Hello,

I was using NGS to analyze the phylogenetic relationship of several K.pneumoniae isolates. One of the isolates does not seem to be K.pneumoniae as indicated by analysis of the cgMLST.

In order to identify the species, I used Kraken (Minkraken 8GB Database). However, Kraken was not able to clearly identify the species: 91% was identified as Enterobacteriaceae and of these only 36% were identified as K.quasipneumoniae and 20% as K.pneumoniae.

Then I used Centrifuge: Similar to kraken, 92.5% were identified as Enterobacteriaceae; but only 43.8 as K.variicola

StrainSeeker (web-based tool) revealed:
Strain: Klebsiella_variicola_strain_HKUOPLA
Relative frequency in sample:100%
Thus, StrainSeeker seems to clearly identify the species.

I also used the web-based tool "ContEst16S" to extract the 16S and run Mole Blast. I am not sure what these results indicate (see picture).

How may I clearly identify the species?

I had a similar problem with Acinetobacter species (see files). Here, Mole Blast indicates that the isolate is A. bereziniae while Centrifuge, Kraken and StrainSeeker are not able to clearly identify the species.
Attached Files
File Type: txt Kraken_Klebsiella.txt (1.1 KB, 3 views)
File Type: txt Centrifuge_Klebsiella.txt (989 Bytes, 2 views)
File Type: pdf MoleBlast_Klebsiella.pdf (12.9 KB, 4 views)
File Type: txt Kraken_Aci.txt (1.6 KB, 3 views)
File Type: txt Centrifuge_Aci.txt (2.9 KB, 2 views)
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Old 04-17-2018, 05:34 AM   #2
SK-N-BE
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Default

Here are the 2 remaining files
Attached Images
File Type: jpg StrainSeeker_Aci.jpg (41.9 KB, 5 views)
Attached Files
File Type: pdf MoleBlast_Aci.pdf (11.9 KB, 3 views)
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Old 04-25-2018, 06:23 AM   #3
ssbiest
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Default

Hi

The reason StrainSeeker outputs multiple related strains is because it is the best answer for the current database (assuming the sample is A. bereziniae).

On the StrainSeeker homepage, there's a file describing the database: http://bioinfo.ut.ee/strainseeker/downloads/info.txt

which contains these Acinetobacter strains:
Quote:
Acinetobacter_baumannii_NCGM_237_DNA
Acinetobacter_sp_TTH0-4
Acinetobacter_baumannii_MDR-ZJ06
Acinetobacter_baumannii_MDR-TJ
Acinetobacter_baumannii_strain_6200
Acinetobacter_baumannii_AB0057
Acinetobacter_baumannii_LAC-4
Acinetobacter_johnsonii_XBB1
Acinetobacter_oleivorans_DR1
Acinetobacter_sp_114
Acinetobacter_baumannii_str_AYE
Acinetobacter_baumannii_strain_AB031
Acinetobacter_baumannii_strain_6411
Acinetobacter_baumannii_D1279779
Acinetobacter_baumannii_strain_AC29
Acinetobacter_baumannii_strain_AB030
Acinetobacter_baumannii_DNA
Acinetobacter_baumannii_BJAB0868
Acinetobacter_calcoaceticus_PHEA-2_chromosome
Acinetobacter_baumannii_Ab04-mff
Acinetobacter_baumannii_strain_XH386
Acinetobacter_baumannii_strain_A1
Acinetobacter_baumannii_ZW85-1
Acinetobacter_baumannii_BJAB07104
Acinetobacter_baumannii_AB307-0294
Acinetobacter_baumannii_strain_AbH12O-A2
Acinetobacter_baumannii_1656-2
Acinetobacter_baumannii_strain_AB5075-UW
Acinetobacter_baumannii_TYTH-1
Acinetobacter_baumannii_ATCC_17978-mff
Acinetobacter_baumannii_genome_assembly_CIP7010
Acinetobacter_baumannii_BJAB0715
Acinetobacter_baumannii_genome_assembly_R2090
Acinetobacter_baumannii_ACICU
Acinetobacter_sp_ADP1_complete_genome
If you're identifying specific strains, you could build your own custom small database with just the species you need.
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Old 04-27-2018, 02:37 AM   #4
SK-N-BE
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Thank you ssbiest. I tried to build my own Kraken Acinetobacter database and used a lot of time. However, I was not able. Thus, I have to wait until I have more time to further work on it.
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