Supplementary Table S1. The five completely sequenced and eleven incompletely sequenced Salmonella genomes used in this study *
Sequencing project / Serovar (Strain) / Non-standard abbreviationComplete / Salmonella enterica serovar Paratyphi A ATCC 9150 (GenBank accession no. CP000026) 14 / SPA
Complete / Salmonella enterica serovar Typhi CT18 (AL513382) 16 / CT18
Complete / Salmonella enterica serovar Typhi Ty2 (AE014613) 15 / Ty2
Complete / Salmonella enterica serovar Typhimurium LT2 (AE006468) 17 / LT2
Complete / Salmonella enterica serovar Choleraesuis SC-B67 (AE017220) 18 / B67
Ongoing / Salmonella enterica serovar Dublin (Univ of Illinois at Urbana-Champaign) / SD
Ongoing / Salmonella enterica serovar Enteritidis LK5 / LK5
Ongoing / Salmonella enterica serovar Enteritidis PT4 / PT4
Ongoing / Salmonella enterica serovar Gallinarum 287/91 / SG287
Ongoing / Salmonella enterica serovar Paratyphi A (Sanger Institute) / SPA2
Ongoing / Salmonella enterica serovar Paratyphi B SPB7 / SPB7
Ongoing / Salmonella enterica serovar Pullorum (Univ of Illinois at Urbana-Champaign) / SP
Ongoing / Salmonella enterica serovar Typhimurium DT104 / DT104
Ongoing / Salmonella enterica serovar Typhimurium SL1344 / SL1344
Ongoing / Salmonella enterica diarizonae serovar 61:1,v:1,5,(7) CDC 01-0005 / SDS61
Ongoing / Salmonella bongori 12419 ATCC 43975 / SB
*Data were derived from the GOLD database 19 available at http://www.genomesonline.org/ (accessed June 2005). The five completely sequenced Salmonella genomes were downloaded from GenBank. Publicly available contigs from the 11 ongoing Salmonella genome sequencing projects were downloaded from corresponding sequencing centres.
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Supplementary Table S2. Results of the Paratyphi A-specific multiplex PCR assay for the 52 Salmonella strains identified as Paratyphi A by serotype testing
Strain / Target CDSspa0185
(159bp) / spa2473
(324bp) / spa2539
(484bp) / spa4289
(627bp)
ATCC 9150 / + / + / + / +
TKL002 / + / + / + / +
TKL003 / + / + / + / +
TKL004 / + / + / + / +
TKL005 / + (~180bp) / + / + / +
TKL006 / + (~180bp) / + / + / +
TKL007 / + / + / + / +
TKL008 / + (~180bp) / + / + / +
TKL009 / + (~180bp) / + / + / +
TKL010 / + / + / + / +
TKL011 / + / + / + / +
TKL012 / + (~180bp) / + / + / +
TKL013 / + (~180bp) / + / + / +
TKL014 / + / + / + / +
TKL015 / + / + / + / +
TKL016 / + (~180bp) / + / + / +
TKL017 / + / + / + / +
TKL018 / + / + / + / +
TKL019 / + / + / + / +
TKL020 / + / + / + / +
TKL021 / + / + / + / +
TKL022 / + / + / + / +
TKL023 / + / + / + / +
TKL024 / + / + / + / +
TKL025 / + (~180bp) / + / + / +
TKL026 / + / + / + / +
TKL027 / + / + / + / +
TKL028 / + (~180bp) / + / + / +
TKL029 / + / + / + / +
TKL030 / + / + / + / +
TKL031 / + / + / + / +
TKL032 / + (~180bp) / + / + / +
TKL033 / + / + / + / +
TKL034 / + / + / + / +
TKL035 / + / + / + / +
TKL036 / + / + / + / +
TKL037 / + / + / + / +
TKL038 / + / + / + / +
TKL039 / + (~180bp) / + / + / +
TKL040 / + / + / + / +
TKL041 / + / + / + / +
TKL042 / + / + / + / +
TKL043 / + / + / + / +
TKL044 / + / + / + / +
TKL045 / + / + / + / +
TKL046 / + / + / + / +
TKL047 / + / + / + / +
TKL048 / + / + / + / +
TKL049 / + / + / + / +
TKL050 / + / + / + / +
TKL051 / + / + / + / +
TKL052 / + / + / + / +
Supplementary Table S3. Results of the Paratyphi A-specific multiplex PCR assay for the 75 Salmonella enterica strains identified as non-Paratyphi A by serotype testing
spa0180
(159bp) / spa2473
(324bp) / spa2539
(484bp) / spa4289
(627bp)
Agona / TKL101 / - / - / - / -
Albany / TKL102 / + / - / - / -
Albany / TKL103 / + / - / - / -
Albany / TKL104 / + / - / - / -
Albany / TKL105 / + / - / - / -
Albany / TKL106 / + / - / - / -
Bareilly / TKL107 / + / - / - / +
Bareilly / TKL108 / + / - / - / +
Bareilly / TKL109 / + / - / - / +
Blockley / TKL110 / - / - / - / -
Bovismorficans / TKL111 / - / - / - / -
Braenderup / TKL112 / - / - / - / -
Chingola / TKL113 / + / - / - / -
Corvallis / TKL114 / - / - / - / -
Dublin / TKL115 / - / - / - / -
Dublin / TKL116 / - / - / - / -
Enteritidis / ATCC 13076 / - / - / - / -
Enteritidis / TKL118 / - / - / - / -
Enteritidis / TKL119 / - / - / - / -
Enteritidis / TKL120 / - / - / - / -
Enteritidis / TKL121 / - / - / - / -
Enteritidis / TKL122 / - / - / - / -
Enteritidis / TKL123 / - / - / - / -
Enteritidis / TKL124 / - / - / - / -
Enteritidis / TKL125 / - / - / - / -
Enteritidis / TKL126 / - / - / - / -
Hadar / TKL127 / - / - / - / -
Haifa / TKL128 / - / - / - / -
Houten / TKL129 / - / - / - / -
Hvittingfoss / TKL130 / - / - / - / -
Infantis / TKL131 / - / - / - / -
Kentucky / TKL132 / + / + / - / -
Kentucky / TKL133 / + / + / - / -
Kentucky / TKL134 / + / + / - / -
Kentucky / TKL135 / + / + / - / -
Kentucky / TKL136 / + / + / - / -
Lomita / TKL137 / + / - / - / -
Matopeni / TKL138 / - / - / - / -
Matopeni / TKL139 / - / - / - / -
Muenchen / TKL140 / - / - / - / -
Newport / TKL141 / + / - / - / -
Okerara / TKL142 / + / - / - / -
Paratyphi B / ATCC 8759 / + / - / - / -
Paratyphi B / TKL144 / + / - / - / -
Paratyphi B / TKL145 / + / - / - / -
Paratyphi B / TKL146 / + / - / - / -
Paratyphi B / TKL147 / + / - / - / -
Paratyphi B / TKL148 / + / - / - / -
Paratyphi B / TKL149 / + / - / - / -
Paratyphi B / TKL150 / + / - / - / -
Paratyphi C / ATCC 9068 / + / - / - / -
Paratyphi C / TKL152 / + / - / - / -
Raus / TKL153 / - / - / - / -
Supplementary Table S3. continued
Serovar / Strain / Target CDS
spa0180
(159bp) / spa2473
(324bp) / spa2539
(484bp) / spa4289
(627bp)
Thompson / TKL154 / - / - / - / -
Tschiongwe / TKL155 / + / - / - / -
Typhi / TKL156 / - / - / - / -
Typhi / TKL157 / - / - / - / -
Typhi / TKL158 / - / - / - / -
Typhi / TKL159 / - / - / - / -
Typhi / TKL160 / - / - / - / -
Typhi / TKL161 / - / - / - / -
Typhi / TKL162 / - / - / - / -
Typhi / TKL163 / - / - / - / -
Typhi / TKL164 / - / - / - / -
Typhi / TKL165 / - / - / - / -
Typhi / TKL166 / - / - / - / -
Typhi / TKL167 / - / - / - / -
Typhi / TKL168 / - / - / - / -
Typhi / TKL169 / - / - / - / -
Typhimurium / ATCC 13311 / - / - / - / -
Typhimurium / TKL171 / - / - / - / -
Virchow / TKL172 / + / - / - / -
Virchow / TKL173 / + / - / - / -
Waycross / TKL174 / - / - / + / -
Weltevreden / TKL175 / - / + / - / -
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Supplementary Table S4. Results of the Paratyphi A-specific multiplex PCR assay for the 14 non-Salmonella bacterial strains
Species / Strain / Target CDSspa0180
(159bp) / spa2473
(324bp) / spa2539
(484bp) / spa4289
(627bp)
Burkhoderia pseudomallei / TKL201 / - / - / - / -
Burkholderia pseudomallei / TKL202 / - / - / - / -
Escherichia coli / TKL203 / - / - / - / -
Escherichia coli / TKL204 / - / - / - / -
Escherichia coli / TKL205 / - / - / - / -
Klebsiella pneumoniae / TKL206 / - / - / - / -
Klebsiella pneumoniae / TKL207 / - / - / - / -
Listeria monocytogenes / ATCC 7644 / - / - / - / -
Pseudomonas aeruginosa / ATCC 27853 / - / - / - / -
Shigella boydii / TKL210 / - / - / - / -
Shigella dysenteriae 2 / TKL211 / - / - / - / -
Shigella flexneri / ATCC 12022 / - / - / - / -
Shigella sonnei / ATCC 11060 / - / - / - / -
Staphylococcus aureus / ATCC29213 / - / - / - / -
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Supplementary Table S5. Details of putative strain-specific CDS in Salmonella enterica serovar Paratyphi A strain ATCC 9150 *
No. / Start / Stop / Strand / Length (bp) / CGH† / Cluster‡ / CDS§ / Gene / Annotated protein product or similarity with representative sequence in database(Blastp E value) ¶
1 / 207989 / 209050 / -1 / 1062 / + / C1 / spa0179 / stkG / putative fimbrial protein
2 / 209062 / 209661 / -1 / 600 / + / C1 / spa0180 / stkF / putative fimbrial protein
3 / 209680 / 210237 / -1 / 558 / + / C1 / spa0181 / stkE / putative fimbrial protei
4 / 210264 / 210836 / -1 / 573 / + / C1 / spa0182 / stkD / putative fimbrial protein (transporter activity)
5 / 210871 / 213468 / -1 / 2598 / + / C1 / spa0183 / stkC / outer membrane usher protein
6 / 213536 / 214288 / -1 / 753 / + / C1 / spa0184 / stkB / putative fimbrial chaperone
7 / 214375 / 214980 / -1 / 606 / + / C1 / spa0185 / stkA / major fimbrial subunit protein
8 / 2507316 / 2507837 / -1 / 522 / - / C5 / spa2395 / - / hypothetical protein
9 / 2509699 / 2510322 / -1 / 624 / - / C5 / spa2399 / - / antitermination protein
10 / 2510319 / 2510507 / -1 / 189 / - / C5 / spa2400 / ninH / Gp68, bacteriophage HK97, AAF31143 (5e-28)
11 / 2510504 / 2510866 / -1 / 363 / - / C5 / spa2401 / Rus / holiday-junction resolvase, bacteriophage HK620, AAK28880 (1e-63)
12 / 2512177 / 2512623 / -1 / 447 / - / C5 / spa2407 / ninB / hypothetical protein Stx2IIp131, NP_859378 (2e-76)
13 / 2512580 / 2512876 / -1 / 297 / - / C5 / spa2408 / - / Orf-98, S. Typhimurium bacteriophage ST64T, NP_720307 (9e-48)
14 / 2513660 / 2515096 / -1 / 1437 / - / C5 / spa2410 / gp12 / DNA replication protein (helicase)
15 / 2515086 / 2515985 / -1 / 900 / - / C5 / spa2411 / gp18 / DNA replication protein
16 / 2568786 / 2569097 / -1 / 312 / + / C2 / spa2469 / - / hypothetical protein
17 / 2576641 / 2577102 / -1 / 462 / + / C2 / spa2472 / - / hypothetical protein
18 / 2577104 / 2577847 / -1 / 744 / + / C2 / spa2473 / - / hypothetical protein
19 / 2638739 / 2639344 / +1 / 606 / + / C3 / spa2539 / - / putative cytoplasmic protein, S. Choleraesuis SC-B67, YP_217668 (1e-63)
20 / 2699408 / 2701108 / -1 / 1701 / - / C6 / spa2602 / - / cell wall hydrolase (lysis/hydrolase activity), Haemophilus phage HP2, NP_536842 (9e-122)
21 / 2701111 / 2701602 / -1 / 492 / - / C6 / spa2603 / - / putative phage protein
22 / 2704925 / 2705500 / -1 / 576 / - / C6 / spa2607 / - / P2-like phage tail formation protein, E. coli E22, ZP_00730573 (5e-68)
23 / 2705505 / 2706638 / -1 / 1134 / - / C6 / spa2608 / - / NAD synthase, E. coli E22, ZP_00730574 (3e-150)
24 / 2706686 / 2707015 / -1 / 330 / - / C6 / spa2609 / - / translation elongation factors GTPases, E.coli E22, ZP_00730575 (1e-32)
25 / 2707012 / 2708982 / -1 / 1971 / - / C6 / spa2610 / - / putative bacteriophage tail protein, Yersinia pseudotuberculosis IP 32953, CAH22391 (5e-128)
26 / 2709170 / 2709427 / -1 / 258 / - / C6 / spa2611 / - / putative phage protein
27 / 2710244 / 2710537 / -1 / 294 / - / C6 / spa2612 / - / putative phage protein
28 / 2710547 / 2711002 / -1 / 456 / - / C6 / spa2613 / - / putative tail tube protein (ORF24), Haemophilus phage HP1, NP_043493 (6e-42)
29 / 2710999 / 2712126 / -1 / 1128 / - / C6 / spa2614 / - / topoisomerase IA, E. coli E22, ZP_00730583 (4e-119)
30 / 2712123 / 2712830 / -1 / 708 / - / C6 / spa2615 / - / putative phage tail protein
31 / 2712827 / 2713333 / -1 / 507 / - / C6 / spa2616 / - / putative phage protein
No. / Start / Stop / Strand / Length (bp) / CGH† / Cluster‡ / CDS§ / Gene / Annotated protein product or similarity with representative sequence in database
(Blastp E value) ¶
32 / 2713330 / 2713782 / -1 / 453 / - / C6 / spa2617 / - / phage head/capsid-completion protein, bacteriophage K139, NP_536652 (2e-20)
33 / 2713879 / 2714538 / -1 / 660 / - / C6 / spa2618 / - / putative terminase, endonuclease subunit, bacteriophage K139, NP_536651 (1e-42)
34 / 2714584 / 2715555 / -1 / 972 / - / C6 / spa2619 / - / phage major capsid protein, Shewanella sp. W3-18-1, ZP_00903018 (4e-83)
35 / 2716629 / 2718404 / +1 / 1776 / - / C6 / spa2620 / - / transposase, E. coli E22, ZP_00730590 (0.0)
36 / 2718401 / 2719462 / +1 / 1062 / - / C6 / spa2621 / - / bacteriophage capsid portal protein, Yersinia bercovieri ATCC 43970, ZP_00821709 (3e-137)
37 / 2719513 / 2719782 / +1 / 270 / - / C6 / spa2622 / - / zinc-finger protein, bacteriophage K139, NP_536645 (5e-19)
38 / 2720087 / 2721619 / -1 / 1533 / - / C6 / spa2623 / - / deoxycytidine deaminase, Yersinia bercovieri ATCC 43970, ZP_00821705 (0.0)
39 / 2722149 / 2722961 / -1 / 813 / - / C6 / spa2624 / - / site-specific DNA methylase, Yersinia frederiksenii ATCC 33641, ZP_00828817 (6e-67)
40 / 2724303 / 2724833 / -1 / 531 / - / C6 / spa2625 / - / regulatory protein CII, bacteriophage 186, Yersinia pseudotuberculosis IP 32953, CAH21008 (1e-47)
41 / 4462603 / 4463598 / -1 / 996 / + / C4 / spa4289 / hsdM / DNA methyltransferase SptAIM; protects DNA against PvuII endonuclease
42 / 4463654 / 4463890 / +1 / 237 / + / C4 / spa4290 / hsdS / subunit S of type I restriction-modification system
43 / 4463887 / 4464450 / +1 / 564 / + / C4 / spa4291 / hsdR / subunit R of type I restriction-modification system
*The strain-specific CDS were identified based on the level of nucleotide similarity of query CDS sequences against the other subject genomes. See the text for further details.
†CDS were flagged as 'Present' (+) or 'Absent' (-) on the basis of previously published comparative genomic hybridization (CGH) data for ATCC 9150 and twelve other Paratyphi A test strains. 14
‡The several contiguous CDS on the ATCC 9150 genome were merged into contigs using ArrayOme 20 and further clustered by physical location by grouping contigs separated by less than 10 kb on the ATCC 9150 genome.
§The four CDS highlighted in orange were selected as target CDS for the Paratyphi A-specific multiplex PCR assay. When these four target CDS were subjected to BLASTN searches against GenBank, no significant similarity was found in non-Paratyphi A genomes except that CDS spa4289 had high level similarity to sbaIM in Salmonella Bareilly (GenBank accession no. AF508974).