Supplementary Table S1: Bacterial Species and Strains Used in This Study

SupplementaryMaterial

Figure S1 A

Figure S1 B

Figure S1 C

Figure S1. Amplification curves for multiplex real-time PCR diagnostics assay. Fig.S1A Real-time amplification curves for 3 strains of P. aeruginosa (DSM 50071T, DSM 19880, DSM 1117) (triangles) targeting the ssrA gene in the HEX channel (523-568 nm); Fig S1B Amplification curves for the Burkholderia genus (circles) targeting the rnpB gene in the FAM channel (483-533 nm); Fig. S1C Amplification curves for the IAC in TYE665 channel (615-670 nm). All samples detected except the non-template control sample (diamonds).

Figure S2 A

Figure S2 B

Figure S2.Sensitivity of the P. aeruginosa specific diagnostics assay.Fig.S2A Real-time amplification curves showing sensitivity (serial dilutions of P. aeruginosa DSM 19880 DNA from 106 GE to 10 GE) of the P. aeruginosa specific diagnostics assay; Fig.S2B Standard curve representing above serial dilutions.

Supplementary Table S1: Bacterial species and strains used in this study.

Species / Strain designationa,b / Remark
P. aeruginosa / DSM 50071 / Type strain
P. aeruginosa PA01 / DSM 19880 / Isolated from human, infected wound
P. aeruginosa / DSM 1117 / Isolated from human blood culture
P. aeruginosa / DSM 288 / NA
P. aeruginosa / DSM 1253 / NA
P. aeruginosa / DSM 1299 / Isolated from human sputum
P. aeruginosa / DSM 1707 / NA
P. aeruginosa / DSM 3227 / Isolated from urine
P. aeruginosa / DSM 11148 / NA
P. aeruginosa / DSM 46349 / Isolated from human
P. aeruginosa / DSM 1128 / Isolated from outer ear infection
P. aeruginosa / DSM 24599 / Isolated from urine
P. aeruginosa / DSM 46358 / Isolated from human
P. aeruginosa / DSM 50073 / NA
P. putida / DSM 291 / Type strain isolated from lactate enrichment
P. alcaligenes / LMG 1224 / Type strain isolated from swimming pool water
P. chlororaphis / LMG 5004 / Type strain isolated from contaminated plate
P. mendocina / LMG 1223 / Type strain isolated from soil enriched with ethanol
P. flavescens / LMG 18387 / Type strain isolated from English walnut tree, canker tissue
P. resinovorans / LMG 2274 / Type strain isolated from soil
P. syringae / LMG1247PVRS / Type strain isolated from Syringa vulgaris
P. fluorescens / LMG 1794 / Type strain isolated from pre-filter water-works tanks
P. nitroreducens / LMG 21614 / Type strain isolated from oil brine
P. oleovorans / LMG 2229 / Type strain isolated from oil-water emulsion used as lubricant and cooling agent in cutting and grinding of metals
P. stutzerii / LMG 11199 / Type strain isolated from spinal fluid
P. pertucinogena / LMG 1874 / Type strain of clinical origin
B. cepacia / DSM 7288 / Type strain isolated from onion
B. contaminans / DSM 22706 / Type strain isolated from milk of sheep with mastitis
B. diffusa / DSM 23434 / Type strain isolated from sputum of patient with cystic fibrosis
B. endofungorum / DSM 19003 / Type strain isolated from fungus Rhizopus microsporus
B. ferrariae / LMG 23612 / Type strain isolated from iron mine
B. rhizoxinica / DSM 19002 / Type strain isolated from fungus Rhizopus microsporus
B. seminalis / DSM 23518 / Type strain isolated from human sputum from cystic fibrosis patient
B. sordidicola / LMG 22029 / Type strain isolated from Phanerochaetesordida collected from Quercus acutissima
B. stabilis / DSM 16586 / Type strain isolated from cystic fibrosis patient
B. tropica / LMG 22274 / Type strain isolated from sugarcane, roots

a*DSM = The German Collection of Microorganisms; * LMG=LaboratoriumvoorMicrobiologie -Belgian Co-ordinated Collections of Micro-organisms

bPVRS= Pathovar reference strain

Supplementary Table S2: Other species and strains of microorganisms used in this study.

Species / Strain designation a / Remark
Ralstoniapickettii / DSM 6297 / Type strain
Ralstoniapickettii / LMG 7009 / Isolated from trachea
Ralstonia sp. / DSM 13640 / Isolated from activated sludge
Ralstoniasyzygii / DSM 7385 / Type strain isolated from clove Syzygium aromaticum
Ralstoniamannitolytica / DSM 17512 / Type strain isolated from blood
Ralstoniainsidiosa / DSM 17714 / Type strain isolated from human sputum of patient with leukemia
Cupriavidusbasilensis / DSM 11853 / Type strain isolated from laboratory fixed bed reactor
Cupriaviduspauculus / DSM 17313 / Type strain isolated from human endotrachea
Cupriavidus necator / DSM 13513 / Type strain isolated from soil
Cupriavidusmetallidurans / DSM 2839 / Type strain isolated from decantation tank of zinc factory
Cupriavidusrespiraculi / DSM 17358 / Type strain isolated from respiratory tract of patient with cystic fibrosis
Cupriavidusgilardii / DSM 17292 / Type strain isolated from whirlpool
Cupriavidusoxalaticus / DSM 1105 / Type strain isolated from garden soil
Cupriavidustaiwanensis / DSM 17343 / Type strain isolated from root nodule of Mimosa pudica
Cupriaviduscampensis / DSM 17293 / Type strain isolated from zinc desertified site
Acinetobacter baumanii / DSM 30007 / Type strain isolated from urine
Acinetobacter iwoffii / DSM 2403 / Type strain
Alcaligenes faecalis / DSM 30030 / Type strain
Bacillus subtilis / DSM 704 / Strain 2a
Bordetella pertussis / DSM 4923 / Serovar: 1,2
Bordetella parapertussis / DSM 13415 / Type strain isolated from patient with whooping cough
Bordetella bronchiseptica / DSM 13414 / Type strain isolated from dog lung
Citrobacter freundii / DSM 30039 / Type strain
Enterobacter aerogenes / DSM 30053 / Type strain isolated from sputum
Haemophilus influenzae / DSM 24049 / Type strain isolated from human sputum, pneumonia patient
Haemophilus parainfluenzae / DSM 8978 / Type strain isolated from septic finger
Klebsiella oxytoca / DSM 5175 / Type strain isolated from pharyngeal tonsil
Klebsiella pneumoniae / DSM 16358 / Type strain isolated from human nose
Legionella pneumophila / DSM 7514 / Type strain isolated from human lung tissue
Moraxella catarrhalis / DSM 11994 / Isolated from transtracheal aspirate from coal miner with chronic bronchitis
Morganella morganii / DSM 30164 / Type strain isolated from stool of summer diarrhea case
Mycobacterium tuberculosis / ATCC 51910 / Isolated from human sputum
Mycoplasma buccale / NCTC 10136 / Type strain isolated from human oropharynx
Neisseria meningitidis / DSM 10036 / Type strain isolated from spinal fluid from fatal case of meningitis
Proteus mirabilis / DSM 4479 / Type strain
Providenciastuartii / DSM 4539 / Type strain
Serratia marcescens / DSM 1608 / NAb
Staphylococcus epidermidis / DSM 20044 / Type strain isolated from nose
Stenotrophomonasmaltophilia / DSM 50170 / Type strain isolated from oropharyngeal region of patient with cancer
Streptococcus pneumoniae / DSM 11865 / Isolated from clinical source
Candida albicans / CBS 562 / Isolated from foot of person with interdigital mycosis

a *DSM=German Collection of Microorganisms and cell cultures; * LMG=LaboratoriumvoorMicrobiologie- Belgian Co-ordinated Collections of Micro-organisms; *NCTC National Collection of Type Cultures; *ATCC American Type Culture Collection; CBS= CentraalbureauvoorSchimmelcultures, Netherlands.

b Information not available (NA)

Supplementary Table S3: Accession numbers of P. aeruginosa strains and Burkholderia species/strains.

Organism / GenBank ID:
P. aeruginosa PAO1 / NC_002516
P. aeruginosa LESB58 / NC_011770.1
P. aeruginosa 39016 / AEEX01000009.1
P. aeruginosa PAb1 / ABKZ01000454.1
P. aeruginosa PACS2 / AAQW01000001.1
P. aeruginosa 2192 / AAKW01000081.1
P. aeruginosa UCBPP-PA14 / CP000438.1
P. aeruginosa C3719 / AAKV01000120.1
P. aeruginosa PA7 / CP000744.1
P. aeruginosa NCGM2.S1 / AP012280.1
P. aeruginosa M18 / CP002496.1
P. aeruginosa 152504 / AEVW01000017
P. aeruginosa AES-1R / AFNF01000829.1
P. aeruginosa 9BR / AFXI01000001.1
P. aeruginosa 19BR / AFXJ01000001.1
P. aeruginosa 213BR / AFXK01000001.1
P. aeruginosa MPAO1/P1 / AHKM01000035.1
Burkholderia sp. Ch1-1 / ADNR02000018
Burkholderia sp. YI23 / NC_016589
Burkholderia sp. 383 / NC_007510
Burkholderia sp. TJI49 / AEXE01000916
Burkholderia sp. CCGE1001 / NC_015136
Burkholderia sp. CCGE1002 / NC_014117
Burkholderia sp. CCGE1003 / NC_014539
Burkholderia sp. H160 / ABYL01000030
Burkholderia sp. SJ98 / AJHK01000006
B. ambifariaMEX-5 / ABLK01000420
B. ambifariaMC40-6 / NC_010551
B. ambifariaAMMD / NC_008390
B. ambifariaIOP40-10 / ABLC01000058
B. cenocepaciaJ2315 / NC_011000
B. cenocepaciaH111 / CAFQ01000050
B. cenocepaciaHI2424 / NC_008542
B. cenocepacia AU 1054 / NC_008060
B. cenocepaciaMC0-3 / NC_010508
B. dolosaAUO158 / AAKY01000118
B. gladioli BSR3 / NC_015381
B. glumaeBGR1 / NC_012724
B. graminisC4D1M / ABLD01000065
B. malleiNCTC 10247 / NC_009080
B. malleiATCC 23344 / NC_006348
B. malleiSAVP1 / NC_008785
B. malleiATCC 10399 / AAHN02000004
B. malleiNCTC 10229 / NC_008836
B. malleiGB8horse4 / AAHO01000003
B. malleiFMH / AAIQ02000022
B. malleiJHU / AAIR02000022
B. mallei 2002721280 / AANX02000066
B. malleiPRL-20 / AAZP01000002
B. multivoransCGD1 / ACFB01000011
B. multivoransCGD2M / ACFD01000014
B. multivoransATCC 17616 / NC_010084
B. oklahomensisEO147 / ABBF01000405
B. oklahomensisC6786 / ABBG01000276
B. phymatumSTM815 / NC_010622
B. phytofirmansPsJN / NC_010681
B. pseudomallei406e / AAMM02000006
B. pseudomallei1106b / AAMB02000020
B. pseudomalleiB7210 / ABBN01000660
B. pseudomallei 7894 / ABBO01000738
B. pseudomallei Pasteur 52237 / AAHV02000073
B. pseudomallei1710a / AAHS03000017
B. pseudomalleiBp22 / AFBJ01000263
B. pseudomallei 576 / ACCE01000003
B. pseudomallei1106a / NC_009076
B. pseudomallei DM98 / ABBI01001062
B. pseudomalleiBCC215 / ABBR01000447
B. pseudomallei1710b / NC_007434
B. pseudomalleiK96243 / NC_006350
B. pseudomallei 668 / NC_009074
B. pseudomallei 305 / AAYX01000005
B. pseudomallei Pakistan 9 / ACKA01000035
B. pseudomallei 112 / ABBP01000585
B. pseudomallei 9 / ABBL01000798
B. pseudomallei 1655 / AAHR02000006
B. pseudomalleiNCTC 13177 / ABBQ01000497
B. pseudomallei 91 / ABBK01000781
B. pseudomallei 14 / ABBJ01000848
B. pseudomalleiMSHR346 / NC_012695
B. rhizoxinicaHKI 454 / NC_014722
B. thailandensisE555 / AECN01000331
B. thailandensisBt4 / ABBH01000528
B. thailandensisTXDOH / ABBD01000514
B. thailandensisE264ATCC 700388 / AACX01000007
B. thailandensisMSMB43 / ABBM01000516
B. ubonensis Bu / ABBE01000351
B. vietnamiensisG4 / NC_009256
B. xenovoransLB400 / NC_007951