Table of Contents
Chapter 1 7
Chapter 2 39
Chapter 3 61
Chapter 4 77
Chapter 5 89
Chapter 6 125
Chapter 7 145
Chapter 8 161
Chapter 9 181
Addendum 197
203
8
A brief history of the Brachyspiraceae
. .
“a .
9 0.02 (~24bp)
Figure 1:
10
.
Figure 2:
11 Chapter 1
4
.
12
. .
Figure 3:
13 Chapter 1
Chapter 9
The various Brachyspira species
Brachyspira hyodysenteriae (hog: pig; dysentery: severe diarrhoea)
14 * * Type of reference strain* of reference Type + + + + + + + + + + 56 + + + + + + + + + + + + Indole Hippurate Species 44 Table 1: Table
15 B.hyodysenteriae B78 'B.suana
A na' AN 4859/03
B.intermedia PWS/A
B.alvinipulli C1
B.murdochii 56-150 'B.pulli' AN304/04
'B.canis' Dog A2
'B.hampsonii' cluster II NSH-24 B.innocens B256
B.aalborgi 513A
'B.ibaraki' HIS24/11/99
'B.hominis' adhucomuHca09 'B.hampsonii' cluster I NSH-16
'B.muridarum' A58/06
'B.muris' A10/06 'B.corvi' AN968/2/04
us' A249/07
T.primi
B.pilosicoli P43/6/78
'B.ra a ZAS-2
0.03 ‘B.hampsonii’ cluster II NSH-24 B
B.hyodysenteriae B78
‘B.hampsonii’ cluster I NSH-16
B.innocens B256 ‘B.suana
na’ AN 4859/03
B.murdochii 56-150
B.intermedia PWS/A T.primi a ZAS-2
‘B.corvi’ AN968/2/04
B.pilosicoli P43/6/78
B.aalborgi 513A ‘B.canis’ Dog A2
‘B.pulli’ AN304/04
0.04
B.alvinipulli C1 Figure 4: 16
Brachyspira innocens (innocens: innocent) .
Brachyspira murdochii (Murdoch: Australian university where much research into .
Brachyspira pilosicoli (pilo: hairy; colon: colon) chapter 9
17 Chapter 1
Brachyspira intermedia (intemediate: referring to the fact that the phenotype is between B. hyodystenteriae and B. innocens) . . In
Brachyspira alvinipulli
18
Brachyspira aalborgi
‘Brachyspira canis’ (canine: dog) p In
‘Brachyspira corvi’ (corvus: crows)
19 Chapter 1
44
‘Brachyspira pulli’
‘Brachyspira muridarum’ and ‘Brachyspira muris’ . . .
(sus: pig ( Anas platyrhynchos))
20
‘Brachyspira hampsonii’ (Prof. Hampson: prominent Brachyspira
‘Brachyspira ibaraki’
21 B. aalborgi B. alvinipullihyodysenteriae B. B. innocens B. intermedia B. murdochii B. pilosicoli ‘B. canis’ ‘B. corvi’ Species Table 2: Table 22 ‘B. hampsonii’ ‘B. hampsonii’ ‘B. hominis’muridarum’ ‘B. ‘B. muris’ ‘B. pulli’ Species
23 Chapter 1
‘Brachyspira hominis’ (hominis: human)
Zoonosis
24
Epidemiological evidence
25 Chapter 1
. . .
26
27 Chapter 1
.
28
Figure 5:
29 Chapter 1
Table 3:
Country Colon biopsies Appendices Faeces*
Concluding
30
Aim of this thesis chapter 2 chapter 4 (chapters 2 8 In chapter 3 Chapter 5 chapter 8. Chapter 6 chapter 7 chapter 5
31 Chapter 1
References 45 88 16 27 12 41 37 17 85 41 86 10 70 33 82 36 22 11 34 189 57 11 31 10 40 1 33 31 1 125 50 63 Int J 49 46 3
32
160 Int J 29 53 Int J 47 136 48 178 35 8 36 67 28 59 9 106 14 53 2 130 67 24 Occurrence 7 153 23 15 52 39
33 Chapter 1
146 146 12 158 52 124 121 137 99 37 21 22 102 134 28 46 53 23 35 47 91 111 63 32 23 105 119 15 53 121 59 36
34
41 34 68 153 12 13 16 61 158 42 59 53 21 39 33 2 64 59 65 J 22 J 31 21 J 141 113 113 48 26 138 93 143 146
35 Chapter 1
4 7 103 45 49 31 7 134 30 179 150 49 35 38 30 38 59 224 101 187 21 13 90 39 74 41 23 134 37 Int J 18
36 37 38 4
4
Chapter 2
Abstract
Methods
Results p
Conclusions
40
4
Jensen
41 Chapter 2
.
Aims of this study
42
Methods Ethics statement
43 Chapter 2
Processing of FFPE biopsy samples
44
®
45 Table 1:
Primer set 5’–––3’ Total length °C Time Purpose
PCR volume PCR consumables PCR protocol
46
m ®
Sequencing
StepB (253bp) 203 445 StepA (212bp) StepC (258bp) 60 271 366 623 Bspp (82bp) 135 216 5’ 3’ 0 100 200 300 400 500 600 700
Primer Amplicon
Figure 1:
47 Chapter 2
48
Results A
PCR results p p p
49 12
10
8
6
4
2
0 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96
-2 B. aalborgi) B. pilosicoli)
Figure 2:
Table 2
Sequence result
50 B. burgdorferi B. pilosicoli B. pilosicoli B. murdochii B. innocens B. hyodysenteriae B. intermedia B. alvinipulli Brachyspira ‘B. hominis’ B. aalborgi Brachyspira aalborgi 0.01 Figure 3:
51 Chapter 2
(p
Table 3: p
# + +
52
Discussion
.
53 Chapter 2
m
54
55 Chapter 2
56
References 48 23 35 53 160 42 2 16 Int J 46 31 40 49 7 67 63 106 41 62 115 41 12 16 2 12 39 53 59 116 39
57 Chapter 2
197 25 Suppl 3 37 27 12 132 83 95 32 23 40 67 136 178 35
58 Supplementary Table S1:
59 60
Chapter 3
Abstract
Methods
Results
Conclusion
62 Appendiceal Spirochaetosis in Children
.
.
63 Chapter 3
.
64 Appendiceal Spirochaetosis in Children
Materials and methods Ethics statement
Sample processing
65 Chapter 3
®
®
66 Table 1:
5’–––3’ Amplicon
PCR volume PCR protocol
67 Chapter 3
Histopathology
® ®
68 Appendiceal Spirochaetosis in Children
Results
Table 2: Immunohistochemistry
PCR result ++++++
p
(p
69 Chapter 3
Discussion
Table 3: Total appendices Control group Other diagnoses 4
70 Appendiceal Spirochaetosis in Children
(p
71 Chapter 3
®
72 Appendiceal Spirochaetosis in Children
References 24 17 39 12 53 27 88 39 90 23 23 8 154 3 52 16 J 38 7 53 160 4 67 31 35 Am J 132 2 55 142 25 Suppl 3 2 51 59 7
73 Chapter 3
37 33 65
74 75 76 4
4
Chapter 4
Abstract (p
78
As a
79 Chapter 4
Materials and methods ® ®
Table 1: a
a
80
Results p
p
81 Chapter 4
Discussion
p
82
83 Chapter 4
84
References 16 48 3 85 7 101 53 21 23 21 59 39 2 70 J 22 82 45 22 82 53 4 132 53 31 J 38 42 16 31 7
85 Supplementary table S1: Sample ID .etrc .jjn S. dysenteriae C. jejuni S. enterica + + * * * + * Bacteria * STEC/EPEC + + + + G. lamblia + + + Parasites .faii C. parvum D. fragilis * * # + +
86 87 88 A 4
4
Chapter 5
Abstract
90
Brachyspira species . (
91 Chapter 5
. In (alp
.
92
Material and methods MLST design
Table 1:
Criterion Database
93 Chapter 5
®
atpG
94
atpG
95 Table 2:
Amplicon (bp) Locus Target Primers** Total Useful Min
atpG
® PCR volume PCR consumables PCR protocol
96 0.02 (~24bp)
Colour-plate A: Colour-plate B: Colour-plate C: 12
10
8
6
4
2
0 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
-2
513A (B. aalborgi) WesB (B. pilosicoli)
Colour-plate D: 12
10
8
6
4
2
0 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
-2
513A (B. aalborgi) WesB (B. pilosicoli)
Colour-plate E: B. aalborgi ‘B. hominis’ B. murdochii B. innocens
B. pilosicoli B. hyodysenteriae B. alvinipulli B. intermedia
Colour-plate F: B. innocens B. aalborgi ‘B. hominis’ B. murdochii B. innocens
B. intermedia B. pilosicoli B. hyodysenteriae B. alvinipulli B. intermedia
Colour-plate G:
Colour-plate H:
Colour-plate I: WA1 B-78 PWS/A Q98.0033.72 513A 56-150 C1 T.primitia_ZAS-2 T1 199800660 200517505 Q97.2110.4.11 WesB OF_11 WF1 K1 201101966 201009139 201102362 200909930 200831665 VTN021f HRM_4B HRM_2B N1 RV1 SC1 Q94.0354.0.6 Q98.0037.6 7072i L72 201013692 200300944 200410620a 200410620b 200709033 200513182a 200513182b 200900828 201009156 200232081 201105386 201204927 201221374 201200678 VTN022f f199600014 D9201243 Q1404.6A 3295.90B HRM7A W015/C138 WW25 WIA8 HRM7 Q95.0635.6 Q95.2078.2 Q95.3281.0 H60-2 Q97.2224.3.1 Q98.0028.3 Q98.0072.31 Q97.000.6.8 Q98.0026.12 Q98.0072.08 H38-2 H4-2 J_F2 QF1 EM1 KP5 Human M1 Q1588.5 9803.1 Pig V1_H141 95/1000 Q91.1223.3 B256 Chicken P43/6/78 201124725 201125230 Dog 200805431 V1_H11 H21
0.05
Colour-plate J: WA1 B-78 PWS/A 56-150 B256 C1 T.primitia_ZAS-2 513A 201101966 T1 Q97.2110.4.11 Q95.0635.6 Q1588.5 9803.1 P43/6/78 A Q91.1223.3 W015/C138 WW25 KP5 WesB OF_11 B WF1 K1 200909930 HRM_4B HRM_2B HRM7A HRM7 N1 RV1 SC1 200517505 200300944 201204927 7072i 201124725 201105386 200513182a 200513182b EM1 200232081 201009156 V1_H141 Q94.0354.0.6 201221374 V1_H11 QF1 201125230 201013692 200900828 200410620a 200410620b 201200678 200805431 95/1000 H60-2 Q97.2224.3.1 C Q98.0072.08 M1 201009139 200709033 201102362 200831665 VTN021f VTN022f JF2 Human H21 WIA8 Q98.0072.31 Pig Q98.0026.12 3295.90B Q95.2078.2 Q98.0028.3 Chicken D9201243 Q1404.6A H38-2 Dog H4-2 Q95.3281.0 Q97.000.6.8 0.05
Colour-plate K: The Netherlands Italy United Kingdom
Human Chicken Pig Dog Australia Papua New Guinea United States of America
Colour-plate L: The Netherlands Italy United Kingdom
Australia Papua New Guinea United States of America
Colour-plate M: Groningen SIR biopsies: 0.89 (0.88 - 0.90) SIR HIS: 0.29 (0.13 - 0.55) Pigs 63.7/km2 Poultry 2.376.6/km2 HIV-centres 1/30
Noord-Holland SIR biopsies: 1.01 (1.01 - 1.02) SIR HIS: 1.84 (1.63 - 2.08) Pigs 9.7/km2 2 Poultry 493.4/km Friesland HIV-centres 9/30 SIR biopsies: 1.04 (1.02 - 1.05) SIR HIS: 0.21 (0.08 - 0.42) Pigs 31.8/km2 Poultry 2,187.2/km2 Drenthe HIV-centres 1/30 SIR biopsies: 0.92 (0.90 - 0.93) Flevoland SIR HIS: 0.54 (0.29 - 0.90) SIR biopsies: 1.20 (1.18 - 1.22) Pigs 107,5/km2 SIR HIS: 2.24 (1.62 - 3.02) Poultry 2,363.8/km2 Pigs 40.8/km2 HIV-centres 0/30 Poultry 1,461.9/km2 Overijssel HIV-centres 2/30 SIR biopsies: 0.94 (0.93 - 0.95) SIR HIS: 0.96 (0.72 - 1.24) Pigs 483.2/km2 Poultry 2,943.3/km2 HIV-centres 2/30 Utrecht SIR biopsies: 0.97 (0.96 - 0.98) SIR HIS: 0.93 (0.71 - 1.20) Pigs 219.1/km2 Poultry 1,227.9/km2 HIV-centres 2/30 Gelderland SIR biopsies: 1.08 (1.08 - 1.09) SIR HIS: 0.48 (0.36 - 0.64) Pigs 442.9/km2 Zuid-Holland 2 SIR biopsies: 0.99 (0.98 - 0.99) Poultry 3,439.3/km SIR HIS: 0.46 (0.37 - 0.57) HIV-centres 2/30 Pigs 56.5/km2 Poultry 390.0/km2 HIV-centres 7/30
Noord-Brabant SIR biopsies: 0.82 (0.81 - 0.82) SIR HIS: 0.58 (0.46 - 0.73) Limburg Pigs 1,078.6/km2 SIR biopsies: 1.27 (1.26 - 1.28) 2 SIR HIS: 2.92 (2.51 - 3.38) Poultry 5,330.5/km 2 HIV-centres 2/30 Pigs 790.6/km Poultry 6,880.0/km2 HIV-centres 1/30
Zeeland SIR biopsies: 0.86 (0.85 - 0.88) SIR HIS: 1.03 (0.64 - 1.58) Pigs 43.6/km2 Poultry 1,015.2/km2 HIV-centres 1/30
Colour-plate N: 4 4
Groningen SIR biopsies: 0.89 (0.88 - 0.90) SIR HIS: 0.29 (0.13 - 0.55) Pigs 63.7/km2 Poultry 2.376.6/km2 HIV-centres 1/30 3 5 3 5 Noord-Holland SIR biopsies: 1.01 (1.01 - 1.02) A C SIR HIS: 1.84 (1.63 - 2.08) Pigs 9.7/km2 2 Poultry 493.4/km Friesland HIV-centres 9/30 SIR biopsies: 1.04 (1.02 - 1.05) SIR HIS: 0.21 (0.08 - 0.42) 2 1 2 1 Pigs 31.8/km2 Poultry 2,187.2/km2 Drenthe 6 6 HIV-centres 1/30 SIR biopsies: 0.92 (0.90 - 0.93) Flevoland SIR HIS: 0.54 (0.29 - 0.90) 7 7 SIR biopsies: 1.20 (1.18 - 1.22) Pigs 107,5/km2 SIR HIS: 2.24 (1.62 - 3.02) Poultry 2,363.8/km2 Pigs 40.8/km2 HIV-centres 0/30 Poultry 1,461.9/km2 Overijssel HIV-centres 2/30 SIR biopsies: 0.94 (0.93 - 0.95) SIR HIS: 0.96 (0.72 - 1.24) Pigs 483.2/km2 Poultry 2,943.3/km2 HIV-centres 2/30 4 4 Utrecht SIR biopsies: 0.97 (0.96 - 0.98) SIR HIS: 0.93 (0.71 - 1.20) Pigs 219.1/km2 Poultry 1,227.9/km2 HIV-centres 2/30 Gelderland SIR biopsies: 1.08 (1.08 - 1.09) SIR HIS: 0.48 (0.36 - 0.64) Pigs 442.9/km2 3 3 Zuid-Holland 2 SIR biopsies: 0.99 (0.98 - 0.99) Poultry 3,439.3/km 5 5 SIR HIS: 0.46 (0.37 - 0.57) HIV-centres 2/30 Pigs 56.5/km2 B D Poultry 390.0/km2 HIV-centres 7/30
Noord-Brabant 2 1 2 1 SIR biopsies: 0.82 (0.81 - 0.82) SIR HIS: 0.58 (0.46 - 0.73) Limburg 6 6 Pigs 1,078.6/km2 SIR biopsies: 1.27 (1.26 - 1.28) 2 SIR HIS: 2.92 (2.51 - 3.38) Poultry 5,330.5/km 2 HIV-centres 2/30 Pigs 790.6/km 7 7 Poultry 6,880.0/km2 HIV-centres 1/30
1 Appendix Zeeland SIR biopsies: 0.86 (0.85 - 0.88) 2 Coecum SIR HIS: 1.03 (0.64 - 1.58) Pigs 43.6/km2 3 Ascending colon Poultry 1,015.2/km2 HIV-centres 1/30 4 Transversing colon 5 Descending colon 6 Sigmoid 7 Rectum
Colour-plate O: A
B
Colour-plate P:
Results Selected MSLT genes ( atpG
atpG
97 201105351b_B.aalborgi igroblaa.B_d153501102
igroblaa.B_e153501102
igroblaa.B_f153501102
201024610_B.aalborgi
201150471_B.aalborgi
201202009_B.aalborgi
201023408_B.aalborgi 201022967i_B.aalborgi
201022967h_B.aalborgi
201022967g_B.aalborgi
201022967f_B.aalborgi
201022967e_B.aalborgi
201022967d_B.aalborgi
201022967c_B.aalborgi
igroblaa.B_c153501102
igroblaa.B_a153501102
201105351g_B.aalborgi 201022967b_B.aalborgi 201111603_B.aalborgi
201114303_B.aalborgi
201123898_B.aalborgi
200101917_B.aalborgi 200918072_B.aalborgi 201150177_B.aalborgi
201104406_B.aalborgi 200917097_B.aalborgi 201050465_B.aalborgi
201014350_B.aalborgi 201015580_B.aalborgi 201040076_B.aalborgi
200813138g_B.aalborgi 200216407_B.aalborgi
200707443_B.aalborgi 200813138f_B.aalborgi 201050211_B.aalborgi
200813138e_B.aalborgi 201024300_B.aalborgi
200922746_B.aalborgi 200813138d_B.aalborgi 200113332_B.aalborgi 200813138c_B.aalborgi 200414761_B.aalborgi
200813138b_B.aalborgi 513A_B.aalborgi
201104608_B.aalborgi 200813138a_B.aalborgi 200813340_B.aalborgi
200805639_B.aalborgi 200501138_B.aalborgi
200709653_B.aalborgi 200904021_B.aalborgi
201103059_B.aalborgi 200914805_B.aalborgi 201120460_B.aalborgi 201150471_B.aalborgi 200602985_B.aalborgi 201003249_B.aalborgi 200900639_B.aalborgi 200900639_B.aalborgi 201110374a_B.aalborgi
201104140_B.hominis 201001908*_B.aalborgi 201110374b_B.aalborgi
201110374d_B.aalborgi 200923973_B.aalborgi 201104149_B.aalborgi 201110374g_B.aalborgi 200430368_B.aalborgi 201102752_B.aalborgi 200902757_B.aalborgi 201129345_B.aalborgi 201129345_B.aalborgi 200702703_B.aalborgi 200608126*_B.hominis 201109833_B.aalborgi 200624827_B.aalborgi
200805639_B.aalborgi 200920244_B.aalborgi 200704900_B.aalborgi
200917337_B.aalborgi 200813138c_B.aalborgi 200430368_B.aalborgi 95/1000_GenBank_B.pilosicoli WesB_B.pilosicoli 200813138f_B.aalborgi 200716125_B.aalborgi P43/6/78_B.pilosicoli ilocisolip.B_502306991 ilocisolip.B_566138002 200917097_B.aalborgi 201113577_B.aalborgi 200513182a_B.pilosicoli 200513182b_B.pilosicoli ilocisolip.B_032521102 ilocisolip.B_669101102 201022967c_B.aalborgi 201122669_B.aalborgi 200232081_B.pilosicoli ilocisolip.B_263201102 ilocisolip.B_683501102 201022967f_B.aalborgi 201108681_B.aalborgi 200410620a_B.pilosicoli 200410620b_B.pilosicoli 201022967g_B.aalborgi 200923973_B.aalborgi 201013692_B.pilosicoli ilocisolip.B_039909002 ilocisolip.B_828009002 201022967d_B.aalborgi 200913478_B.aalborgi ilocisolip.B_931900102 ilocisolip.B_449003002 200918072_B.aalborgi 200901135_B.aalborgi ilocisolip.B_505715002 ilocisolip.B_729402102 200813138g_B.aalborgi 201111933_B.aalborgi ilocisolip.B_651900102 ilocisolip.B_473122102 ilocisolip.B_876002102 200813138d_B.aalborgi 200816817_B.aalborgi ilocisolip.B_134508002
200901634_B.aalborgi 200813138a_B.aalborgi ilocisolip.B_527421102 ilocisolip.B_330907002 201122867_B.aalborgi
201129144_B.aalborgi
201004769_B.aalborgi
C1_B.alvinipulli B256_B.innocens 201018213_B.aalborgi 56-150_B.murdochii PWS/A_B.intermedia WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 200808214_B.aalborgi ilocisolip.B_066008991
200703075_B.aalborgi
200813138h_B.aalborgi
201119045_B.aalborgi
201024466_B.aalborgi
201124639_B.aalborgi
201007259_B.aalborgi
200811646_B.aalborgi sinimoh.B_b295300102 200925995_B.hominis
200803874_B.hominis sinimoh.B_115509002
sinimoh.B_207415002
sinimoh.B_343806002
201021258_B.hominis
201104140_B.hominis
200608126*_B.hominis 201024348_B.hominis
201003592a_B.hominis
201003592c_B.hominis
201003592d_B.hominis
201003592e_B.hominis sinimoh.B_300706002
sinimoh.B_566207002 201108603_B.hominis sinimoh.B_700611102
T.primitia_ZAS-2
0.05
Figure 1: 19
98 igroblaa.B_009407002
igroblaa.B_441921102
201004769_B.aalborgi
201050465_B.aalborgi sinimoh.B_843420102
201150177_B.aalborgi
200914805_B.aalborgi
200816817_B.aalborgi
200913478_B.aalborgi
201113577_B.aalborgi
201109833_B.aalborgi
201104149_B.aalborgi
sinimoh.B_478308002 200607003_B.hominis igroblaa.B_307207002
igroblaa.B_831105002 201023408_B.aalborgi 200813138b_B.aalborgi 201024610_B.aalborgi
201105351b_B.aalborgi 200813138e_B.aalborgi 201105351c_B.aalborgi 201105351d_B.aalborgi
201105351e_B.aalborgi 200813138h_B.aalborgi 201105351f_B.aalborgi
201105351g_B.aalborgi 201022967b_B.aalborgi 201111603_B.aalborgi
201022967e_B.aalborgi 201114303_B.aalborgi
200101917_B.aalborgi 201022967i_B.aalborgi 201007259_B.aalborgi
200716125_B.aalborgi 201040076_B.aalborgi
201119045_B.aalborgi 200702665_B.hominis
201003592a_B.hominis 201123898_B.aalborgi 201003592b_B.hominis
201105351a_B.aalborgi 201003592c_B.hominis
201003592d_B.hominis 201122867_B.aalborgi 201003592e_B.hominis
200608343_B.hominis 201104608_B.aalborgi
200813340_B.aalborgi 200113332_B.aalborgi
200901634_B.aalborgi 201021258_B.hominis 200905511_B.hominis 201104406_B.aalborgi 201103059_B.aalborgi i 201150471_B.aalborgi 201120460_B.aalborgi 201003249_B.aalborgi i 200900639_B.aalborgi 201124639_B.aalborgi 201110374a_B.aalborg 201110374a_B.aalborgi borgi 201110374b_B.aalborg 201104140_B.hominis 201110374b_B.aalborgi 201110374d_B.aalalborgi 200923973_B.aalborgi 201110374d_B.aalborgi 201110374g_B.a i 200430368_B.aalborgi 201110374g_B.aalborgi 200902757_B.aalborg i 201129345_B.aalborgi 200902757_B.aalborgi 200702703_B.aalborg i 200608126*_B.hominis 200216407_B.aalborgi 200624827_B.aalborg i 201108603_B.hominis 200704900_B.aalborg 200805639_B.aalborgi i 513A_B.aalborgi 200917337_B.aalborg 200813138c_B.aalborgi WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 200813138f_B.aalborgi
ilocisolip.B_066008991 200917097_B.aalborgi ilocisolip.B_828009002
200410620a_B.pilosicoliilocisolip.B_296310102 201022967c_B.aalborgi 200410620b_B.pilosicoliilocisolip.B_032521102
201022967f_B.aalborgi
201009139_B.pilosicoli 201022967g_B.aalborgi ilocisolip.B_651900102 ilocisolip.B_876002102
201022967d_B.aalborgi 95/1000_GenBank_B.pilosicoli ilocisolip.B_134508002 P43/6/78_B.pilosicoli
200918072_B.aalborgi ilocisolip.B_330907002 200513182a_B.pilosicoli ilocisolip.B_566138002 200513182b_B.pilosicoli 200813138g_B.aalborgi ilocisolip.B_263201102
200813138d_B.aalborgi
ilocisolip.B_180232002 200813138a_B.aalborgi ilocisolip.B_473122102 201024466_B.aalborgi WesB_B.pilosicoli
200602985_B.aalborgi i ilocisolip.B_683501102
ilocisolip.B_527421102 201102752_B.aalborgi C1_B.alvinipulli
ilocisolip.B_039909002
ilocisolip.B_502306991 200920244_B.aalborg B256_B.innocens ilocisolip.B_729402102
ilocisolip.B_449003002 PWS/A_B.intermedia ilocisolip.B_505715002
201122669_B.aalborgi ilocisolip.B_669101102
56-150_B.murdochii 201111933_B.aalborgi
200917337_B.aalborgi
201015580_B.aalborgi
201116007_B.hominis
201050211_B.aalborgi
200925995_B.hominis
200514702_B.hominis
201003249_B.aalborgi
200624827_B.aalborgi
200811646_B.aalborgi
igroblaa.B_647229002 igroblaa.B_*809100102
201014350_B.aalborgi
201018213_B.aalborgi
201024300_B.aalborgi
200414761_B.aalborgi
200808214_B.aalborgi
201022967h_B.aalborgi
200709653_B.aalborgi 201202009_B.aalborgi
201108681_B.aalborgi igroblaa.B_570307002
200707443_B.aalborgi igroblaa.B_531109002
200904021_B.aalborgi
T.primitia_ZAS-2
0.06
Figure 2:
99 igroblaa.B_053410102 igroblaa.B_936421102
200702703_B.aalborgi
201111603_B.aalborgi
200917337_B.aalborgi
201104140_B.hominis 201003592b_B.hominis
201003592c_B.hominis
201003592d_B.hominis
200803874_B.hominis
201021258_B.hominis
201150177_B.aalborgi 200904021_B.aalborgi 200905511_B.hominis igroblaa.B_941401102 sinimoh.B_843420102 200923973_B.aalborgi
200925995_B.hominis 200602985_B.aalborgi
200805639_B.aalborgi200922746_B.aalborgi 201111933_B.aalborgi 201123898_B.aalborgi
201105351c_B.aalborgi 200920244_B.aalborgi 201105351b_B.aalborgi
201105351d_B.aalborgi 200624827_B.aalborgi
200811646_B.aalborgi 200414761_B.aalborgi
201103059_B.aalborgi
201015580_B.aalborgi 513A_B.aalborgi 200707443_B.aalborgi 201007259_B.aalborgi 201108681_B.aalborgi
200808214_B.aalborgi 200709653_B.aalborgi
200914805_B.aalborgi 201119045_B.aalborgi 201102752_B.aalborgi 200816817_B.aalborgi 201129345_B.aalborgi 200702665_B.hominis 200813138a_B.aalborgi 200904021_B.aalborgi 200608343_B.hominis 200813138g_B.aalborgi 201003249_B.aalborgi 200704900_B.aalborgi 200514702_B.hominis 200430368_B.aalborgi 200813138c_B.aalborgi 200716125_B.aalborgi 201116007_B.hominis 200113332_B.aalborgi 201113577_B.aalborgi 201003249_B.aalborgi 200501138_B.aalborgi 201122669_B.aalborgi
201129144_B.aalborgi 201050211_B.aalborgi 201108681_B.aalborgi 201122669_B.aalborgi 200902757_B.aalborgi 200923973_B.aalborgi WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 200816817_B.aalborgi 201114303_B.aalborgi PWS/A_B.intermedia 200917337_B.aalborgi 201024610_B.aalborgi C1_B.alvinipulli 200914805_B.aalborgi 56-150_B.murdochii 201018213_B.aalborgi B256_B.innocens 201015580_B.aalborgi
200900639_B.aalborgi 201202009_B.aalborgi
201150471_B.aalborgi 200913478_B.aalborgi 201150177_B.aalborgi P43/6/78_B.pilosicoliilocisolip.B_669101102 201104406_B.aalborgi 201116007_B.hominis
201104406_B.aalborgi
200513182a_B.pilosicoli 200918072_B.aalborgi 201050465_B.aalborgi ilocisolip.B_473122102 200513182b_B.pilosicoli
200716125_B.aalborgi201050465_B.aalborgi ilocisolip.B_180232002
201122867_B.aalborgi WesB_B.pilosicoli
201024300_B.aalborgi
2 ilocisolip.B_505715002 201104608_B.aalborgi ilocisolip.B_449003002
201202009_B.aalborgi 95/1000_GenBank_B.pilosicoli
201022967d_B.aalborgi ilocisolip.B_039909002
ilocisolip.B_566138002 ilocisolip.B_263201102
201022967c_B.aalborgi ilocisolip.B_330907002 ilocisolip.B_683501102
200813138e_B.aalborgi ilocisolip.B_52742110
200901135_B.aalborgi ilocisolip.B_729402102 200813138d_B.aalborgi 201150471_B.aalborgi ilocisolip.B_032521102
ilocisolip.B_296310102 201022967e_B.aalborgi 200917097_B.aalborgi
201110374d_B.aalborgi ilocisolip.B_828009002
201110374b_B.aalborgi
ilocisolip.B_931900102
ilocisolip.B_134508002 ilocisolip.B_651900102
ilocisolip.B_876002102
ilocisolip.B_a026014002 200813138b_B.aalborgi ilocisolip.B_b026014002
T.primitia_ZAS-2 0.06 Figure 3:
100 igroblaa.B_806401102
sinimoh.B_e295300102
201040076_B.aalborgi
201014350_B.aalborgi
200703075_B.aalborgi
200101917_B.aalborgi
201123898_B.aalborgi
201114303_B.aalborgi
200501138_B.aalborgi
_599529002
201022967h_B.aalborgi200514702_B.hominis
201022967g_B.aalborgi
201022967d_B.aalborgi
sinimoh.B_d295300102 sinimoh.B
igroblaa.B_647229002 201022967c_B.aalborgi 200813340_B.aalborgi 201124639_B.aalborgi
201110374a_B.aalborgi
201110374b_B.aalborgi
201110374d_B.aalborgi 200608343_B.hominis 201110374g_B.aalborgi 200902757_B.aalborgi
201129144_B.aalborgi 200803874_B.hominis 513A_B.aalborgi
200917097_B.aalborgi 200900639_B.aalborgi
200901135_B.aalborgi 200813138h_B.aalborgi 201018213_B.aalborgi
200813138g_B.aalborgi 200913478_B.aalborgi
200608126*_B.hominis 200813138f_B.aalborgi 200602985_B.aalborgi
200813138c_B.aalborgi 200805639_B.aalborgi
200813138a_B.aalborgi 200813138b_B.aalborgi 200813138d_B.aalborgi
200709653_B.aalborgi 200813138e_B.aalborgi
201022967i_B.aalborgi 200607003_B.hominis 201023408_B.aalborgi 201001908*_B.aalborgi 201105351a_B.aalborgi
201104149_B.aalborgi 201105351b_B.aalborgi
201105351c_B.aalborgi 201102752_B.aalborgi i 201105351d_B.aalborgi 201129345_B.aalborgi 201105351g_B.aalborgi 200813138a_B.aalborgi i 200904021_B.aalborgi 201111603_B.aalborgi 200813138g_B.aalborg 201003249_B.aalborgi 200808214_B.aalborgi i 200704900_B.aalborg 201007259_B.aalborgi 200430368_B.aalborgi 200813138c_B.aalborgi 200811646_B.aalborgi 200716125_B.aalborgi 201003592a_B.hominis 200113332_B.aalborg i 201113577_B.aalborgi 201003592b_B.hominis 200501138_B.aalborg i 201122669_B.aalborgi 201003592c_B.hominis 201050211_B.aalborg 201108681_B.aalborgi 200901634_B.aalborgi i 201122669_B.aalborg 200905511_B.hominis 200923973_B.aalborgi 200805431_B.pilosicoli 95/1000_GenBank_B.pilosicoli 200816817_B.aalborgi P43/6/78_B.pilosicoli
200831665_B.pilosicoli ilocisolip.B_931900102 200917337_B.aalborgi ilocisolip.B_330907002 ilocisolip.B_263201102 200914805_B.aalborgi
ilocisolip.B_180232002 201015580_B.aalborgi 200900828_B.pilosicoli 200410620b_B.pilosicoliilocisolip.B_473122102 200410620a_B.pilosicoli 201202009_B.aalborgi ilocisolip.B_876002102
21102 ilocisolip.B_651900102 201150471_B.aalborgi 200513182b_B.pilosicoli 200513182a_B.pilosicoli 201150177_B.aalborgi 201101966_B.pilosicoli 201024466_B.aalborgi ilocisolip.B_296310102 WesB_B.pilosicoli 201116007_B.hominis ilocisolip.B_0325 ilocisolip.B_502306991 ilocisolip.B_039909002 201104406_B.aalborgi ilocisolip.B_729402102 ilocisolip.B_683501102 201050465_B.aalborgi
ilocisolip.B_449003002 WA1_GenBank_B.hyodysenteriae 201021258_B.hominis B-78_B.hyodysenteriae ilocisolip.B_505715002
ilocisolip.B_527421102 201004769_B.aalborgi
200113332_B.aalborgi PWS/A_B.intermedia
C1_B.alvinipulli 200414761_B.aalborgi
56-150_B.murdochii 201122867_B.aalborgi B256_B.innocens
ilocisolip.B_066008991 200702703_B.aalborgi
201108603_B.hominis
200216407_B.aalborgi
201120460_B.aalborgi
201103059_B.aalborgi
200707443_B.aalborgi
200702665_B.hominis
201105351f_B.aalborgi sinimoh.B_041401102 igroblaa.B_112050102
igroblaa.B_728426002
201105351e_B.aalborgi 201024610_B.aalborgi 201024348_B.hominis
201022967f_B.aalborgi
201022967e_B.aalborgi
201022967b_B.aalborgi 200918072_B.aalborgi
201109833_B.aalborgi
200920244_B.aalborgi
201111933_B.aalborgi
201024300_B.aalborgi igroblaa.B_009407002
igroblaa.B_540911102
T.primitia_ZAS-2
0.06
Figure 4:
101 201114303_B.aalborgi
igroblaa.B_646118002 201104149_B.aalborgi
200917337_B.aalborgi
200501138_B.aalborgi
200702703_B.aalborgi
201050211_B.aalborgi
201122669_B.aalborgi
201018213_B.aalborgi
200900639_B.aalborgi
200913478_B.aalborgi
200624827_B.aalborgi
201105351d_B.aalborgi 513A_B.aalborgi
200902757_B.aalborgi
201129144_B.aalborgi
201103059_B.aalborgi
201105351b_B.aalborgi 201124639_B.aalborgi
200702665_B.hominis
200707443_B.aalborgi 201123898_B.aalborgi 201024610_B.aalborgi
201111603_B.aalborgi 200922746_B.aalborgi 200813138c_B.aalborgi
201105351c_B.aalborgi 200813138g_B.aalborgi
200709653_B.aalborgi
200805639_B.aalborgi 200813138a_B.aalborgi
200923973_B.aalborgi 201150177_B.aalborgi 201108681_B.aalborgi
201021258_B.hominis 200914805_B.aalborgi
200816817_B.aalborgi 200925995_B.hominis 201104406_B.aalborgi 200803874_B.hominis 201116007_B.hominis
201015580_B.aalborgi 200113332_B.aalborgi
201119045_B.aalborgi 201024300_B.aalborgi
200514702_B.hominis 200602985_B.aalborgi 200414761_B.aalborgi 200920244_B.aalborgi 200704900_B.aalborgi
201111933_B.aalborgi 201003249_B.aalborgi
201104140_B.hominis 200904021_B.aalborgi
200608343_B.hominis 201014350_B.aalborgi WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 201007259_B.aalborgi PWS/A_B.intermedia
200808214_B.aalborgi 56-150__B.murdochii B256_B.innocens 201024348_B.hominis C1_B.alvinipulli
200905511_B.hominis
201003592d_B.hominis 201110374b_B.aalborgi
201003592c_B.hominis 201110374d_B.aalborgi
201003592b_B.hominis T.primitia_ZAS-2
201050465_B.aalborgi
201122867_B.aalborgi 200909930_B.pilosicoli ilocisolip.B_669101102
200813138e_B.aalborgi 201009156_B.pilosicoli 200813138d_B.aalborgi
201022967c_B.aalborgi ilocisolip.B_180232002
201022967d_B.aalborgi
201022967e_B.aalborgi ilocisolip.B_828009002
201104608_B.aalborgi WesB_B.pilosicoli ilocisolip.B_296310102 201202009_B.aalborgi 200513182b_B.pilosicoli ilocisolip.B_032521102 200901135_B.aalborgi 200513182a_B.pilosicoli 201150471_B.aalborgi 200918072_B.aalborgi 200917097_B.aalborgi 200716125_B.aalborgi ilocisolip.B_527421102
ilocisolip.B_134508002 200410620a_B.pilosicoli
ilocisolip.B_931900102
ilocisolip.B_263201102
ilocisolip.B_566138002 ilocisolip.B_729402102
200813138b_B.aalborgi ilocisolip.B_683501102
ilocisolip.B_505715002
ilocisolip.B_449003002
ilocisolip.B_876002102
P43/6/78_B.pilosicoli
ilocisolip.B_473122102 ilocisolip.B_b026014002
95/1000_GenBank_B.pilosicoli
ilocisolip.B_330907002 0.06 Figure 5:
102
atpG
Table 3:
Length Locus MLST Length (bp) AAT variable sites variable sites
atpG
T.primitia_Z AS-2 **
103 B. aalborgi B. pilosicoli B. murdochii B. innocens
‘B. hominis’ B. hyodysenteriae B. alvinipulli B. intermedia
Figure 6:
104 B. aalborgi B. pilosicoli B. murdochii B. innocens
B. hyodysenteriae B. intermedia ‘B. hominis’ B. alvinipulli B. intermedia
Figure 7:
105 Chapter 5
106
Figure 8:
107 Chapter 5
Discussion
108
As
atpG .
109 Chapter 5
.
110
111 Chapter 5
References 32 2 4 154 36 52 39 J 38 16 36 7 3 53 77 53 153 23 43 136 14 12 5 43 2 62
112
4 138 1 7 102 13 95 29 51 27 12 23 28 13 67 41 132 39
113 201104140_B.hominis
igroblaa.B_863034002 201111933_B.aalborgi 201104608_B.aalborgi igroblaa.B_775311102
201103059_B.aalborgi 201109833_B.aalborgi
200608126*_B.hominis
200918072_B.aalborgi
201024348_B.hominis 201003592a_B.hominis
201003592b_B.hominis
sinimoh.B_599529002 201003592c_B.hominis sinimoh.B_478308002
igroblaa.B_936508002 201003592d_B.hominis igroblaa.B_412808002
200923973_B.aalborgi
200917337_B.aalborgi
201202009_B.aalborgi 201003592e_B.hominis 201150177_B.aalborgi 201122867_B.aalborgi
201150471_B.aalborgi 201104406_B.aalborgi 200902757_B.aalborgi
200905511_B.hominis 200702665_B.hominis
201110374a_B.aalborgi 200703075_B.aalborgi
200813138h_B.aalborgi
201110374b_B.aalborgi 201102752_B.aalborgi
200901135_B.aalborgi 201110374d_B.aalborgi 201116007_B.hominis
201110374g_B.aalborgi 201024300_B.aalborgi
200514702_B.hominis
201021258_B.hominis 200608343_B.hominis 201003249_B.aalborgi 201114303_B.aalborgi 200607003_B.hominis
201018213_B.aalborgi 201111603_B.aalborgi 201024610_B.aalborgi 200900639_B.aalborgi 200901634_B.aalborgi
200101917_B.aalborgi 201129144_B.aalborgi
201004769_B.aalborgi 200913478_B.aalborgi 200920244_B.aalborgi 200813340_B.aalborgi
201040076_B.aalborgi 201023408_B.aalborgi 200811646_B.aalborgi 201022967i_B.aalborgi 201104149_B.aalborgi 201021258_B.hominis 201022967h_B.aalborgi 201007259_B.aalborgi 201024348_B.hominis 201022967g_B.aalborgi 201124639_B.aalborgi 200918072_B.aalborgi 201014350_B.aalborgi 201022967f_B.aalborgi 201050465_B.aalborgi 201003592b_B.hominis 201022967e_B.aalborgi 200624827_B.aalborgi 201003592a_B.hominis 201022967d_B.aalborgi 200414761_B.aalborgi 201003592d_B.hominis
201022967c_B.aalborgi 201124725_B.pilosicoli ilocisolip.B_729402102 201003592c_B.hominis 200831665_B.pilosicoli 200813138g_B.aalborgi ilocisolip.B_330907002 200905511_B.hominis ilocisolip.B_263201102 200813138f_B.aalborgi 200513182a_B.pilosicoliilocisolip.B_651900102 200901634_B.aalborgi 200513182b_B.pilosicoliilocisolip.B_180232002 200813138e_B.aalborgi ilocisolip.B_134508002 WesB_B.pilosicoli ilocisolip.B_669101102 201015580_B.aalborgi P43/6/78_B.pilosicoli 199603205_B.pilosicoli 200813138d_B.aalborgi 201119045_B.aalborgi
200410620b_B.pilosicoli 200410620a_B.pilosicoli ilocisolip.B_039909002 200813138c_B.aalborgi 201050465_B.aalborgi 201024466_B.aalborgi ilocisolip.B_505715002 95/1000_GenBank_B.pilosicoli
200813138b_B.aalborgi 201122867_B.aalborgi
200813138a_B.aalborgi ilocisolip.B_876002102 200805639_B.aalborgi ilocisolip.B_683501102 ilocisolip.B_828009002 200709653_B.aalborgi 200602985_B.aalborgi
ilocisolip.B_032521102 201129345_B.aalborgi 201104608_B.aalborgi ilocisolip.B_296310102
ilocisolip.B_931900102 201122669_B.aalborgi ilocisolip.B_449003002 201007259_B.aalborgi ilocisolip.B_473122102
201108681_B.aalborgi 201102752_B.aalborgi 200816817_B.aalborgi
200914805_B.aalborgi
201050211_B.aalborgi
200113332_B.aalborgi
200501138_B.aalborgi
200704900_B.aalborgi
201108603_B.hominis
200707443_B.aalborgi
201119045_B.aalborgi ilocisolip.B_066008991
B-78_B.hyodysenteriae 200904021_B.aalborgi B256_B.innocens
igroblaa.B_064021102
200716125_B.aalborgi
56-150_B.murdochii 513A_B.aalborgi
200602985_B.aalborgi igroblaa.B_f153501
C1_B.alvinipulli 200702703_B.aalborgi 201001908*_B.aalborgi 201015580_B.aalborgi
201105351a_B.aalborgi 200922746_B.aalborgi
201123898_B.aalborgi
201105351c_B.aalborgi igroblaa.B_790719002
201105351b_B.aalborgi
201105351e_B.aalborgi
201105351d_B.aalborgi
aidemretni .B_A/SWP
102
airetnsdy B_knaBneG_1AW . nesydoyh t e r i ea
T.primitia_ZAS-2
0.06
114 igroblaa.B_942300102
201024300_B.aalborgi sinimoh.B_343806002
200913478_B.aalborgi sinim
201202009_B.aalborgi
201111603_B.aalborgi
oh.B_300706002 201105351d_B.aalborgi
200702665_B.hominis
200101917_B.aalborgi
200902757_B.aalborgi
sinim o h.B _ 2 0 7 4 1 5 0 0 2 igro bla a.B _ 1 6 7 4 1 4 0 0 2
sinim o h.B _ 7 0 0 6 1 1 1 0 2 201023408_B.aalborgi
201129144_B.aalborgi 201103059_B.aalborgi 201114303_B.aalborgi
201105351b_B.aalborgi
201105351c_B.aalborgi 200704900_B.aalborgi
200716125_B.aalborgi 200501138_B.aalborgi
200113332_B.aalborgi
200917337_B.aalborgi 201050211_B.aalborgi
201110374g_B.aalborgi 200914805_B.aalborgi
200816817_B.aalborgi 201004769_B.aalborgi 201108681_B.aalborgi
200925995_B.hominis 201122669_B.aalborgi
201129345_B.aalborgi 200803874_B.hominis
200709653_B.aalborgi 200624827_B.aalborgi 200813138a_B.aalborgi
200608126*_B.hominis 200813138c_B.aalborgi
200813138d_B.aalborgi 201109833_B.aalborgi
200813138e_B.aalborgi 200920244_B.aalborgi 200920244_B.aalborgi 200813138f_B.aalborgi 201040076_B.aalborgi 201111933_B.aalborgi i 200813138g_B.aalborgi 200811646_B.aalborgi 201104140_B.hominis 201022967b_B.aalborgi i 201104149_B.aalborg 201021258_B.hominis 201022967c_B.aalborgi 201007259_B.aalborg i 201022967d_B.aalborgi 201024348_B.hominis 201124639_B.aalborg i 201022967e_B.aalborgi 200918072_B.aalborgi 201014350_B.aalborg i 201022967f_B.aalborgi 201050465_B.aalborg 201003592b_B.hominis 201022967g_B.aalborgi i 200624827_B.aalborg 201003592a_B.hominis 201022967h_B.aalborgi i 200414761_B.aalborg 201003592d_B.hominis 201022967i_B.aalborgi
201003592c_B.hominis 200813340_B.aalborgi
201108603_B.hominis 200905511_B.hominis
201024610_B.aalborgi 200901634_B.aalborgi
WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 201015580_B.aalborgi PWS/A_B.intermedia
201119045_B.aalborgi C1_B.alvinipulli
201050465_B.aalborgi 56-150_B.murdochii
201122867_B.aalborgi
200805639_B.aalborgi
1 200602985_B.aalborgi T.primitia_ZAS-2 201110374d_B.aalborgi o cisil olip.B _ 0 6 6 0 0 8 9 9
201104608_B.aalborgi 201150471_B.aalborgi
201007259_B.aalborgi 200901135_B.aalborgi
200517505_B.pilosicoli 201102752_B.aalborgi
201014350_B.aalborgi
201124639_B.aalborgi o cis olip.B _ 5 6 6 1 3 8 0 0 2 201102362_B.pilosicoli il
200811646_B.aalborgi o cis olip.B _ 0 3 9 9 0 9 0 0 2 il 201104406_B.aalborgi
200808214_B.aalborgi 201024466_B.aalborgi 513A_B.aalborgi o cis olip.B _ 9 3 1 9 0 0 1 0 2 il
WesB_B.pilosicoli o cis olip.B _ 6 6 9 1 0 1 1 0 2 201110374b_B.aalborgi il 201105351g_B.aalborgi
201018213_B.aalborgi
200900639_B.aalborgi
200702703_B.aalborgi
o cis olip.B _ 4 7 3 1 2 2 1 0 2 il 201104149_B.aalborgi 09002 200513182a_B.pilosicoli o cis olip.B _ 8 7 6 0 0 2 1 0 2 il 200513182b_B.pilosicoli
200410620a_B.pilosicoli o cis olip.B _ 1 8 0 2 3 2 0 0 2
200410620b_B.pilosicoli il 200923973_B.aalborgi o cis olip.B _ 6 8 3 5 0 1 1 0 2
il P43/6/78_B.pilosicoli il 200904021_B.aalborgi il ocisolip.B_330907002 igroblaa.B_570307002 o cis olip.B _ 8 2 8 0
ocisolip.B_729402102 201123898_B.aalborgi 201113577_B.aalborgi il 201150177_B.aalborgi o cis olip.B _ 6 5 1 9 0 0 1 0 2 200922746_B.aalborgi il
200707443_B.aalborgi
B256_B.innocens
200917097_B.aalborgi
o cis olip.B _ 0 3 2 5 2 1 1 0 2 200813138b_B.aalborgi
o cis olip.B _ 4 4 9 0 0 3 0 0 2 il
il o cis olip.B _ 5 2 7 4 2 1 1 0 2
o cis olip.B _ 2 9 6 3 1 0 1 0 2
il
il 200805431_B.pilosicoli
o cis olip.B _ k n a B n e G _ 0 0 0 1/5 9
il
0.05
115 201003249_B.aalborgi
igroblaa.B_412808002
igroblaa.B_936009002 201108603_B.hominis
201114303_B.aalborgi 200514702_B.hominis
201202009_B.aalborgi 201024610_B.aalborgi200925995_B.hominis
201129144_B.aalborgi
200902757_B.aalborgi
sinim o h.B _ 3 4 3 8 0 6 0 0 2
igro bla a.B _ 0 5 3 4 1 0 1 0 2 200811646_B.aalborgi sinim o h.B _ 5 6 6 2 0 7 0 0 2 201119045_B.aalborgi sinim o h.B _ 7 0 0 6 1 1 1 0 2
201120460_B.aalborgi 201018213_B.aalborgi 200816817_B.aalborgi 201004769_B.aalborgi
200920244_B.aalborgi 200414761_B.aalborgi
201015580_B.aalborgi 200914805_B.aalborgi 200707443_B.aalborgi
200709653_B.aalborgi 201104406_B.aalborgi 201108681_B.aalborgi
201007259_B.aalborgi 201129345_B.aalborgi
200608126*_B.hominis 200704900_B.aalborgi
200624827_B.aalborgi 201104140_B.hominis 200501138_B.aalborgi 201021258_B.hominis 200113332_B.aalborgi
200803874_B.hominis 201050211_B.aalborgi
201122669_B.aalborgi 201024348_B.hominis 200813138a_B.aalborgi 201003592c_B.hominis 200813138b_B.aalborgi
201003592b_B.hominis 200813138c_B.aalborgi
201003592d_B.hominis 200813138d_B.aalborgi
200813138e_B.aalborgi 200901135_B.aalborgi 200813138g_B.aalborgi 201105351c_B.aalborgi
201022967b_B.aalborgi 200624827_B.aalborgi 201105351b_B.aalborgi 201022967c_B.aalborgi 200430368_B.aalborgi 201105351d_B.aalborgi 201022967d_B.aalborgi
201050465_B.aalborgi 201105351f_B.aalborgi 201022967e_B.aalborgi
201022967f_B.aalborgi 201108681_B.aalborgi 201110374g_B.aalborgi 201022967g_B.aalborgi 201104406_B.aalborgi 200602985_B.aalborgi 201040076_B.aalborgi 201104149_B.aalborgi 201150177_B.aalborgi 200813340_B.aalborgi
201110374a_B.aalborgi 201105351e_B.aalborgi WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae PWS/A_B.intermedia 200923973_B.aalborgi 201001908*_B.aalborgi 200716125_B.aalborgi 513A_B.aalborgi 200914805_B.aalborgi C1_B.alvinipulli B256_B.innocens 201103059_B.aalborgi 200816817_B.aalborgi 200918072_B.aalborgi
200805639_B.aalborgi 56-150_B.murdochii 201129144_B.aalborgi
201105351g_B.aalborgi 201021258_B.hominis 201110374b_B.aalborgi 200922746_B.aalborgi 201024610_B.aalborgi 201110374d_B.aalborgi
201123898_B.aalborgi 200813138c_B.aalborgi 199603205_B.pilosicoli 201150471_B.aalborgi
122102 200702703_B.aalborgi 200805431_B.pilosicoli
200917097_B.aalborgi o cis olip. B _ 4 7 3 il P43/6/78_B.pilosicoli 201104149_B.aalborgi 200513182b_B.pilosicoli
200917337_B.aalborgi o cis olip.B _ 6 5 1 9 0 0 1 0 2 il 200513182a_B.pilosicoli 201023408_B.aalborgi
201111603_B.aalborgi
201104608_B.aalborgi o cis olip.B _ 5 0 5 7 1 5 0 0 2 il
201124639_B.aalborgi 95/1000_GenBank_B.pilosicoli
201110374a_B.aalborgi o cis olip.B _ 1 8 0 2 3 2 0 0 2 200607003_B.hominis il o cis olip.B _ 8 2 8 0 0 9 0 0 2 il 200905511_B.hominis WesB_B.pilosicoli
200410620a_B.pilosicoli o cis olip.B _ 4 4 9 0 0 3 0 0 2
200410620b_B.pilosicoli il 201111933_B.aalborgi o cis olip.B _ 9 3 1 9 0 0 1 0 2 il
200216407_B.aalborgi il 201102362_B.pilosicoli il il
ocisolip.B_039909002
ocisolip.B_669101102
ocisolip.B_527421102 o cis olip.B _ 0 3 2 5 2 1 1 0 2 200913478_B.aalborgi il
200923973_B.aalborgi 200904021_B.aalborgi o cis olip.B _ 2 9 6 3 1 0 1 0 2 il
201024300_B.aalborgi
o cis olip.B _ 8 7 6 0 0 2 1 0 2 201105351a_B.aalborgi201024466_B.aalborgi
o cis olip.B _ 6 8 3 5 0 1 1 0 2 201050465_B.aalborgi o cis olip.B _ 5 6 6 1 3 8 0 0 2 o cis olip.Bil _ 7 2 9 4 0 2 1 0 2 o cis olip.B _ 3 3 0 9 0 7 0 0 2
il il
201122867_B.aalborgi il
il
200430368_B.aalborgi
T.primitia_ZAS-2 0.07
116 igroblaa.B_270819002 201024348_B.hominis
201150177_B.aalborgi
200113332_B.aalborgi
2 00925995_B.hominis 201150471_B.aalborgi
201110374b_B.aalborgi
201122669_B.aalborgi
sinim o h.B _ b 2 9 5 3 0 0 1 0 2 201050211_B.aalborgi sinim o h.B _c2 9 5 3 0 0 1 0 2 sinim o h.B _ d 2 9 5 3 0 0 1 0 2 201109833_B.aalborgi
o cissinim olip.B o h.B _ 6 6_ 1 9 1 1 5 0 5 1 0 1 9 0 0 2 0201113577_B.aalborgi 2
201111933_B.aalborgi il 201104140_B.hominis 513A_B.aalborgi 200501138_B.aalborgi 201114303_B.aalborgi
200920244_B.aalborgi 200902757_B.aalborgi 201001908*_B.aalborgi 200702703_B.aalborgi
201110374d_B.aalborgi 201119045_B.aalborgi
200608343_B.hominis 201111603_B.aalborgi 200901135_B.aalborgi 201003249_B.aalborgi
201105351c_B.aalborgi
200514702_B.hominis 200922746_B.aalborgi
201123898_B.aalborgi 201116007_B.hominis
200707443_B.aalborgi 200702665_B.hominis
200808214_B.aalborgi 200709653_B.aalborgi 201007259_B.aalborgi 200913478_B.aalborgi 201103059_B.aalborgi
200900639_B.aalborgi 200917337_B.aalborgi 201122867_B.aalborgi 201018213_B.aalborgi 200813138g_B.aalborgi 201015580_B.aalborgi i 201022967b_B.aalborgi 200624827_B.aalborgi 200716125_B.aalborgi i 201022967c_B.aalborg 200430368_B.aalborgi 201040076_B.aalborgi 201022967d_B.aalborg lborgi 200414761_B.aalborgi 201050465_B.aalborgi 201022967e_B.aa i 201105351b_B.aalborgi 201022967f_B.aalborg 201108681_B.aalborgi lborgi 201124639_B.aalborgi 201022967g_B.aa 201104406_B.aalborgi i 201105351e_B.aalborgi 201040076_B.aalborg 201104149_B.aalborgi i 201105351a_B.aalborgi 200813340_B.aalborg
201110374a_B.aalborgi 201105351d_B.aalborgi
200923973_B.aalborgi 95/1000_GenBank_B.pilosicoli WesB_B.pilosicolio cisil olip.B _ 3 3 0 9 0 7 0 0 2
200914805_B.aalborgi o cisil olip.B _ 6 8 3 5 0 1 1 0 2 200410620b_B.pilosicolio cis olip.B _ 5 0 2 3 0 6 9 9 1 200410620a_B.pilosicoli il o cisil olip.B _ 5 6 6 1 3 8 0 0 2 200816817_B.aalborgi o cisil olip.B _ 8 7 6 0 0 2 1 0 2 201022967d_B.aalborgi 201022967c_B.aalborgi o cis olip.B _ 2 6 3 2 0 1 1 0 2 200813138e_B.aalborgi il 200813138b_B.aalborgi 200813138d_B.aalborgi
200513182a_B.pilosicoli 201129144_B.aalborgi 200513182b_B.pilosicoli o cis olip.B _ 9 3 1 9 0 0 1 0 2 201022967e_B.aalborgi il o cis olip.B _ 5 0 5 7 1 5 0 0 2 P43/6/78_B.pilosicoli il o cis olip.B _ 5 2 7 4 2 1 1 0 2 il 201021258_B.hominis 200900828_B.pilosicoli o cis olip.B _ 1 3 4 5 0 8 0 0 2 il
201024610_B.aalborgi
o cis olip.B _ 7 2 9 4 0 2 1 0 2 il 200813138c_B.aalborgi
o cis olip.B _ 4 4 9 0 0 3 0 0 2 o cis olip.B _ 4 7 3 1 2 2 1 0 2 il 200704900_B.aalborgi il
sinimo cis o h.B olip.B _ a 2 _ 9 6 5 5 3 1 0 9 0 0 1 0 2 1 0 2 o ciso cis olip.B olip.B _ 0 3 _ 9 1 9 8 0 0 9 2 0 3 0 2 2 0 0 2
o cis olip.B _ 2 9 6 3 1 0 1 0 2 o cis olip.B _ 0 3 2 5 2 1 1 0 2 il il il
il il 201022967h_B.aalborgi
201022967b_B.aalborgi
il
ocisolip.B_066008991
200813138g_B.aalborgi
201014350_B.aalborgi
200813138a_B.aalborgi
200917097_B.aalborgi
201024300_B.aalborgi
200904021_B.aalborgi
200803874_B.hominis
201120460_B.aalborgi
200703075_B.aalborgi
200811646_B.aalborgi
200805639_B.aalborgi 200602985_B.aalborgi
B256_B.innocens
PWS/A_B.intermedia
201104608_B.aalborgi
B-78_B.hyodysenteriae
201202009_B.aalborgi
C1_B.alvinipulli 56-150_B.murdochii
WA1_GenBank_B.hyodysenteriae
0.06 T.primitia_ZAS-2
117 igroblaa.B_670040102
201003592c_B.hominis sinimoh.B_566207002 201104608_B.aalborgi
200901634_B.aalborgi 200813340_B.aalborgi 201103059_B.aalborgi
200905511_B.hominis 201124639_B.aalborgi 201120460_B.aalborgi 201110374b_B.aalborgi 201110374a_B.aalborgi 201110374g_B.aalborgi
sinimoh.B_b295300102
201110374d_B.aalborgi igroblaa.B_646118002 sinimoh.B_a295300102igroblaa.B_344707002
sinimoh.B_d295300102 201007259_B.aalborgi 201014350_B.aalborgi 200703075_B.aalborgi 200808214_B.aalborgi sinimoh.B_e295300102 201111603_B.aalborgi 201108603_B.hominis 200101917_B.aalborgi 201024348_B.hominis 200902757_B.aalborgi 201024610_B.aalborgi 201022967i_B.aalborgi 201023408_B.aalborgi 201022967g_B.aalborgi 201129144_B.aalborgi 201022967h_B.aalborgi 513A_B.aalborgi 201022967e_B.aalborgi 201122867_B.aalborgi 201022967f_B.aalborgi 201022967c_B.aalborgi 200702703_B.aalborgi 201022967d_B.aalborgi 200917097_B.aalborgi 200624827_B.aalborgi 200918072_B.aalborgi 200704900_B.aalborgi 200813138g_B.aalborgi 200813138h_B.aalborgi 200904021_B.aalborgi 200813138e_B.aalborgi 201003249_B.aalborgi 200813138f_B.aalborgi 200813138c_B.aalborgi 200514702_B.hominis 200813138d_B.aalborgi 200813138a_B.aalborgi 200608343_B.hominis 200813138b_B.aalborgi 200414761_B.aalborgi 200709653_B.aalborgi
200501138_B.aalborgi 200805639_B.aalborgi 200813138b_B.aalborgi 201114303_B.aalborgi 200602985_B.aalborgi 200607003_B.hominis 201110374b_B.aalborgi 200803874_B.hominis 201102752_B.aalborgi 95/1000_GenBank_B.pilosicoli 200925995_B.hominis 201104149_B.aalborgi 201001908*_B.aalborgi 200113332_B.aalborgi 200608126*_B.hominis
201021258_B.hominis WA1_GenBank_B.hyodysenteriae P43/ 56-150__B.murdochii 6/78_B.pilosicoli B-78_B.hyodysenteriae 201004769_B.aalborgi B256_B.innocens PWS/A_B.intermedia 21102 ilocisolip.B_5274
201050211_B.aalborgi
ol ip.B_032521102 C1_B.alvinipulli ilocis
201024300_B.aalborgi ol ip.B_683501102
201104406_B.aalborgi ilocis ol ip.B_729402102
201050465_B.aalborgi ilocis
so l i p .B_473122102 201119045_B.aalborgi iloci
201116007_B.hominis
cisol ip.B_039909002 ilocisolip.B_066008991 ilo
201150471_B.aalborgi ilocisolip.B_527421102 200703075_B.aalborgi 201150177_B.aalborgi ilocisolip.B_729402102
201015580_B.aalborgi ilocisolip.B_502306991 ilocisolip.B_330907002 B_876002102 201202009_B.aalborgi ilocisolip.B_566138002 200900639_B.aalborgi ilocisolip. 200914805_B.aalborgi 200513182b_B.pilosicoli ilocisolip.B_039909002 200513182a_B.pilosicoli 200917337_B.aalborgi ilocisolip.B_473122102 200410620b_B.pilosicoli 200901135_B.aalborgi 200410620a_B.pilosicoli ilocisolip.B_683501102 201104140_B.hominis ilocisolip.B_180232002 200816817_B.aalborgi
P43/6/78_B.pilosicoli ilocisolip.B_651900102 201018213_B.aalborgi WesB_B.pilosicoli 95/1000_GenBank_B.pilosicoli
201024466_B.aalborgi ilocisolip.B_828009002 201111933_B.aalborgi
igroblaa.B_e153501102 200923973_B.aalborgi igroblaa.B_d153501102 200913478_B.aalborgi 201122669_B.aalborgi ilocisolip.B_263201102 201108681_B.aalborgi 200716125_B.aalborgi 201113577_B.aalborgi ilocisolip.B_449003002 200920244_B.aalborgi ilocisolip.B_931900102 200430368_B.aalborgi ilocisolip.B_505715002 201129345_B.aalborgi ilocisolip.B_669101102 201109833_B.aalborgi ilocisolip.B_032521102
201105351a_B.aalborgi200922746_B.aalborgi ilocisolip.B_296310102 201123898_B.aalborgi
ilocisolip.B_134508002
201105351c_B.aalborgi
201105351b_B.aalborgi
igroblaa.B_f153501102
0.07
2-SAZ_ai rp.T imi t
118
201119045_B.aalborgi 201150177_B.aalborgi
201015580_B.aalborgi 201050465_B.aalborgi 201104140_B.hominis 201021258_B.hominis
200920244_B.aalborgi
200925995_B.hominis
201111933_B.aalborgi 201004769_B.aalborgi
201102752_B.aalborgi 200624827_B.aalborgi 201109833_B.aalborgi 201122867_B.aalborgi
200602985_B.aalborgi
200803874_B.hominis 200608126*_B.hominis 200922746_B.aalborgi
200918072_B.aalborgi
200805639_B.aalborgi 200704900_B.aalborgi
201123898_B.aalborgi 200702703_B.aalborgi 201003249_B.aalborgi 201024348_B.hominis
201007259_B.aalborgi 200904021_B.aalborgi 200808214_B.aalborgi 200608343_B.hominis
201003592a_B.hominis 200514702_B.hominis 200501138_B.aalborgi
201014350_B.aalborgi 200414761_B.aalborgi
201003592c_B.hominis 200113332_B.aalborgi
201003592b_B.hominis 201024300_B.aalborgi
201104608_B.aalborgi 201050211_B.aalborgi
201003592d_B.hominis 201104406_B.aalborgi
200905511_B.hominis 201116007_B.hominis
200901634_B.aalborgi 201202009_B.aalborgi
200716125_B.aalborgi 200914805_B.aalborgi
200917337_B.aalborgi 200900639_B.aalborgi
201104149_B.aalborgi 200816817_B.aalborgi 201110374g_B.aalborgi 201018213_B.aalborgi
200917097_B.aalborgi 200913478_B.aalborgi
200813138b_B.aalborgi 200923973_B.aalborgi
201110374b_B.aalborgi 201108681_B.aalborgi
95/1000_GenBank_B.pilosicoli
201122669_B.aalborgi
B256_B.innocens 201113577_B.aalborgi
P43/6/78_B.pilosicoli 201129345_B.aalborgi
o cisil olip.B _ 5 2 7 4 2 1 1 0 2 2 0 0 6 0 7 0 0 3 _ h.B o sinim
i lpB_032521102 0 1 1 2 5 2 3 0 _ olip.B cis o
il igro bla a.B _ 3 5 6 9 0 7 0 0 2
i lpB_683501102 0 1 1 0 5 3 8 6 _ olip.B cis o il igro bla a.B _ a 8 3 1 3 1 8 0 0 2
200813138c_B.aalborgi
i lpB_729402102 0 1 2 0 4 9 2 7 _ olip.B cis o il
200813138d_B.aalborgi i lpB_473122102 0 1 2 2 1 3 7 4 _ olip.B cis o
il 200813138e_B.aalborgi
solioci i lpB_039909002 0 0 9 0 9 9 3 0 _ olip.B cis o
il il
200703075_B.aalborgi PWS/A_B.intermedia B-78_B.hyodysenteriae il WA1_GenBank_B.hyodysenteriae
200813138g_B.aalborgi igro bla a.B _f8 3 1 3 1 8 0 0 2 201024466_B.aalborgi
201022967b_B.aalborgi
201022967c_B.aalborgi
i lpB_296310102 0 1 0 1 3 6 9 2 _ olip.B cis o
il 201022967d_B.aalborgi
. _134508002 p.B 201022967e_B.aalborgi
ocisoli il
201022967f_B.aalborgi
ciso olip.B _ 5 0 5 7 1 5 0 0 2
il 201022967g_B.aalborgi
o cis olip.B _ 6 6 9 1 0 1 1 0 2 201022967h_B.aalborgi il
201022967i_B.aalborgi
200410620b_B.pilosicoli
o cis olip.B _ 4 4 9 0 0 3 0 0 2 C1_B.alvinipulli
il 56-150_B.murdochii
201023408_B.aalborgi
200410620a_B.pilosicoli
o cis olip.B _ 9 3 1 9 0 0 1 0 2 201024610_B.aalborgi il
201105351b_B.aalborgi
201105351c_B.aalborgi
201105351d_B.aalborgi 200513182b_B.pilosicoli
201105351g_B.aalborgi
200513182a_B.pilosicoli
o cis olip.B _ 2 6 3 2 0 1 1 0 2 il 201111603_B.aalborgi
201114303_B.aalborgi
o cis olip.B _ 3 3 0 9 0 7 0 0 2
il 200101917_B.aalborgi 08991
200702665_B.hominis
200232081_B.pilosicoli 200707443_B.aalborgi
200811646_B.aalborgi
200813340_B.aalborgi
201103059_B.aalborgi
201124639_B.aalborgi
o cis olip.B _ 0 6 6 0 200902757_B.aalborgi
201200678_B.pilosicoli 201108603_B.hominis
il 201129144_B.aalborgi
513A_B.aalborgi
o cis olip.B _ 8 2 8 0 0 9 0 0 2
il
WesB_B.pilosicoli
o cis olip.B _ 6 5 1 9 0 0 1 0 2
200901135_B.aalborgi
il
201150471_B.aalborgi o cis olip.B _ 5 6 6 1 3 8 0 0 2
il
201110374d_B.aalborgi T.primitia_ZAS-2
0.05
119 201022967g_B.aalborgi
201022967d_B.aalborgi
igroblaa.B_804320102 201022967c_B.aalborgi
201022967b_B.aalborgi sinimoh.B_843420102
200917097_B.aalborgi 200813138g_B.aa
200813138e_B.aalborgi
200813138d_B.aalborgi
200813138c_B.aalborgi
200813138b_B.aalborgi
200813138a_B.aalborgi
200805639_B.aalborgi
igroblaa.B_f769220102 lborgi igroblaa.B_e769220102
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201105351d_B.aalborgi
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200607003_B.hominis 201105351f_B.aalborgi
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201129345_B.aalborgi 201040076_B.aalborgi
200702665_B.hominis 200920244_B.aalborgi 200707443_B.aalborgi
201122669_B.aalborgi 201003592b_B.hominis
201108681_B.aalborgi 201003592c_B.hominis
201003592d_B.hominis 200923973_B.aalborgi 201104608_B.aalborgi 200811646_B.aalborgi 200813340_B.aalborgi
200913478_B.aalborgi 200905511_B.hominis
201103059_B.aalborgi 201018213_B.aalborgi 201024300_B.aalborgi 201120460_B.aalborgi 201111933_B.aalborgi 201124639_B.aalborgi
201104140_B.hominis 201110374g_B.aalborgi 200925995_B.hominis 200816817_B.aalborgi 200902757_B.aalborgi 200113332_B.aalborgi 200216407_B.aalborgi 200917337_B.aalborgi 200414761_B.aalborgi 201108603_B.hominis 200901135_B.aalborgi 201129144_B.aalborgi 200514702_B.hominis 200900639_B.aalborgi 513A_B.aalborgi 200608343_B.hominis 200914805_B.aalborgi 200918072_B.aalborgi 56-150_B.murdochii B256_B.innocens 200803874_B.hominis 201015580_B.aalborgi PWS/A_B.intermedia 200904021_B.aalborgi WA1_GenBank_B.hyodysenteriae 201202009_B.aalborgi B-78_B.hyodysenteriae 201003249_B.aalborgi 200716125_B.aalborgi 201150471_B.aalborgi C1_B.alvinipulli 200704900_B.aalborgi 201150177_B.aalborgi 201122867_B.aalborgi 201119045_B.aalborgi 201110374b_B.aalborgi
201116007_B.hominis 201110374d_B.aalborgi 200901135_B.aalborgi 199603205_B.pilosicoli 201104406_B.aalborgi
201050211_B.aalborgi 201200678_B.pilosicoli
201024300_B.aalborgi
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201004769_B.aalborgi 402102
200925995_B.hominis ilocisolip.B_039909002
ilocisolip.B_473122102 200922746_B.aalborgi 200513182b_B.pilosicoli
200513182a_B.pilosicoli ilocisolip.B_729 200113332_B.aalborgi ilocisolip.B_683501102
200414761_B.aalborgi 200410620b_B.pilosicoli ilocisolip.B_180232002 200410620a_B.pilosicoli
200501138_B.aalborgi ilocisolip.B_651900102
200514702_B.hominis ilocisolip.B_828009002
igroblaa.B_a473011102 P43/6/78_B.pilosicoli
ilocisolip.B_134508002 95/1000_GenBank_B.pilosicoli
ilocisolip.B_296310102 200608343_B.hominis
200803874_B.hominis ilocisolip.B_263201102
200904021_B.aalborgi ilocisolip.B_330907002
201003249_B.aalborgi
200702703_B.aalborgi ilocisolip.B_449003002
ilocisolip.B_BseW ilocisolip.B_931900102 200624827_B.aalborgi ilocisolip.B_505715002 201105351a_B.aalborgi201024466_B.aalborgi ilocisolip.B_669101102 200704900_B.aalborgi ilocisolip.B_032521102 201050465_B.aalborgi ilocisolip.B_527421102
201122867_B.aalborgi
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T.primitia_ZAS-2
120 200813138c_B.aalborgi
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200920244_B.aalborgi
200430368_B.aalborgi
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200923973_B.aalborgi igro bla a.B _ g 8 3 1 3 1 8 0 0 2
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201024610_B.aalborgi 201111933_B.aalborgi 201105351a_B.aalborgi 201105351b_B.aalborgi 201105351d_B.aalborgi 201104140_B.hominis 201105351e_B.aalborgi 200816817_B.aalborgi 201111603_B.aalborgi 201114303_B.aalborgi 200917337_B.aalborgi 200808214_B.aalborgi 201007259_B.aalborgi 200914805_B.aalborgi 201014350_B.aalborgi 201040076_B.aalborgi 201015580_B.aalborgi 200702665_B.hominis 201150471_B.aalborgi 200707443_B.aalborgi 200811646_B.aalborgi 201150177_B.aalborgi 201003592b_B.hominis 201119045_B.aalborgi 201003592c_B.hominis 201003592d_B.hominis 201116007_B.hominis 200905511_B.hominis 201104406_B.aalborgi 201103059_B.aalborgi
201050465_B.aalborgi 201124639_B.aalborgi
i 201110374a_B.aalborgi 201024300_B.aalborgi 201120460_B.aalborgi 201110374b_B.aalborgi i 201124639_B.aalborg 201021258_B.hominis 201110374d_B.aalborgi 201110374g_B.aalborg i 200925995_B.hominis 200902757_B.aalborgi 200902757_B.aalborg i 201129144_B.aalborgi 200113332_B.aalborgi 200216407_B.aalborg 513A_B.aalborgi s 200414761_B.aalborgi ocisolip.B_669101102il 201108603_B.homini i 201129144_B.aalborg 200514702_B.hominis WA1_GenBank_B.hyodysenteriae B-78_B.hyodysenteriae 513A_B.aalborgi PWS/A_B.intermedia 200608343_B.hominis 56-150_B.murdochii 200803874_B.hominis B256_B.innocens
200904021_B.aalborgi C1_B.alvinipulli
201003249_B.aalborgi 200909930_B.pilosicoli 200704900_B.aalborgi 2002
201122867_B.aalborgi o cisil olip.B _ 1 8 0 2 3
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0.06
T.primitia_ZAS-2
121
122
123 124 4 4 4 A
4
Chapter 6
Abstract
126
chapter 5
127 Chapter 6
Materials and methods
Brachyspira pilosicoli
128
chapter 5
Sequence analysis
atpG
129 Chapter 6
Results Biopsy samples
aptG
130 Table 1:
Sample ID Country of origin County Host Type of sample ST
Human Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
131 Table 1:
Sample ID Country of origin County Host Type of sample ST
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human Human
132 WA1 B-78 PWS/A 513A 56-150 C1 T.primitia_ZAS-2 T1 @ 199800660 @ 200517505 @ WesB @ K1 @ 201101966 @ 201009139 @ 201102362 @ 200909930 @ 200831665 @ HRM_4B @ HRM_2B @ N1 @ RV1 @ SC1 @ 7072i @ 201013692 @ 200300944 @ 200410620a @ 200410620b @ 200709033 @ 200513182a @ 200513182b @ 200900828 @ 201009156 @ 200232081 @ 201105386 @ 201204927 @ 201221374 @ 201200678 @ f199600014 @ HRM7A @ HRM7 @ H60-2 @ H38-2 @ H4-2 @ J_F2 @ QF1 @ EM1 @ M1 @ V1_H141 @ @: Human B256 201124725 @ 201125230 @ 200805431 @ V1_H11 @ H21 @
0.05 Figure 1:
133 WA1 B-78 PWS/A 56-150 B256 C1 T.primitia_ZAS-2 513A 201101966 @ T1 A WesB @ B K1 @ 200909930 @ HRM_4B @ HRM_2B @ HRM7A @ HRM7 @ N1 @ RV1 @ SC1 @ 200517505 @ 200300944 @ 201204927 @ 7072i @ 201124725 @ 201105386 @ 200513182a @ 200513182b @ EM1 @ 200232081 @ 201009156 @ V1_H141 @ 201221374 @ V1_H11 @ QF1 @ 201125230 @ 201013692 @ 200900828 @ 200410620a @ 200410620b @ 201200678 @ 200805431 @ H60-2 @ C M1 @ 201009139 @ 200709033 @ 201102362 @ 200831665 @ JF2 @ H21 @ @: Human Q98.0028.3 H38-2 @ H4-2 @ 0.05 Figure 2:
134 Table 2:
MLST Length Locus alleles (bp) sites
44
atpG
Human Chicken Pig Dog
Figure 3:
135 The Netherlands Italy United Kingdom Australia Papua New Guinea United States of America
Figure 4:
136
Discussion
137 Chapter 6
138
139 Chapter 6
140
References 2 64 7 65 4 31 J 22 J 31 51 40 146 141 63 12 106 29 153 95 2 J 24 23 27 119 12 28 53 23 35 13 21 In Press. 33
141 Chapter 6
13
142 143 144 A 4 4
4
Chapter 7
Abstract
146 VSH-1 in Brachyspira Aalborgi
In
4 In .
147 Chapter 7
Materials and methods Ethics statement
Analysis of genomic sequence
Primer design 4
148 VSH-1 in Brachyspira Aalborgi
Table 1:
Presence of svp38 Species
®
149 Chapter 7
Sequencing
150 VSH-1 in Brachyspira Aalborgi
Results Analysis of genome sequence .
Table 2:
Primer name Sequence Set
151 Chapter 7
152 Hvp 38 VSH-1 associated protein B. intermedia PWS/A (GenBank) B. intermedia PWS/A B. alvinipulli C1 Cluster A1 B. hyodysenteriae WA1 (GenBank) B. hyodysenteriae B-78 Cluster A B. intermedia HB60 (GenBank) B. murdochii 56-150 (GenBank) B. murdochii 56-150 Cluster A2 B. innocens B256 T57 (B. aalborgi) U14 (B. aalborgi) U70 (B. aalborgi) 23 (B. aalborgi) 125 (B. aalborgi) 192 (B. aalborgi) 258 (B. aalborgi) Cluster B1 259 (B. aalborgi) 261 (B. aalborgi) 263 (B. aalborgi) 266 (B. aalborgi) 39 (B. aalborgi) B. pilosicoli P43/6/78 (GenBank) B. pilosicoli P43/6/78 U32 (B. pilosicoli) U49 (B. pilosicoli) U38 (B. aalborgi) 243 (B. pilosicoli) L09 (B. aalborgi) V01a (B. pilosicoli) 153 (B. pilosicoli) Cluster B 154 (B. pilosicoli) 95 (B. aalborgi) 225 (B. pilosicoli) 8 (B. aalborgi) 175 (B. aalborgi) Cluster B2 0. 01 B. pilosicoli WesB (GenBank) U22 (B. aalborgi) T24 (B. pilosicoli) 150 (B. pilosicoli) 85 (B. aalborgi) 140 (B. aalborgi) B. pilosicoli B2904 (GenBank) B. pilosicoli 95/1000 (GenBank) B. pilosicoli WesB 37 (B. aalborgi) 75 (B. aalborgi) 128 (B. aalborgi) 256 (B. aalborgi) 257 (B. aalborgi)
Figure 1:
153 Chapter 7
Discussion
154 VSH-1 in Brachyspira Aalborgi
155 Chapter 7
156 VSH-1 in Brachyspira Aalborgi
157 Chapter 7
References 134 27 12 187 23 179 13 224 13 12 31 74 132 134 38 2 3 59 52 39 J 16 68 29 41 4 67 51 95 7
158 159 160 4 A
4
Chapter 8
Abstract
Design
Results p p p p
Conclusion
162 Epidemiology of HIS in the Netherlands
Figure 1:
163 Chapter 8
Methods Ethics statement
164 Epidemiology of HIS in the Netherlands
January 1991 for presence of HIS December 2011
Search term ‘colon + biopsy’ HIS not present 20% randomly selected as controls All colon-biopsies n = 1,205,676 50.28% females 49.82% males
HIS-cases Controls Search term n = 1,243 n = 351 ‘spirochaete’ 28.96% females 60.32% females (+ related spellings) 71.04% males 39.68% males
n = 3,003 Requested from 47.25% females pathology laboratories 52.75% males
Figure 2:
as
165 Chapter 8
p
166 Epidemiology of HIS in the Netherlands
Results
p p
p
167 pathology laboratories
HIS-cases Controls
for processing n = 5
PCR Brachyspira
n = 631 n = 100
Internal control
n = 78 n = 22
PCR
n = 33 n = 45
Exclusion Inclusion
HIS-cases Controls Figure 3:
168 Table 1:
Complaint without Complaint with B. Complaint Complaint present p B. pilosicoli pilosicoli
4
Table 2:
n Diagnosis
44
169 Chapter 8
p p
170 Groningen SIR biopsies: 0.89 (0.88 - 0.90) SIR HIS: 0.29 (0.13 - 0.55) Pigs 63.7/km2 Poultry 2.376.6/km2 HIV-centres 1/30
Noord-Holland SIR biopsies: 1.01 (1.01 - 1.02) SIR HIS: 1.84 (1.63 - 2.08) Pigs 9.7/km2 2 Poultry 493.4/km Friesland HIV-centres 9/30 SIR biopsies: 1.04 (1.02 - 1.05) SIR HIS: 0.21 (0.08 - 0.42) Pigs 31.8/km2 Poultry 2,187.2/km2 Drenthe HIV-centres 1/30 SIR biopsies: 0.92 (0.90 - 0.93) Flevoland SIR HIS: 0.54 (0.29 - 0.90) SIR biopsies: 1.20 (1.18 - 1.22) Pigs 107,5/km2 SIR HIS: 2.24 (1.62 - 3.02) Poultry 2,363.8/km2 Pigs 40.8/km2 HIV-centres 0/30 Poultry 1,461.9/km2 Overijssel HIV-centres 2/30 SIR biopsies: 0.94 (0.93 - 0.95) SIR HIS: 0.96 (0.72 - 1.24) Pigs 483.2/km2 Poultry 2,943.3/km2 HIV-centres 2/30 Utrecht SIR biopsies: 0.97 (0.96 - 0.98) SIR HIS: 0.93 (0.71 - 1.20) Pigs 219.1/km2 Poultry 1,227.9/km2 HIV-centres 2/30 Gelderland SIR biopsies: 1.08 (1.08 - 1.09) SIR HIS: 0.48 (0.36 - 0.64) Pigs 442.9/km2 Zuid-Holland 2 SIR biopsies: 0.99 (0.98 - 0.99) Poultry 3,439.3/km SIR HIS: 0.46 (0.37 - 0.57) HIV-centres 2/30 Pigs 56.5/km2 Poultry 390.0/km2 HIV-centres 7/30
Noord-Brabant SIR biopsies: 0.82 (0.81 - 0.82) SIR HIS: 0.58 (0.46 - 0.73) Limburg Pigs 1,078.6/km2 SIR biopsies: 1.27 (1.26 - 1.28) 2 SIR HIS: 2.92 (2.51 - 3.38) Poultry 5,330.5/km 2 HIV-centres 2/30 Pigs 790.6/km Poultry 6,880.0/km2 HIV-centres 1/30
Zeeland SIR biopsies: 0.86 (0.85 - 0.88) SIR HIS: 1.03 (0.64 - 1.58) Pigs 43.6/km2 Poultry 1,015.2/km2 HIV-centres 1/30
Figure 4:
171 150000 200
150 100000
100
50000 HIS Biopsies 50
0 0
199119921993199419951996199719981999200020012002200320042005200620072008200920102011 Year Figure 5:
1 Appendix (3.7%) 4 2 Coecum (13.2%) 3 Ascending colon (10.9%) 4 Transversing colon (7.8%) 5 Descending colon (10.1%) 3 6 Sigmoid (13.0%) 5 7 Rectum (10.4%)
2 1 6 7
Figure 6:
172 4 4
3 3 A 5 C 5 2 1 2 1 6 6 7 7
4 4
3 3 B 5 D 5 2 1 2 1 6 6 7 7
Figure 7:
Table 3:
B. pilosicoli B. pilosicoli p (n = 150) absent present
B. pilosicoli B. pilosicoli p (n = 126) absent present
173 Chapter 8
Discussion
4
174 Epidemiology of HIS in the Netherlands
175 Chapter 8
176 Epidemiology of HIS in the Netherlands
177 Chapter 8
References 95 16 3 2 82 2 7 Int J 4 18 J 22 21 45 101 63 85 62 27 106 59 146 21 51 53 59 132 39 70 82 29 22
178 Epidemiology of HIS in the Netherlands
39 31 31 J 31 40 141 12 41 303 42 32
179 180 182 Discussion
Aim of this thesis
Pathogenicity chapter 4
chapters 2 8 As chapter 4 chapter 8 chapters 2 8 .
183 A
B
Figure 1:
184 Discussion
.
185 Chapter 9
(chapter 2
chapter 1 chapter 1 chapter 1
186 Discussion
Chapter 5
atpG chapter 7
187 Chapter 9
Epidemiology chapter 1 chapter 6
chapter 8
188 Discussion
chapters 4 8 chapter 4 chapter 8 chapter 4
Chapter 8 p chapter 3
Zoonosis chapter 5 chapter 6
189 B`åckhäns et al. EnvironB`åckhäns Rep, Microbiol 2010. 2(6): p. 720-7. ‘Brachyspira muridarum’ ‘Brachyspira rattus’ ‘Brachyspira muris’ 2010 Chander et al. J Vet Invest, Diagn 2012. 24(5): p. 903-10. ‘Brachyspira hampsonii’ Jansson et al. Anaerobe, 2008. 14(5): p. 287-95. ‘Brachyspira corvi’ 2012 2008 ‘Brachyspira suanatina’ Råsbäck et al. EnvironRåsbäck Microbiol, 2007. 9(4): p. 983-91. 2007 ‘Spirochaeta steonogyrata’ ‘Spirochaeta eurygyrata’ Werner. Centralbl. f. Bakt. Orig., 1909. 1(lii): p. 241-3. 1909 ‘Borrelia eurygyrata’ Harland et al.Harland BMJ, 1967. 3(5567): p. 718-9. 1967 Hovind-Hougen et al. JCM, 1982. 16(6): p. 1127-36. Brachyspira aalborgi 1982 Stephens et al. Avian Pathol, 1999. 28(5): p. 447. ‘Brachyspira pulli’ 1999 B. hyodysenteriae B. intermedia B. murdochii B. alvinipulli B. innocens Brachyspiraceae B. pilosicoli B. aalborgi Treponema hyodysenteriae Harris et al.Harris Vet Small Anim Clin, 1972. 160(4): p. Med 561-5. 2013 1972 'B. muridarum' 'B. hampsonii' 'B. suanatina' 'B. rattus' 'B. muris' 'B. canis' 'B. corvi' Brachyspira hyodysenteriae 'B. pulli' Ochiai et al.Ochiai Immunol, 1997. 41(6): p. Microbiol 445-52. Brachyspira innocens Brachyspira pilosicoli Duhamel et al.Duhamel J Clin Microbiol, 1998. 36(8): p. 2264-70. ‘Brachyspira canis’ 1997 Serpulina hyodysenteriaeSerpulina 1998 Stanton J Syst Int 1992. 42(1): p. Bacteriol, 189-90. Serpulina innocens Serpulina Serpula hyodysenteriaeSerpula Stanton et al. J Syst Int 1991. 41(1): p. Bacteriol, 50-8. Serpula innocens Serpula 1992 1991 Kinyon et al. J Syst Int 1979. 29(2): p. Bacteriol, 102-9. Treponema innocens Hampson et al. J Syst Int Evol Microbiol, 2006. 56(5): p. 1009-12. 1979 Brachyspira intermedia Brachyspira murdochii Brachyspira alvinipulli Stanton et al. J Syst Int 1998. 48(3): p. Bacteriol, 669-76. Brachyspira alvinipulli Trott et al. J Syst Int 1996. 46(1): p. Bacteriol, 206-15. Serpulina pilosicoli Serpulina 2006 1998 1996 Lee et al. Vet Microbiol, 1993. 34(3): p. 273-85. ‘Anguilina coli’ 1993 2: Figure Stanton et al. J Syst Int 1997. 47(4): p. Bacteriol, 1007-12. Serpulina intermedia Serpulina Stanton et al. J Syst Int 1997. 47(4): p. Bacteriol, 1007-12. Serpulina murdochii Serpulina 1997 1997
190 Discussion
4 chapters 5 6 44
Conclusion
191 Chapter 9
References 45 3 2 39 51 4 23 J 22 141 45 8 303 67 121 27 53 16 2 86 37 J 38 38 165 74 160 224 67 134
192 Discussion
47 111 9 24 119 21 63 33 64 65 32 48 13
193 194 A 196
en met
en
197 Addendum
met en
In
198
In .
tussen en
199 Addendum
In
200
. en .
201 202 Dankwoord
203 Addendum
204 Dankwoord
205 Addendum
206 Dankwoord
207