Pseudomonas aeruginosa outliers

Bacterial Taxonomy
1

What is the status of Pseudomonas paraeruginosa? This was formerly referred to as “PA7-clade” or “P. aeruginosa phylogroup 3”. It has been proposed to be a new species:

https://lpsn.dsmz.de/species/pseudomonas-paraeruginosa

based on newer criteria such as AAI and ANI instead of solely rRNA. I am preparing a manuscript on the comparative genomics of 77 strains. NCBI uses “P. aeruginosa” (taxid:287) for some and P. paraeruginosa " (taxid: 2994495) for others; the change has not been done consistently.

2

Hi,

P. paraeruginosa will be introduced into the GTDB in the next release (R220). We are currently working on this release and expect to release it in March or April next year. This release isn’t finalized, but initial results indicate that:

  • GTDB representative genome for P. paraeruginosa will be GCF_002601815.1
  • This GTDB cluster will contain 58 genomes (see below)

This information could change before the final release, but this is unlikely. Hope this is helpful.

Cheers,
Donovan

[58 genomes in the P. paraeruginosa cluster]

G003839875,G001449385,G003411505,G000790465,G030131645,G003837245,G024648925,G900608035,G025717095,G001909445,G026127105,G003968475,G000791105,G003968965,G001280745,G001454675,G024495345,G901420175,G001450355,G000789725,G026127045,G016743035,G002968755,G000017205,G001444975,G006971785,G026191435,G003032395,G900706985,G026191395,G001450165,G001294675,G001402955,G001280755,G003968155,G024464635,G026126985,G026191415,G021460625,G008802575,G001452985,G004351335,G003025345,G024464615,G001280765,G025908315,G001449465,G000335395,G001449965,G001451945,G024464665,G002563335,G026284155,G001450465,G003839025,G003073695,G901542305,G003057595
3

Hi Donovan,

 Thanks for your reply.  It's nice to know that the name will be officially approved.  I looked up your assembly numbers to get the strain names, and compared your list to our spreadsheet.  I have 36 more P. paraeruginosa that are not on your list:

AS012511
14ARS-STU0205
14ARS-NKI0055
20DM006058
14ARS-GMH0014
AS012673
PSA00730
PSA01132
13ARS_VSM0177
13ARS_VSM0105
PSA00579
PSA00588
PSA00358
PSA00289
PSA00486
NMI5282_13
14ARS-EVR0071
ARLG-9239
PSA00304
ESP077
PSA00944
PSA00320
ARLG-10319
PSA00554
PSA009022
PSA00985
PSA-BAB-IMI-102528
PSA-BAB-IMI-102527
PSA00066
ARLG-10516
13ARS_BGH0067
NCGM2990
PSA00043
PSA00465
PSA00464
PSA00407
A few of your strains are newer than the cutoff date for our genomic analysis; also, in our manuscript we am omitting a few strains for poor sequence quality or for too many (>200) contigs >500 nt. Finally, strain 88 (G004351335) has been suppressed and strain NCTC11569 (G901542305) was incorrectly identified as S. dysgalactiae by the submitter but it is P. paraeruginosa.

Hope this helps,

Paul

4

Hi again Donovan,

 Here are a few recent Pseudomonas paraeruginosa strains that were not on either of our lists:

SSI-PA24 JAWLON 30-OCT-2023
PaG5 JAVRMG 24-SEP-2023
IHMA2121768 JAPUYX 09-FEB-2023
IHMA2121764 JAPUXN 09-FEB-2023
also:
PSA-BAB-IMI-102932 STNW (large number of contigs)
ATCC 9027 NIQD (another 9027)
PA09ZY10 MKEN (large number of contigs)

Paul