Genetic array for simultaneous detection of multiple <i>Salmonella </i>serovars

Abstract

Disclosed are novel genetic arrays for use in the molecular detection of multiple Salmonella serovars, common food-borne and water-borne pathogens. The arrays may be used to simultaneously detect multiple food safety Salmonella serovars. The multiplex-detection methods have improved sensitivity and specificity for the detection of multiple high-impact food-borne pathogens simultaneously. Real-time PCR assaying techniques using such serovars include microarrays.

Claims

1. A multiplex real-time PCR system for use in simultaneously testing for a plurality of Salmonella serovars that are foodborne pathogens or food threat agents, said system comprising: a container for receiving test samples, said container containing two or more primer pairs, said two or more primer pairs being adapted to detect and distinguish with specificity DNA from at least two different Salmonella serovars that are foodborne pathogens or food threat agents, wherein all said primer pairs have similar melting temperatures such that they can be simultaneously run under the same polymerase chain reaction (PCR) conditions, and wherein said primer pairs comprise at least one primer selected from SEQ ID NO: 1 and SEQ ID NO: 2, wherein the container further contains a different oligonucleotide probe for each primer pair, the oligonucleotide probes each being designed to bind to DNA regions flanked by the regions in genomes of the at least two different Salmonella serovars targeted by the primer pairs, each probe labeled with a different reporter dye having emission capabilities distinguishable from other ones of said probes.

2. The system according to claim 1, wherein said probes are capable of selectively detecting two or more target microorganisms selected from the group consisting of Salmonella serovar Heidelberg, Hadar, Enteritidis, Kentucky, and Dublin.

3. The system according to claim 1, wherein the nucleotide sequence of one of the probes consists of the sequence shown in SEQ ID NO: 3.

4. A method for detecting Salmonella serovars in a sample, said method comprising: performing polymerase chain reaction (PCR) using an array for testing a sample simultaneously for a plurality of Salmonella serovars that are foodborne pathogens or food threat agents, said array comprising: two or more primer pairs placed on a microplate for receiving test samples, said two or more primer pairs being adapted to detect and distinguish with specificity DNA from at least two different Salmonella serovars that are foodborne pathogens or food threat agents, wherein all said primer pairs have similar melting temperatures such that they can be simultaneously run under the same polymerase chain reaction (PCR) conditions, and wherein said primer pairs comprise at least one primer selected from SEQ ID NO: 1 and SEQ ID NO: 2.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

(2) FIG. 1 illustrates various gels obtained from PCR under equivalent conditions for amplification of multiple strains of Salmonella serovars; Enteritidis strains, Heidelberg strains, Kentucky strains and control positive strains for each serovar and further illustrate validation of those primers as having a very specific detection profile.

(3) FIG. 2 illustrates the unique amplification of target serovars in the validation of serovar specific primers, including: panel 2a, serovar Kentucky specific amplifications of S. kentucky C3 11-12-1 and S. kentucky 8195 in lanes 5 and 16; panel 2b, serovar Heidelberg specific amplification of S. heidelberg b 11-21-13 in lane 9; panel 2c, serovar Hadar specific amplification of S. hadar 11025; panel 2d serovar Enteritidis specific primers providing target amplification S. enteritidis (ATCC® 13076TM) on lane 80 and cross reaction with Salmonella O:gim:—11663-31 in lane 17.

(4) FIG. 3 provides multiplex conventional PCR amplification produced testing the selectivity of various primers developed, including for the detection of serovars Enteritidis, Heidelberg, Hadar, Kentucky and Dublin, of the five-pooled Salmonella serovars serially diluted 10 fold inoculated artificially to milk samples.

(5) FIG. 4 provides TAQMAN® PCR results for detecting and quantification of Salmonella Heidelberg from naturally contaminated chicken samples obtained from retail supermarkets using embodiments of the present invention.

(6) FIG. 5 illustrates the detection and quantification of Salmonella Enteritidis from naturally contaminated chicken samples obtained from retail supermarkets using TAQMAN® assay, after enrichment steps. Quantitative assay determined minimum amount of 18 CFU of Salmonella Enteritidis from sample number E2 at around 33 cycles, and maximum amount of Salmonella Enteritidis contamination was observed from sample number C1 giving 2.3×105 CFU.

(7) FIG. 6 illustrates an example of a multiple multiplex serovar microarray with two or more primer pairs placed on a microplate for receiving test samples.

DETAILED DESCRIPTION OF THE INVENTION

(8) Experiments

(9) The various experiments described herein illustrate the novel plasmid target-based PCR assays and testing methodology utilizing the same for the detection of Salmonella serovars. These experiments also provide support for the effectiveness of the unique targets for identifying Salmonella serovars heidelberg, hadar, enteritidis, kentucky and dublin which are important from a public health and economic perspective. Further, these experiments demonstrate improved assays for detecting multiple Salmonella serovars, which include delivery of results in a shorter amount of time.

(10) Materials

(11) A total of one hundred and sixteen (116) Salmonella serovars, and thirty-five (35) non-Salmonella serovars were used for in-vitro validation of the present invention. The Salmonella serovars and strains were obtained from different sources: American Type Culture Collection (ATCC) (Manassas, Va.); United States Department of Agriculture (USDA) diagnostic Lab (Athens, Ga.); Auburn University College of Veterinary Medicine (Auburn, Ala.); Department of Poultry Science, Auburn University; Department of Biological Sciences, Auburn University and National Veterinary Service laboratories (NVSL) (Ames, Iowa). Prior to use all the Salmonella serovars were confirmed by culture on Xylose Lysine Tergitol.sub.4 agar (XLT4) Salmonella selective media and analyzed for the presence of the invasive invA gene (specific to Salmonella) following the procedure performed by Woubit et al. 2012 (62).

(12) Various bacterial strains used in the experiments to establish exclusivity of the PCR detection are listed in Table 1 below. The 35 pure cultures of non-Salmonella strains listed in Table 1 were used for exclusivity test after further verification for Salmonella invA gene amplification. All the non-Salmonella strains yielded negative PCR results when tested using with any of the five primers specific for S. heidelberg, s. enteritidis, s. hadar, s. kentucky and S. dublin, as illustrated in FIG. 2.

(13) TABLE-US-00001 TABLE 1 Non Salmonella organisms used for the assay validation Salmonella Serial Lab Id/strain Specific No. ID. Non salmonella strains number invA PCR 1 28 Bacillus cereus 14579 — 2 9 Campylobacter jejuni 29428 — 3 25 Campylobacter coli 43478 — 4 21 Campylobacter jejuni 33291 — 5 32 Clostridium perfringens 8432 — 6 33 Clostridium perfringens 43402 — 7 34 Clostridium perfringens 3631 — 8 35 Clostridium perfringens 9865 — 9 1 E. coli O145 2.3636 — 10 2 E. coli O157 6.1593 — 11 3 E. coli O111 0.2056 — 12 4 E. coli O121 5.0959 — 13 5 E. coli O103 90.1219 — 14 6 E. coli O104 11.1587 — 15 7 E. coli O26 99.0704 — 16 8 E. coli O45 11.1079 — 17 12 Listeria monocytogenes Auburn — USDA lab 18 13 Listeria monocytogenes 13932 — 19 16 Listeria monocytogenes 35 — 20 19 Listeria monocytogenes 51 — 21 20 Listeria monocytogenes 33 — 22 22 Listeria monocytogenes 38 — 23 24 Listeria monocytogenes 13912 — 24 27 Listeria monocytogenes 18 — 25 14 Pseudomonas aerogenes NR-15 — 26 10 Shigella dysenteriae ATCC 11456A — 27 18 Shigella sonnei NA — 28 29 Staphylococcus aureus 12600 — 29 30 Staphylococcus aureus 13565 — 30 31 Staphylococcus aureus 27664 — 31 11 Yersinia ATCC 11960 — 32 15 Yersinia pestis NA — 33 17 Yersinia pestis NR -624 — 34 23 Yersinia enterocolitica ATCC 700823 — 35 26 Yersinia ATCC908 —

(14) TABLE-US-00002 TABLE 2 Specificity and Sensitivity Testing of the Designed Primers by both Conventional and Real Time PCR invA ID Salmonella enterica serovars gene Heidelberg Hadar Kentucky Enteritidis Dublin  1 Salmonella Montevideo o-group C1 + − − − − −  2 Salmonella Senftenberg E4 11-21-13 + − − − − −  3 Salmonella Kiambu ATCC MC 319 + − − − − − TX B  4 Salmonella Javiana Ps 11-21-13 + − − − − −  5 Salmonella Kentucky C3 11-12-13 + − − + − −  6 Salmonella Enteritidis D1 11-21-13 + − − − + −  7 Salmonella Muenchen C 2 11-21-13 + − − − − −  8 Salmonella Typhimurium B 11-21-13 + − − − − −  9 Salmonella Heidelberg b 11-21-13 + + − − − − 10 Salmonella Mbandaka C1 11-21-13 + − − − − − 11 Salmonella Weltevreden E 1 11-21-13 + − − − − − 12 Salmonella Pensacola 11272 11-21-13 + − − − − − 13 Salmonella Worthington 9409 11-21- + − − − − − 13 14 Salmonella Heidelberg 4124 11-21-13 + + − − − − 15 Salmonella Newport 9152 + − − − − − 16 Salmonella Kentucky 8195 + − − + − − 17 Salmonella O:gim:-11663-31 + − − − + − 18 Salmonella Ohio 8068-11 + − − − − − 19 Salmonella Braenderup 8895 + − − − − − 20 Salmonella Uganda 12269 + − − − − − 21 Salmonella 4, 5, 12:I:-10470 + − − − − − 22 Salmonella 6, 7:k:-7642-31 + − − − − − 23 Salmonella Hadar 11025 + − + − − − 24 Salmonella Paratyphi B-VAN-2 + − − − − − TARTNATE 12634 T 25 Salmonella Thompson 7642-13 A + − − − − − 26 Salmonella Typhimurium + − − − − − 27 Salmonella Infantis + − − − − − 28 Salmonella Reading + − − − − − 29 Salmonella Typhimurium SN en + − − − − − 30 Salmonella Infantis + − − − − − 31 Salmonella Typhimurium SN en + − − − − − 32 Salmonella Paratyphi A ATCC 11511 + − − − − − 33 Salmonella Typhimurium + − − − − − 34 Salmonella Typhimurium ATCC + − − − − − BAA 1836 35 Salmonella Typhimurium ATCC + − − − − − 700730 36 Salmonella Typhi os ATCC 6539 + − − − − − 37 Salmonella Schwarzengrund 12-1 + − − − − − 38 Salmonella Schwarzengrund 11-1 + − − − − − 39 Salmonella Schwarzengrund 11-2b R + − − − − − 40 Salmonella Schwarzengrund 11-3 + − − − − − 41 Salmonella Schwarzengrund 37-1 + − − − − − 42 Salmonella Enteritidis 35-1 + − − − + − 43 Salmonella Enteritidis 35-2 + − − − + − 44 Salmonella Enteritidis 35-3 + − − − + − 45 Salmonella Schwarzengrund 37-3 + − − − − − 46 Salmonella Schwarzengrund 11-2a Y + − − − − − 47 Salmonella Schwarzengrund 12-2 + − − − − − 48 Salmonella Enteritidis 35 + − − − + − 49 Salmonella Schwarzengrund 12 + − − − − − 50 Salmonella Enteritidis 35-4 + − − − + − 51 Salmonella Typhimurium 56 + − − − − − 52 Salmonella Typhimurium 3 + − − − − − 53 Salmonella Enteritidis 35-5 + − − − + − 54 Salmonella Schwarzengrund 37 + − − − − − 55 Salmonella Typhimurium 56-2 + − − − − − 56 Salmonella Typhimurium 56-3 + − − − − − 57 Salmonella Saintpaul 7-14-11 ATCC + − − − − − 9712 58 Salmonella Adelaide + − − − − − 59 Salmonella Reading + − − − − − 60 Salmonella arizonae + − − − − − 61 Salmonella Senftenberg + − − − − − 62 Salmonella Rubislaw + − − − − − 63 Salmonella Anatum + − − − − − 64 Salmonella Newport + − − − − − 65 Salmonella Mbandaka + − − − − − 66 Salmonella Oranienburg + − − − − − 67 Salmonella Liverpool + − − − − − 68 Salmonella Muenster + − − − − − 69 Salmonella Litchfield + − − − − − 70 Salmonella 6 7:k:- + − − − − − 71 Salmonella Rough o:gim:- + − − − − − 72 Salmonella Inverness + − − − − − 73 Salmonella Dublin M06-53175-Dr + − − − − + Ogi 74 Salmonella Dublin M07-17378-Dr + − − − − + Ogi 75 Salmonella Tennessee (ATCC ® + − − − − − 10722TM) 76 Salmonella Agona (ATCC ® + − − − − − 51957TM) 77 Salmonella Paratyphi C (ATCC ® + − − − + − 13428TM) 78 Salmonella Bareilly (ATCC ® + − − − − − 9115TM) 79 Salmonella Pullorum (ATCC ® + − − − − − 13036TM) 80 Salmonella Enteritidis (ATCC ® + − − − + − 13076TM) 81 Salmonella Newport (ATCC-6962) + − − − − − 82 Salmonella Paratyphi B (ATCC 8759) + − − − − − 83 Salmonella Javiana (ATCC-BAA- + − − − − − 1593) 84 Salmonella arizonae (ATCC-13314) + − − − − − 85 Salmonella Muenchen (ATCC-BAA- + − − − − − 1674) 86 Salmonella diarizonae (ATCC-12325) + − − − − − 87 Salmonella Thompson (ATCC-8391) + − − − − − 88 Salmonella Choleraesuis (ATCC- + − − − − − 55105) 89 Salmonella Infantis (ATCC 51741) + − − − − − 90 Salmonella Cerro (ATCC 10723) + − − − − − 91 Salmonella Gaminara (ATCC 8324) + − − − − − 92 Salmonella Johannesburg (14-5818) + − − − − − 93 Salmonella Wandsworth (11-7160) + − − − − − 94 Salmonella 4-5-12i (14-5821) + − − − − − 95 Salmonella Subsp. arizonae + − − − − − 48:g, Z51:_(13-1516) 96 Salmonella Baildon (14-4442) + − − − − − 97 Salmonella Choleraesuis (14-3829) + − − − − − 98 Salmonella Infantis (14-4189) + − − − − − 99 Salmonella Newport (14-2911) + − − − − − 100  Salmonella Schwarzengrund (13- + − − − − − 5829) 101  Salmonella Enteritidis 145352 + − − − + −  1a Salmonella Enteritidis 12D14456 + − − − + −  2a Salmonella Enteritidis 775 + − − − + −  3a Salmonella Enteritidis 420 + − − − −.sup.1 −  4a Salmonella Enteritidis 1614 + − − − + −  5a Salmonella Enteritidis 2640 + − − − + −  13a Salmonella Enteritidis + − − − + −  6a Salmonella Dublin 598 + − − − − +  7a Salmonella Dublin 941 + − − − − +  8a Salmonella Dublin 1225 + − − − − +  9a Salmonella Dublin 1958 + − − − − +  10a Salmonella Dublin 1618 + − − − − +  11a Salmonella Heidelberg + − − − − −  14a Salmonella Heidelberg + + − − − −  12a Salmonella Kentucky + + − − − −  15a Salmonella Kentucky + − − + − − .sup.1A very weak amplification of similar size observed.

(15) The suitability of the various serovar/strain specific primers designed by Applicants for both highly selective and highly sensitive use was confirmed, as described in the various examples and experiments below. Other preferred primers, and preferred uses of the primers in combination with other primers, are identified in the various examples that follow.

(16) Genomic DNA from all Salmonella serovars and non-Salmonella organisms, unless otherwise noted herein, was extracted according to the manufacturer's procedure used in bacterial DNA extraction (QiaAmp® DNA Mini Kit (Qiagen™, Valencia, Calif.). All organisms were cultured in Tryptic Soy Broth and incubated for 18 h at 37° C. before DNA extraction. All artificially and naturally contaminated food samples were pre-enriched in non-selective Buffered Peptone Water (BPW) followed by selective enrichment in Rappaport-Vassiliadis Salmonella Enrichment Broth (RVS). For DNA extraction, 1 ml of selective enrichment culture from artificial and natural inoculation were collected in 1.5 ml tube and centrifuged at 5000 g for 10 minutes at +4° C. The supernatant was carefully discarded without disrupting the pellet; the pellet was then used for DNA xtraction using DNeasy® Blood and Tissue kit following the manufacturer's instructions (Qiagen™, Valencia, Calif.). The quality of DNA was assayed both by using NANODROP 2000C spectrophotometers (Thermo Fisher Scientific®, Carlsbad, Calif.) and by agarose gel electrophoresis. Extracted DNA was stored at −20° C.

(17) Unless otherwise indicated herein in the various specific laboratory examples, all PCR reactions were set up in an isolated PCR station (AirClean® Systems, NC) that was ultraviolet (UV)-sanitized daily and after each use.

(18) As noted above, primers are not available which are highly sensitive and specific while still being suitable for use in a simultaneous multi-serovar array. As such, Applicants designed various primers as disclosed herein that would be suitable for use in simultaneous detection systems. To this end, Applicants used text mining, genomic data mining, sequence analysis and comparison tools to design the various primers listed in Table 3 below. Indeed, the primers for some serovars of S. enteritidis were designed from a target gene reported to be unique for this serovar because of obstacles of finding unique targets from genome mining and some of the targets obtained cross-reacted in vitro with other Salmonella serovars. All primers were independently designed based upon direct genomic information without earlier reference to other known primers.

(19) During the process of selection and design, the primers were initially validated for unique site recognition and strength of binding by using genomic DNA template of the respective organism. For each of the organisms selected, Applicants obtained genome sequences for the organisms and a BLAST (Basic Local Alignment Search Tool) search was used in selecting target regions. During design, Applicants also analyzed oligo-dimer and hair-loop characteristics of potential primer sequences in an effort to standardize primers to have similar melting temperatures, a prerequisite for simultaneous PCR usage. All of the Salmonella serovars and strains used in the development of the primers and tests were positive for the invA gene specific for the genus Salmonella. Most of the virulent Salmonella serotypes have the invA gene, which is responsible for invasion of epithelia cells and for pathogenicity (52).

(20) Completed and incomplete (contigs) genome sequence data for the five selected Salmonella serovars; other serovars and non-Salmonella organisms were retrieved to VECTOR NTI 11 database (Thermo Fisher Scientific®, Carlsbad, Calif.) from National Center for Biotechnology Information (NCBI) microbial genome-sequencing database. To identify specific unique target sequences for each of the five selected Salmonella serovars, approximately 4500 annotated protein-coding sequences (CDSs) of each of the selected strain of a serovar were screened for the similarity of nucleotide sequence against genomes from other Salmonella serovars and non-Salmonella organisms available at NCBI through the Basic Local Alignment Search Tool (BLAST) for nucleotide. The CDSs of a given serovar were selected as the potential targets for detection if it matched with those of the same serovars in the database, with lowest E 10-50 values, more than 98% query coverage and 100% identity coverage. The target CDSs sequences were then uploaded to VECTOR NTI database along with closely Salmonella serovar and non-Salmonella organisms from NCBI databases and blasted and aligned to further evaluate the uniqueness of the target amino acid sequence and its nucleotide counterpart. Similarly the targets were also tested against the Salmonella and non-Salmonella organisms found in Pathosystems Resource Integration Center (PATRIC) databases (64). When the target matched 100% to the selected serovars and did not cross-react with other Salmonella and non-Salmonella organisms, it was selected for primer design from its most polymorphic site. The designed primer was further blasted on 268 complete, 2395 scaffold and 4543 contig's of Salmonella serovars on both PATRIC and NCBI databases. In addition, primers were validated for non-specific binding on the genome sequences of 15 closely related species including Escherichia coli and other members of the family Enterobacteriaceae. Primers were then used to run in-silico PCR of target serovar and to verify none-target amplification with other serovars on 45 fully sequenced Salmonella. Primers were further used to analyze motif search to check inter and intra-genomic specificities, this later validation was performed using VECTOR NTI motif search engine. This allowed confirmation of single site binding within the target genome and no cross binding to other Salmonella serovars and closely related organisms. Primers that fulfilled these criteria were analyzed for their thermodynamic properties including dimer and hair-loop formation, palindromes, Tm, and 3′GC content before final ordering. Probes for multiplex TAQMAN® assay were designed for three serovars, i.e., Enteritidis, Heidelberg and Dublin using PrimerQuest™ of Integrated DNA Technologies® (IDT, Ames, Iowa). The reporter dyes for serovars Enteritidis, Heidelberg and Dublin were FAM™, ROX™ and CY5™, respectively; all the probes were modified to carry a Black Hole Quencher™ Dye (BHQ) at their 3′end. The primers and probe were ordered from Integrated DNA Technologies®.

(21) Virtual PCR results provided an initial indication regarding the specificity of the developed primers for the serovars, and conventional PCR specific amplification from different organisms species was confirmed the in-silico findings. Specifically, primers were validated in-silico on a wide range of target and non-target organisms, including 45 fully sequenced Salmonella serovars, 268 complete, 2395 scaffold and 4543 contig's of Salmonella serovars on both PATRIC and NCBI databases. In addition, primers were validated for non-specific binding on the genome sequences of 15 closely related species including Escherichia coli and other members of the family Enterobacteriaceae.

(22) Following this in-silico testing, those primers identified in Table 3 below were tested further using conventional PCR. Initial validation involved testing of these primers with the genomic DNA of the corresponding Salmonella serovars. The PCR was performed in a total of 20 μl volume containing 10 μl of PWO master mix (DNA Polymerase, reaction buffer with 4 mM MgCl2 and PCR-grade dNTP's (each 0.4 mM) in a total volume of 250 μl) (SIGMA, Mannheim, Germany), 8 μl of PCR water, 1 μl of 20 μM of primer pair and 1 μl of 30 ng/μl genomic DNA. The thermal cycling program (Mastercycler® Pro, Eppendorf®, Hamburg, Germany) included: initial denaturation for 2 min at 94° C., followed by 30 cycles of 15 seconds at 94° C., 15 seconds at 60° C., and 15 seconds at 72° C. then 1 cycle of 72° C. for 5 min. Four microliters of the PCR product was mixed with 2 μl of 6× loading dye and loaded onto 1.5% agarose gel, which ran for 40 minutes at 100 volts. The PCR product was analyzed for the presence of bands after the gel was stained using GelRed® (Biotium, Hayward, Calif.), images were analyzed using AlphaView® software (AlphaView® software, San Leandro, Calif.).

(23) In addition to conventional PCR confirmation, SYBR Green Real Time PCR assay was performed using MX3000PTM (Agilent® Technologies Inc., Santa Clara, Calif.) for further validations of primers provided a specific single band with the conventional PCR assay. The PCR was done in a 20 μl reaction volume comprising 7.7 μl of PCR grade water, 10 μl of 2× SYBR® Green master mixes (Roche™ Life Science, Indianapolis, Ind.), 0.5 μL of forward and reverse primer and 1 μl of DNA. The thermal cycling program for the real-time PCR were as follows: 95° C. for 15 min, followed by 30 cycles of denaturation at 94° C. for 30 seconds, annealing at 60° C. for 30 seconds, and extension at 72° C. for 30 seconds. The PCR results were analyzed using MxPro® software (Agilent® Technologies Inc.).

(24) The real time PCR assays using the newly created primers were tested by five-fold serial dilutions of the genomic DNA of each of the five serovars, in order to determine the minimum concentration of DNA that can be detected. Before the assay, the initial concentration of stock DNA was measured using NANODROP 2000C spectrophotometers. DNA was serially diluted using PCR grade water to femtogram (fg) concentrations.

(25) TABLE-US-00003 TABLE 3a Sequences of primers and probes designed GenBank accession Target no. Primers Size SEQ ID size or strain and probes (bp) Sequences (5′ to 3′) NO: (bp) (position) Primer-probe combinations for assays Heidelerg- 20 GCAGTTCATTCGCTTTGTCG 1 156 NC_021810 1R-s (1677692- 1677980) Heidelberg- 21 CGGAAAATACGTCTCATGTCC 2 1F Heidelberg 24 ROX/TAGTCCATCACCCAGCGCAGTTTC/I 3 probe ABkFQ Enteritidis- 19 CTGGCATCAAGAATGTCGT 4 325 U66901.1 all-2R (609-933) Enteritidis- 20 CGCAAAAATCAGGATGGCTC 5 all-2F Enteritidis 23 FAM/TACGGCGATTTCTACCGTGTCGT/IA 6 probe BkFQ Dublin-1R- 27 GATTTACGACTGTTGGTGTTTAAGCTG 7 118 NC_011204 s.sup.2 (46817- 46934) Dublin-1F- 26 GTGAGAAATCCAGATACCAGAAAGAA 8 p.sup.a Dublin 23 CY5/AGAACTACGCACGGCAATTTCGA/IA 9 probe BkFQ Primer combinations for conventional and SYBR Green PCR assay validation Heidelberg- 21 CGGAAAATACGTCTCATGTCC 10 289 NC_021810 1F.sup.a (1677692- 1677980) Heidelberg- 21 GATTCTTCACGCACAATATCC 11 1R.sup.a Hadar-1F.sup.a 24 AATCTGAACTTGAGAAATCAATCC 12 354 FR686852.1 (93097- 93120 Hadar-1R.sup.a 22 CCGTGAGGAGATTATTTAGCCC 13 Kentucky- 21 ACGTTGAGCGAGTTTATCGCT 14 246 EDX46695.1 2F.sup.a Kentucky- 20 CAATGGTCTGTTATGGGGAA 15 2R.sup.a Enteritidis- 19 CTGGCATCAAGAATGTCGT 16 325 U66901.1 a11-2R.sup.a (609-933) Enteritidis- 20 CGCAAAAATCAGGATGGCTC 17 all-2F.sup.a Dublin-1F 26 GTGAGAAATCCAGATACCAGAAAGAA 18 286 NC_011204 (46817- 47102) Dublin-1R 23 CGGGATGGTTTAATTATCAATGA 19 .sup.2Primers used for multiplex conventional PCR assay.

(26) TABLE-US-00004 TABLE 3b Sequences of primers and probes designed with Targeted Sequence SEQ SEQ Primer Size ID Target Target ID Name (bp) Sequence (5′-3′) NO: (bp) gene Targeted Sequence NO: Javiana- 20 GTTGAATGGA 20 136 Type V GTTGAATGGAGGAAGCG 93 3mF GGAAGCGTCC secretory TCCAGGTTGAAGGTAAT pathway TATGGCATTTTGATGCTC adhesin TATAATAATTCACAAGC AIDA CACCCTGATGGGCACCG AGGTCACCGCAACGGCG GAAACAACTAGCGGCAT AGTGTCACAGCAAGGC Javiana- 20 CCTTGCTGTG 21 3R ACACTATGCC G Oranienburg- 23 CATTAGATAT 22 188 Hypothetical CATTAGATATGAACAAG 94 SS- GAACAAGCGA protein CGACCGGACTCAACCGT new-2R CCG ATTAAAGCGCATATAAA TACTGCTAACAAATTCA CCCACATTTATTGGCATT GGTGAATTTTTTGGTTCT TTACGCTTTCCAATTGTC TTGGCTTCAATAACTACC ATTCTATTTAAAAAACCC GTCCCAGCCTCACGGCTT GAAAATGCACTC Oranienburg- 21 AGTGCATTTT 23 SS- CAAGCCGTGA new-2F G Oranienburg- 23 GAGTTTTACC 24 175 Hypothetical AGTTTTACCAACTGATGT 95 SS- AACTGATGTC Protein CGGGGCTAAAACTGCAA new-1R GGG TATATAAATTACTCGTTA GCGTTCCCTTATATGACC ATCTGCCAGAAATTAAA GAAGCCATTGACGCAAC GGAAAACGCCAATGCTA ATTCAGGGCAATATGTT CTAGTGTTTTCAATTTGC CAATCAAACAAGCCAGT T Oranienburg- 21 AACTGGCTTG 25 SS- TTTGATTGGC new-1F A Paratyphi 20 ATGAGTCCAA 26 213 SPAB_0 ATGAGTCCAATCGTGCC 96 B-4R TCGTGCCTGC 5693 - TGCGATACTAATATATA EcoKI GATCGTTTTTACTTATGG restriction- TGTAATTGCTGATAGCA modification GATAAGTATCGGAGTCT system AAATACTTAATCGTGGA protein AAGATTTACGCTTCCATT HsdS TTCGAAGTCAGTAACTCT AATATATGGATGTTCTGT TGCGGTATTAAGTAAAG CTTTACCTTTGGGAAGCC TTTTTCCACCCTTTACTT CA Paratyphi 23 TGAAGTAAAG 27 B-4F GGTGGAAAAA GGC Paratyphi 23 GGACTATTCA 28 111 SSPA22 GGACTATTCAGGATGCT 97 A-SF GGATGCTGTG 66- GTGAAGTTTTGCAGGGA AAG hypothetical GACTGGAAGACAAGATG protein CTGGCTCAGCCATGGAG GCATGGAATGCCTGCCG CACCGCCATGCTCCAAG GTAGCCAAC Paratyphi 19 GTTGGCTACC 29 A- TTGGAGCAT 5R Paratyp 19 TGAGGTCGCC 30 264 SSPA22 GACTTGTCGATATTGATT 98 hi A- AAGTTCTGC 66- CAGGCGCAGAGGATCAT 4R hypothetical TGGAAATATTCAACTCA protein GTGCATAACACCTGCAT CTGGAAAGACGTACCGT ATTGAGTCTATTCCTCTC TACACAGTCTCGCAACC AGTACCAGTACCAGAAC GCGAACGTATTCGCCGT GAACATGCTGAATGGTC TGATGCCACATTCGGCG ATGTTGGCCCCATCGGTC CACTGAAGCACCTCTCA AAAGAGGCATTGGAAAC TGCCGCAGAACTTGGCG ACCTCA Paratyp 24 GACTTGTCGA 31 hi A-4F TATTGATTCA GGCG Tennes- 24 CCACAGCAGT 32 198 DNA CCACAGCAGTACATAGA 99 4F ACATAGAAAG transfer AAGGACCGGGAGAACCG GACC protein CAAACGTACTTAGAAAC CTTGACTCGGGCCTGTCC AGCGTAACCAGCACTGT CCTCAATGCTATAGCCA ACTCCACATCAGGTGCT GTTGTTGGCGGTGCAGG TGGAGGGATTGCTGGCG CTGCTGCCGGGGCGTTG GCTGGAGCGGGACTGAA AGGCATCGTT Tennes- 20 AACGATGCCT 33 4R TTCAGTCCCG Tennes- 22 AATCTGTTTGT 34 100 DNA AATCTGTTTGTCTCCTGG 100 3R CTCCTGGCAC mismatch CACCTATAATATCCTCTC C repair CATTTTCCACATCTTGTT protein CATCTATGTTATTAATGG AGTAAACACTATCCCTC AATGATTTCGC Tennes- 22 GCGAAATCAT 35 3F TGAGGGATAG TG Hadar- 22 CCGTGAGGAG 36 354 FR6868 AATCTGAACTTGAGAAA 101 1R ATTATTTAGC 52.1 TCAATCCGTACAGCCTAT CC (93097 CTTGCCACAAATATACT to AGCCTATTGGGCAATAC 93120, AAGATGGTAATGCAAAA integrative CAAGCCCTCTATGTATCG and GAGCGTTGCCTGCTATG conjugative GGTATGGCACCGTATTC element ACCTTGAAAAAAGTCCA ICESe4 CAACAATACTTCTCTGCC ATTAATATTATATGGCA AAACTATATTAATATCTC CGCAGAATACTTTTCCA AACTTCAACCCTATTTTC ACGAAAAATATCTTCTG TCGTCATACTCTGCCGAT AGCGCATTAATTAATCTT ACTATATTTGAACAAAT AGGTATACTCTCTACTAT CGGGCTAAATAATCTCC TCACGG Hadar- 24 AATCTGAACT 37 1F TGAGAAATCA ATCC Enteritidis- 19 CTGGCATCAA 38 225 U66901. CTGGCATCAAGAATGTC 102 all- GAATGTCGT 1 (609 to GTCTCGTGCTGGCCATA 2R 933) GGCAGCCAAACGTTCAG fimbrial TTTGACCTGACAATGTAC biosynthesis TCAACTCCAGTACTCCTC protein CACTGACAGGATTCCCA Prot6e TAGCTGTAGCTTTGTTTT TCAACAAAACAACGCGA ACCATGCTCAGCTGCTCC ACTTGGTTCAAACCTCGC CCTCACATTCATAAAAA CGACACGGTAGAAATCG CCGTACACGAGCTTATA GATTTTTGAGATGGGGG TCACCACACTTAAATTAT TGCTATTTTGCCCTGTAC ACTGCATCCCTGTCACA ACATTCCATGAGCCATC CTGATTTTTGCG Enteritidis- 20 CGCAAAAATC 39 all- AGGATGGCTC 2F Heidelberg- 21 GATTCTTCAC 40 289 fig|1124 CGGAAAATACGTCTCAT 103 1R GCACAATATC 936.4. GTCCGCTCTTCTTTACGC C peg.1672,  AGCAAAGATGAAACCTT Type II TAGAGGTCGCCTCGAAG restriction ATAACAGTACCTATCAG enzyme, AAACTGCGCTGGGTGAT methylase GGACTACTGGTGTGCGC subunits TATGGTTCTGGCCAATCG ACAAAGCGAATGAACTG CCGGATCGCGGTATGTG GCTAATGGAGATGGAGA CACTGATCGACGGTATT GTCGTCACGGAAAGAGT CACTGAAGTTGCAGAGC AGGCCACCGGCAATCTG TTTGCCGACGAGGATAT TGTGCGTGAAGAATC Heidelberg- 21 CGGAAAATAC 41 1F GTCTCATGTC C Kentucky- 20 CAATGGTCTG 42 246 EDX466 CAATGGTCTGTTATGGG 104 2R TTATGGGGAA 95.1, GAAAATCATAAATATTT hypothet TTAAAGAGTTGAGAGGC ical GGGATTTTATTTGGTGAA protein AGGAACGACTACGCTAA AATTTGGCAAGAAAAAT ACCTTTCCACATCTGGGG TTGTTTCTGAGTTTGATG ATAATGTATTTTCATCAG CATATGATTATTGGCGTT CTCTTGAAGGGCCTTGG AGAGAATTATTTGTTTGT TTTTGGAACAAAGTTAG CGATAAACTCGCTCAAC GT Kentucky- 21 ACGTTGAGCG 43 2F AGTTTATCGC T Baildon- 25 CGTCAGGGAA 44 266 gb|AFC TCCCTGACGACAAAATT 105 1F-m AACTGTATTT K01000924. CAATCCATTGTACTCAG AATCG 11:2 GCTATTATTCTGTGGAAA 454- GACTGAAACACTAACAG 4682, CCACTTTTAATAAAAATT hypothetical TCAAAAAAATTGTACCC protein GTTCATTTTGCGACCGAA LTSEB ATATCAAATTTTAGAAA AI_3067 TGACTTTACAATGTTGGG ATATTTAACAGAAAAGA CTAGTGGATGGGTTACC AAGTTTGTTGATTTTTCA ATCAACGAAATTGAGAA AAACTCAGCAGACATTA AAGGATTTCACGACGAG TTTAGG Baildon- 22 GGATGCTAAG 45 1R-m TGAAGTGTTG GG Baildon- 23 CGACCATTGC 46 223 gb|AFC GGTGAGAATAGCAAGTC 106 2F-m ACTGATTCAT K01000924. GTACTCTGATTACATTAA CAT 11:2 TAAAATAAAAGAAATAA 454- CTAAAACATCTAAGTAC 4682, GGATATAAAGAGAAAGT hypothetical TCTAAACTATGTTAAAGT protein AGGATTAGATGGTCAAA LTSEB CATTTCAGATCGATGGT AI_3067 AAAAAACTAGAAATTCA ATCAGATGGAACAAATT CTTTCAAATACATTGAA ATATTTCTATCCCTGTTA ATATCCCTTACAAGAA Baildon- 25 TACAAAATTA 47 2R-m GAACGACGAG AAGCA Mississipi- 21 ACCCTTTCAA 48 138 PATRIC ACCCTTTCAATGTTCCTA 107 1F TGTTCCTACG ID: CGCTCAAAATGTGATCG C fig|913080.3.  TGAGCTATATTTGTCACT peg. ACATGAAGATTCCGAAT 4734, TGGATGCTAATTCAATG hypothetical CCAGTGCCCCTTCAGGC protein GCGTCCAGGAATCGGAG TGCTTCAAACTGCTGGA Mississipi- 20 TCCAGCAGTT 49 1R TGAAGCACTC Mississipi- 20 AGCGGTTCTT 50 217 PATRIC AGCGGTTCTTCTACATTG 108 2R CTACATTGCA ID: CAGCTAGCCAATTTTGAT fig|913080.3. TTAGCGATTGCAATGGC peg. GACCGGAGATGTATCTA 4735, TTCCCCATGCTGAGAGC hypothetical CCTAACGTTCGGGCTGC protein AAACAGTGAAGTCCCCC TTCCACAGAAAGGGTCG AGGATAACCGGAGTGTC CTTTCGATGTTTTTTTAG CACTTGGTAAGGATACT CAAGGGGAAACATCGTA AAATAAGGAC Mississipi- 23 GTCCTTATTTT 51 2F ACGATGTTTC CC Newport- 20 GGAATGAACT 52 130 Restriction GTTCCAGTTGATCGCAG 109 1F-m TGCCAAGGCT endonuclease AGGGACATGAGTTTATC subunit AACACGTGAAACAATTC S GCAGTTGCTCCTGGATA GGAGCTAATTCGATGAC AGCCTGCTGAGCTTTTTC TGTACCAAGCCTTGGCA AGTTCATTCC Newport- 20 ATTCCAGTTG 53 1R- ATCGCAGAGG m Newport- 23 ATTCGATGAC 54 Probe 1- AGCCTGCTGA Probe GCT Newport- 19 TTCCAGTTGA 55 128 PATRIC TTCCAGTTGATCGCAGA 110 1R-3 TCGCAGAGG ID: GGGACATGAGTTTATCA fig|877468.3. ACACGTGAAACAATTCG peg. CAGTTGCTCCTGGATAG 920, GAGCTAATTCGATGACA Type I GCCTGCTGAGCTTTTTCT restriction- GTACCAAGCCTTGGCAA modification GTTCATTC system, specificity subunit S Newport- 20 GAATGAACTT 56 1F-3 GCCAAGGCTT Shwazengrund- 20 CTCAAGACCT 57 368 YP_002 CTCAAGACCTCCAGTGC 111 2F-m CCAGTGCCTC 115706. CTCGCCAATCCGCCCAA 1, TCCATGTTCGAACCATTT hypothetical TGGCAAGCTCAACGAGG protein AGCATCCAATCTTCCATT SeSA_ TCTGGAGCTTCGAGCGTT A2894 ACCCAAAGATTACCCTG CCCCTCATATACACAGG TCAGCCGTTGCGCTTCAA GATCATCAATTGATGCG TAGCACTTGCTCTGACGC TCGGTGGGAAAGAAATC TTCTGCCGAAGGCCTCAT CACTCGATGCCATTTACC ATTGTTGTCACTAATGCG ATGCCGGTCATATCCTGT GTCTGCCGCTATTCGTAT ACCACGGAGTAAATTCG TGGGAATCATTAACATT AGCGGGTGTTCCGGTGT GATACGGTCATCTGGTA A Shwazengrund- 23 TTACCAGATG 58 2R-m ACCGTATCAC ACC Shwazengrund- 22 CTTTCAGTTGC 59 381 YP_002115706. ATTACGAGCAAGTGAGA 112 1R-m TGTACGTCCC 1, GGTCCTTACATTCGATAA T hypothetical CGAGAACTTGATTGCGG protein TCTGAGCGCCAGGCAAG SeSA_ AAGATCAATATCCCCCG A2894 GATCACCTGGTAGATTC CTGCGAAGAATTTCAGG AAAGCCTATGCCACGTC GAACTGTCCAGCCTATTT CACGAAGTTCTCTCTCCA AAGTTTTTTCGAATGTGT GTCCTTCCCGCGCTCCAC CTAACCAAGTGTCTCTCA TACCCTCTGTGCGAAAG AAGTCACGCTTAAATTG CCCAGTGTATGCGCCAT CGAAAACGTATTTAAGG GACAGATTCAAGAGTCC TGGTGCGATAACAATTA GTGGATCGTGACTCTCTT CAATCTGTAACAAGGGA CGTACAGCAACTGAAAG Shwazengrund- 23 ATTACGAGCA 60 1F-m AGTGAGAGGT CCT Shwazengrund- 24 GAATTTCAGG 61 Probe probe-1 AAAGCCTATG CCAC Choleraesuis- 21 TTACGCCCTG 62 190 antirepressor TCCCAACCCTCGATCAA 113 2R-m TTACATCGGT (YP_216185.1) CCTGAACTTTGCGTTATT G GATGGCAAAGTCGTTAC TTCCTCACTGGCTGTTGC CGATTATTTCCATAAGCC ACATAAAGACGTACTGG CTAAGATTTCCCGCCTGG ATTGTTCTGTCGAATTTA CCGAGCGAAATTTCTCG CTCAGCAAATACACCGA TGTAACAGGGCGTAA Choleraesuis- 18 TCCCAACCCT 63 2F-m CGATCAAC Agona- 27 CATTATCAGT 64 158 YP_008863900.  TGATATTGCTAGGCTGTT 114 1R AGGGAGTTTT 1, AGTTTGTGATGCCTGGA GTCTGAG hypothetical AAGCACAGGTTAAAGGG protein ATACCAGCCGGTTGTTTT Q786_ CTACTTGCATTTTACGAT 22240 GGTGAAGACGGTGTTGA AGAGGCTGTATTGCTTA GAGCACTTTCTCAGACA AAACTCCCTACTGATAA TG Agona- 24 TGATATTGCT 65 1F AGGCTGTTAG TTTG Agona- 25 GTAAACTCAG 66 414 YP_008863900. TTTAGAATGTAGGGTTCT 115 2R ATGTTTCAGG 1, TGGAGTATTTTATAGAA AGAAG hypothetical CACAGAAAGGGAATATA protein GAATTTGGTGCTGACCTT Q786_ GAGAACTTTTATGCAGC 22240 TAATAATTACACTGTATA CAAAGCCAATAGAGATG TTCTTGAATTTATAGTAA ATCAACGAGATGATGGC GGTTTAGTTGGTCAGGA CTCTGAATTTAAAATTGG TAGTGTAAGATATTCATC TAGCCGTAGACATCAAT CTCAAGAGGAAAATGTT AATGTATGGGTAAATCC TAAAGATTTTTTAGGAA AAAGGTCTGCTATGTTTG GGATGACCCGTACTGGT AAGTCGAATACTGTAAA GAAAGTGATAGAAGCAA CAGAGGAAATTTCAAGA AAAGCTTTAATACTATTG GATTCAGCTTCTCCTGAA ACATCTGAGTTTAC Agona- 25 TTTAGAATGT 67 2F AGGGTTCTTG GAGTA Arizoniae- 21 TCATTTGGCA 68 249 PATRICIA: TCATTTGGCACTTCAACA 116 1R- CTTCAACACG fig|41514. CGGAAGTGTGGACGCAT m G 7.peg.3 ATCGTTAGTTATATTGTC 248, GTCAGCAATACCAGTGT Large CATTGATCAGTTCGATGC repetitive TATTAATCGCGATTTGCG protein TATCCACTTTCACTGTTA SARI_ ATGGTGTGGACTGGCGA 03417 ATATTTCCCGCCTCATCT TCCACCGTCACTTGCAGT GTATAGCTGCCATCATCC CACGTGCTGGCAGGTGT AAATACCCAGTTACCGC CATCTTGAGTCAGTACA ATC Arizoniae- 23 GATTGTACTG 69 1F- ACTCAAGATG m GCG Bareilly- 23 CCAGATCTTC 70 95 PATRICID: CCAGATCTTCGCAGGGT 117 1F-k GCAGGGTCAA fig|1196348. CAAGCTGTGTTTGAGTG GCT 3.peg. AGTTCAAAATAGCGATC 3599,  AACCATTGAGCCGACAA hypothetical TCTTGCTTATTCCATTCC protein GACAGTCAC SEEB0189_ 09420 Bareilly- 24 GTGACTGTCG 71 1R-k GAATGGAATA AGCA Bareilly- 24 GGTTCTTAAC 72 423 PATRICID: GGTTCTTAACGCTGTAA 118 2F-k GCTGTAAGCA fig|1196348. GCAACTCAATATTAACG ACTC 3.peg. GATTCAAGATTTCCTTCT 3599, GCACGTAGAATCTCCAG hypothetical ACAAGCGGCATACAAAA protein TTGTCTCAGAATACCTGT SEEB0189_ ATTTTGATTCGCATTGCA 09420 GAGTCGCAAGCTCGGGA AGAGTGGGAACCTTTGA AGCAATAAAATCCAGAC AATTTCTTAATGCCCCCC GAACCAGTTTGTCGTCA CCAAATTCTAATTCAATT CTTTCCGGAAGCATGAG CACAAGTTCTGCAAAAC GCACCAGACAACCCCAG TGAAGACCTCGTTCTAC AATATCTCTGTTTTCATT AACGAATTCTATATTTTT GGCGTGGATCTCTCGTTG CCTTCTATCATAGCGGTT CATCTTTCGGCTATGTCT GAATCTCAAGTGCTGGT GCTTTCGCTCAGATAATT TCAT Bareilly- 23 ATGAAATTAT 73 2R CTGAGCGAAA GCA Braenderup- 22 TCACCTATCG 74 228 PATRICID: TCACCTATCGCTGGTATA 119 2F CTGGTATAGC fig|930771. GCCTATTATTCCACTAGA CT 3.peg. ATGCATAATGCTAATAA 3431, AACACATAGATCAATCA hypothetical ATGTAGTATTACCACCTA protein AAGCTACTTACAAACAG ATAATAGCTCAAGAATA TTGCCCGCGCTTACAGG CTTTATTTCATTTTACAC CTCCTGTCTCGTGGCAGG TTCTAAAAACTTTAGACT ATCAATTTGTCGGAGAA AGAACTCCTGACCAAGC T Braenderup- 23 AGCTTGGTCA 75 2R GGAGTTCTTT CTC Braenderup- 22 GAAATAAAGC 76 Probe 2- CTGTAAGCGC Probe GG Braenderup- 27 AATTCTACAG 77 349 PATRICID: AATTCTACAGTCAGATA 120 1F-m TCAGATAGAG fig|1182171. GAGTTTCCCCGCCCCTTA TTTCCCC 3.peg. CACTTGAATCAGATATC 3553, GTGTCAGACTTTAAAGA Hypothetical ACGATGCGAGTACTATA protein TCGATTCCCTTAAAAAAT ATGACAAAGAAAACAAT ACCAAAATAAACTTCGA CTTAATGATCAAGCGAA TTTCGATTATAGTTAATG GGATTACAAAATGCCTT GAAGAATTTTTGTCTGG AGATATAAAATCTGCTT ACGATGTATTTAACGAT ATTTTTTCATCTAGCACT ATTAATAAACACATAAG GAGAATAACCATTCCCC TTTATGATGTCTGCAATG AAAAAAGACCTTTATTT CGAGTAAGGAAATCTGA CGCA Braenderup- 21 TGCGTCAGAT 78 1R-m TTCCTTACTCG Thornson- 21 ACAATTTAAC 79 132 PATRICID: ACAATTTAACACCCCCT 121 2R ACCCCCTACC fig|935705. ACCAAGGGATTTACCTA A 3.peg. AAGCCTTTTGAATTTTTT 4176, TAACTTCTCTCGCTCTAT Putative CTAAACGATTAAAGTTTT Rhs CAAATAGACTTTCTTTTA family CCTTAACGGCAGATTCA protein AATAACCTC Thornson- 21 GAGGTTATTT 80 2F GAATCTGCCG T Wandsworth- 22 GAAGAGTATT 81 288 PATRICID- CAATATCACAGCTAAGA 122 1R TGCCATTGCA fig|913086. ACCGTAAATAATGCATC AA 3.peg. CGAAGGGATGCGCATTC 806, TAGTTAAGGCATATATTC Phage AAGGGACGAATATCGGA tail GGTGGTGAATTCAGTTG fibers GAACTCCACAACCACTC AAGCTGATGATGGCGGG TACATCATTAGGCCAAC TGGAATTGTTACTGGCG CCTGGATTAGAATCAGC AAAACAAGCAAGGTTTA TCTGACTGAGTATGGGG CAACCGGCGATGATACC GACGTATCAACTAAGAT ATCATCTGTTTTTGCAAT GGCAAATACTCTTC Wandsworth- 25 CAATATCACA 82 1F GCTAAGAACC GTAAA Montevideo- 22 GTGAATAATC 83 256 PATRICID- GTGAATAATCCTCATCG 123 2R-m-2 CTCATCGGTT fig|859199. GTTCGCAATAATTGGTAT CG 4.peg. TGATACCCTTCAAGGAC 4528, AAGCTCTCTCGCCAGTCT Hypothetical ATGCTGATCGGGTTGTTG protein TGAAGCAAAATCTCTCC CTAACACTCTATTCTGGA AATTATTAGCTCTGGTTA TTGCATTAGCATTTAGAT CATTTTCATCATTATTAA TTTCAATGAAACGAACA GGGACTTTAACTTGATA AATTCTATCTCCTAGCAC ATCCATAACGCTGCCTA AACTACTCAC Montevideo- 25 GTGAGTAGTT 84 2F-m-2 TAGGCAGCGT TATGG Paratyp 18 TAGCTTGGCA 85 hi C- TTGGGTCG 1R-s Paratyp 19 GGTTCAGGCG 86 315 PATRICID: TAGCTTGGCATTGGGTC 124 hi C- GAGATTGTG fig|476213. GTCTGTTAATCATTAAAT 1F-s 4.peg. CAGAACGTGTAAATATC 928, TTTTCCCAAAGCTCTTTA hypothetical AACTCTTTTATTTTTTCA protein TTTTGAACAAGTCTTGGT SPC_0871 GTCTCGGATAAAAAATC TTTAATGCCATAAATAA AATTACCAAGTTGAGCA CCATCGAAGGATGAACT GGTTTTTGATTGAATGAA TGTTATATCTACATCTAA ATAGCTGTAATTATTAGC GATATCATCAAACGCTT CGATAGAAGTTATAATC CTTCCGTTAATGGAAAT AACTAATCCATCTATAG CACAATCTCCGCCTGAA CC Diarizonae- 23 ACAACAGACA 87 101 PATRICID: GTGGTGTCAACGGTAAA 125 1R TCACTGAGGG fig|1173780. GTTCAGCGTCCGCGTCG TGT 3.peg. CCGTGTTCCCTGCGATAT 2392, CGGTCGCTTCCACCGTCA hypothetical GCGTGTGTACACCCTCA protein GTGATGTCTGTTGT Diarizonae- 23 GTGGTGTCAA 88 1F CGGTAAAGTT CAG Paratyp 21 CCTGCACTAT 89 335 bp SPAB_05347 - GCTATTGGCCTGTCTGAT 126 hi B- CCTCTTCCTCC DNA CCAGAGTGTAGTTCTCTT 1R-s topoisomerase CTTTCAGGTCTAAATACT III TCGTTTGTTTCGCGTATA TGGAACGACAAAAAAAT CACAGCTCACCATGGCA TTATCCCTACCCGAAAC GCGTTTAAGTTTTCTGCG TTAAGTGAGGCAGAGCG AAGGGTATACACCCTTA TCCGCCGAAATTATCTG GCACAATTTCTTCCCCTG CACGAATCTGATATTACT CGTCTGCAGTTTGACATT GGCGGGCAACTGTTCCG CACAACAGGAAGGACGG AGATTGTAATGGGCTGG AAGGTCCTTTTCAGTAA GGAGGAAGAGGATAGTG CAGG Paratyp 20 GCTATTGGCC 90 hi B- TGTCTGATCC 1F-s Pullorum- 20 GGACGCACAG 91 163 bp Hypothetical GGACGCACAGGTCAGGT 127 1R GTCAGGTATG Protein ATGTAAAAGCAGCCGCA GCAGCAATAACGACTGC CCACCCAGCCCACTTCG GCCAGGCGCCATCTGTT GGCTCCGGAACGGCCAC ATCCGCTTCAAATCCGG CCAGTGCCGCATCCAGC ACCGCCCCCCCTATCAC GGTTCCTGCA Pullorum- 19 TGCAGGAACC 92 1F GTGATAGGG

Example 1: Multiple Conventional PCR for Five Salmonella Serovars

(27) Primers for Salmonella Dublin and Salmonella Heidelberg were modified to allow better band separation on gel, as illustrated in Table 3. DNA from five Salmonella serovars, each with the same concentration of ˜30 ng/μl, was pooled for running a multiplex PCR. The PCR was performed in three different sets of reactions: Primer set 1 (Set 1) as a triplex, primer set 2 (Set 2) as a duplex and primer set 3 for invA gene (Set 3). The constraint in the use of invA gene in multiplex sets is that the DNA fragment size was too close to that of serovar Kentucky, and resolution of more than three bands in one reaction did not turn optimal. Therefore, we decided to use three different tubes, tube one providing three bands for serovars Hadar, Heidelberg and Dublin; Tube two providing double bands for serovars Enteritidis and Kentucky and Tube 3 amplifying invA gene that would be run in parallel with the other two tubes. Single PCR reactions for each of the serovars were run along with the multiplex. Set 1 detected Hadar, Heidelberg and Dublin. The reaction mixture in Set 1 contained 30 μl of reaction volume: 6 μl of PCR grade water, 15 μl of PWO Master Mix and 0.5 μl of each primer (forward and reverse) for S. hadar, s. heidelberg and 1 μl of each forward and reverse primer for S. dublin. Increasing the concentration of Dublin primers to 0.66 μM in the 30 μl reaction volume increased the band intensity for this serovar, and an equal signal band was detected for all the targets while the concentration for other two primers for S. heidelberg and S. hadar were 0.33 μM. Primer concentrations were adjusted by decreasing those pairs that resulted in relatively strong signal and increasing the ones producing too weak bands in steps of 0.1 μM. This adjustment led to final multiplex system, resulted in equal signal strength for all targets when a mix of standardized template DNA was used.

(28) Set 2 detected Salmonella serovars Enteritidis and Kentucky. The reaction mixture in set 2 contained 20 μl of reaction volume, consisting of 3 μl of PCR grade water, 10 μl of PWO Master Mix and 0.5 μl of forward and reverse primers for S. enteritidis and S. kentucky. The single PCR reactions for each of the serovars were run with each primer to check the sensitivity of the multiplex PCR and to compare PCR product fragments with those generated from sets 1 and 2. For single serovar PCR, 15 μl reaction volume containing 1.5 μl of PCR grade water, 7.5 μl of PWO Master Mix and 0.5 μl of each forward and reverse primers were used. All PCR reactions were processed using the same program as described above. A mixture of 1 μl of the PCR product, 7 μl of PCR grade water and 2 μl of 6× loading dye was loaded onto 2.5% agarose gel in TAE buffer and ran for 2.5 hours at 100 volts and examined using ALPHAIMAGER (Alpha Innotech® Corporation, San Leandro, Calif.) under ultraviolet light. Annotation and modification of the gel pictures were performed using AlphaView® Software (San Leandro, Calif.).

(29) The conventional multiplex assay was able to detect serovars Hadar (354 bp fragment), Heidelberg (289 bp fragment) and Dublin (118 bp fragment) in Set 1 at a DNA concentration of 266 pg/μl. As illustrated in FIG. 3, Set 2 demonstrated detection of serovars Enteritidis (325 bp fragment) and Kentucky (246 bp fragment) at a DNA concentration of 400 pg/μl. InvA gene and individual serovars were also detected by single PCR primer sets at a DNA concentration of 533 pg/μl per reaction volume.

(30) Similar results were also obtained from artificially contaminated milk samples, as provided below at Examples 4 and 5.

Example 2: Triplex TAQMAN® PCR for Salmonella Serovars

(31) The following experiment was performed to confirm the specificity of Applicants' designed primer pairs to detect by triple TAQMAN® PCR. Due to the limitation of the number of detection filters in the PCR machine, three Salmonella serovars, S. heidelberg, s. enteritidis, s. dublin, were selected to develop a triplex TAQMAN® assay. An internal positive control (IPC) at 5 fg/25 μl concentration was assigned to one detection filter (VIC). Quantities of DNA used ranged from 30 ng to 15.36 fg (6*106 to 3*100 Genomic Equivalent, provided by 5 fg of DNA per E. coli cell (57) (GE), 2.18 ng to 1.1 fg (4.36*105 to 3*10-2GE) and 11 ng to 5.6 fg (2.2×106 to 1×100GE) for S. heidelberg s. dublin and S. enteritidis, respectively. The dyes FAM™, ROX™, CY5™, and JOE™ were used to generate signals for the detection of S. enteritidis, s. heidelberg, s. dublin and IPC, respectively. The TAQMAN® assay was operated and analyzed using MxPro® software (Agilent® Technologies Inc., Santa Clara, Calif.). The total volume of reaction was 25 μl consisting of 12.5 μl of 2× Brilliant III QPCR TAQMAN® master mix, 1 μl of 1 μM of each primer, 1 μl of 1 μM of each probe, 2.5 μl of 10×IPC containing primer and probe and 1 μl of DNA from internal positive control and each of the three Salmonella serovars. The PCR cycling conditions were 95° C. for 10 minutes followed by 35 cycles of 95° C. for 10 seconds then 60° C. for 1 minute. The result was considered positive when cycle threshold (Ct) value was less than the Ct value of the IPC.

(32) Internal Positive Control.

(33) Internal positive control was used in the TAQMAN® multiplex assay to exclude the presence of PCR inhibitors. For this purpose, an exogenous 10×Exo IPC Mix (VIC) and 50×IPC DNA were purchased from Applied Biosystem (Life Technologies, California, USA). Internal Positive Control detection limit was tested in triplicate to obtain the minimum detection limit by using serially diluted IPC DNA at 80 pg, 16 pg, 3.2 pg, 0.64 pg and 128 μg with constant amount of DNA from Salmonella serovars Heidelberg, Enteritidis, and Dublin. After obtaining the optimal IPC DNA, multiplex TAQMAN® Real Time assay was performed with the target Salmonella DNA from serovars Heidelberg, Enteritidis and Dublin in decreasing concentration to evaluate the optimal co-amplification.

(34) The multiplex TAQMAN® assay was performed to determine the level of detectable DNA and the corresponding genomic equivalent (GE) per ml for each of S. heidelberg, s. enteritidis and S. dublin. The standard curve was generated using various concentrations of DNA from the three serovars, performed in quadruplet. The slopes for the standard curve of S. enteritidis on FAM™, S. heidelberg on ROX™ and S. dublin on CY5™ were −3.460, −3.592 and −4.093, respectively. The regression curves were generated for these three serovars based on the varying amounts of bacterial DNA. A good linearity response was shown for each of the standard curves of the serovars. The R2 value was 1.000 for S. enteritidis, 0.998 for S. heidelberg and 0.992 for S. dublin. The results indicated that the multiplex Real-Time PCR successfully detected the minimum amount of DNA in the assay and corresponding GE/ml, which was 75.8 fg (1.53*101) for S. heidelberg, 140.8 fg (2.8*101) for S. enteritidis, and 3.48 pg (6.96*102) for S. dublin. PCR efficiencies calculated from the standard curve gave efficiency of 89.8% for S. heidelberg; 94.5% for Enteritidis, and 75.5% for S. dublin.

(35) As illustrated in FIG. 3, the current study successfully developed a multiplex conventional PCR assay that was able to detect five Salmonella serovars in three sets of PCR reactions run in parallel. The multiplex TAQMAN® assay developed in this study also successfully detected a small amount of DNA from serovars Heidelberg, Enteritidis and Dublin. In previous studies, real-time PCR assay was used only for identification of Salmonella at species level or other foodborne pathogens (23, 24, 48) or only for detecting one or two serovars (10, 51, 54).

Example 3: Determination of the Sensitivity and Efficiency

(36) The following experiment was conducted to test the sensitivity and efficiency of each of the primers identified in Table 3. The sensitivity of the TAQMAN® assay was determined by five-fold serial dilution of the genomic DNA of each of the target Salmonella serovar. The PCR was done in quadruplicate to plot the standard curve and evaluate both the sensitivity and the reaction efficiency. Each of the reactions contained the IPC. PCR efficiency was calculated from the standard curves using the formula E=(10−1/slope−1)×100.

(37) SYBR Green Real Time PCR was performed to determine the detection limit for the five serovars. The sensitivities for DNA detection were found to be 58.8 fg/tl for S. heidelberg, 42.2 fg/tl for S. kentucky, 200 fg/tl for S. hadar, 63.4 fg/tl for S. enteritidis and 26 pg/tl for S. dublin, which corresponded with ˜11.8, 8.4, 40, 13, 5200 CFU/ml, respectively.

(38) Therefore, under these conditions, Applicants found that these five primers were able to achieve a high sensitivity of detection combined with the high specificity as described above. Similar sensitivity assays of various other primers achieved results confirming them as having suitable sensitivities for use.

(39) This sensitivity assay was very sensitive detecting femto gram amounts of DNA for serovars Hadar, Heidelberg, Kentucky, Enteritidis and pictogram levels of DNA for S. dublin. The lower sensitivity for Dublin may be explained in part by the fact that we used whole genome extraction kit because most of the DNAs in the current study were of bacterial genomic 467 origin. As observed by others, plasmids could be depleted during extractions with salting-out kits except for larger plasmids of 362 kb (3). The use of plasmid extraction kit later in the study resulted a band with higher signal with S. dublin (data not shown). S. dublin has an 80 kb plasmid that is responsible for systemic infection in cattle (12) and causes high mortality. On the other hand, plasmid-free strains cause less severe conditions and are responsible for only enteric infection. The virulent plasmid is very conserved in the host cell (37) and is necessary for its pathogenesis. This plasmid has efficient stability with an estimated loss less than 10-7 per generation per cell (11). The stability of the S. dublin plasmid depends on a multimer resolution system that consists of a resolvase, encoded by the crs gene, and a resolution site, rsd. This system is also present in other Salmonella plasmids. A locus called vagC/vagD may also be involved in the maintenance of the S. dublin plasmid; delaying cell division until replication has been completed (18, 37, 56, 67). This is the primary reason why plasmid bearing S. dublin was targeted in Applicants' study.

Example 4: Artificial Contamination of Food Samples

(40) Food matrices provide a critical challenge in amplification-based pathogen detection approaches because, among other things, pre-analytical sample processing techniques must be streamlined to reduce the time needed to arrive at diagnosis and decision-making. In this experiment, Applicants performed a preliminary experiment to evaluate the real time detection of S. serovars spiked in milk to evaluate whether real-time detection as described herein would be compatible with DNA isolated from bacteria in food matrix.

(41) Milk samples including whole milk, 2% fat, fat free and chocolate milk were confirmed Salmonella-free by standard cultural method (47) where 25 ml milk sample was pre-enriched in 225 ml of Buffered Peptone Water at 37° C. for 20 h. Equal amounts of overnight cultures of S. heidelberg, s. hadar, s. kentucky, s. enteritidis and S. dublin were pooled after each serovar was adjusted to same OD value of 0.5 using NANODROP 2000C spectrophotometers. The pooled samples were then 10-fold serially diluted up to 108. Each dilution was plated on both Tryptic Soya agar and XLT4 media to evaluate the number of colony forming units (CFU). Serially diluted pooled bacteria were used to artificially inoculate the Salmonella-free milk. Briefly 25 ml of milk was transferred into sterile Nasco Whirl-Pak® (Universal Medical Inc, Norwood, USA) containing 225 ml of sterile BPW and inoculated with pooled cultures containing 0 CFU to 1×107 CFU. The mixture was homogenized with Stomacher® 400 Circulator (Seward Laboratory Systems Inc., Florida, USA) and incubated at 37° C. for 20 h for pre-enrichment. After pre-enrichment, 100 μL of the pre-enriched sample was inoculated into 10 ml of RVS and incubated at 41.5° C. for 12 h. DNA was extracted from RVS (selective enriched) and stored at −20° C. for further use.

Example 5: Detection of Natural Contamination of Salmonella from Milk and Chicken Meat Samples

(42) Thirty pasteurized milk and thirty raw chicken samples were sourced from different suppliers to for the presence of Salmonella using the newly developed PCR assay. Different types of milk samples were collected from different brands. The raw chicken samples were from wings, necks, gizzards, and leg quarters. Twenty-five grams of meat from each sample were weighed and added to 225 ml of BPW then homogenized with a Stomacher® 400 Circulator machine. For the milk samples, 25 ml were measured and processed using the same procedure as used for chicken samples. The homogenized samples were then incubated at 37° C. for 20 h after which 100 μl of each pre-enriched sample was transferred into 10 ml of RVS and incubated at 41.5° C. for 12 h. DNA was extracted from 1 ml of the RVS cultures and kept at −20° C. until further use.

(43) The purpose of analyzing the milk samples was to test if Salmonella could be detected in commercial dairy products. All milk samples tested negative for Salmonella using both culture and PCR. As provided in Table 4, among the thirty chicken samples, twelve (40%) were positive by both cultural and conventional PCR targeting the Salmonella specific invA gene. Those twelve positive samples were individually tested by conventional PCR using our serovar-specific primers (data not shown). The result of serovar-specific PCR showed six positive samples (20.0% of the total 30 samples) for serovar Kentucky (B1, B2, B3, C1, C2 and C3). Analysis using the S. enteritidis-specific PCR revealed seven positive samples (20% of the total) for S. enteritidis (B1, B3, C1, C2, C3 and 12). Results also showed that five of the 30 samples (16.6%) (B1, B3, C1, C2 and C3) were dually contaminated with both S. kentucky and S. enteritidis. Tests using the S. heidelberg-specific PCR primers did not detect any of the twelve samples as positive. Using the TAQMAN® assay, targeting only S. heidelberg, s. enteritidis and S. dublin, same results were obtained as in the conventional PCR for S. enteritidis and S. dublin. However, this assay also amplified eleven samples (out of the 30 total) as S. heidelberg, among which six were co-detected with serovar Enteritidis (FIGS. 4 and 5). Single colonies randomly picked from all the twelve positive samples were sent to USDA laboratory, Athens, Ga. for further identification. Briefly, the method involved extraction of DNA from purified colonies inoculated on Brilliant Green Sulpha agarose (Hardy Diagnostics®, Santa Maria, Calif.), followed by amplification and sequencing of Intergenic sequence ribotyping (ISR) to evaluate single nucleotide polymorphisms occurring in a 5S ribosomal gene region and flanking sequences bordering the gene dkgB (26). The laboratory confirmed five samples (B1, B2, C1, C2 and C3) as S. kentucky, which was also detected by our assays as S. kentucky. It is possible that serovar Kentucky colony was not picked or was likely over grown by other non-Salmonella organisms, which could explain absence of Kentucky in sample B3. It is also important to remember that organisms that are viable but none-cultivable (VBNC) could be missed in culturing step but their genomic DNA could easily be amplified by PCR directly from the RV broth (19). The USDA laboratory also detected I1, I2 and I3 as Typhimurium, but Typhimurium primers were not used in the present assay, although we have already developed and validated specific S. Typhimurium primers in our previous work (65), Table 5 presents comparison of results obtained using the two approaches.

(44) FIGS. 4 and 5 illustrate the standard curve method was used to estimate the initial concentration of both S. enteritidis and S. heidelberg in all the positive samples. Results showed that minimum numbers of S. enteritidis detected from the meat samples were approximately 18 cells (sample E2) and that of S. heidelberg were 40 cells (sample E2), respectively.

(45) The multiplex conventional assay and multiplex TAQMAN® assay developed were sensitive enough to successfully detect 1 to 10 CFU from artificially inoculated milk after enrichment. Both multiplex conventional and TAQMAN® assay also yielded 100% similar results. The use of Internal Positive Control (IPC) in the TAQMAN® assay made the assay more robust and reliable. IPC is required to exclude the presence of PCR inhibitors and also to check the quality of PCR reagents and thermal cycler conditions (30).

(46) Results from our experiments to detect natural contamination of chicken samples using our new assay proved to be successful, as the bacteria isolated as S. kentucky was also confirmed by sequencing in USDA laboratory at Athens, Ga. This gives further confidence that the developed assay is very reliable to detect the contamination from different food samples and therefore from potential outbreak samples directly from RV broth. This study detected multiple Salmonella contaminations of single food source, which were not otherwise detected by randomly selected colonies from Salmonella specific plates. In this study, we also observed that TAQMAN® assay was more sensitive than conventional PCR assay. Unlike the TAQMAN® assay, conventional assay could not detect S. heidelberg and S. enteritidis from naturally contaminated chicken samples. This finding is supported by others who had reported TAQMAN® assay is more sensitive than conventional PCR assay (2, 22).

(47) The assay developed in this study employs unique targets for the serovars Heidelberg, Hadar, Enteritidis, Kentucky and Dublin, all of which are important from public health and economic perspectives in the USA and worldwide. However, we strongly believe the conventional multiplex PCR assay will be a valuable tool for diagnostic laboratories as well as for other food processing units to detect in a single run these five major Salmonella serovars. This tool would be also very helpful for low resource environment where Real Time PCR may not be possible. Also the TAQMAN® assay will be a useful tool for the detection and quantitation of serovars Heidelberg, Enteritidis and Dublin. Finally, we believe that our developed assays would be useful for routine laboratory diagnosis of Salmonella, as well as for rapid diagnostic testing during an outbreak. These developments could replace the conventional diagnostic technique that requires almost 7 days, while the assay developed here requires only one or two days.

(48) In this manner, the experiments described herein demonstrate the suitability of the various assays, kits and primers discovered by Applicants for combined simultaneous use in real-time PCR screens for detecting and identifying Salmonella serovars as food threat agents and food-borne pathogens with levels of specificity and sensitivity not previously obtained by others in the art.

(49) Having described preferred embodiments of the invention; it will now become apparent to those of ordinary skill in the art that other embodiments incorporating these concepts may be used. Accordingly, it is submitted that that the invention should not be limited to the described embodiments but rather should be limited only by the spirit and scope of the appended claims.

(50) Although the invention has been described and illustrated with a certain degree of particularity, it is understood that the present disclosure has been made only by way of example, and that numerous changes in the combination and arrangement of steps, ingredients, or processes can be resorted to by those skilled in the art without departing from the spirit and scope of the invention, as will be claimed hereafter.

(51) TABLE-US-00005 TABLE 4 Detection of invA gene, Salmonella Heidleberg, Salmonella Enteritidis, and Salmonella Dublin from commercially obtained chicken samples PCR results TaqMan assay Salmonella Salmonella Conventional Eteritidis Heidelberg Salmonella Dublin Sample ID (invA) C.sub.T GE/mL.sup.a C.sub.T GE/mL C.sub.T B1 + 23.94 1.727 × 10.sup.6 25.13 8.494 × 10.sup.5 — B2 + — — B3 + 21.81 7.118 × 10.sup.6 24.74 1.087 × 10.sup.6 — C1 + 19.01  4.59 × 10.sup.7 23.8 1.997 × 10.sup.6 — C2 + 23.6  2.172 × 10.sup.6 25.02 9.114 × 10.sup.5 — C3 + 22.97 3.284 × 10.sup.6 — E1 + — 23.12  3074 × 10.sup.5 — E2 + — 32.39  8.08 × 10.sup.3 — E3 + — 24.22 1.527 × 10.sup.6 — I1 + — 29.7 4.512 × 10.sup.4 — I2 + 20.82  1.37 × 10.sup.7 26.93 2.668 × 10.sup.5 — I3 + — 31.65 1.294 × 10.sup.4 — GE = Genomic Equivalent, Genomic Equivalent, provided by 5 fg of DNA per E. coli cell (54) .sup.aThe number of GE/ml of enriched sample was determined by comparing the CT value to the standard curve and then multiplying the GE by 100 as 1 μl of 200 μl DNA which was extracted from 1 ml of sample was used in the TaqMan PCR assay for natural contamination

(52) TABLE-US-00006 TABLE 5 Detection of Salmonella serovars from commercial chicken samples by using conventional and TaqMan PCR assays and ISR-specific sequencing.sup.3 Salmonella serovars detected Sample ID PCR assays ISR sequencing B1 Kentucky, Enteritidis, and Heidelberg Kentucky B2 Kentucky and Heidelberg Kentucky B3 Kentucky, Enteritidis, and Heidelberg Not Salmonella C1 Kentucky Enteritidis, and Heidelberg Kentucky C2 Kentucky and Heidelberg Kentucky C3 Kentucky, Enteritidis, and Heidelberg Kentucky E1 Heidelberg Not Salmonella E2 Heidelberg Not Salmonella E3 Not Salmonella I1 Heidelberg and Enteritidis Typhimurium I2 Enteritidis and Heidelberg Typhimurium I3 Heidelberg Typhimurium .sup.3Conventional and TaqMan PCR assays were conducted in our laboratory, and ISR-specific sequencing was conducted at the USDA laboratory (Athens, GA).

REFERENCES

(53) 1. Abubakar, I., L. Irvine, C. F. Aldus, G. M. Wyatt, R. Fordham, S. Schelenz, L. Shepstone, A. Howe, M. Peck, and P. R. Hunter. 2007. A systematic review of the clinical, public health and cost-effectiveness of rapid diagnostic tests for the detection and identification of bacterial intestinal pathogens in faeces and food. Health Technol Assess. 11:1-216. 2. Balamurugan, V., K. D. Jayappa, M. Hosamani, V. Bhanuprakash, G. Venkatesan, and R. K. Singh. 2009. Comparative efficacy of conventional and TaqMan polymerase chain reaction assays in the detection of capripoxviruses from clinical samples. Journal of veterinary diagnostic investigation. 21:225-231. 3. Becker, L., M. Steglich, S. Fuchs, G. Werner, and U. Nübel. 2016. Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing. Scientific Reports. 6:28063. 4. Braden, C. R. 2006. Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. Clin Infect Dis. 43:512-7. 5. Bugarel, M., A. Tudor, G. H. Loneragan, and K. K. Nightingale. 2017. Molecular detection assay of five Salmonella serotypes of public interest: Typhimurium, Enteritidis, Newport, Heidelberg, and Hadar. J Microbiol Methods. 134:14-20. 6. CDC. 1984. Salmonella Dublin and raw milk consumption California. MMWR. 33:196-8. 7. CDC. 2003. Salmonella Surveillance Summary, 2002. In US Department of Health and Human Services (ed.) CDC, Atlanta, Ga. 8. CDC. 2014. Notes from the Field: Multistate Outbreak of Human Salmonella Infections Linked to Live Poultry from a Mail-Order Hatchery in Ohio March-September 2013. p. 222. In, MMWR, vol. 63. 9. Cernela, N., M. Nüesch-Inderbinen, H. Hächler, and R. Stephan. 2014. Antimicrobial resistance patterns and genotypes of Salmonella enterica serovar Hadar strains associated with human infections in Switzerland, 2005-2010. Epidemiology and infection. 142:84-89. 10. Chen, J., L. Zhang, G. C. Paoli, C. Shi, S.-I. Tu, and X. Shi. 2010. A real-time PCR method for the detection of Salmonella enterica from food using a target sequence identified by comparative genomic analysis. International journal of food microbiology. 137:168-174. 11. Chikami, G. K., J. Fierer, and D. G. Guiney. 1985. Plasmid-Mediated Virulence in Salmonella Dublin Demonstrated by Use of a Tn5-oriT Construct. American Society for Microbiology. 50:420-424. 12. Chu, C., Y. Feng, A.-C. Chien, S. Hu, C.-H. Chu, and C.-H. Chiu. 2008. Evolution of genes on the Salmonella Virulence plasmid phylogeny revealed from sequencing of the virulence plasmids of S. enterica serotype Dublin and comparative analysis. Genomics. 92:339-343. 13. Demczuk, W., G. Soule, C. Clark, H.-W. Ackermann, R. Easy, R. Khakhria, F. Rodgers, and R. Ahmed. 2003. Phage-based typing scheme for Salmonella enterica serovar Heidelberg, a causative agent of food poisonings in Canada. Journal of clinical microbiology. 41:4279-4284. 14. Dietz, H. H., M. Chriél, T. H. Andersen, J. C. Jorgensen, M. Torpdahl, H. Pedersen, and K. Pedersen. 2006. Outbreak of Salmonella Dublin-associated abortion in Danish fur farms. Canadian veterinary journal. 47:1201. 15. Dinjus, U., I. Hanel, W. Müller, R. Bauerfeind, and R. Helmuth. 1997. Detection of the induction of Salmonella enterotoxin gene expression by contact with epithelial cells with RT-PCR. FEMS microbiology letters. 146:175-179. 16. Doran, J. L., S. K. Collinson, C. M. Kay, P. A. Banser, J. Burian, C. K. Munro, S. H. Lee, J. M. Somers, E. C. Todd, and W. W. Kay. 1994. fimA and tctC based DNA diagnostics for Salmonella. Mol Cell Probes. 8:291-310. 17. DuPont, H. L. 2007. The growing threat of foodborne bacterial enteropathogens of animal origin. Clinical infectious diseases. 45:1353-1361. 18. Ebersbach, G., and K. Gerdes. 2005. Plasmid segregation mechanisms. Annu Rev Genet. 39:453-79. 19. Fakruddin, M., K. S. B. Mannan, and S. Andrews. 2013. Viable but Nonculturable Bacteria: Food Safety and Public Health Perspective. ISRN Microbiology. 2013:6. 20. Ferretti, R., Mannazzu, I, Cocolin, Luca, Comi, Giuseppe, & Clementi, Francesca. 2001. Twelve-hour PCR-based method for detection of Salmonella spp. in food. Applied and environmental microbiology. 67(2) 977-978. 21. Fricke, W. F., P. F. McDermott, M. K. Mammel, S. Zhao, T. J. Johnson, D. A. Rasko, P. J. Fedorka-Cray, A. Pedroso, J. M. Whichard, J. E. LeClerc, D. G. White, T. A. Cebula, and J. Ravel. 2009. Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic Escherichia coli Strains in Salmonella enterica Serovar Kentucky Isolates from Poultry. Applied and Environmental Microbiology. 75:5963-5971. 22. Garland, S., J. Wood, and L. F. Skerratt. 2011. Comparison of sensitivity between real-time detection of a TaqMan assay for Batrachochytrium dendrobatidis and conventional detection. Dis Aquat Organ. 94:101-5. 23. Gillespie, B., and S. Oliver. 2005. Simultaneous detection of mastitis pathogens, Staphylococcus aureus, Streptococcus uberis, and Streptococcus agalactiae by multiplex real-time polymerase chain reaction. Journal of dairy science. 88:3510-3518. 24. Grant, M. A., J. Hu, and K. C. Jinneman. 2006. Multiplex real-time PCR detection of heat-labile and heat-stable toxin genes in enterotoxigenic Escherichia coli. Journal of Food Protection®. 69:412-416. 25. Greene, H., and D. Dempsey. 1986. Bovine neonatal salmonellosis: An outbreak in a dairy calf rearing unit. Irish Veterinary Journal. 40:30-34. 26. Guard, J., R. Sanchez-Ingunza, C. Morales, T. Stewart, K. Liljebjelke, J. Van Kessel, K. Ingram, D. Jones, C. Jackson, P. Fedorka-Cray, J. Frye, R. Gast, and A. Hinton, Jr. 2012. Comparison of dkgB-linked intergenic sequence ribotyping to DNA microarray hybridization for assigning serotype to Salmonella enterica. FEMS Microbiol Lett. 337:61-72. 27. Guo, X., J. Chen, L. R. Beuchat, and R. E. Brackett. 2000. PCR Detection of Salmonella entericaSerotype Montevideo in and on Raw Tomatoes Using Primers Derived from hilA. Applied and environmental microbiology. 66:5248-5252. 28. Hadjinicolaou, A. V., V. L. Demetriou, M. A. Emmanuel, C. K. Kakoyiannis, and L. G. Kostrikis. 2009. Molecular beacon-based real-time PCR detection of primary isolates of Salmonella Typhimurium and Salmonella Enteritidis in environmental and clinical samples. BMC Microbiol. 9:97. 29. Hohmann, E. L. 2001. Nontyphoidal salmonellosis. Clin Infect Dis. 32:263-9. 30. Hoorfar J, C. N., Malorny B, Wagner M, De Medici D, Abdulmawjood A, Fach P. 2004. Diagnostic PCR: making internal amplification control mandatory. J Appl Microbiol. 96(2). 31. ISO. 2003. ISO 6579:2002. In, Microbiology of food and animal feeding stuffs. Horizontal method for the detection of Salmonella spp. 32. Jackson, B. R., P. M. Griffin, D. Cole, K. A. Walsh, and S. J. Chai. 2013. Outbreak-associated Salmonella enterica serotypes and food Commodities, United States, 1998-2008. Emerg Infect Dis. 19:1239-44. 33. Kim, H., S. Park, T. Lee, B. Nahm, Y. Chung, K. Seo, and H. Kim. 2006. Identification of Salmonella enterica serovar Typhimurium using specific PCR primers obtained by comparative genomics in Salmonella serovars. Journal of Food Protection®. 69:1653-1661. 34. Kim, H.-J., S.-H. Park, T.-H. Lee, B.-H. Nahm, Y.-R. Kim, and H.-Y. Kim. 2008. Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics. Biosensors and Bioelectronics. 24:238-246. 35. Kimura, A. C., V. Reddy, R. Marcus, P. R. Cieslak, J. C. Mohle-Boetani, H. D. Kassenborg, S. D. Segler, F. P. Hardnett, T. Barrett, and D. L. Swerdlow. 2004. Chicken consumption is a newly identified risk factor for sporadic Salmonella enterica serotype Enteritidis infections in the United States: a case-control study in FoodNet sites. Clinical Infectious Diseases. 38:S244-S252. 36. Kingsley, R. A., and A. J. Balmier. 2000. Host adaptation and the emergence of infectious disease: the Salmonella paradigm. Molecular microbiology. 36:1006-1014. 37. Krause, M., and D. G. Guiney. 1991. Identification of a multimer resolution system involved in stabilization of the Salmonella dublin virulence plasmid pSDL2. Journal of Bacteriology. 173:5754-5762. 38. Kubota, K., E. Iwasaki, S. Inagaki, T. Nokubo, Y. Sakurai, M. Komatsu, H. Toyofuku, F. Kasuga, F. J. Angulo, and K. Morikawa. 2008. The human health burden of foodborne infections caused by Campylobacter, Salmonella, and Vibrio parahaemolyticus in Miyagi Prefecture, Japan. Foodborne Pathog Dis. 5:641-8. 39. Lampel, K., S. Keasler, and D. Hanes. 1996. Specific detection of Salmonella enterica serotype Enteritidis using the polymerase chain reaction. Epidemiology and infection. 116:137-145. 40. Le Hello, S., A. Bekhit, S. A. Granier, H. Barua, J. Beutlich, M. Zajac, S. Munch, V.

(54) Sintchenko, B. Bouchrif, K. Fashae, J. L. Pinsard, L. Sontag, L. Fabre, M. Gamier, V. Guibert, P. Howard, R. S. Hendriksen, J. P. Christensen, P. K. Biswas, A. Cloeckaert, W. Rabsch, D. Wasyl, B. Doublet, and F. X. Weill. 2013. The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain. Front Microbiol. 4:395. 41. Le Hello, S., D. Harrois, B. Bouchrif, L. Sontag, D. Elhani, V. Guibert, K. Zerouali, and F. X. Weill. 2013. Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study. Lancet Infect Dis. 13:672-9. 42. Le Hello, S., R. S. Hendriksen, B. Doublet, I. Fisher, E. M. Nielsen, J. M. Whichard, B. Bouchrif, K. Fashae, S. A. Granier, N. Jourdan-Da Silva, A. Cloeckaert, E. J. Threlfall, F. J. Angulo, F. M. Aarestrup, J. Wain, and F.-X. Weill. 2011. International Spread of an Epidemic Population of Salmonella enterica Serotype Kentucky ST198 Resistant to Ciprofloxacin. Journal of Infectious Diseases. 43. Liu, Z. M., X. M. Shi, and F. Pan. 2007. Species-specific diagnostic marker for rapid identification of Staphylococcus aureus. Diagn Microbiol Infect Dis. 59:379-82. 44. Majowicz, S. E., J. Musto, E. Scallan, F. J. Angulo, M. Kirk, S. J. O'Brien, T. F. Jones, A. Fazil, and R. M. Hoekstra. 2010. The global burden of nontyphoidal Salmonella gastroenteritis. Clinical Infectious Diseases. 50:882-889. 45. Malorny, B., C. Bunge, and R. Helmuth. 2007. A real-time PCR for the detection of Salmonella Enteritidis in poultry meat and consumption eggs. J Microbiol Methods. 70. 46. Malorny, B., J. Hoorfar, C. Bunge, and R. Helmuth. 2003. Multicenter validation of the analytical accuracy of Salmonella PCR: towards an international standard. Applied and environmental microbiology. 69:290-296. 47. Malorny, B., D. Made, and C. Löfström. 2013. Real-time PCR Detection of Food-borne Pathogenic Salmonella spp. p. 57-77. In D. Rodriguez-Lázaro (ed.), Real-Time PCR in Food Science: Current Technology and Applications Caister Academic Press. 48. Malorny, B., E. Paccassoni, P. Fach, C. Bunge, A. Martin, and R. Helmuth. 2004. Diagnostic real-time PCR for detection of Salmonella in food. Appl Environ Microbiol. 70:7046-52. 49. Marcus, R., J. Varma, C. Medus, E. Boothe, B. Anderson, T. Crume, K. Fullerton, M. Moore, P. White, and E. Lyszkowicz. 2007. Re-assessment of risk factors for sporadic Salmonella serotype Enteritidis infections: a case-control study in five FoodNet Sites, 2002— 2003. Epidemiology and Infection. 135:84-92. 50. Mateus, A., D. J. Taylor, D. Brown, D. J. Mellor, R. Bexiga, and K. Ellis. 2008. Looking for the unusual suspects: a Salmonella Dublin outbreak investigation. Public Health. 122:1321-3. 51. Maurischat, S., B. Baumann, A. Martin, and B. Malorny. 2015. Rapid detection and specific differentiation of Salmonella enterica subsp. enterica Enteritidis, Typhimurium and its monophasic variant 4,[5], 12: i:—by real-time multiplex PCR. International journal of food microbiology. 193:8-14. 52. Murugkar, H. V., H. Rahman, and P. K. Dutta. 2003. Distribution of virulence genes I Salmonella serovars isolated from man & animals. Indian J Med Res. 117:66-70. 53. Nielsen, L. R., B. van den Borne, and G. van Schaik. 2007. Salmonella Dublin infection in young dairy calves: transmission parameters estimated from field data and an SIR-model. Prev Vet Med. 79:46-58. 54. O'Regan, E., E. McCabe, C. Burgess, S. McGuinness, T. Barry, G. Duffy, P. Whyte, and S. Fanning. 2008. Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples. BMC microbiology. 8:156. 55. Ou, H. Y., C. T. Ju, K. L. Thong, N. Ahmad, Z. Deng, M. R. Barer, and K. Rajakumar. 2007. Translational genomics to develop a Salmonella enterica serovar Paratyphi A multiplex polymerase chain reaction assay. J Mol Diagn. 9:624-30. 56. Pullinger, G. D., and A. J. Lax. 1992. A Salmonella Dublin virulence plasmic locus that affects bacterial growth under nutrient-limited conditions. Molecular Microbiology. 6:1631-1643. 57. Raghunathan, A., H. R. Ferguson, Jr., C. J. Bornarth, W. Song, M. Driscoll, and R. S. Lasken. 2005. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol. 71:3342-7. 58. Sint, D., L. Raso, and M. Traugott. 2012. Advances in multiplex PCR: balancing primer efficiencies and improving detection success. Methods in Ecology and Evolution. 3:898-905. 59. Sivapalasingam, S., C. R. Friedman, L. Cohen, and R. V. Tauxe. 2004. Fresh produce: a growing cause of outbreaks of foodborne illness in the United States, 1973 through 1997. Journal of Food Protection®. 67:2342-2353. 60. Song, J.-H., H. Cho, M. Y. Park, Y. S. Kim, H. B. Moon, Y. K. Kim, and C. H. Pai. 1994. Detection of the H1-j strain of Salmonella typhi among Korean isolates by the polymerase chain reaction. The American journal of tropical medicine and hygiene. 50:608-611. 61. Uzzau, S., D. J. Brown, T. Wallis, S. Rubino, G. Leori, S. Bernard, J. Casadesús, D. J. Platt, and J. E. Olsen. 2000. Host adapted serotypes of Salmonella enterica. Epidemiology and infection. 125:229-255. 62. Vandegraaff, R., and J. Malmo. 1977. Salmonella Dublin in dairy cattle. Australian veterinary journal. 53:453-455. 63. Voetsch, A. C., T. J. Van Gilder, F. J. Angulo, M. M. Farley, S. Shallow, R. Marcus, P. R. Cieslak, V. C. Deneen, R. V. Tauxe, and G. Emerging Infections Program FoodNet Working. 2004. FoodNet estimate of the burden of illness caused by nontyphoidal Salmonella infections in the United States. Clin Infect Dis. 38 Suppl 3:S127-34. 64. Wattam, A. R., J. J. Davis, R. Assaf, S. Boisvert, T. Brettin, C. Bun, N. Conrad, E. M. Dietrich, T. Disz, J. L. Gabbard, S. Gerdes, C. S. Henry, R. W. Kenyon, D. Machi, C. Mao, E. K. Nordberg, G. J. Olsen, D. E. Murphy-Olson, R. Olson, R. Overbeek, B. Parrello, G. D. Pusch, M. Shukla, V. Vonstein, A. Warren, F. Xia, H. Yoo, and R. L. Stevens. 2017. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 45:D535-D542. 65. Woubit, A. S., T. Yehualaeshet, T. Habtemariam, and T. Samuel. 2012. Simultaneous, specific and real-time detection of biothreat and frequently encountered food-borne pathogens. Journal of food protection. 75:660-670. 66. Wray, C., and W. J. Sojka. 1977. Bovine salmonellosis. Journal of Dairy Research. 44:383-425. 67. Yarmolinsky, M. B. 1995. Programmed cell death in bacterial populations. Science. 267:836-7.