Löfström Et Al 2008 Pre-print FANM 1(1), 23-37

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    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:

    [email protected]

    This article is published in: Food Analytical Methods, 2008, 1(1), 23-27

    The original publication is available at www.springerlink.com

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    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

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    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

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    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

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    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

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    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

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    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

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    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

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    ethidium bromide, and bands were visualized with the GelDoc 1000 system (Bio-Rad, Hercules,75

    CA) using the Molecular Analyst software (Bio-Rad).76

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    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

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    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

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    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

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    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

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    Innovation Systems (VINNOVA), and the Foundation of the Swedish Farmers' Supply and174

    Crop Marketing Cooperation (SL-stiftelsen).175

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    References177

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    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

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    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

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    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

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    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

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    FIGURE LEGEND218

    Fig. 1. Overview of the validation study set-up.219220

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    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