DOI: 10.1128/JCM.42.12.5644-5649.2004
Article Figures & Data
Tables
- TABLE 1.
Properties of the P. aeruginosa strains used for validationa
Strain ST BURST group Allelic profile Sero- type toxA type Hospital, center, or geographic source Isolation site Date of isolation (mo-yr) Soil isolate (n = 2) 145 17, 35, 36, 3, 14, 4, 7 NA Wellesbourne, UK Soil Jan-99 Midlands 1 epidemic 116 17, 20, 1, 3, 13, 6, 7 NA NA Sputum 8623 110 15, 5, 1, 3, 2, 12, 7 NA 07.06.06 T6 NA NA PA0093 83 1 11, 5, 1, 3, 14, 17, 7 PA Folkestone, UK Tissue sample Nov-01 PA0092 82 1 32, 5, 24, 3, 14, 17, 7 O11 Wycombe, UK Blood Nov-01 1353 M 100 33, 3, 3, 3, 4, 12, 7 NA Wellesbourne, UK Mushroom compost 7874 129 2 6, 5, 6, 7, 2, 6, 7 O3 07.03.22 T31 West Yorkshire, UK NA 7916 119 2 6, 5, 6, 7, 3, 6, 7 O11 10.08.10 T13 Bristol, UK NA 8184 27 2 6, 5, 6, 7, 4, 6, 7 O11 04.08.10 T5 Queen Mary's, UK NA 8101 27 2 6, 5, 6, 7, 4, 6, 7 O11 10.08.17 T7 Stourbridge, UK NA 6954 27 2 6, 5, 6, 7, 4, 6, 7 O4 04.06.11 T10 Glasgow, UK NA 6338 27 2 6, 5, 6, 7, 4, 6, 7 O12 02.02.02 T17 NA NA 4587 27 2 6, 5, 6, 7, 4, 6, 7 O11 10.08.09 T14 Boston, UK NA 7627 11 2 6, 5, 6, 7, 4, 6, 3 O4 01.01.01 T1 Croydon, UK NA 2359 Canada 7 2 6, 5, 6, 7, 4, 6, 1 NA Canada Oil-contaminated aquifer Jan-87 8281 15 2 12, 5, 6, 7, 4, 6, 7 NA NA NA 8122 128 2 6, 5, 6, 8, 21, 6, 7 O1 03.10.15. T12 Mid-Glamorgan, UK NA 5798 122 2 6, 5, 6, 8, 2, 6, 7 NA NA NA 6563 10 8, 5, 8, 8, 4, 6, 7 O3 01.01.01 T1 Blackburn, UK NA PA0051 44 4, 5, 6, 7, 1, 16, 7 O9 Luton, UK Sputum Aug-02 PA0074 66 30, 10, 23, 5, 4, 2, 7 O4 Dorset, UK Blood Mar-02 PA0050 43 25, 5, 17, 5, 4, 15, 7 O11 Chelsea, UK Wound swab Sep-02 PA0040 33 19, 5, 15, 3, 4, 12, 7 O11 Birmingham, UK NA Nov-02 PA0029 25 19, 5, 12, 7, 4, 10, 7 O6 Manchester, UK Sputum Jan-03 Clone C 142 3 11, 5, 1, 7, 9, 26, 7 NA Sputum 8735 17 3 11, 5, 1, 7, 9, 4, 7 O1 01.01.01 T1 Birmingham, UK NA 8277 14 3 11, 5, 1, 7, 9, 8, 7 O1 01.01.01 T1 Durham, UK NA Clone C genotype P10118 117 3 11, 20, 1, 7, 9, 4, 32 NA NA Sputum Clone C genotype P10119 115 3 11, 20, 1, 7, 9, 4, 7 NA NA Sputum PA0100 90 39, 25, 9, 7, 9, 20, 7 O1 Northampton, UK NA Sep-01 PA0072 64 28, 4, 22, 7, 9, 10, 7 O15 Ormskirk, UK Urine Apr-02 Melbourne 141 11, 33, 11, 31, 23, 4, 7 NA NA Sputum PA0105 95 7, 4, 7, 5, 2, 7, 7 O6 London, UK NA Aug-01 PA0049 42 4, 13, 16, 5, 2, 7, 7 O11 London, UK Bronccoalveolar lavage fluid Sep-02 PA0075 67 31, 4, 6, 5, 2, 6, 7 O11 Birmingham, UK NA Mar-02 PA0057 50 26, 17, 11, 5, 2, 4, 7 O6 Newcastle, UK Blood Jul-02 Manchester 143 17, 34, 11, 18, 4, 13, 3 NA NA Sputum PA0044 37 23, 16, 11, 4, 4, 6, 3 O7 Leeds, UK Blood Oct-02 PA0036 124 4 20, 8, 5, 4, 4, 4, 3 O6 Cheshire, UK NA Dec-02 8756 113 4 17, 5, 5, 4, 19, 4, 3 O12 06.04.00 T4 France NA 8722 111 4 17, 5, 5, 4, 4, 4, 3 O12 06.04.00 T4 Belfast, UK NA 6950 102 4 15, 5, 5, 3, 4, 4, 3 O12 06.04.00 T4 Southport, UK NA PA0108 97 4 11, 5, 1, 4, 4, 20, 3 O1 Bristol, UK NA Jul-01 PA0061 53 4 11, 5, 19, 4, 4, 4, 3 PA Brighton, UK Sputum Jun-02 1330 M 4 3, 3, 4, 4, 4, 4, 3 NA Wellesbourne, UK Mushroom compost 8103 133 1, 20, 32, 3, 4, 25, 3 O3 07.08.17 T34 St. Mary's, UK NA 7272 134 23, 20, 7, 30, 4, 4, 10 O6 04.08.05 T24 Cumbria, UK NA PA0098 88 22, 4, 17, 7, 4, 13, 7 PA London, UK Blood Oct-01 PA0068 60 28, 4, 17, 15, 4, 4, 3 O4 Nottingham, UK Tissue sample May-02 8440 132 6, 20, 1, 3, 4, 4, 2 O6 10.08.03 T41 Carmarthen, UK NA PA0094 84 6, 11, 1, 5, 4, 4, 27 O4 Bristol, UK NA Nov-01 PA0107 96 6, 5, 1, 11, 17, 7, 2 O6 Leicester, UK Sputum Aug-01 PA0020 18 6, 4, 1, 11, 4, 7, 10 PA Stafford, UK NA Feb-03 7306 135 6, 20, 11, 7, 1, 12, 19 6 06.09.13 T25 Queen Elizabeth II NA 8113 106 22, 20, 11, 23, 1, 3, 3 O11 10.08.09 T4 Conquest NA PA0076 68 32, 20, 24, 3, 1, 17, 15 O11 Dublin, Ireland Blood Mar-02 PA0043 36 11, 15, 11, 3, 1, 14, 15 O1 York, UK NA Oct-02 PA0034 28 15, 10, 11, 3, 2, 7, 12 NT London, UK Blood Dec-02 PA0022 20 15, 5, 11, 3, 1, 7, 11 O6 Cheshire, UK Sputum Feb-03 Liverpool a 114 11, 20, 11, 3, 4, 23, 1 NA Liverpool, UK Sputum PA0067 59 11, 4, 11, 11, 4, 12, 20 O11 London, UK NA May-02 8364 130 5, 8, 25, 28, 4, 24, 34 O3 01.02.18 T38 University College, UK NA PA0097 87 5, 24, 25, 21, 4, 4, 7 O3 London, UK Bronccoalveolar lavage fluid Oct-01 8405 127 43, 30, 31, 26, 4, 24, 32 O8 Atyp 4 T49 Bangor, UK NA 5973 131 6, 5, 11, 29, 11, 15, 1 NA NA NA 8734 112 6, 5, 1, 25, 1, 12, 1 O6 06.03.14 T11 Stoke/Trent, UK NA PA0089 125 36, 1, 28, 1, 1, 7, 1 PA London, UK NA Dec-01 NCTC 10662 1 1, 1, 1, 1, 1, 1, 1 NA NA NA Apr-69 7186 103 17, 5, 12, 22, 14, 22, 29 O11 04.08.10 T5 Truro, UK NA PA0084 76 17, 21, 12, 5, 1, 17, 1 O4 London, UK Blood Jan-02 PA0024 21 16, 5, 12, 11, 1, 2, 1 O3 Bedford, UK Skin Jan-03 PA0026 123 17, 5, 5, 1, 10, 12, 2 O6 Sheffield, UK NA Jan-03 PA0101 91 17, 5, 5, 1, 1, 21, 1 O11 Windsor, UK Blood Sep-01 PA0054 47 17, 5, 5, 12, 1, 10, 16 PA London, UK Sputum Aug-02 PA0070 62 2, 5, 5, 16, 3, 1, 19 O11 London, UK Blood May-02 PA0062 54 2, 5, 5, 11, 4, 4, 16 O11 Leeds, UK Hospital sink Jun-02 8386 121 11, 5, 7, 27, 1, 7, 33 O1 09.11.10 T40 Wexham, UK NA 5670 8 7, 5, 7, 3, 7, 1, 6 O11 10.08.04 T16 Scunthorpe, UK NA PA0102 92 40, 5, 30, 3, 1, 4, 8 O9 London, UK NA Sep-01 PA0053 46 5 4, 5, 16, 3, 1, 17, 13 O9 Lincoln, UK Urine Aug-02 PA0045 38 5 4, 5, 16, 3, 1, 4, 13 O3 Wolverhampton, UK Blood Oct-02 PA0046 39 5 18, 5, 5, 3, 1, 6, 13 O11 Folkestone, UK Blood Oct-02 PA0038 31 5 21, 5, 5, 3, 1, 4, 13 O14 Ashton under Lyme, UK NA Nov-02 PA0037 30 5 15, 12, 5, 3, 1, 4, 13 O10 London, UK Blood Nov-02 PA0090 81 37, 5, 29, 3, 4, 4, 26 O6 Folkestone, UK NA Nov-01 8318 108 39, 5, 20, 5, 1, 6, 31 O6 01.01.23 T3 Sutton, UK NA PA0081 73 33, 5, 25, 20, 1, 6, 24 O10 London, UK Blood Jan-02 PA0104 94 24, 5, 3, 5, 16, 6, 28 O6 Leicester, UK Hospital floor Aug-01 PA0111 126 5, 27, 5, 13, 1, 13, 4 O6 Nottingham, UK Blood Jul-01 PA0095 85 5, 11, 3, 13, 1, 4, 4 O4 London, UK Blood Oct-01 PA0103 93 22, 5, 11, 13, 1, 15, 4 O14 Leeds, UK Blood Sep-01 PA0066 58 4, 5, 16, 13, 1, 2, 4 O4 Nottingham, UK NA May-02 PA0055 48 6, 5, 4, 13, 1, 4, 4 PA Newcastle on Tyne, UK Blood Jul-02 PA0063 55 27, 5, 20, 13, 1, 2, 8 O6 Bedford, UK Blood Jun-02 PA0083 75 17, 5, 26, 13, 1, 17, 25 O6 Brompton, UK NA Jan-02 PA0099 89 13, 8, 5, 13, 1, 7, 25 O7 Folkestone, UK Sputum Sep-01 8297 16 13, 8, 9, 3, 1, 9, 9 O11 10.08.17 T7 Ports; mouth, UK NA 8382 109 6 4, 4, 16, 24, 1, 6, 3 O10 05.03.05 T2 Whippscross, UK NA 8202 107 6 4, 4, 16, 21, 1, 6, 1 O10 05.03.05 T2 St. Thomas, UK NA 7215 104 6 4, 4, 16, 3, 1, 6, 30 O11 05.03.05 T2 Bath, UK NA 8237 13 10, 4, 5, 10, 1, 6, 3 O10 05.03.05 T2 St. Bar, UK NA PA0077 69 7 28, 4, 3, 3, 1, 6, 11 O11 Dudley, UK Sputum Mar-02 PA0069 61 7 13, 4, 9, 3, 1, 6, 11 O15 Gloucester, UK Sputum May-02 PA0096 86 38, 4, 3, 3, 15, 15, 3 PA London, UK Blood Oct-01 PA0087 79 34, 11, 3, 12, 1, 13, 3 O11 London, UK Staff hands, intensive care Dec-01 PA0056 49 8 24, 5, 3, 12, 1, 6, 3 NT Surrey, UK NA Jul-02 1346 M 41 8 24, 3, 3, 12, 1, 7, 3 NA Wellesbourne, UK Mushroom compost PA0065 57 8 11, 5, 1, 12, 1, 12, 3 O12 London, UK Blood May-02 PA0060 52 8 11, 19, 12, 12, 1, 6, 3 O11 Wycombe, UK Sputum Jun-02 PA0052 45 8 11, 5, 12, 12, 1, 6, 3 O9 Lincoln, UK Sputum Aug-02 PA0085 77 17, 22, 12, 12, 1, 18, 3 O4 Nottingham, UK Hospital floor Jan-02 PA0073 65 29, 4, 16, 12, 1, 18, 21 O10 London, UK Blood Apr-02 PA0082 74 4, 5, 1, 19, 13, 7, 23 O3 Wycombe, UK Blood Jan-02 PA0080 72 4, 4, 16, 19, 13, 10, 23 PA York, UK Sputum Feb-02 PA0047 40 4, 5, 16, 11, 11, 7, 14 O7 Chelsea, UK Wound swab Sep-02 PA0041 34 4, 5, 16, 3, 3, 7, 3 O9 Luton, UK Sputum Nov-02 PA0078 70 4, 4, 16, 17, 10, 12, 22 PA London, UK Sputum Feb-02 7193 120 17, 22, 5, 3, 4, 14, 3 O4 09.08.11 T22 Milton Keynes, UK NA 4785 101 7, 22, 5, 3, 3, 14, 19 O4 04.06.11 T10 Kings College, UK NA PA0064 56 13, 17, 5, 14, 3, 6, 19 O6 Telford, UK Wound swab Jun-02 8420 118 9 6, 6, 4, 3, 20, 4, 7 O1 01.13.15 T15 Hope, UK NA 5757 9 9 6, 6, 4, 3, 3, 4, 7 O1 01.01.01 T1 Toulouse, France NA 7433 105 42, 28, 4, 3, 18, 4, 7 O1 03.10.15 T12 Leicester, UK NA PA0109 98 41, 12, 4, 3, 3, 4, 14 O10 Cheshire, UK Blood Jul-01 PA0110 99 17, 26, 5, 3, 3, 4, 7 O11 Brighton, UK NA Jul-01 PA0079 71 28, 4, 5, 18, 3, 4, 7 O11 Bristol, UK NA Feb-02 PA0086 78 11, 11, 11, 3, 3, 19, 19 PA Stoke, UK Catheter Dec-01 PA0042 35 22, 14, 17, 3, 3, 6, 7 O6 Glasgow, UK Sputum Oct-02 PA0035 29 7, 11, 14, 3, 3, 2, 7 O11 London, UK Blood Dec-02 PA0030 26 16, 8, 1, 3, 3, 13, 3 PA Cheshire, UK NA Dec-02 PA0025 22 6, 4, 4, 3, 3, 11, 2 O4 Northampton, UK Tissue sample Jan-03 1329 M 3 1, 2, 3, 3, 3, 3, 2 NA Wellesbourne, UK Mushroom compost 1997 PA0059 51 24, 19, 3, 3, 11, 10, 18 NT Luton, UK Eye Jul-02 PA0088 80 35, 23, 27, 6, 6, 4, 5 O1 London, UK Trachea Dec-01 PA0021 19 14, 9, 10, 6, 6, 10, 5 PA Dudley, UK Vaginal swab Feb-03 2351 M 6 5, 4, 5, 6, 6, 5, 5 NA Wellesbourne, UK Mushroom compost PA0071 63 5, 4, 21, 5, 12, 10, 15 O15 Ormskirk, UK Urine Apr-02 PA0027 23 10 18, 4, 5, 5, 5, 4, 4 O15 Tyne and Wear, UK Urine Jan-03 1349 M 5 10 4, 3, 5, 5, 5, 4, 4 NA Wellesbourne, UK Mushroom compost PA0039 32 18, 13, 13, 11, 11, 4, 14 O11 London, UK Venous line Nov-02 PA0028 24 18, 5, 13, 11, 2, 6, 2 PA Tyne and Wear, UK Urine Jan-03 8079 12 9, 7, 2, 9, 8, 7, 8 NA NA NA 1327 M 2 2, 2, 2, 2, 2, 2, 2 NA Wellesbourne, UK Mushroom compost ↵a Symbols and abbreviations: NA, not available; NT, nontypeable; UK, United Kingdom; boldface, epidemic clones.
- TABLE 2.
Functions and genome positions of the seven loci used in the P. aeruginosa typing scheme
Locus Putative function of gene (strain) Position in PAO1 genome (base pair) acsA Acetyl coenzyme A synthetase (PA0887) 969670 aroE Shikimate dehydrogenase (PA0025) 26711 guaA GMP synthase (PA3769) 4227237 mutL DNA mismatch repair protein (PA4946) 5551681 nuoD NADH dehydrogenase I chain C, D (PA2639) 2983963 ppsA Phosphoenolpyruvate synthase (PA1770) 1914037 trpE Anthralite synthetase component I (PA0609) 670980 - TABLE 3.
Dideoxyoligonucleotide primers used for P. aeruginosa MLST
Locus and function Primer sequence (5′ to 3′) Amplicon size (bp) Forward Reverse acsA Amplification ACCTGGTGTACGCCTCGCTGAC GACATAGATGCCCTGCCCCTTGAT 842 Sequencing GCCACACCTACATCGTCTAT GTGGACAACCTCGGCAACCT 390 aroE Amplification TGGGGCTATGACTGGAAACC TAACCCGGTTTTGTGATTCCTACA 825 Sequencing ATGTCACCGTGCCGTTCAAG TGAAGGCAGTCGGTTCCTTG 495 guaA Amplification CGGCCTCGACGTGTGGATGA GAACGCCTGGCTGGTCTTGTGGTA 940 Sequencing AGGTCGGTTCCTCCAAGGTC TCAAGTCGCACCACAACGTC 372 mutL Amplification CCAGATCGCCGCCGGTGAGGTG CAGGGTGCCATAGAGGAAGTC 940 Sequencing AGAAGACCGAGTTCGACCAT ATGACTTCCTCTATGGCACC 441 nuoD Amplification ACCGCCACCCGTACTG TCTCGCCCATCTTGACCA 1,042 Sequencing ACGGCGAGAACGAGGACTAC TTCACCTTCACCGACCGCCA 366 ppsA Amplification GGTCGCTCGGTCAAGGTAGTGG GGGTTCTCTTCTTCCGGCTCGTAG 989 Sequencing GGTGACGACGGCAAGCTGTA TCCTGTGCCGAAGGCGATAC 369 trpE Amplification GCGGCCCAGGGTCGTGAG CCCGGCGCTTGTTGATGGTT 811 Sequencing TTCAACTTCGGCGACTTCCA GGTGTCCATGTTGCCGTTCC 441 - TABLE 4.
Analysis of the seven loci in the P. aeruginosa population sampled
Locus Fragment size (bp) No. of alleles No. of variable sites % Variable sites dN/dS acsA 390 43 32 8.2 0.03 aroE 495 35 33 6.7 0.087 guaA 372 36 24 6.5 0.02 mutL 441 31 26 5.9 0.051 nuoD 366 23 25 6.8 0.033 ppsA 369 26 25 6.8 0.06 trpE 441 35 37 8.4 0.017
