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


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, 2 views)
File Type: txt Centrifuge_Aci.txt (2.9 KB, 1 views)
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Old 04-17-2018, 04:34 AM   #2
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Here are the 2 remaining files
Attached Images
File Type: jpg StrainSeeker_Aci.jpg (41.9 KB, 3 views)
Attached Files
File Type: pdf MoleBlast_Aci.pdf (11.9 KB, 2 views)
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