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Bacterial strains and plasmids

3. Materials and Methods

3.3. Microbiological methods

3.3.1. Bacterial strains and plasmids

In Table 8 and Table 9 bacterial strains and plasmids used in this study are listed. The additional Y. enterocolitica strains tested for validation of the patho-serotyping PCR are listed in Table 10.

Table 8 Bacterial strains used in this study.

(FBI-Zoo: Food-Borne Zoonotic Infections of Humans, BMBF project; FLI: Friedrich-Löffler Institute; MvPI:

Max-von-Pettenkofer Institute) Y. enterocolitica strains

Bacterial strain ID Features Reference

8081 Bioserotype 1B/O:8, American human isolate (Portnoy et al., 1981)

WA-314 (ATCC 51871) Bioserotype 1B/O:8, clinical isolate (Heesemann and Laufs, 1983) Y11 (DSMZ 13030) Bioserotype 4/O:3, human isolate (Neubauer et al., 2000a) W22703 Bioserotype 2/O:9, mutant from strain W227 (Cornelis and Colson, 1975)

Y5.27P Bioserotype 3/O:5,27 MvPI collection

NF-O Bioserotype 1A/O:5, clinical isolate (Ratnam et al., 1982) IP2222 Bioserotype 1A/O:36, Japanese isolate from

water (Grant et al., 1999)

Y8265/556 Bioserotype 4/O:3, French human isolate MvPI collection Y5307/647 Bioserotype 4/O:3, Finnish human isolate MvPI collection

P1 (BR6319) Bioserotype O:3, German isolate from pig Prof. Neubauer, FLI Jena P4 (BR0055) Bioserotype O:3,German isolate from pig Prof. Neubauer, FLI Jena 149 (CN-Y641) Bioserotype 4/O:3, Belgian isolate from puppy MvPI collection

150 (CN-Y486) Bioserotype 4/O:3, Belgian isolate form calf MvPI collection D1 (M1-S3405) Bioserotype 4/O:3, German human isolate MvPI collection D2 (M2-S3547) Bioserotype 4/O:3,German human isolate,

obtained 45 days after D1 from same patient MvPI collection D3 (CN-35) Bioserotype 4/O:3, German human isolate MvPI collection D4 (CN-142) Bioserotype 4/O:3, Belgian isolate from pig MvPI collection D5 (CN-146) Bioserotype 4/O:3, Danish isolate from pig MvPI collection D6 (CN-243/Y745) Bioserotype 3/O:3, Japanese isolate MvPI collection D7 (P8/FBI-00033) Bioserotype 4/O:3, German isolate from pig FBI-Zoo collection D8 (P14/FBI-03871) Bioserotype 4/O:3, German isolate from pig FBI-Zoo collection D9 (P15/04247) Bioserotype 4/O:3, German isolate from pig FBI-Zoo collection

Other strains

Species Features Reference

E. coli T7 express (BL21 derivative, no λ-prophage)

fhuA2 lacZ::T7 gene1 [lon] ompT gal sulA11 R(mcr-73::miniTn10--TetS)2 [dcm] R(zgb-210::Tn10--TetS) endA1

D(mcrCmrr)114::IS10

New England Biolabs, Frankfurt

Y. frederiksenii CN-113 Strain H56-36/81, serotype O:60 MvPI collection Y. intermedia CN-114 Strain H9-36/83, serotype O:17 MvPI collection Y. kristensenii CN-115 Strain H17-36/83, serotype O:12.25 MvPI collection Y. rohdei CN-116 Strain H274-36/85, serotype O:76 MvPI collection Y. bercovieri CN-117 Strain H632-36/85, serotype O:16 MvPI collection Y. mollaretii CN-118 Strain H279-36/86, serotype O:59 MvPI collection Y. pseudotuberculosis Strain IP32953, serotype O:1 (Chain et al., 2004)

Y. pestis CN-691 Strain KIM, biotype Medievalis (Fetherston and Perry, 1994)

E. coli Strain UTI89, serotype O18:K1:H7 Prof. Stecher, MvPI

E. coli Strain CFT073, serotype O6:H1 Prof. Stecher, MvPI

S. enterica subsp.I Strain C5, serovar Typhimurium Prof. Stecher, MvPI S. enterica subsp.I Strain ATCC 14028, serovar Typhimurium Prof. Stecher, MvPI

C. jejuni Strain L11, serotype Lior 11 MvPI collection

C. jejuni Strain G23 MvPI collection

L. pneumophila Strain 2020 Prof. Hilbi, MvPI

Table 9 List of plasmids.

Plasmid Features Reference

pET-30a Expression vector, T7 promoter, N-ter and C-ter

His·Tag, KanR Novagen, Darmstadt

pET-30b Expression vector, T7 promoter, N-ter and C-ter

His·Tag, KanR Novagen, Darmstadt

pET-30c Expression vector, T7 promoter, N-ter and C-ter

His·Tag, KanR Novagen, Darmstadt

Table 10 Y. enterocolitica strains used for validation of the patho-serotyping PCR-based method.

When necessary, re-serotyping of these strains was performed by Dr. Bader (MvPI, Munich).

(CVUA: Chemisches und Veterinäruntersuchungsamt Stuttgart; FBI-Zoo: Food-Borne Zoonotic Infections of Humans, BMBF project; FLI: Friedrich-Löffler-Institute; MvPI: Max-von-Pettenkofer Institute; RKI:

Robert Koch Institute, Wernigerode)

Strain ID Features Source

CN-32 Serotype 0:3, strain 108P MvPI collection

CN-36 Bioserotype 1A/O:5, human isolate MvPI collection CN-38 Bioserotype 1A/O:4,33, isolate from milk MvPI collection CN-39 Bioserotype 1A/O:7,8, isolate from milk MvPI collection CN-40 Bioserotype 1A/O:6.30, isolate from milk MvPI collection CN-41 Bioserotype 1A/O:10,K1, isolate from milk MvPI collection

CN-42 Bioserotype 2/O:5,27 MvPI collection

CN-44 Bioserotype 4/O:9, human isolate MvPI collection CN-45 Bioserotype 4/O:5,27, human isolate MvPI collection CN-47 Bioserotype 3/O:5,27, human isolate MvPI collection CN-49 Bioserotype 2/O:5,27, human isolate MvPI collection

CN-52 Bioserotype 1A/O:48 MvPI collection

CN-53 Bioserotype 1A/O:41,43 MvPI collection

CN-54 Bioserotype 1A/O:5 MvPI collection

CN-55 Bioserotype 1B/O:8, strain CDC 544 MvPI collection CN-56 Bioserotype 1B/O:8, strain CDC 540/84 MvPI collection CN-57 Bioserotype 1B/O:8, strain E 661 Montana MvPI collection CN-58 Bioserotype 1B/O:13, strain USA 329/82 MvPI collection CN-59 Bioserotype 1B/O:20, strain CDC 3039/85 MvPI collection CN-60 Bioserotype 1B/O:21, strain CDC 209/84 MvPI collection

CN-101 Bioserotype 1A/O:36 MvPI collection

CN-170 Serotype O:3, strain 59/03 MvPI collection CN-233 Bioserotype 1B/O:8, strain IP636 MvPI collection CN-235 Bioserotype 2/O:9, strain IP22393 MvPI collection CN-237 Bioserotype 2-3/O:5,27, strain IP199 MvPI collection CN-238 Bioserotype 2-3/O:5,27, strain IP885 MvPI collection CN-239 Bioserotype 2-3/O:5,27, strain IP1607 MvPI collection CN-240 Bioserotype 2-3/O:5,27, strain IP22460 MvPI collection CN-242 Bioserotype 4/O:3, strain IP24231 MvPI collection CN-244 Bioserotype 4/O:3, strain IP24231 MvPI collection CN-245 Bioserotype 4/O:3, strain IP21981 MvPI collection

CN-249 Bioserotype 4/O:3, strain IP23357 MvPI collection CN-252 Bioserotype 4/O:3, strain IP7032 MvPI collection CN-254 Bioserotype 4/O:3, strain IP3692 MvPI collection CN-256 Bioserotype 4/O:3, strain IP4115 MvPI collection CN-262 Bioserotype 4/O:3, strain IP22274 MvPI collection CN-266 Bioserotype 4/O:3, strain IP23227 MvPI collection CN-272 Bioserotype 1A/O:5, strain IP124 MvPI collection CN-584 Bioserotype 1A/O:5, strain NF-O MvPI collection

260 Not typeable, strain FBI-4465 Klinikum der Universität München 267 Serotype O:3, strain FBI-4848 Klinikum der Universität München 282 Not typeable, strain FBI-5620 Klinikum der Universität München 292 Serotype O:27, strain FBI-6584 Klinikum der Universität München 343 Serotype O:9, strain FBI-5634 Klinikum der Universität München 377 Serotype O:3, strain FBI-6821 Klinikum der Universität München

H-82 Strain Ty 4726/85 MvPI collection

H-89 Strain Ty 448/87 MvPI collection

H-93 Strain Ty 822/88 MvPI collection

H-395 Serotype O:5,27 MvPI collection

H-522 Serotype O:1,2a,3, strain H 523/88 MvPI collection H-523 Serotype O:2a,2b,3, strain H 518/88 MvPI collection H-534 Bioserotype 2/O:5,27, strain D113 MvPI collection H-556 Bioserotype 4/O:3, strain 8265 MvPI collection H-568 Bioserotype 2/O:5,27, strain YE873 MvPI collection H-647 Bioserotype 4/O:3, strain 5307 MvPI collection H-678 Bioserotype 2/O:5,27, strain SZ 3801/03 MvPI collection H-679 Bioserotype 2/O:5,27, strain SZ 81/04 MvPI collection

H-744 Strain S11136 MvPI collection

H-745 Strain S11149 MvPI collection

H-746 Serotype O:3, strain S11925 MvPI collection H-747 Serotype O:3, strain S12723 MvPI collection H-748 Serotype O:3, strain S12891 MvPI collection H-749 Serotype O:3, strain S12982 MvPI collection H-750 Serotype O:3, strain S13559 MvPI collection

P2 Bioserotype 4/O:3, strain 0350, from pig Dr. Rau, CVUA, Stuttgart P3 Bioserotype 4/O:3, strain 5819, from pig Dr. Rau, CVUA, Stuttgart P5 Serotype O:3, strain BR0056, from pig Prof. Neubauer, FLI, Jena P6 Serotype O:3, strain BR0057, from pig Prof. Neubauer, FLI, Jena

P7 Serotype O:3, strain BR0058, from pig Prof. Neubauer, FLI, Jena P9 Bioserotype 4/O:3, strain FBI-03524, from pig FBI-Zoo collection P10 Bioserotype 4/O:3, strain FBI-03540, from pig FBI-Zoo collection P11 Bioserotype 4/O:3, strain FBI-03585, from pig FBI-Zoo collection P12 Bioserotype 4/O:3, strain FBI-03855, from pig FBI-Zoo collection P13 Bioserotype 4/O:3, strain FBI-03870, from pig FBI-Zoo collection P16 Bioserotype 4/O:3, strain FBI-05198, from pig FBI-Zoo collection P17 Bioserotype 4/O:3, strain FBI-05680, from pig FBI-Zoo collection

06-03972 Bioserotype 3/rough Dr. Tietze, RKI

06-04957 Bioserotype 3/rough Dr. Tietze, RKI

07-05684 Bioserotype 3/rough Dr. Tietze, RKI

08-00920 Bioserotype 1A/rough Dr. Tietze, RKI

08-02627 Bioserotype 1A/O:5 Dr. Tietze, RKI

09-05064 Bioserotype 4/O:3 Dr. Tietze, RKI

09-05074 Bioserotype 4/O:3 Dr. Tietze, RKI

09-05075 Bioserotype 4/O:3 Dr. Tietze, RKI

09-05076 Bioserotype 4/O:3 Dr. Tietze, RKI

09-05259 Bioserotype 3/rough Dr. Tietze, RKI

09-08364 Bioserotype 3/rough Dr. Tietze, RKI

10-00826 Bioserotype 1B/O:8 Dr. Tietze, RKI

10-00827 Bioserotype 1A/O:8 Dr. Tietze, RKI

11-01204 Bioserotype 3/O:5,27 Dr. Tietze, RKI

11-06758 Bioserotype 3/O:5,27 Dr. Tietze, RKI

11-07058 Bioserotype 1A/rough Dr. Tietze, RKI

11-08263 Bioserotype 3/O:5,27 Dr. Tietze, RKI

11-08388 Bioserotype 3/O:5,27 Dr. Tietze, RKI

11-08389 Bioserotype 3/O:5,27 Dr. Tietze, RKI

12-00565 Bioserotype 3/O:9 Dr. Tietze, RKI

12-00586 Bioserotype 3/O:9 Dr. Tietze, RKI

12-00587 Bioserotype 3/O:9 Dr. Tietze, RKI

12-00821 Bioserotype 1A/rough Dr. Tietze, RKI

12-01019 Bioserotype 3/O:9 Dr. Tietze, RKI

12-01336 Bioserotype 1A/O:8 Dr. Tietze, RKI

12-01511 Bioserotype 1A/O:5 Dr. Tietze, RKI

12-01512 Bioserotype 1A/O:8 Dr. Tietze, RKI

12-01527 Bioserotype 3/O:9 Dr. Tietze, RKI

12-01557 Bioserotype 1A/O:8 (re-serotyped as rough) Dr. Tietze, RKI

12-01616 Bioserotype 1A/O:8 Dr. Tietze, RKI

12-01779 Bioserotype 1A/O:5 Dr. Tietze, RKI

12-01805 Bioserotype 3/O:9 Dr. Tietze, RKI

12-01910 Bioserotype 3/O:9 Dr. Tietze, RKI

12-02272 Bioserotype 1A/O:5 Dr. Tietze, RKI

12-02439 Bioserotype 1A/O:5 Dr. Tietze, RKI

12-02966 Bioserotype 1A/O:8 Dr. Tietze, RKI

12-03062 Bioserotype 1A/O:5 Dr. Tietze, RKI

12-03266 Bioserotype 1A/rough Dr. Tietze, RKI

12-03276 Bioserotype 4/O:3 Dr. Tietze, RKI

12-03288 Bioserotype 1A/rough Dr. Tietze, RKI

12-03324 Bioserotype 1A/rough Dr. Tietze, RKI

12-03401 Bioserotype 1A/rough Dr. Tietze, RKI

12-03475 Bioserotype 4/O:3 Dr. Tietze, RKI

12-03489 Bioserotype 4/O:3 Dr. Tietze, RKI

12-03561 Bioserotype 4/O:3 Dr. Tietze, RKI

12-03562 Bioserotype 4/O:3 Dr. Tietze, RKI

12-03803 Bioserotype 3/rough Dr. Tietze, RKI

12-04470 Bioserotype 1A/rough Dr. Tietze, RKI

12-05220 Bioserotype 1B/O:8 Dr. Tietze, RKI

13-00330 Bioserotype 4/O:5,27 Dr. Tietze, RKI