Article Figures & Data
Figures
- Fig 1
Discriminatory power (D) provided by CRISPR-MVLST and PFGE. Pie charts show the number of distinct groups that were defined by (a) CRISPR-MVLST (38 groups; D = 0.9597) or (b) PFGE (62 groups; D = 0.9907). The most frequent NSTs and PFGE patterns are indicated on the representative pie charts.
- Fig 2
Closely related NSTs share PFGE patterns. BURST analysis revealed the relationships between different NSTs. Within a BURST group, the NSTs in the outer ring differ from the core NST at one of the four CRISPR-MVLST loci. NSTs that could not be assigned to a group are listed as singletons. Individual PFGE patterns that were found in isolates that had different NSTs are shown as colored ovals, and the PFGE pulsotype is indicated by the numbers that follow JJPX01, i.e., JJPX01.0061 is shown as 0.0061.
- Fig 3
Closely related PFGE patterns share NSTs. The dendrogram shows the relationship among the 62 PFGE patterns identified in this study. Single NSTs that were found in isolates with different PFGE pulsotypes are shown in colored boxes.
- Fig 4
Correlation of CRISPR-MVLST and PFGE data. Individual PFGE dendrograms, comprising portions from the full dendrogram in Fig. 3, show all the NSTs from within a single BURST group. This analysis included all groups from Fig. 2, with the exception of group 3 and the singleton NSTs. Group 3 was excluded because it did not contain a core NST.
- Fig 5
Rapid separation of Salmonella serovar Newport isolates based on size of CRISPR PCR products. PCR products of CRISPR1 (top) and CRISPR2 (bottom) were run on 1.2% agarose gels. Samples NST 46-1 and NST 46-2 are two different representative isolates from the tomato outbreak and share the same PCR product sizes at both loci. The other lanes correspond to single representatives of the remaining eight NSTs. The size differences between CRISPR1 NST 24 and NST 48 and between CRISPR2 NST 17 and NST 47 represent a single spacer repeat unit (or 61 bp). M, marker. The molecular sizes (in kb) of the marker are shown to the right.
Tables
- Table 1
List of the 84 Salmonella serovar Newport isolates from the Pennsylvania Department of Health that were analyzed
Isolate CRISPR-MVLSTa PFGE PA regionb Isolation date 07E00097 NST 7 JJPX01.0061 NE Jan-07 M10013735001A NST 7 JJPX01.0061 NE Jun-10 08E00210 NST 7 JJPX01.0267 SE Feb-08 09E00125 NST 7 JJPX01.0267 SE Jan-09 08E01607 NST 8 JJPX01.0005 SW Sep-08 07E00155 NST 8 JJPX01.0119 SE Jan-07 08E01537 NST 8 JJPX01.0119 NW Aug-08 M11030458001A NST 8 JJPX01.0239 SW Dec-11 07E00399 NST 9 JJPX01.2015 SW Mar-07 07E00461 NST 10 JJPX01.2010 SE Apr-07 07E01951 NST 11 JJPX01.0014 SE May-07 07E00747 NST 12 JJPX01.0289 NE May-07 M11000510001A NST 12 JJPX01.2721 SE Jan-11 07E00929 NST 13 JJPX01.2261 SW Jun-07 07E02078 NST 14 JJPX01.0011 SE Oct-07 08E01356 NST 14 JJPX01.0011 SC Aug-08 M09016624001A NST 14 JJPX01.0011 SW Jul-09 M09024074001A NST 14 JJPX01.0011 SE Oct-09 M10028778001A NST 14 JJPX01.0011 SW Dec-10 M10018416001A NST 14 JJPX01.0030 SE Aug-10 M11019990001A NST 14 JJPX01.0030 NE Aug-11 07E00925 NST 14 JJPX01.0057 NE Jun-07 M11018046001A NST 14 JJPX01.0213 SE Jul-11 08E00500 NST 14 JJPX01.0394 SW Apr-08 M11015863001A NST 14 JJPX01.0872 SW Jun-11 07E01217 NST 15 JJPX01.2301 SW Jul-07 07E01261 NST 16 JJPX01.2263 SE Jul-07 M11014659001A NST 17 JJPX01.0105 SE Jun-11 07E01662 NST 17 JJPX01.0177 SE Sep-07 M11022592001A NST 17 JJPX01.0309 SE Sep-11 07E02298 NST 17 JJPX01.2282 SE Nov-07 M10026897001A NST 17 JJPX01.3088 SW Oct-10 07E02137 NST 18 JJPX01.0025 SW Oct-07 08E00166 NST 18 JJPX01.0242 SE Jan-08 08E00335 NST 18 JJPX01.2775 SE Mar-08 08E02126 NST 18 JJPX01.0497 SW Nov-08 07E02409 NST 19 JJPX01.0149 NC Dec-07 M10029131001A NST 20 JJPX01.0014 SE Dec-10 09E00792 NST 20 JJPX01.0383 SC Apr-09 07E01395 NST 20 JJPX01.0383 SC Aug-07 M11026343001A NST 20 JJPX01.0422 SW Oct-11 M10003908001A NST 20 JJPX01.1811 SE Feb-10 08E00177 NST 20 JJPX01.2232 SE Feb-08 09E01543 NST 20 JJPX01.3251 SC Jun-09 08E00291 NST 21 JJPX01.0023 SW Mar-08 M09018506001A NST 21 JJPX01.0358 SE Aug-09 M09019440001A NST 21 JJPX01.0358 NE Aug-09 M09016172001A NST 21 JJPX01.0847 SW Jul-09 08E00513 NST 22 JJPX01.0235 SE May-08 M10011785001A NST 22 JJPX01.3528 SW May-10 08E01026 NST 23 JJPX01.0438 NC Jun-08 08E00966 NST 24 JJPX01.0538 SW Jul-08 09E01420 NST 24 JJPX01.0538 NE Jun-09 08E01066 NST 25 JJPX01.0170 SW Jul-08 M09023181001A NST 25 JJPX01.0687 SW Sep-09 08E01928 NST 27 JJPX01.1824 NE Oct-08 M11010588001A NST 27 JJPX01.3681 SE Mar-11 M11010828001A NST 27 JJPX01.3681 SE Apr-11 08E02388 NST 29 JJPX01.0025 SC Dec-08 M10027390001A NST 29 JJPX01.0025 SE Nov-10 M10006936001A NST 29 JJPX01.0534 SW Mar-10 M10013705001A NST 29 JJPX01.3115 SE Jun-10 08E02500 NST 30 JJPX01.0497 SE Dec-08 09E00195 NST 31 JJPX01.0267 SE Jan-09 09E00491 NST 32 JJPX01.0514 SE Mar-09 09E00565 NST 33 JJPX01.1846 NE Mar-09 09E01249 NST 34 JJPX01.0241 SE May-09 09E01236 NST 34 JJPX01.0241 SC May-09 M09032450001A NST 35 JJPX01.0696 NW Nov-09 M10001733001A NST 36 JJPX01.0472 NC Jan-10 M10015969001A NST 37 JJPX01.0032 SE Jul-10 M11004830001A NST 37 JJPX01.0032 SW Feb-11 M10015025001A NST 37 JJPX01.0038 SE Jul-10 M10007077001A NST 37 JJPX01.1477 SE Mar-10 M10008806001A NST 38 JJPX01.0629 SE Apr-10 M10011150001A NST 39 JJPX01.3105 SW May-10 M10017951001A NST 40 JJPX01.0206 SW Aug-10 M10020055001A NST 41 JJPX01.0061 SE Sep-10 M10021286001A NST 42 JJPX01.0023 SE Sep-10 M11007253001A NST 43 JJPX01.0742 SE Mar-11 M11012736001A NST 44 JJPX01.0005 SW May-11 M11030097001A NST 45 JJPX01.3896 SW Nov-11 M09021254001A NST 47 JJPX01.0413 SE Sep-09 M09029283001A NST 51 JJPX01.0238 NE Nov-09 - Table 2
Primers used for CRISPR-MVLST PCR and sequencing
Marker Orientation Primer sequence (5′–3′) Annealing temp (°C)a Primer used for: PCR Sequencing CRISPR1-5 Forward TGAAAACAGACGTATTCCGGTAGATT 55.5 Yes Yes CRISPR1-1 Reverse CAGCATATTGACAAGGCGCT Yes Yes CRISPR1-6 Forward AATTGGGTAGATTTAGGGTGT Yes CRISPR2-3 Forward ATTGTTGCGATTATGTTGGT 57 Yes Yes CRISPR2-1 Reverse TCCAGCTCCCTTATGATTTT Yes CRISPR2-4 Reverse GCAATACCCTGATCCTTAACGCCA Yes fimH-1 Forward AGGTGAACTGTTCATCCAGTGG 56.7 Yes Yes fimH-2 Reverse GCGGGCTGAACAAAACACAA Yes Yes sseL-1 Forward AAAATCAGGTCTATGCCTGATTTAATATATC 60 Yes sseL-5 Reverse GGCTCTAAGTACTCACCATTACT Yes sseL-3 Forward ACCAGGAAACAGAGCAAAATGAATATATGT Yes sseL-4 Forward TTCTCTCGGTAAACTATCCTATTGGGC Yes ↵a The annealing temperature is shown for the PCR primers.
- Table 3
List of all NSTs identified in this study, showing the allelic combination of all four markers, fimH, sseL, CRISPR1, and CRISPR2, that define each NST
NST Allelea fimH sseL CRISPR1 CRISPR2 NST 7 4 17 101 130 NST 8 5 17 110 131 NST 9 3 56 111 133 NST 10 5 17 112 134 NST 11 3 56 112 132 NST 12 5 17 113 135 NST 13 5 17 114 131 NST 14 5 57 7 136 NST 15 5 17 115 131 NST 16 3 56 116 137 NST 17 5 17 103 11 NST 18 5 17 7 138 NST 19 5 57 119 139 NST 20 3 56 181 132 NST 21 5 57 7 139 NST 22 5 17 103 140 NST 23 5 17 109 11 NST 24 3 56 121 142 NST 25 5 17 122 143 NST 27 3 56 123 142 NST 29 5 17 7 144 NST 30 5 17 113 145 NST 31 4 17 101 146 NST 32 3 55 101 148 NST 33 3 56 124 150 NST 34 3 56 181 152 NST 35 5 17 125 11 NST 36 5 17 7 153 NST 37 4 17 101 147 NST 38 5 17 126 11 NST 39 5 17 127 154 NST 41 4 17 101 151 NST 42 3 56 7 139 NST 43 3 56 111 142 NST 44 5 17 110 155 NST 45 3 56 128 157 NST 46 3 56 121 132 NST 47 3 56 161 202 NST 48 3 56 162 142 NST 49 5 17 163 204 NST 50 51 17 164 203 NST 51 3 56 180 149 ↵a New alleles identified in this study and assigned a new numerical identifier are shown in bold.
- Table 4
Salmonella serovar Newport isolates analyzed by CRISPR-MVLST and PFGE as part of the tomato outbreak studya
Isolate PFGE CRISPR-MVLST PA regionb Isolation date M12012060001A JJPX01.0238 NST 46 OS Jun-12 M12012090001A JJPX01.0238 NST 46 SE Jun-12 M12012292001A JJPX01.0238 NST 46 SE Jun-12 M12012137001A JJPX01.0238 NST 46 SE Jun-12 M12012364001A JJPX01.0238 NST 46 SE Jun-12 M12012100001 JJPX01.0238 NST 46 SE Jun-12 M12012372001A JJPX01.0238 NST 46 SE Jun-12 M12012369001A JJPX01.0238 NST 46 SE Jun-12 M12012471001A JJPX01.0238 NST 46 SE Jun-12 M12012531001A JJPX01.0238 NST 46 SE Jun-12 M12012312001A JJPX01.0415 NST 17 SE Jun-12 M12012826001A JJPX01.0413 NST 47 SE Jun-12 M12012889001A JJPX01.0025 NST 49 SC Jun-12 M12012888001A JJPX01.0011 NST 14 SC Jun-12 M12013292001A JJPX01.0546 NST 24 SE Jul-12 M12014067001A JJPX01.0011 NST 14 SE Jul-12 M12014796001A JJPX01.0111 NST 48 SE Jul-12 M12014789001A JJPX01.0061 NST 7 SE Jul-12 M12014624001A JJPX01.0011 NST 14 SE Jul-12 M12014798001A JJPX01.0301 NST 50 SE Jul-12
