Löfström Et Al 2008 Pre-print FANM 1(1), 23-37
-
Upload
rodolfograna -
Category
Documents
-
view
219 -
download
0
Transcript of Löfström Et Al 2008 Pre-print FANM 1(1), 23-37
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
1/16
1
2
3
4
5
6
7
8
9
0
1
2
34
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
01
2
3
4
5
6
7
8
9
0
1
2
34
5
6
7
8
9
0
1
2
3
4
5
1
Validation of a Diagnostic PCR Method for Routine Analysis ofSalmonella spp.
in Animal Feed Samples
Running head: Validation of PCR for Salmonellain feed
Charlotta Lfstrma,b, Charlotta Engdahl Axelssonband Peter Rdstrma*
aApplied Microbiology, Lund Institute of Technology, Lund University, P.O. Box 124,
SE-221 00 Lund, bLantmnnen AnalyCen AB, P.O. Box 905, SE-531 19 Lidkping, Sweden
* Corresponding author. Mailing address: Applied Microbiology, Center for Chemistry and
Chemical Engineering, Lund Institute of Technology, Lund University, P.O. Box 124, SE-221 00
Lund, Sweden. Phone: +46 46 222 3412, Fax: +46 46 222 4203, E-mail:
This article is published in: Food Analytical Methods, 2008, 1(1), 23-27
The original publication is available at www.springerlink.com
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
2/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
2
Abstract
As a part of a validation study, a comparative study of a PCR method and the standard culture-
based method NMKL-71, for detection of Salmonella,was performed according to the validation
protocol from the Nordic validation organ for validation of alternative microbiological methods
(NordVal) on 250 artificially or naturally contaminated animal feed samples. The PCR method is
based on culture enrichment in buffered peptone water followed by PCR using the DNA
polymerase Tthand an internal amplification control. No significant difference was found between
the two methods. The relative accuracy, relative sensitivity and relative specificity were found to be
96.0%, 97.3% and 98.8%, respectively. PCR inhibition was observed for rape seed samples. For the
acidified feed samples, more Salmonella-positive samples were found with the PCR method
compared to the NMKL method. This study focuses on the growing demand for validated
diagnostic PCR methods for routine analysis of animal feed and food samples to assure safety in the
food production chain.
Keywords: animal feed, NordVal,Salmonella, validation, PCR, polymerase chain reaction
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
3/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
3
Introduction1
Food borne diseases such as salmonellosis are recognized as one of the most serious public health2
concerns today.1The problem of salmonellosis related to the food industry is cyclic and animal feed3
may serve as a reservoir for Salmonella contributing to the spread of the bacteria along the food4
chain.2The conventional culture method used today for detection of Salmonella in feed is laborious5
and takes 3-7 days to complete.3 Hence, there is a growing demand for rapid methods for the6
detection of Salmonella in feed samples. PCR is considered to be one of the most promising7
techniques to meet this demand and several PCR-based detection methods for Salmonella in food8
and feed have been developed.4-89
Although the PCR-based methods meet the demands of diagnostic laboratories on detection10
methods regarding sensitivity, specificity and ease of use, the introduction of the technique for11
diagnostic use has so far been slow. The technological novelty of the technique, the high investment12
cost and the lack of officially approved, validated and standardized methods have been mentioned13
as reasons for this delay.8, 9 Validation is an important step in the process of standardizing a method,14
because it provides evidence that the new method gives results at least as good and in agreement15
with the currently used reference method, as well as proving confirmation of the reproducibility and16
specificity when used by other laboratories.8, 9These data are needed to gain acceptance among17
authorities and end users of a method, and to speed up the implementation of new rapid PCR-based18
detection systems in diagnostic laboratories.19
The aim of this study was to perform a comparative study of a diagnostic PCR procedure6and20
the currently used NMKL reference method3 for the detection of Salmonella in animal feed21
samples. The PCR method, based on a simple PCR-compatible enrichment procedure, has been22
evaluated and found to specifically detect low numbers of viable Salmonella spp. in feed samples23
without any sample pre-treatment such as DNA extraction or cell lysis prior to PCR. The24
probability of detecting 1 CFU/25 g feed in the presence of natural background flora was found to25
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
4/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
4
be 0.81.6It is therefore of great value to perform a validation study for this method in order to gain26
acceptance for use on a routine basis. In the first part of this study a comparative study of the PCR27
and NMKL methods for 250 artificially inoculated or naturally contaminated feed samples of both28
animal and vegetable origin were performed according to the protocol of NordVal.10, 11
29
Furthermore, a small interlaboratory study was performed to assess the reproducibility of the PCR30
method.31
32
Materials and methods33
Feed samples.For the comparative study samples of each of the two main categories of feed, i.e. of34
animal and vegetable origin, as well as other feed related samples, were used (Table 1). For feed of35
animal origin, 30 samples were not inoculated (not containing salmonella as determined previously36
by the NMKL method3), 14 were inoculated with 1-10 CFU Salmonella/25 g feed, 12 with 10-10037
CFU/25 g, and 17 were naturally contaminated (unknown salmonella status before analysis). For38
feed of vegetable origin, 26 samples were not inoculated, 18 were inoculated with 1-10 CFU39
Salmonella/25 g feed, 16 with 10-100 CFU/25 g and 94 were naturally contaminated. Twenty-three40
other feed related samples (naturally contaminated) were included in the study (Table 1). For the41
artificially contaminated samples, half of the samples at each level were inoculated with S.42
Livingstone and the other half with S. Senftenberg. The inoculation level of S. Senftenberg was 843
CFU at the 1-10 CFU level, and 75 CFU at the 10-100 level. The corresponding values for S.44
Livingstone were 9 CFU at the 1-10 CFU level and 92 CFU at the 10-100 CFU level.45
46
Salmonella strains. Salmonella enterica ssp. enterica serovar Senftenberg S57 (S. Senftenberg, an47
animal feed isolate from AnalyCen Nordic AB, Kristianstad, Sweden) and S. Livingstone CCUG48
39481 (obtained from the Culture Collection, University of Gteborg, Gothenburg, Sweden) were49
obtained by growth in tryptone soy broth (TSB, Merck, Darmstadt, Germany) at 37C overnight.50
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
5/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
5
The concentration of cells was determined by viable counts on tryptone glucose extract (TGE,51
Merck) agar plates. The cell suspensions were diluted in saline (0.9% (w/v) NaCl) to concentrations52
corresponding to 1-10 CFU/ml and 10-100 CFU/ml.53
54
Sample preparation.Twenty-five grams of each feed was homogenized in 225 ml buffered peptone55
water (BPW, Lab 46, LabM, Bury, UK) in a sterile plastic bag. The feed homogenates (Table 1)56
were inoculated with Salmonella and enriched at 37C for 18 h. A small aliquot (0.1 ml) of the57
samples from this pre-enrichment was analysed further using the NMKL method3, including58
selective enrichment in Rappaport-Vassiliades soy broth (RVS, Oxoid, CM866, Basingstoke, UK)59
overnight at 42C, plating on selective agar xylose lysine decarboxylase (XLD, Neogen, Acumedia,60
7166, Lansing, Michigan, USA) and brilliant green agar (BGA, Oxoid, CM329), followed by61
biochemical and serological identification (see Fig. 1). Samples were withdrawn after the pre-62
enrichment step for PCR analysis and stored at 20C. Before PCR, samples were thawed and63
diluted 1:10 in saline and 5 l of the diluted sample was added to the PCR tube.64
65
PCR conditions. PCR, amplifying a part of the invA gene was run as previously described6using a66
mixture consisting of: 0.2 M of each primer12 (Scandinavian Gene Synthesis AB, Kping,67
Sweden), 200 M of each dNTP (Roche Molecular Biochemicals, Mannheim, Germany), 1 PCR68
buffer (Roche), 0.75 U of TthDNA polymerase (Roche) and 3 104copies of an internal control69
DNA fragment.8The sample volume used was 5 l and the final volume 25 l. A GeneAmp 970070
PCR System thermocycler (Applied Biosystems, Foster City, CA) was used. The temperature71
program started with a denaturation step of 5 min at 94C, followed by 36 cycles at 94C for 30 s,72
60C for 30 s and 72C for 40 s, and then 1 cycle at 72C for 7 min. Finally, the samples were73
cooled to 4C. Samples were analyzed with gel electrophoresis using 1% agarose gels stained with74
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
6/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
6
ethidium bromide, and bands were visualized with the GelDoc 1000 system (Bio-Rad, Hercules,75
CA) using the Molecular Analyst software (Bio-Rad).76
77
Data analysis and statistics. After confirmation of the results obtained by PCR, the relative78
accuracy (AC), relative sensitivity (SE) and relative specificity (SP) were calculated according to79
the NordVal validation protocol.10 AC is defined as the degree of correspondence between the80
response obtained by the alternative method and the reference method on identical samples, as81
follows: (PA + NA + FP) 100 / (PA + NA + TP + FN + FP), where PA refers to positive82
agreement, NA to negative agreement, FP to false positives, TP to true positives, and FN to false83
negatives. SE is defined as the ability of the alternative method to detect the target microorganism84
compared to the reference method, as follows: (PA + TP) 100 / (PA + FN). SP is defined as the85
ability of the alternative methodnot to detect the target microorganism when it is not detected by the86
reference method, as follows: (NA 100) / (NA + FP). In this study, FP was defined as a negative87
result for NMKL and a positive result for the PCR method not confirmed by growth; TP was88
defined as a negative result for NMKL and a positive result for the PCR method confirmed by89
growth, and FN positive result for NMKL, and a negative result for PCR.90
To verify that there was no significant difference in the results obtained by the two methods the91
McNemar test was performed according to Annex F in ISO 16140:2003.13, 14Cohens kappa () was92
calculated as described by NMKL to quantify the degree of agreement between the two methods 1593
( > 0.80 means very good agreement between methods).94
95
Results and discussion96
The comparative trial was conducted in accordance with the guidelines provided by NordVal10, 1197
and included the matrix animal feed of both animal and vegetable origin (Table 1). In a comparative98
trial, parameters such as the relative accuracy, detection level, sensitivity and specificity are99
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
7/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
7
evaluated. The relative selectivity in terms of inclusivity and exclusivity of the PCR method have100
been determined previously.6 Salmonella strains (n = 101) representing 33 serotypes were correctly101
identified as Salmonellaby both the NMKL and the PCR methods. Strains (n = 43) representing 27102
bacterial species other than Salmonellawere negative according to both methods. Furthermore, a103
recent study of PCR using the same primer pair showed a 99.6% inclusivity and 100% exclusivity104
for 364 strains.8Several other studies have also confirmed the selectivity of the primers.12, 16105
In this study, no significant differences (using the McNemar test) were found between the two106
methods for a total of 250 artificially or naturally contaminated samples including animal feed of107
both vegetable and animal origin. Furthermore, a very good agreement between the two methods108
was obtained using Cohens kappa (Table 1). The relative accuracy, sensitivity and specificity were109
evaluated for the PCR method in comparison to the standard culture based method currently in use110
for detection of Salmonella3according to the NordVal protocol (Table 1). The relative sensitivity111
for the matrices animal feed of animal and vegetable origin, as well as when all 249 samples were112
analysed together were above 95% which is the limit considered acceptable according to NordVal.10113
No recommendations concerning the levels for the relative accuracy and relative specificity are114
given in the standard.10To further assess the reproducibility of the PCR method, when performed115
by different persons in different laboratories, 40 randomly selected artificially contaminated116
samples were analysed with PCR at two different laboratories. No significant differences were117
found between the results obtained at the two laboratories (data not shown).118
When analysing the data in more detail two major trends were noted: (i) the inability to detect119
Salmonella in acidified feed samples by the NMKL method, and (ii) difficulties in detecting120
Salmonellain rape seed samples by PCR. The inability of the NMKL method to detect Salmonella121
in acidified feed samples has been observed previously.6One possible reason for this may be that122
the cells were stressed after acidification and did not recover sufficiently to be able to survive and123
multiply in the selective RVS broth. Furthermore, it has been shown that Salmonellamust reach124
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
8/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
8
levels of 104CFU/ml in RVS broth to enable successful transfer and further growth on the selective125
agar plates employed in the NMKL method17. A total of six false negative results were found in the126
comparative study. Out of these six, two were rapeseed or rapeseed meal (Table 1). Furthermore,127
one rapeseed sample totally inhibited the PCR even at 1:100 dilution with no amplification of either128
the specific product or the internal control. Rapeseed has previously been noted to be PCR-129
inhibitory6 with reduced amplification efficiency using the same PCR method. In contrast,130
Salomonsson et al. (2005) did not have problems with PCR inhibition caused by rape seed samples131
when detecting salmonella after pre-enrichment in BPW.5However, a larger volume was used for132
the PCR (50 l instead of 25 l in this study) which diluted the inhibitors. Furthermore, the use of133
another DNA polymerase (rTthinstead of Tth) can also explain the differences. The use of alternate134
DNA polymerases is a convenient way to overcome PCR inhibition and has successfully been135
applied for different biological matrices.5, 6, 18 Additionally, Salmonella in one spiked sample136
(compound feed containing fishmeal and coccidiostatics) was not detected by the PCR method,137
although the internal control was amplified. As a control, this sample was re-analysed after the138
validation study was completed using four new 25 g samples inoculated with 4 CFU of Salmonella.139
All four samples were positive with the PCR method. The other two false negative results for the140
feed of animal origin were obtained for samples not inoculated with Salmonella(meat meal and fish141
meal). The samples also proved negative with NMKL when three new 25 g portions were analysed,142
which indicates that the sample included in the validation study was false positive with the NMKL143
method, possibly due to cross contamination.144
Special routines are needed to avoid carry-over contamination during the entire PCR145
procedure. Particular attention should be paid to the handling of samples to avoid transfer of146
amplified PCR product to the samples and reaction mixture, as well as to avoid the possibility of147
contamination of negative wells by adjacent positive wells during gel electrophoresis. One non-148
spiked sample was false positive with the PCR method. The amplified PCR product showed a faint149
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
9/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
9
band in the gel, which could indicate contamination or the presence of low amounts of Salmonella150
in the sample. Reasons for this result might be carry-over contamination during preparation of the151
samples or contamination from adjacent wells during gel electrophoresis. The sample was152
reanalysed using both the NMKL and PCR methods with negative results. However, there is a153
possibility that the sample might have been contaminated with Salmonellaat a low level, which was154
not detectable. The issue of weak bands should therefore be considered in the final protocol for the155
alternative method. To circumvent these problems and further speed up the analysis, real-time PCR156
or PCR-ELISA might be used instead of electrophoresis to detect the amplicon. Several recent157
studies have successfully detected the same amplicon using PCR followed by ELISA19 and real-158
time PCR using SYBRGreen19, 20or TaqMan probes19-21for detection.159
In conclusion, the PCR method validated in this study enabled the detection of low numbers160
of Salmonellain less than 24 h, compared to at least 3 days using the NMKL method (Fig. 1). For161
the problematic sample type rapeseed further studies are needed to achieve better pre-PCR162
processing to overcome the inhibitory effect. For acidified soy samples more positives were found163
with the PCR method than with the NMKL method, indicating difficulties in the recovery of164
sublethally damaged Salmonella cells by selective enrichment. To obtain NordVal approval the165
study needs to be supplemented with an additional interlaboratory study. However, the specificity,166
simplicity and speed of the PCR method makes it suitable for routine analysis of large numbers of167
samples and the implementation of the method in industry will help improve safety in the food168
production chain.169
170
Acknowledgements171
The authors wish to thank Dr. Halfdan Grage for help with the statistical analysis and Desire172
Andersson for technical assistance. This work was financially supported by the Swedish Agency for173
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
10/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
10
Innovation Systems (VINNOVA), and the Foundation of the Swedish Farmers' Supply and174
Crop Marketing Cooperation (SL-stiftelsen).175
176
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
11/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
11
References177
178
1. C. Tirado and K. Schmidt, J Infect 43, 80 (2001).179
2. R.H. Davies and M.H. Hinton, In: Salmonella in Domestic Animals, edited by C. Wray and A.180
Wray (Cabi Publishing, Wallingford, UK, 2000), p. 285.181
3. Anonymous,Method no 71, 5th ed (Nordic Committee on Food Analysis (NMKL), bo,182
Finland 1999).183
4. J. Hoorfar, P. Ahrens and P. Rdstrm, J Clin Microbiol 38, 3429 (2000).184
5. A.C. Salomonsson, A. Aspn, S. Johansson, A. Heino and P. Hggblom, J Rapid Methods Auto185
Microbiol 13, 96 (2005).186
6. C. Lfstrm, R. Knutsson, C. Engdahl Axelsson and P. Rdstrm, Appl Environ Microbiol 70,187
69 (2004).188
7. B. Malorny, E. Paccassoni, P. Fach, C. Bunge, A. Martin and R. Helmuth, Appl Environ189
Microbiol 70, 7046 (2004).190
8. B. Malorny, J. Hoorfar, C. Bunge and R. Helmuth, Appl Environ Microbiol 69, 290 (2003).191
9. B. Malorny, P.T. Tassios, P. Rdstrm, N. Cook, M. Wagner and J. Hoorfar, Int J Food192
Microbiol 83, 39 (2003).193
10. Anonymous,NV-DOC.D-20021022 (NordVal, Sborg, Denmark 2002).194
11. S. Qvist, Food Control 18, 113 (2007).195
12. K. Rahn, S.A. De Grandis, R.C. Clarke et al., Mol Cell Probes 6, 271 (1992).196
13. Agresti A,An introduction to categorical data analysis(John Wiley, New York, NJ 1996)197
14. Anonymous,ISO 16140 (International Organisation for Standardization, Geneva, Switzerland198
2003).199
15. Anonymous,NMKL procedure no. 20 (Nordic Method Commitee on Food Analysis (NMKL),200
Oslo, Norway 2007).201
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
12/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
12
16. S. Chen, A. Yee, M. Griffiths et al., Int J Food Microbiol 35, 239 (1997).202
17. H.J. Beckers, J. vd Heide, U. Fenigsen-Narucka and R. Peters, J Appl Bacteriol 62, 97 (1987).203
18. W. Abu Al-Soud and P. Rdstrm, Appl Environ Microbiol 64, 3748 (1998).204
19. S. Perelle, F. Dilasser, B. Malorny, J. Grout, J. Hoorfar and P. Fach, Mol Cell Probes 18, 409205
(2004).206
20. P.F. Wolffs, K. Glencross, R. Thibaudeau and M.W. Griffiths, Appl Environ Microbiol 72,207
3896 (2006).208
21. I. Hein, G. Flekna, M. Krassnig and M. Wagner, J Microbiol Methods 66, 538 (2006).209
210
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
13/16
13
Table 1 Comparison of the results in the comparative trial obtained by PCR and the reference culture methoda.211
Category Sample type PA NA FN TP FP Totalb
AC
(%)
SE
(%)
SP
(%)
Animal origin Fishmeal 8 12 1 0 0 21 95.2 88.9 100.0
Meat meal and bone meal 8 21 1 2 0 32 90.6 111.1 100.0
Compound feed (pet food pellets) 4 6 0 0 0 10 100.0 100.0 100.0
Compound feed (containing fish meal and coccidiostatics) 5 4 1 0 0 10 90.0 83.3 100.0
Animal total 25 43 3 2 0 73 93.2 96.4 100.0 0.85
Vegetable origin Ingredients, not heat treated (cereals, pulses and rape seed) 7 18 1 1 0 27 92.6 100.0 100.0
Ingredients, acidified (soybean meal, rape seed meal) 7 48 0 1 1 57 98.2 114.3 98.0
Compound feed (pellets) 8 9 0 0 0 17 100.0 100.0 100.0
Ingredients, heat treated (soybean meal, rapeseed meal, palm
kernel expeller)
14 36 1 0 1 52 98.1 93.3 97.3
Vegetable total 36 111 2 2 2 153 97.4 100.0 98.2 0.90
Other Environmental 0 3 0 0 0 3 100.0 -c 100.0
Feed concentrate 7 12 1 0 0 20 95.0 87.5 100.0
Other total 7 15 1 0 0 23 95.7 87.5 100.0 0.90
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
14/16
14
Total 68 169 6 4 2 249 96.0 97.3 98.8 0.88
aPA: Positive Agreement, NA: Negative Agreement, TP: True Positive, FN: False Negative,212
FP: False Positive, AC: Relative Accuracy, SE: Relative Sensitivity, SP: Relative Specificity, N = PA +NA + FN + TP + FP213
bThe PCR for one rape seed sample was totally inhibited (no specific product or internal control band produced) even at 1:100 dilution.214
This result is considered inconclusive and was not included in the analysis. The total number of samples included in the statistical analysis was215
therefore 249.216
c-, calculation of SE was not possible because PA + FN = 0217
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
15/16
1
2
3
4
5
6
7
8
9
0
12
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
30
31
32
33
34
35
36
37
3839
40
41
42
43
44
45
46
47
48
49
0
1
2
3
4
5
6
7
8
9
60
61
62
63
64
65
15
FIGURE LEGEND218
Fig. 1. Overview of the validation study set-up.219220
-
8/12/2019 Lfstrm Et Al 2008 Pre-print FANM 1(1), 23-37
16/16
25 g feed + 225 ml BPW
Enrichment
Biochemical and serological
identification
Dilution in saline PCR (invA)
37C, 18 h
Enrichment
(RVS)42C, 24 h
Selective plating (XLD, BGA) 37C, 24 h
Day 0
Day 1
Day 2
Day 3