Article Figures & Data
Figures
- FIG. 1.
Genetic regions of diversity in serovar Enteritidis, Dublin, and Gallinarum isolates compared to serovar Enteritidis PT4. (A) Regions that distinguish serovar Enteritidis isolates. (B) Additional regions of difference detected in serovar Dublin and Gallinarum isolates. (C) Further regions of difference detected in unusual SARB isolates. Presence status is color coded: red, absent; light red, mostly absent; gray, uncertain; light blue, mostly present; blue, present. Strain designations correspond to the numbers in Table 1. Regions are described in detail in Table 2 (panels A and B) and Table S2 in the supplemental material (panel C).
- FIG. 2.
Lineages of serovar Enteritidis strains based on presence of a subset of phage regions. Isolates in this study were grouped based on absence/presence patterns of regions A06 (ST64B-like phage), A19 (Fels-2 regions), and the Typhi CT18 phage regions A22 to A24. Deviation of one character status was allowed. The strains in italics are phage types of the PT4-like lineage, and strains in boldface are PT8-like phage types, according to Guard-Petter (9). Strain numbers correspond to Table 1.
Tables
- TABLE 1.
Strains used in this study
Strain no. Strain name Serovar/biovar Phage or MLEE type Isolationb Source 1 MZ 648 Enteritidis PT1 Denmark, 1985, human J. Garaizar 2 MZ 649 Enteritidis PT2 Denmark, 1987, human J. Garaizar 3 MZ 634 Enteritidis PT4 Spain, 1983, human J. Garaizar 4 MZ 636 Enteritidis PT4b Spain, 1993, water J. Garaizar 5 MZ 637 Enteritidis PT5 Spain, 1993, food J. Garaizar 6 MZ 638 Enteritidis PT6a Spain, 1994, water J. Garaizar 7 MZ 635 Enteritidis PT7a Spain, 1983, human J. Garaizar 8 SGSC2377 Enteritidis PT8 Canada K. Sanderson 9 MZ 650 Enteritidis PT8 Denmark, 1983, chicken J. Garaizar 10 21027 Enteritidis PT13a P. Fields 11 21046 Enteritidis PT13a P. Fields 12 MZ 655 Enteritidis PT23 Denmark, 1997, chicken J. Garaizar 13 MZ 646 Enteritidis PT25 Denmark, 1996, human J. Garaizar 14 MZ 672 Enteritidis ? Germany, pigeon A. Helm 15 MZ743 Enteritidis PT6a USA, KS, 1948, guinea pig P. Fields 16 MZ744 Enteritidis PT13a USA, 1948, guinea pig P. Fields 17 MZ745 Enteritidis PT35 USA, GA, 1949 P. Fields 18 MZ746 Enteritidis PT13a USA, 1949 P. Fields 19 MZ747 Enteritidis PT8 USA, NJ, 1950 P. Fields 20 MZ748 Enteritidis PT13a USA, 1950, mouse P. Fields 21 MZ749 Enteritidis PT4b USA, CA, 1950, rat P. Fields 22 MZ750 Enteritidis PT8 USA, TX, 1950, P. Fields 23 SARB16 Enteritidis En1, PT13a USA, Rhode Island K. Sanderson 24 SARB18 Enteritidis En3, PT4 USA, Connecticut K. Sanderson 25 MZ 647 Dublin Denmark, 1984, human J. Garaizar 26 SARB12 Dublin Du1 USA, Idaho, cattle, 1986 K. Sanderson 27 SARB13 Dublin Du3 France, bovine, 1982 K. Sanderson 28 99113 Gallinarum/Pullorum Canada, 1999 J. Guard-Bouldin 29 99117 Gallinarum/Pullorum Canada, 1999 J. Guard-Bouldin 30 7865L Gallinarum/Pullorum USA, 1997 J. Frye 31 17368L Gallinarum/Pullorum USA, 2003 J. Frye 32 SARB51 Gallinarum/Pullorum Pu3 Germany K. Sanderson 33 Sg9 Gallinarum/Gallinarum T. Wallis 34 SgJ91 Gallinarum/Gallinarum T. Wallis 35 287/91 Gallinarum/Gallinarum Sequenced isolate, 1991 Sanger Center 36 SARB52 Gallinarum/Pullorum Pu4 Germany K. Sanderson 37 SARB17 Enteritidis En2, RDNCa Brazil K. Sanderson 38 SARB20 Enteritidis En7, RDNC Switzerland K. Sanderson 39 MZ630 Enteritidis PT4 sequenced isolate Sanger Center - TABLE 2.
Regions differing from the sequenced serovar Enteritidis PT4 isolate in serovar Enteritidis, Dublin, and Gallinarum strainsa
Region no.a Location start Approx size (kb) Gene rangec Gene and description Differing strainsd Enteritidis Dublin Gallinarum Other SARB Genes present in PT4 A01b 0249806 1.8 24 28-35 38 A02 0309634 6.7 STM0266-0289 24 28-35 36,37 A03 1275768 7.9 STM1834-1843 rrmA 3 A04b 1469682 11.6 Phage? 15,17 25-27 28-35 36-38 A05 1659634 3.2 STM1489-1491 ynfK 18 A06b 2020515 38.4 ST64B phage? 2,8-11,12,15-24 28-35 36-38 A07 2302417 2.5 STM2200-2201 lysP 18-20 A08 2875524 12.6 STM2844-2858 Hydrogenase 3 operon 7 A09 2911415 4.6 STM2883-2886 sipBCD, sicA, part of SPI1 7 A10 4366609 50.4 STM4270-4312 dcu, pmr, nrf, mel operon 7 A11b 4608741 9.4 DNA restriction/methylation? 1 36,37 A12 p_00096 5.4 pSLT001-009 DNA replication, rck 14 27 29 36-38 A13 p_07550 11.2 pSLT012-026 pef fimbriae 14,24 25-27 28-35 36-38 A14 p_19482 23.3 pSLT027-051 spv operon, resolvase, ccd 14 29 36-38 A15_all p_43200 16.1 pSLT052-055, pSLT068-084 par, sam, SOS inhibition psi, part of tra locus 14 25-27 29,33,35 36-38 A15_sub p_52504 2.0 pSLT073-077 Part of tra locus 10,11,15 25-27 29,33,35 36-38 B01 0093701 3.7 STM0081-0084 25,26 B02 0353500 2.4 STM0330-0332 Transcriptional regulator? 32 36,37 B03 0593150 3.7 STM0554-0558 yfd glycosyltransferase 26 36 B04 0866128 1.5 STM0839-0840 ybiV(2) 28,30-32 36,38 B05b 0890919 25.7 29 B06 1013381 8.2 STM1004-1056 sspH2 28-35 37 B07_all 1242709 7.7 STM0910-0907 plus SPT spec Similar to parts of phage Fels-1 28,30,31 37 B07_sub 1249229 1.2 STM0910-0909 Similar to parts of phage Fels-1 25-27 28-31 37 B08 1447962 10.8 STM1664-1675 Yersinia invC homolog 28,30-32 B09b 1520211 5.6 MFS transport? 25-27 36-38 B10b 1533858 1.6 29 B11 1549742 5.7 STM1590-1594 srfA 34 B12 1591291 6.4 STM1558-1560 Glycosyl hydrolases 27 B13_a 1600655 8.9 STM1544-1555 pqaA 25-27 29,33-35 B13_b 1595657 4.9 STM1556-1558 32 B14 1668378 2.1 STM1481-1483 Cation transport 32,35 B15b 1720290 4.7 29 B16 1873762 6.6 STM1283-1286 Chemotaxis? 29,33-35 B17b 2128623 22.0 29 B18 2331001 2.8 STM2226-2228 yejKL 35 B19 2939355 4.2 STM2912-2915 30 B20 2947941 3.3 STM2921-2924 rpoS 32 B21 3071210 12.3 STM3022-3033 std fimbriae 29,33-35 B22 3898009 2 STM3823-3824 tor system 28,30-32 B23_a 4602467 2.7 STM4519-4521 plus SPT spec 28-35 B23_bb 4606076 1.8 28-35 36,37 Genes absent in PT4 A16 0309924 3.9 STM0271-0272 24 25-27 28-35 36,38 A17_a 1099565 4.6 STM1006-1009 Parts of phage Gifsy-2 24 25-27 36 A17_b 1104740 4.3 STM1010-1018 Parts of phage Gifsy-2 24 25-27 A17_c 1109305 3.7 STM1019-1024 Parts of phage Gifsy-2 24 25-27 36 A17_d 1116857 9.1 STM1031-1040 Parts of phage Gifsy-2 24 25-27 28-35 38 A17_e 1126009 6.7 STM1041-1047 Parts of phage Gifsy-2 24 25-27 28-35 36,38 A18 2762064 1.7 STM2616-2618 Part of phage Gifsy-1 24 A19_a 2844714 7.2 STM2695-2702 Parts of phage Fels-2 2,8-12,15-20,22,23 25-27 36,38 A19_b 2852212 1.2 STM2703-2704 Parts of phage Fels-2 15,17 A19_c 2855566 18.0 STM2707-2730 Parts of phage Fels-2 2,8-12,15-20,22,23 25 30,31 36 A20 48285 6.9 pSLT056-067 ssbB 24 27 28,30-35 A21 67516 25.8 pSLT085-110 tra, trb 15,17,24 27 28,30-35 A22 2766359 1.7 STY2887-2888 Part of serovar Typhi phage ST27 2,8-12,16-20,22,23 25 28,30,31 36,38 A23 3517867 2.7 STY3662-3667 cII, dam, part of serovar Typhi phage ST35 2,8-12,16,18-20,22,23 28,30,31 36 A24 3526926 12.8 STY3674-3691 nuc, part of ST35 2,8-12,15-20,22,23 25-27 28,30,31 36,38 A25 4498909 4.2 STY4632-4636 Dam, part of serovar Typhi phage SopEST 15 38 A26 2699408 25.4 SPA2602-2625 Serovar Paratyphi A phage SPA-3 20 38 B24 0306723 9.9 STM0268-0275 25-27 38 B25_a 0318679 13.4 STM0279-0289 25-27 38 B25_b 0332086 1.6 STM0290-0291 25-27 B26 2873542 4.3 STM2731-2738 Parts of phage Fels-2 25-27 B27_all 46_00830 31.6 R001-R046 26 B27_sub 46_14184 7.5 R022-R027 fip, tra, stb 26 34 B28 1883033 5.2 STY2003-2011 Restr/modification, hydrolase, start of Typhi phage ST18 29,35 B29 1912209 1.2 STY2043-2045 Part of ST18 26,27 B30 1921304 1.3 STY2060-2061 Part of ST18 27 B31 2761219 7.6 STY2882-2889 Part of ST27 28,30,31 B32 3540251 0.8 STY3693-3694 Part of ST35 28,30,31 B33 4409652 64.1 STY4521-4597 SPI7: samB pil topB 27 B34 4508347 21.4 STY4648-4666 SPI7: vex/tvi 27 B35_a 2488061 7.6 SPA2387-2391 Part of serovar Paratyphi A phage SPA-1 32,34 B35_b 2496420 10.7 SPA2393-2394 Parts of SPA-1 25,26 32,34 B35_c 2510504 17.1 SPA2401-2431 Part of SPA-1 32,34 ↵ a Regions A are different among serovar Enteritidis strains; regions B have been identified in serovar Dublin and Gallinarum strains.
↵ b Regions are not present in sequenced and annotated genomes of serovar Typhimurium LT2, serovar Typhi CT18, serovar Typhi Ty2, or serovar Paratyphi A SARB42; pSLT, serovar Typhimurium LT2 plasmid; R46, transmission plasmid.
↵ c Range of homologous region in STM, STY, or SPA is indicated. STM, S. enterica serovar Typhimurium LT2; STY, S. enterica serovar Typhi CT18; SPA, S. enterica serovar Paratyphi A SARB42.
↵ d Strain numbers are as in Table 1.
HTML Page - index.htslp
Files in this Data Supplement:
- Supplemental file 1
-
Table S1, Absence/presence prediction for every gene represented by a probe on the Salmonella array in surveyed Salmonella strains; Table S2, Absence/presence predictions for all regions of divergence identified in arrayed S. enterica serovar Enteritidis, Dublin, and Gallinarum isolates; Table S3, Subspecies I signature genes after compilation of data on
all subspecies and 24 S. enterica subspecies I serovars.
Zipped Excel document, 2MB.
- Supplemental file 1
-
Table S1, Absence/presence prediction for every gene represented by a probe on the Salmonella array in surveyed Salmonella strains; Table S2, Absence/presence predictions for all regions of divergence identified in arrayed S. enterica serovar Enteritidis, Dublin, and Gallinarum isolates; Table S3, Subspecies I signature genes after compilation of data on
all subspecies and 24 S. enterica subspecies I serovars.
