1
Source attribution, prevalence and enumeration of Campylobacter spp. from
2
retail liver.
3
4
Strachan NJC1*, MacRae M2, Thomson A2, Rotariu O1, Ogden ID2 & Forbes KJ2.
5
6
7
1
8
University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB23
9
8GN
Instutute of Biological and Environmental Sciences, School of Biological Sciences,
10
2
11
AB25 2ZD
School of Medicine and Dentistry, University of Aberdeen, Foresterhill, Aberdeen
12
13
14
* Corresponding Author:
15
Norval Strachan, Institute of Biological and Environmental Sciences, School of
16
Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24
17
3UU, UK. (email: n.strachan@abdn.ac.uk, Tel: +44 1224 272699, Fax: +44 1224
18
272703).
19
20
Running headline: Campylobacter in retail liver
21
22
Abstract
23
24
Campylobacter prevalence from retail liver (chicken, cattle, pig and sheep) was found
25
to be 81%, 69%, 79% and 78% respectively. Molecular source attribution
26
demonstrated that strains from chicken liver were most similar to those found
27
commonly in humans. This provides further evidence of liver being a probable source
28
of human infection.
29
30
Keywords: Campylobacter, outbreak, liver, source attribution, pâté
31
32
1
33
Campylobacter jejuni and C. coli are the major recognised cause of bacterial
34
gastroenteritis worldwide. There is a growing epidemic of human campylobacteriosis
35
in the UK (Strachan et al., 2010) with laboratory reports showing 69,281 cases in the
36
UK in 2010 a 35 % increase since 2005. These rates are likely to be substantial
37
underestimates of the actual disease burden because it is estimated that only 1 in 7
38
cases are reported in the United Kingdom (Wheeler et al., 1999). But, despite its
39
significance as a public health problem, the relative contributions of different sources
40
of infection remains complex with food (Adak et al., 2005), water (Said et al., 2003),
41
and environmental sources (Strachan et al., 2009) also being recognised contributing.
42
Source attribution methods employing multi-locus sequence typing (MLST) have
43
indicated that between 40 to 80% of cases are associated with chicken meat (Sheppard
44
et al., 2009) and it is known that 65% of broiler meat at retail is contaminated with
45
Campylobacter in the UK (Anonymous, 2011) (Gormley et al., 2008).
46
47
Although outbreaks of Campylobacter are apparently uncommon there have been a
48
growing number associated with chicken liver pâté (or parfait) particularly from food
49
service establishments (Little et al., 2010). Indeed, in England and Wales during
50
2010, out of the 16 recognised foodborne outbreaks of Campylobacter infection, 10
51
were linked to poultry liver pâté or parfait consumption and one other to pâté prepared
52
from duck liver. Further, in Scotland three recent events have been associated with the
53
consumption of chicken liver pâté (Oshin, 2005; Forbes et al., 2009; O'Leary et al.,
54
2009).
55
56
Surveys of Campylobacter in raw liver from different animal species have revealed
57
diverse contamination rates. High prevalence (>90%) of Campylobacter in chicken
58
livers were reported in Chile (Fernandez and Pison, 1996) and in New Zealand
59
(Whyte et al., 2006) but in the USA (Cox et al., 2009), significantly lower values of
60
13% and 17% were observed in two separate flocks and in the UK prevalence ranged
61
widely between 8 and 54 % (Jennings et al., 2011). Two Japanese studies of cattle
62
livers showed a low prevalence of 1.4% (Matsumoto et al., 2008) and 5% (Enokimoto
63
et al., 2007). In N. Ireland (Moore and Madden, 2003) a prevalence of 6% was found
64
in pig livers whilst in New Zealand (Cornelius et al., 2005) 62% of sheep livers were
65
contaminated with Campylobacter. The aims of the current study were to provide
66
further evidence for the potential of liver from a number of host species to cause
2
67
infection in humans by determining (i) the prevalence and concentration of
68
Campylobacter and (ii) the MLST genotypes found and whether these were typical of
69
both the host species and those observed commonly in human clinical cases.
70
71
Materials and Methods
72
73
Sampling and microbiology
74
Liver samples were purchased from retail supermarkets and butcher’s shops in
75
Aberdeen, NE Scotland between April 2006 and March 2008. Choice of liver types
76
was determined by availability in sentinel shops. Samples were chilled for transport
77
back to the laboratory for testing. Whole samples (median 382g) were rinsed in 300
78
mL Campylobacter enrichment broth (see below) and 0.1mL decimal dilutions plated
79
directly onto the modified Campylobacter Blood-Free Selective Agar Base (CCDA
80
base, CM0739; Oxoid, Basingstoke, UK) with CCDA selective supplement (SR 155;
81
Oxoid) for target enumeration (minimum detection limit of the plate count was
82
therefore 3 x103 cfu/ sample). The presence or absence of Campylobacter was
83
ascertained by incubating the remaining enrichment broth microaerobically in an
84
atmosphere of 10% CO2, 5% O2, balance N2, 100mL volumes of nutrient broth base
85
(Mast, Bootle, UK) with 5% horse blood, growth supplement (Mast Selectavial
86
SV61), amphotericin (2 mg/mL), cefoperazone (15 mg/mL), and trimethoprim (10
87
mg/mL); polymixin B (2500 IU/L) and rifampicin (5 mg/mL) were added, and the
88
broths incubated for 2 days at 37ºC (Bull et al., 2006). All antimicrobials were
89
purchased from Sigma-Aldrich (Gillingham, UK). Enrichment broths (0.1 mL) were
90
plated onto mCCDA agar incubated microaerobically for 2 days at 37ºC. Five
91
colonies were taken from each plate and presumptively identified as Campylobacter
92
by agglutination with Microscreen latex (Microgen, Camberley, UK). Individual
93
colonies were stored (-80ºC, nutrient broth, glycerol added to 15% [v/v]) for MLST.
94
Campylobacter presence was confirmed as C. jejuni or C. coli using isolate ST as
95
determined by MLST.
96
97
Genotyping
98
Presumptive positive isolates were genotyped by traditional 7 locus multilocus
99
sequence typing (MLST) as described previously (Sheppard et al., 2009) and allele
3
100
profiles and STs were assigned using the public Campylobacter MLST profile
101
database (http://www.pubmlst.org).
102
103
Attribution
104
Data (MLST) at the level of sequence type were used to identify the reservoir origin
105
(cattle, chicken, sheep, pigs or wild birds) based on source attribution scores
106
generated from the software programme STRUCTURE (Pritchard et al., 2000)
107
calibrated with data from the CaMPS study (Sheppard et al., 2009; Forbes, 2009). The
108
PopTools (available from http://www.cse.csiro.au/poptools) add-in to Microsoft Excel
109
was used to generate 95% confidence intervals. The percentage of strains (ST) from
110
each of the liver source species that were identical by MLST to the 10 most common
111
human clinical strains from the pan Scotland 2005/06 CaMPS study (Forbes, 2009)
112
was determined; these 10 strains accounted for nearly 50% of all clinical cases.
113
Binomial confidence intervals were calculated and significant differences were
114
calculated using @RISK software (Palisade, Ivybridge, UK) with the assumption that
115
the data were binomially distributed.
116
117
Results and Discussion
118
119
The prevalence of Campylobacter ranged from 81% to 69% (chicken and cattle livers
120
respectively) indicating significant contamination across all liver types tested and
121
confirming the putative role of this food as a source of infection for humans (Table 1).
122
The high prevalence in chicken is in line with a 2006 Campylobacter study in retail
123
chicken meat which showed 90.4% positive from 114 samples tested (Gormley et al.,
124
2008). Further, it has been demonstrated (Whyte et al., 2006) that 90% of positive
125
Campylobacter chicken liver samples contained the pathogen in internal tissue and
126
that flash frying, as recommended in many recipes, to leave the centre of the liver
127
pink, may be ineffective at killing all Campylobacter present because there is a very
128
small margin of error between pink and undercooked.
129
130
Enumeration data showed the majority of samples were positive only after enrichment
131
(79%) indicating low numbers of Campylobacter on many retail livers. The higher
132
counts observed from direct plating were most frequently from associated with
133
chicken and cattle liver washes (>25%). This was not unexpected for chicken
4
134
(Gormley et al., 2008) which showed 65% retail chicken meat with Campylobacter
135
concentrations >100 cfu / sample). Only 3% of pig and 10% of sheep livers had
136
higher counts.
137
138
In comparison to published studies, prevalence and counts here agreed with the sheep
139
data from New Zealand (Cornelius et al., 2005) but differed from the two Japanese
140
cattle studies (Matsumoto et al., 2008; Enokimoto et al., 2007) and the N. Ireland pig
141
data (Moore and Madden, 2003) (all with lower prevalence values). The chicken data
142
reported here is in line with the high prevalence and enumeration data in the reports
143
from Chile (Fernandez and Pison, 1996) and New Zealand (Whyte et al., 2006) but
144
USA studies (Cox et al., 2009) (2009) showed significantly lower values of 13% and
145
17% in two separate flocks. Meanwhile, the large variation in flock prevalence in the
146
UK (Jennings et al., 2011) does encompass the findings of the current study but it
147
must be remembered that there may be opportunity for cross contamination of livers
148
post abattoir. Finally, the difference in reported data may reflect microbiological
149
methodology, animal husbandry in the country of origin and source (animal species)
150
of the liver samples tested.
151
152
Source attribution showed that the MLST types found in chicken livers were more
153
similar to those found in retail broiler meat compared to other sources (Table 1).
154
There was relatively poor attribution of cattle isolates (29%) which was not
155
significantly better than random (25%). However, most of the misclassifications of
156
liver isolates from cattle were as sheep (and vice-versa) and when the analysis was
157
repeated treating sheep and cattle as one “ruminant” species then the attribution was
158
much improved (81%). This commonality of MLST genotypes from cattle and sheep
159
has already been reported elsewhere (McCarthy et al., 2007).
160
161
Comparison of the MLST genotypes from liver with those commonly found in
162
humans showed that those of chicken origin had the greatest overlap (56%, P<0.05).
163
This provides further evidence, beyond outbreak case questionnaires, that chicken
164
livers are a risk to humans. It is unclear why the degree of overlap was less for the
165
other species but this could be due to a number of reasons that include: less
166
consumption of livers from species other than chicken; the strains found in these other
5
167
hosts are less infectious to humans and livers/liver products from hosts other than
168
chicken may be more likely to be cooked correctly.
169
170
The growing number of chicken liver outbreaks may not explain the whole reason for
171
the recent rise of human campylobacteriosis in the UK, since these outbreaks only
172
encompass a small of fraction of cases. However, here we have shown that the
173
prevalence of Campylobacter in chicken livers is high and that a number of these
174
strains are identical to those found commonly in humans. Further, we have also
175
shown that there is a high prevalence in all the species of livers tested and although
176
the most common human strains are not so frequently found in these other livers, they
177
presumably do pose a risk to human health. Therefore it is important that food
178
caterers treat raw liver as a foodstuff likely to be contaminated with Campylobacter
179
and that it should be handled in a manner to minimise cross contamination with other
180
foodstuffs and surfaces as well as requiring adequate cooking to ensure successful
181
killing of this pathogen. Only once this has been achieved will the number of reported
182
outbreaks decline.
183
184
185
186
187
188
189
190
Acknowledgements
We thank Food Standards Agency, Scotland for funding this work.
References
191
192
Adak, G.K., Meakins, S.M., Yip, H., Lopman, B.A., O'Brien, S.J.,2005. Disease risks
193
from foods, England and Wales, 1996-2000. Emerging infectious diseases (Print) 11,
194
365-372.
195
Anonymous. (2011). Campylobacter infections by year in england and wales, 1989-
196
2010.
197
http://www.hpa.org.uk/Topics/InfectiousDiseases/InfectionsAZ/Campylobacter/Epide
198
miologicalData/campyDataEw/
199
Bull, S.A., Allen, V.M., Domingue, G., Jorgensen, F., Frost, J.A., Ure, R., Whyte, R.,
200
Tinker, D., Corry, J.E., Gillard-King, J., Humphrey, T.J.,2006. Sources of
Retrieved
10/6,
2011,
from
6
201
Campylobacter spp. colonizing housed broiler flocks during rearing. Applied and
202
Environmental Microbiology 72, 645-652.
203
Cornelius, A., Nicol, C., Hudson, J.,2005. Campylobacter spp. in New Zealand raw
204
sheep liver and human campylobacteriosis cases. International journal of food
205
microbiology 99, 99-105.
206
Cox, N., Richardson, L., Buhr, R., Fedorka Cray, P.,2009. Campylobacter species
207
occurrence within internal organs and tissues of commercial caged Leghorn laying
208
hens. Poultry science 88, 2449-2456.
209
Enokimoto, M., Kubo, M., Bozono, Y., Mieno, Y., Misawa, N.,2007. Enumeration
210
and identification of Campylobacter species in the liver and bile of slaughtered cattle.
211
International journal of food microbiology 118, 259-263.
212
Fernandez, H., Pison, V.,1996. Isolation of thermotolerant species of Campylobacter
213
from commercial chicken livers. International journal of food microbiology 29, 75-80.
214
Forbes, K.J.,2009. The Molecular Epidemiology of Scottish Campylobacter Isolates
215
from Human Cases of Infection using Multilocus Sequence Typing.S14006, 1-150.
216
Forbes, K.J., Gormley, F.J., Dallas, J.F., Labovitiadi, O., MacRae, M., Owen, R.J.,
217
Richardson, J., Strachan, N.J., Cowden, J.M., Ogden, I.D., McGuigan, C.C.,2009.
218
Campylobacter immunity and coinfection following a large outbreak in a farming
219
community. Journal of clinical microbiology 47, 111-116.
220
Gormley, F.J., Macrae, M., Forbes, K.J., Ogden, I.D., Dallas, J.F., Strachan,
221
N.J.,2008. Has retail chicken played a role in the decline of human
222
campylobacteriosis? Applied and Environmental Microbiology 74, 383-390.
223
Jennings, J., Sait, L., Perrett, C., Foster, C., Williams, L., Humphrey, T.,2011.
224
Campylobacter jejuni is associated with, but not sufficient to cause vibrionic hepatitis
225
in chickens. Veterinary microbiology 149, 193-199.
7
226
Little, C., Gormley, F., Rawal, N., Richardson, J.,2010. A recipe for disaster:
227
outbreaks of campylobacteriosis associated with poultry liver pate in England and
228
Wales. Epidemiology and infection 138, 1691-1694.
229
Matsumoto, N., Taniwaki, T., Kinuta, M., Murase, T.,2008. Isolation of
230
Campylobacter jejuni and coliform bacilli from bile and liver obtained from slaughter
231
cattle in western Japan. Journal of food protection 71, 1228-1231.
232
McCarthy, N.D., Colles, F.M., Dingle, K.E., Bagnall, M.C., Manning, G.,
233
Maiden,M.C.J.and Falush, D.,2007. Host-associated genetic import in Campylobacter
234
jejuni. Emerging infectious diseases 13, 267.
235
Moore, J., Madden, R.,2003. Comparison of eight phenotypic methods for subspecies
236
characterization of thermophilic Campylobacter spp. isolated from pig liver. Journal
237
of food protection 66, 1079-1084.
238
O'Leary, M., Harding, O., Fisher, L., Cowden, J.,2009. A continuous common-source
239
outbreak of campylobacteriosis associated with changes to the preparation of chicken
240
liver pate. Epidemiology and infection 137, 383-388.
241
Oshin, F.,2005. Campylobacter outbreak in North Ayrshire. Health Protection
242
Scotland Weekly Report 39, 232.
243
Pritchard, J.K., Stephens, M., Donnelly, P.,2000. Inference of population structure
244
using multilocus genotype data. Genetics 155, 945-959.
245
Said, B., Wright, F., Nichols, G., Reacher, M., Rutter, M.,2003. Outbreaks of
246
infectious disease associated with private drinking water supplies in England and
247
Wales 1970-2000. Epidemiology and infection 130, 469-479.
248
Sheppard, S.K., Dallas, J.F., Strachan, N.J.C., MacRae, M., McCarthy, N.D., Wilson,
249
D.J., Gormley, F.J., Falush, D., Ogden, I.D., Maiden, M.C., Forbes, K.J.,2009.
250
Campylobacter
251
Clin.Infect.Dis. 48, 1072-1078.
genotyping to
determine
the source of human
infection.
8
252
Strachan, N.J.C., Gormley, F.J., Rotariu, O., Ogden, I.D., Miller, G., Dunn, G.M.,
253
Sheppard, S.K., Dallas, J.F., Reid, T.M.S., Howie, H., Maiden, M.C., Forbes,
254
K.J.,2009. Attribution of Campylobacter infections in northeast Scotland to specific
255
sources using multi-locus sequence typing (MLST). The Journal of infectious diseases
256
199, 1205-1208.
257
Strachan, N.J.C., Forbes, K.J.,2010. The growing UK epidemic of human
258
campylobacteriosis. Lancet 376, 665-7.
259
Wheeler, J.G., Sethi, D., Cowden, J.M., Wall, P.G., Rodrigues, L.C., Tompkins, D.S.,
260
Hudson, M.J., Roderick, P.J.,1999. Study of infectious intestinal disease in England:
261
rates in the community, presenting to general practice, and reported to national
262
surveillance. The Infectious Intestinal Disease Study Executive. BMJ (Clinical
263
research ed.) 318, 1046-1050.
264
Whyte, R., Hudson, J., Graham, C.,2006. Campylobacter in chicken livers and their
265
destruction by pan frying. Letters in applied microbiology 43, 591-595.
266
9
267
Table 1 Campylobacter spp. from retail livera: prevalence, counts, attribution of
268
genotypes to source species and similarity to common human genotypes.
269
Animal
Prevalence
species
Campylobacter
of High
countsb Liver isolates’ Percentage of all
(%)
(%)
genotype
liver
isolates
correctly
belonging to the
attributed
to top 10 human
source species genotypes (%)
(%)
Chicken
21/26 (81)
7/26 (27)
64
56
Cattle
22/32 (69)
8/32 (25)
30
20
Pig
23/29 (79)
1/29 (3)
41
18
Sheep
31/40 (78)
4/40 (10)
43
13
Total
97/127 (76)
20/127 (16)
45
26
270
a
271
information.
272
b
273
x103 cfu/ sample).
Full details on samples and types of individual isolates are in the supplementary
High counts are designated as those samples that gave direct plate counts (i.e.> 3
274
275
276
277
10
278
279
280
281
282
283
284
Isolate
R014
7496B
R071
7494A
7498B
R022
R066
R067
R068
7499A
10011
8920
R029
R001
R080
R027
R050
7499B
R081
7439
R019
7553B
7591B
R010
R079
R006
R039
R052
R082
7486
7506
7771
7843
8094
8289
8945
8962
R035
R062
R044
Supplementary information
The following table contains details on each of the samples:
Table S1 Sample details, enumeration and STs of C. jejuni/coli in retail liver
Date
collected
13/11/2007
12/04/2006
26/02/2008
12/04/2006
12/04/2006
04/12/2007
19/02/2008
19/02/2008
19/02/2008
12/04/2006
10/10/2006
22/06/2006
11/12/2007
06/11/2007
04/03/2008
04/12/2007
22/01/2008
12/04/2006
11/03/2008
31/03/2006
27/11/2007
24/04/2006
26/04/2006
13/11/2007
04/03/2008
06/11/2007
14/01/2008
24/01/2008
11/03/2008
07/04/2006
12/04/2006
23/05/2006
31/05/2006
05/07/2006
19/07/2005
27/09/2006
04/10/2006
08/01/2008
12/02/2008
14/01/2008
Animal
species
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
sheep
Counts
Counts
Sample
Counts MLST
Campylobacter per
per ml
weight (g) per g
Sequence
present / absent sample
wash
typea
present
<900
<3
420
<2
42
present
<900
<3
416
<2
50
present
<900
<3
400
<2
50
present
99000
330
332
298
52
present
<900
<3
310
<3
53
present
<900
<3
315
<3
61
present
<900
<3
205
<4
61
present
<900
<3
200
<5
61
present
<900
<3
600
<2
190
present
15000
50
226
66
206
present
<900
<3
273
present
<900
<3
526
<2
422
present
<900
<3
368
<2
422
present
<900
<3
418
<2
520
present
<900
<3
426
<2
618
present
<900
<3
500
<2
822
present
<900
<3
372
<2
822
present
<900
<3
226
<4
827b
present
<900
<3
236
<4
827 b
present
<900
<3
210
<4
962 b
present
<900
<3
356
<3
2340
present
<900
<3
342
<3
2666
present
<900
<3
356
<3
2670
present
12000
40
252
48
UA
present
<900
<3
398
<2
UA
present
<900
<3
512
<2 Camp. spp.
present
<900
<3
315
<3 Camp. spp.
present
<900
<3
604
<1
UA
present
3000
10
264
11
UA
present
<900
<3
300
<3 Camp. spp.
present
<900
<3
300
<3 Camp. spp.
absent
425
absent
absent
384
absent
556
absent
392
absent
absent
424
absent
234
absent
294
11
7593
R036
R090
R091
7732
R056
R047
R032
7592
R016
R075
R076
R013
R058
8095
100551
R072
R005
R028
R070
R085
R042
R055
7495
7497
7554
7672
8946
R002
8776
R008
7941
R031
R063
R087
7362
7474B
R078
R088
R025
R043
R077
R034
R020
R073
R059
8425B
R048
R049
R060
26/04/2006
08/01/2008
18/03/2008
18/03/2008
17/05/2006
24/01/2008
22/01/2008
12/12/2007
26/04/2006
27/11/2007
04/03/2008
04/03/2008
13/11/2007
12/02/2008
05/07/2006
24/10/2006
26/02/2008
06/11/2007
04/12/2007
26/02/2008
11/03/2008
14/01/2008
24/01/2008
12/04/2006
12/04/2006
24/04/2006
10/05/2006
27/09/2006
06/11/2007
05/09/2006
13/11/2007
07/06/2006
11/12/2007
19/02/2008
18/03/2008
14/03/2006
07/04/2006
04/03/2008
18/03/2008
04/12/2007
14/01/2008
04/03/2008
08/01/2008
27/11/2007
26/02/2008
12/02/2008
02/08/2006
22/01/2008
22/01/2008
12/02/2008
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
pig
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
chicken
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
absent
absent
absent
absent
absent
absent
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
<900
3000
<900
<900
<900
<900
<900
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
<3
10
<3
<3
<3
<3
<3
<900
<900
<900
1200
<900
<900
<900
<900
<900
<900
33000
<900
<900
12000
<900
<900
291000
<900
27000
12000
3000
<3
<3
<3
40
<3
<3
<3
<3
<3
<3
110
<3
<3
40
<3
<3
970
<3
90
40
10
209
458
382
459
502
336
471
340
382
424
434
300
249
340
367
393
242
488
360
439
414
516
340
340
394
340
380
400
400
227
400
238
400
10
250
400
400
400
400
400
400
400
400
400
400
400
400
<4
<2
<2
<2
<2
<3
<2
<3
<2
<2
<2
<3
<4
<3
<2
8
<4
<2
<3
<2
<2
19
21
21
21
58
206
270
1058 b
1096 b
1096 b
1096 b
1096 b
1143 b
2219
2508 b
2697
3609
UA
UA
UA
UA
Camp. spp.
UA
<2
<2
<4
30
<4
<2
90
<4
<2
<2
83
<2
<2
30
<2
<2
728
68
30
8
19
22
45
45
45
50
257
257
257
257
574
574
574
586
699
828 b
872 b
2687
UA
UA
UA
12
7297
7324
7325
7326
R089
7473B
8426
7555
R011
R004
R069
R084
R024
10057
R057
8098
8065
R054
8919
7493B
R053
R033
7590B
7939A
7939B
R017
R086
7733
7772
7940
8288
8293
10012
R009
R023
R064
R065
285
286
287
27/02/2006
07/03/2006
07/03/2006
07/03/2006
18/03/2008
07/04/2006
02/08/2006
24/04/2006
13/11/2007
06/11/2007
26/02/2008
11/03/2008
04/12/2007
24/10/2006
12/02/2008
05/07/2006
28/06/2006
24/01/2008
22/09/2006
12/04/2006
24/01/2008
11/12/2007
26/04/2006
07/06/2006
07/06/2006
27/11/2007
11/03/2008
17/05/2006
23/05/2006
07/06/2006
19/07/2005
19/07/2005
10/10/2006
13/11/2007
04/12/2007
19/02/2008
19/02/2008
a
b
chicken
chicken
chicken
chicken
chicken
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
cattle
absent
absent
absent
absent
absent
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
present
absent
absent
absent
absent
absent
absent
absent
absent
absent
absent
<900
<900
<900
15000
6000
<900
21000
<900
<900
<900
<900
<900
<900
<900
<900
30000
15000
<900
9000
<900
15000
12000
<3
<3
<3
50
20
<3
70
<3
<3
<3
<3
<3
<3
<3
<3
100
50
<3
30
<3
50
40
19
400
250
241
211
373
379
442
385
492
550
255
253
498
418
362
440
413
414
386
470
470
386
449
360
250
412
626
484
205
219
<4
<4
<4
40
16
<2
55
<2
<2
<4
<4
<2
<2
<2
<2
73
36
<2
19
<2
39
27
19
21
50
61
206
206
206
262
266
273
505
574
575
806
827 b
827 b
854 b
2669
2676
2677
Camp. spp.
UA
Unassigned to sequence type (UA)
C. coli
13