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Table 3 Comparative pathogenomics of mutations present in the major virulence factors of RP isolates respect to the prototype strain PAO1 and evaluation in others P. aeruginosa sequenced strains

From: Comparative genomics and biological characterization of sequential Pseudomonas aeruginosa isolates from persistent airways infection

Virulence factors

ORFs

PAO11

PA141

LESB581

PA71

RP12

RP452

Mutation in RP45

RP732

Mutation in RP73

Type IV Pili biosynthesis

pilA

PA4525

PA14_58730

PLES_49071

PSPA7_5161

deleted3

deleted3

 

deleted

 

pilC

PA4527

PA14_58760

PLES_49101

PSPA7_5163

deleted3

deleted3

 

deleted

 

pilO

PA5042

PA14_66640

PLES_54321

PSPA7_5779

present

present

stop codon after 138 aa

present

stop codon after 138 aa

pilV

PA4551

deleted

PLES_49341

PSPA7_5191

present

deleted4

 

deleted

 

pilW

PA4552

PA14_60290

PLES_49351

PSPA7_5192

present

deleted4

 

deleted

 

pilY2

PA4555

deleted

PLES_49381

PSPA7_5195

present

deleted4

 

deleted

 

fimT

PA4549

deleted

PLES_49321

PSPA7_5189

present

deleted3

 

deleted

 

Alginate regulation

algP/algR3

PA5253

PA14_69370

PLES_56471

PSPA7_5998

present

present

 

present

 

Pyochelin

pchD

PA4228

PA14_09240

PLES_06991

PSPA7_0872

present

present

stop codon after 276 aa

present

stop codon after 276 aa

Pyoverdin

pvdD

PA2399

PA14_33650

PLES_28971

deleted

present5

present

 

present

stop codon after 839 aa

Phospholipase D

pldA

PA3487

PA14_18970

deleted

deleted

deleted4

deleted4

 

deleted

 

N-(3-oxo-dodecanoyl)-L-homoserine lactone QS system

lasR

PA1430

PA14_45960

PLES_39841

PSPA7_3898

present

present

stop codon after 220 aa

present

stop codon after 220 aa

Type III Secretion System

pscQ

PA1694

PA14_42610

PLES_36321

deleted

present

present

 

deleted

 

pscP

PA1695

PA14_42600

deleted

deleted

present

present5

 

deleted

 

pscO

PA1696

PA14_42580

PLES_36311

deleted

present

present

 

deleted

 

pscN

PA1697

PA14_42570

PLES_36301

deleted

present

present

 

deleted

 

poPN

PA1698

PA14_42550

PLES_36291

deleted

present

present

 

deleted

 

pcr1

PA1699

PA14_42540

PLES_36281

deleted

present

present

 

deleted

 

pcr2

PA1700

PA14_42530

PLES_36271

deleted

present

present

 

deleted

 

pcr3

PA1701

PA14_42520

PLES_36261

deleted

present

present

 

deleted

 

pcr4

PA1702

PA14_42510

PLES_36251

deleted

present

present

 

deleted

 

pcrD

PA1703

PA14_42500

PLES_36241

deleted

present

present

 

deleted

 

pcrR

PA1704

PA14_42490

PLES_36231

deleted

present

present

 

deleted

 

pcrG

PA1705

PA14_42480

PLES_36221

deleted

present

present

 

deleted

 

pcrV

PA1706

PA14_42470

PLES_36211

deleted

present

present

 

deleted

 

pcrH

PA1707

PA14_42460

deleted

deleted

present

present

 

deleted

 

poPB

PA1708

PA14_42450

PLES_36201

deleted

present

present

 

deleted

 

poPD

PA1709

PA14_42440

PLES_36191

deleted

present

present

 

deleted

 

exsC

PA1710

PA14_42430

PLES_36181

deleted

present

present

 

deleted

 

exsE

PA1711

PA14_42410

deleted

deleted

present

present

 

deleted

 

exsB

PA1712

PA14_42400

PLES_36171

deleted

present

present

 

deleted

 

exsA

PA1713

PA14_42390

PLES_36161

deleted

present

present

 

deleted

 

exsD

PA1714

PA14_42380

PLES_36151

deleted

present

present

 

deleted

 

pscB

PA1715

PA14_42360

PLES_36141

deleted

present

present

 

deleted

 

pscC

PA1716

PA14_42350

PLES_36131

deleted

present

present

 

deleted

 

pscD

PA1717

PA14_42340

PLES_36121

deleted

present5

present

 

deleted

 

pscE

PA1718

PA14_42320

PLES_36111

deleted

present

present

 

deleted

 

pscF

PA1719

PA14_42310

PLES_36101

deleted

present

present

 

deleted

 

pscG

PA1720

PA14_42300

PLES_36091

deleted

present

present

 

deleted

 

pscH

PA1721

PA14_42290

PLES_36081

deleted

present

present

 

deleted

 

pscI

PA1722

PA14_42280

PLES_36071

deleted

present

present

 

deleted

 

pscJ

PA1723

PA14_42270

PLES_36061

deleted

present

present

 

deleted

 

pscK

PA1724

PA14_42260

PLES_36051

deleted

present

present

 

deleted

 

pscL

PA1725

PA14_42250

PLES_36041

deleted

present

present

 

deleted

 

LPS

lpxO2

PA0936

PA14_52150

PLES_43801

PSPA7_4774

present

present

 

present

stop codon after 145 aa

Efflux pumps

mexA

PA0425

PA14_05530

PLES_04231

PSPA7_0525

present

present

+29 aa at N-ter

present

+29 aa at N-ter

 

mexT

PA2492

PA14_32410

pseudogene

PSPA7_2746

present

present

N-ter not conserved

present

N-ter not conserved

Antibiotic resistance

arr

PA2818

deleted

deleted

PSPA7_2339

deleted3

deleted3

 

deleted

 
  1. 1Sources for PAO1, PA14, LESB58 and PA7 information are the Virulence Factor Database
  2. (http://www.mgc.ac.cn/VFs/) and Pseudomonas Database (www.pseudomonas.com)
  3. 2Identified by local blast (>90 % query coverage, >90 % sequence similarity) using the PAO1 gene sequences as query
  4. 3Presence of at least one flanking region (500 bp) confirmed by blast search on contigs; gene not located at contig edge
  5. 4Flanking regions not found, but absence of the gene is consistent with a deletion in isolate RP73
  6. 5Gene is present, but separated onto multiple contigs