Patent Publication Number: US-2019177773-A1

Title: Method of detecting salmonella typhimurium

Description:
CROSS-REFERENCE TO RELATED APPLICATION 
     This application claims the benefit of U.S. Application 62/351,130 filed on Jun. 16, 2016 which is hereby incorporated by reference in its entirety. 
    
    
     SEQUENCE LISTING 
     The instant application contains a Sequence Listing which has been submitted electronically herewith and is hereby incorporated by reference in its entirety. The ASCII copy, created on Jun. 7, 2017, is named 1050901_SEQ_ST25.txt, and is 5,026 bytes in size. 
     BACKGROUND 
       Salmonella  is a leading cause of foodborne illnesses worldwide, with poultry and pork products being a primary source of infection to humans. Detecting  Salmonella  can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. The genus  Salmonella , member of the Enterobacteriaceae family, comprises two species  Salmonella enterica  and  Salmonella bongori. Salmonella enterica  is further divided into six subspecies, of which  S. enterica  subsp.  enterica  is the most clinically significant, causing 99% of  Salmonella  infections. The subspecies are further sub-divided into more than 2,500 serovars defined by somatic and flagellar antigens.  Salmonella enterica  subsp.  enterica  serovar  Typhimurium  and  Salmonella enterica  subsp.  enterica  serovar  Enteritidis  are the most frequently reported serovars associated with human cases of  Salmonella  infection from foodborne outbreaks. In the EU, a regulation in force since 2003 governs the mandatory detection of  Salmonella . In 2011, this regulation was supplemented with the mandatory testing for  S. Enteritidis  and  S. Typhimurium . According to Commission Regulation (EU) No. 1086/2011, all fresh poultry must be examined for  S. Enteritidis  and  S. Typhimurium  contamination. In the United States, the Food and Drug Administration (FDA) has published the Final Rule “Prevention of  Salmonella Enteritidis  in Shell Eggs During Production, Storage, and Transportation” (74 FR 33030), which will introduce methods requiring egg producers to test for  S. Enteritidis . For non-egg producers, the FDA also published the guidance document for testing of human foods for  salmonella : “Guidance for Industry: Testing for  Salmonella  Species in Human Foods and Direct-Human-Contact Animal Foods”. 
     Conventional microbiological methods for the detection and identification of  Salmonella  serovars are very time consuming. The current accepted method for isolation of  Salmonella  from food and environmental primary production samples takes up to 5 days according to the ISO 6579. The most widely-used method used to characterize  Salmonella  into its subspecies is the Kauffman-White serotyping system, based on the variability of the O, H and Vi antigens. 
     SUMMARY 
     Described herein are methods and compositions for detecting  Salmonella Typhimurium.    
     In an embodiment, a method of selectively detecting the presence of  Salmonella Typhimurium  in a sample comprises (a) providing a reaction mixture comprising a suitable primer pair for amplification of residues 749 to 2136 (1388 bp), or a portion thereof, of  Salmonella Typhimurium  ACCESSION CP007235 (SEQ ID NO:1); (b) performing PCR amplification of the nucleic acids of the sample using the reaction mixture of step (a); and (c) selectively detecting the presence of  Salmonella Typhimurium  by detecting the amplified nucleic acids. In some embodiments, the step (b) is performed in partitions. In some embodiments, the detecting the presence of  Salmonella Typhimurium  comprises sequencing the amplified nucleic acids. 
     In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence 95%, 97% or 99% homologous to SEQ ID NO:1 or a portion thereof. In certain embodiments, the reaction mixture comprises a primer pair for amplification of residues 749 to 1697 (947 bp), or portions thereof, of  Salmonella Typhimurium  ACCESSION CP007235 (SEQ ID NO:2). In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence 95%, 97% or 99% homologous to SEQ ID NO:2 or a portion thereof. In certain embodiments, the reaction mixture comprises a primer pair for amplification of residues 755 to 1063 (309 bp), or portions thereof, of  Salmonella Typhimurium  ACCESSION CP007235 (SEQ ID NO:3). In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence 95%, 97% or 99% homologous to SEQ ID NO:3 or a portion thereof. 
     In an embodiment, the primer pair for amplification of the nucleic acid region of SEQ ID NO:3 comprises the polynucleotide sequences set forth in SEQ ID NO:4 and SEQ ID NO:5. In an embodiment, the reaction mixture further comprises a probe for the nucleic acid region to be detected. In some embodiments, the probe comprises a detectable label. In some embodiment, the probe comprises the polynucleotide sequences set forth in SEQ ID NO:6 and SEQ ID NO:7. In certain embodiments, the probe comprises the polynucleotide sequences set forth in SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or SEQ ID NO:9. 
     In an embodiment, an isolated polynucleotide comprises a polynucleotide sequence having at least 95% sequence identity based on the BLASTN method of alignment to the polynucleotide sequence set forth in SEQ ID NO:1. In some embodiments, the isolated polynucleotide sequence comprises a polynucleotide sequence set forth in SEQ ID NO:1. In an embodiment, an isolated polynucleotide comprises a polynucleotide sequence having at least 95% sequence identity based on the BLASTN method of alignment to the polynucleotide sequence set forth in SEQ ID NO:2. In some embodiments, the isolated polynucleotide sequence comprises a polynucleotide sequence set forth in SEQ ID NO:2. In an embodiment, an isolated polynucleotide comprises a polynucleotide sequence having at least 95% sequence identity based on the BLASTN method of alignment to the polynucleotide sequence set forth in SEQ ID NO:3. In some embodiments, the isolated polynucleotide sequence comprises a polynucleotide sequence set forth in SEQ ID NO:3. 
     In an embodiment, a kit for the detection of  Salmonella Typhimurium  in a sample comprises a primer pair comprising SEQ ID NO:4 and SEQ ID NO:5. In some embodiments, the kit further comprises a probe comprising SEQ ID NO:6 and SEQ ID NO:7. In some embodiments, the kit further comprises a probe comprising comprising SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or SEQ ID NO:9. In certain embodiments, the kit further comprises at least one component selected from a lysis reagent, a DNA polymerase, at least one dNTP, a buffer, a negative control, a positive control, and instructions for performing a method to detect the presence of  Salmonella Typhimurium  in a nucleic acid sample. 
    
    
     DETAILED DESCRIPTION 
     Provided herein are methods of selectively detecting the presence of  Salmonella Typhimurium  in a sample. Also provided are compositions for use in the detection of  Salmonella Typhimurium  in a sample by nucleic acid amplification, e.g., by real-time PCR. 
     The disclosed detection method finds utility in the detection of  S. Typhimurium  in any type of sample, for example in samples for food testing, environmental testing, or human/animal diagnostic testing. Exemplary food samples include, but are not limited to, meats products, poultry (e.g., chicken, turkey), eggs, fish (e.g, cod), cookie dough, produce (e.g, lettuce, tomatoes), dairy (e.g, cheese, milk), milk powder (e.g., infant formula), chocolate (e.g., milk), cocoa, nacho cheese seasoning, pasta, pet food, peanut butter, soy flour, spices, and ready-to-eat food. Environmental samples include, but are not limited to, plastic, sealed concrete, and stainless steel. Other types of samples include, but are not limited to, water, stool, blood, urine, and tissue. Another type of sample includes weeds. The methods may be performed at the farm or processing facility prior to initial packaging, after packaging (e.g., prior to or after export from one country to another), or at the point of sale. 
     I. DEFINITIONS 
     Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. See, e.g., Lackie, D ICTIONARY OF  C ELL AND  M OLECULAR  B IOLOGY , Elsevier (4 th  ed. 2007); Green et al., M OLECULAR  C LONING, A  L ABORATORY  M ANUAL  (F OURTH  E DITION ), Cold Spring Harbor Laboratory Press (Cold Spring Harbor, N.Y. 2012). 
     The term “a” or “an” is intended to mean “one or more.” The term “comprise” and variations thereof such as “comprises” and “comprising,” when preceding the recitation of a step or an element, are intended to mean that the addition of further steps or elements is optional and not excluded. Any methods, devices and materials similar or equivalent to those described herein can be used in the practice of this invention. The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure. 
     The term “nucleic acid” refers to polymers of deoxyribonucleotides or ribonucleotides in either single- or double-stranded form, and complements thereof. The term “polynucleotide” refers to a linear sequence of nucleotides. Nucleotides can be ribonucleotides, deoxyribonucleotides, or modified versions thereof. Examples of polynucleotides contemplated herein include single and double stranded DNA, single and double stranded RNA (including siRNA), and hybrid molecules having mixtures of single and double stranded DNA and RNA. 
     “Polymerase chain reaction” is abbreviated PCR. 
     The term “isolated” refers to materials, such as nucleic acid molecules and/or proteins, which are substantially free or otherwise removed from components that normally accompany or interact with the materials in a naturally occurring environment. Isolated polynucleotides can be purified from a host cell in which they naturally occur. Conventional nucleic acid purification methods known to skilled artisans can be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides. 
     The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acid sequence”, and “nucleic acid fragment” are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide can be a polymer of RNA or DNA that is single- or double-stranded, that optionally contains synthetic, non-natural, or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA can be comprised of one or more strands of cDNA, genomic DNA, synthetic DNA, or mixtures thereof. 
     The term “amplification product” refers to nucleic acid fragments produced during a primer-directed amplification reaction. Typical methods of primer-directed amplification include polymerase chain reaction (PCR), ligase chain reaction (LCR), or strand displacement amplification (SDA). If PCR methodology is selected, the replication composition can comprise the components for nucleic acid replication, for example: nucleotide triphosphates, two (or more) primers with appropriate sequences, thermostable polymerase, buffers, solutes, and proteins. 
     The term “primer” refers to a synthetic oligonucleotide that is capable of acting as a point of initiation of nucleic acid synthesis or replication along a complementary strand when placed under conditions in which synthesis of a complementary strand is catalyzed by a polymerase. A primer can further contain a detectable label, for example a 5′ end label. 
     The term “probe” refers to a synthetic oligonucleotide that is complementary (though not necessarily fully complementary) to a polynucleotide of interest and forms a duplexed structure by hybridization with at least one strand of the polynucleotide of interest. A probe can further contain a detectable label. 
     As used herein, the terms “label”, “detectable label”, and such refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorescers, chemiluminescers, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal sols, semiconductor nanocrystals, and ligands (e.g., biotin, avidin, streptavidin, or haptens). A detectable label can also include a combination of a reporter and a quencher. 
     The term “reporter” refers to a substance or a portion thereof which is capable of exhibiting a detectable signal, which signal can be suppressed by a quencher. The detectable signal of the reporter is, e.g., fluorescence in the detectable range; thus, a reporter can also be a label. 
     The term “quencher” refers to a substance which is capable of suppressing, reducing, inhibiting, etc., the detectable signal produced by the reporter. 
     As used herein, the term “quenching” refers to a process whereby, when a reporter and a quencher are in close proximity, and the reporter is excited by an energy source, a substantial portion of the energy of the excited state non-radiatively transfers to the quencher where it either dissipates nonradiatively or is emitted at a different emission wavelength than that of the reporter (e.g., by fluorescence resonance energy transfer or FRET). 
     The reporter can be selected from fluorescent organic dyes modified with a suitable linking group for attachment to the oligonucleotide, such as to the terminal 3′ carbon or terminal 5′ carbon. The quencher can also be selected from organic dyes, which may or may not be fluorescent, depending on the embodiment of the invention. Generally, whether the quencher is fluorescent or simply releases the transferred energy from the reporter by non-radiative decay, the absorption band of the quencher should at least substantially overlap the fluorescent emission band of the reporter to optimize the quenching. 
     Non-fluorescent quenchers or dark quenchers typically function by absorbing energy from excited reporters, but do not release the energy radiatively. 
     Selection of appropriate reporter-quencher pairs for particular probes can be undertaken in accordance with known techniques. Fluorescent and dark quenchers and their relevant optical properties from which exemplary reporter-quencher pairs can be selected are listed and described, for example, in R. W. Sabnis, H ANDBOOK OF  F LUORESCENT  D YES AND  P ROBES , John Wiley and Sons, New Jersey, 2015, the content of which is incorporated herein by reference. 
     Reporter-quencher pairs can be selected from xanthene dyes including fluoresceins and rhodamine dyes. Many suitable forms of these compounds are available commercially with substituents on the phenyl groups, which can be used as the site for bonding or as the bonding functionality for attachment to an oligonucleotide. Another group of fluorescent compounds for use as reporters are the naphthylamines, having an amino group in the alpha or beta position. Included among such naphthylamino compounds are 1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include 3-phenyl-7-isocyanatocoumarin; acridines such as 9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide; benzoxadiazoles; stilbenes; pyrenes and the like. 
     Suitable examples of quenchers can be selected from 6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoic acid (DABCYL), tetramethylrhodamine (TAMRA), BHQ-OTM, BHQ-1 TM, BHQ-2TM, and BHQ-3TM, each of which are available from Biosearch Technologies, Inc. of Novato, Calif., Qy7TM QSY-9TM, QSY-21 TM and QSY-35TM, each of which are available from Molecular Probes, Inc, Iowa Black™ FQ available from Integrated DNA Technologies. 
     Suitable examples of reporters can be selected from dyes such as SYBR green, 5-carboxyfluorescein (5-FAMTm available from Applied Biosystems of Foster City, Calif.), 6-carboxyfluorescein (6-FAM), tetrachloro-6-carboxyfluorescein (TET), 2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein, hexachloro-6-carboxyfluorescein (HEX), 6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TETTm available from Applied Biosystems), carboxy-X-rhodamine (ROX), 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOETM available from Applied Biosystems), VICTM dye products available from Molecular Probes, Inc., NEDTM dye products available from Applied Biosystems, Cal Fluor dye products (such as, e.g., Cal Fluor Gold 540, Orange 560, Red 590, Red 610, Red 635) available from Biosearch Technologies, Quasar dye products (such as, e.g., Quasar 570, 670, 705) available from Biosearch Technologies, and the like. 
     The term “percent identity,” in the context of two or more nucleic acids, refers to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters, or by manual alignment and visual inspection. See e.g., the NCBI web site at ncbi.nlm.nih.gov/BLAST. Such sequences are then said to be “substantially identical.” Percent identity is typically determined over optimally aligned sequences, so that the definition applies to sequences that have deletions and/or additions, as well as those that have substitutions. The algorithms commonly used in the art account for gaps and the like. Typically, identity exists over a region comprising a sequence that is at least about 25 nucleotides in length, or over a region that is 50-100 nucleotides in length, or over the entire length of the reference sequence. 
     The terms “selectively” or “selective” with respect to nucleic acids refers to the discrimination between the target nucleic acid sequence (e.g., target sequence of  Salmonella Typhimurium ) over the non-target nucleic acid sequences (e.g., non-target sequence  Salmonella Typhimurium ). An assay is selective for a sequence if little or no hybridization of the primer or probe occurs with non-target sequence. 
     The terms “partitioning” or “partitioned” refer to separating an aqueous solution having one or more of a sample and reactant into a plurality of portions, or “partitions.” Partitions can be solid or fluid. In some embodiments, a partition is a solid partition, e.g., a microchannel. In some embodiments, a partition is a fluid partition, e.g., a droplet. In some embodiments, a fluid partition (e.g., a droplet) is a mixture of immiscible fluids (e.g., water and oil). In some embodiments, a fluid partition (e.g., a droplet) is an aqueous droplet that is surrounded by an immiscible carrier fluid (e.g., oil). 
     II. NUCLEIC ACIDS 
     Genome Detection Regions 
     A detection method is provided herein that is based on the identification of residues 749 to 2136 (1388 bp) of  Salmonella Typhimurium  ACCESSION CP007235 (see SEQ ID NO: 1 in Table 1). 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Sequences 
               
            
           
           
               
               
               
            
               
                 SEQ 
                   
                   
               
               
                 ID 
                   
                   
               
               
                 NO 
                 DESCRIPTION 
                 SEQUENCE 
               
               
                   
               
               
                 1 
                 1388 bp fragment 
                 ATGTAGCTTAAGATATCTATAGTGATATCAGTGTAATACTTATTGGTTAG 
               
               
                   
                 from the 3315 bp 
                 ATCGGTATGATCTTGAATATTTTTATATCGATAGTTTGGATTACATAGTA 
               
               
                   
                 gene of 
                 GAGTTATTTCACTTTGCAATACAGCTTTAATTATAGTTTTGTCAAGTTGT 
               
               
                   
                 
                   Salmonella 
                 
                 AATTTATCTATAAAAATATTATTTATAGTATTTTCTATTAGGAGAAGTGT 
               
               
                   
                 Typhimurium 
                 TTCGACTAACTTGATATTTGTATTGATTTTTTGTTTGTAGATATTCCGTA 
               
               
                   
                 ACCESSION 
                 GCAATTGAGTTGAATTGTGTTCAAGCAATGGTGAACAAACATAATCCCAT 
               
               
                   
                 CP007235 
                 GATTGCTCTTGAGAGTCCCAGTCATTTTTAGCTATTTCAATAGCATTGGT 
               
               
                   
                   
                 GACTAATTCGATAATTTCATCTTCAATTTCTGGATATGGTACTGAGGCTA 
               
               
                   
                   
                 ATTCACCACTAGTAAAGCTAAGTGTGGGGGCTAGTATTGATAAATAATGG 
               
               
                   
                   
                 TTTACAACCGGAGTGCACATTAATCCCGCAGCGTAAAGCAACTCATTTTT 
               
               
                   
                   
                 GTTATTTGAAAAGCCGCAACGGCCTGTATCATCAAAAACAAACCCTTTTG 
               
               
                   
                   
                 GACGATATCTCACGCAAAAATTACCTTGGCTTATTTTTGACCATGTTATG 
               
               
                   
                   
                 CCTTCTCTAAAGTAATACTCATCATTTCTTACGGCAGAGCGAGTTTTGCC 
               
               
                   
                   
                 ATTCTCAAATTTAAAATTTCGTATTTCGTAACCATTATTTTCCCAATTTA 
               
               
                   
                   
                 CAACTATTTCGTTATTACCATACCACTTTCGATATTCACCTCCACTACTA 
               
               
                   
                   
                 CAAGGAAACCATTTGATATTATGAATGTCGATTTTTGTATTTGATTCTTT 
               
               
                   
                   
                 ATTTGTGATAAGGGTTTTTTTTATTGAAACCTCGTACCAATATCTTTGAA 
               
               
                   
                   
                 ATTTAATATTGTCACCGGTGGACATGCCTGCTTTTAATGCTATTTTTTCT 
               
               
                   
                   
                 CCAAGTTTTTTATGGTGGCGAAAAGATAATAGACTCGGTAAGTCTATCCA 
               
               
                   
                   
                 ATATGCTATTGGCATTCCTGGTATGTTTTTAAAATCATGCTGTGTAAATT 
               
               
                   
                   
                 TATCAAATATATTTTTCCTTAGAAGTAGATCGCTTTTCTTTACTTCTTCC 
               
               
                   
                   
                 CTACCATCTATAAGTCTAAAAAATACAGGTTGGTAACGTTCGGAGTGTTG 
               
               
                   
                   
                 GTTTTTAATCACCCAGGCAGTTGTCTGTACAACCTCTCCAGAAATTTGCC 
               
               
                   
                   
                 CAAAAGCCCGAGCTCCCAAATGTGCCATCGTAATAAATGTTTTATTGTCC 
               
               
                   
                   
                 AATAACCAGTTACGTAGTGCTTCATAACTTGACAAAAACATCCATGATTG 
               
               
                   
                   
                 CATATTGACTTGAGCATTAAACCCATTTTCTTTAAGCAAAGAAAATGCAT 
               
               
                   
                   
                 TCTGCATAAACATTGCAAACAAATCAGCTTTACTATCCGGGAAGTTATTT 
               
               
                   
                   
                 TTGGCAAACTCTTTCAGCTCACTATTCATTCCCTTGCC 
               
               
                   
               
               
                 2 
                 947 bp fragment 
                 ATGTAGCTTAAGATATCTATAGTGATATCAGTGTAATACTTATTGGTTAG 
               
               
                   
                 of  Salmonella   
                 ATCGGTATGATCTTGAATATTTTTATATCGATAGTTTGGATTACATAGTA 
               
               
                   
                 Typhimurium 
                 GAGTTATTTCACTTTGCAATACAGCTTTAATTATAGTTTTGTCAAGTTGT 
               
               
                   
                 ACCESSION 
                 AATTTATCTATAAAAATATTATTTATAGTATTTTCTATTAGGAGAAGTGT 
               
               
                   
                 CP007235 
                 TTCGACTAACTTGATATTTGTATTGATTTTTTGTTTGTAGATATTCCGTA 
               
               
                   
                   
                 GCAATTGAGTTGAATTGTGTTCAAGCAATGGTGAACAAACATAATCCCAT 
               
               
                   
                   
                 GATTGCTCTTGAGAGTCCCAGTCATTTTTAGCTATTTCAATAGCATTGGT 
               
               
                   
                   
                 GACTAATTCGATAATTTCATCTTCAATTTCTGGATATGGTACTGAGGCTA 
               
               
                   
                   
                 ATTCACCACTAGTAAAGCTAAGTGTGGGGGCTAGTATTGATAAATAATGG 
               
               
                   
                   
                 TTTACAACCGGAGTGCACATTAATCCCGCAGCGTAAAGCAACTCATTTTT 
               
               
                   
                   
                 GTTATTTGAAAAGCCGCAACGGCCTGTATCATCAAAAACAAACCCTTTTG 
               
               
                   
                   
                 GACGATATCTCACGCAAAAATTACCTTGGCTTATTTTTGACCATGTTATG 
               
               
                   
                   
                 CCTTCTCTAAAGTAATACTCATCATTTCTTACGGCAGAGCGAGTTTTGCC 
               
               
                   
                   
                 ATTCTCAAATTTAAAATTTCGTATTTCGTAACCATTATTTTCCCAATTTA 
               
               
                   
                   
                 CAACTATTTCGTTATTACCATACCACTTTCGATATTCACCTCCACTACTA 
               
               
                   
                   
                 CAAGGAAACCATTTGATATTATGAATGTCGATTTTTGTATTTGATTCTTT 
               
               
                   
                   
                 ATTTGTGATAAGGGTTTTTTTTATTGAAACCTCGTACCAATATCTTTGAA 
               
               
                   
                   
                 ATTTAATATTGTCACCGGTGGACATGCCTGCTTTTAATGCTATTTTTTCT 
               
               
                   
                   
                 CCAAGTTTTTTATGGTGGCGAAAAGATAATAGACTCGGTAAGTCTAT 
               
               
                   
               
               
                 3 
                 123 bp fragment 
                 TAGGAGAAGTGTTTCGACTAACTTGATATTTGTATTGATTTTTTGTTTGT 
               
               
                   
                 of  Salmonella   
                 AGATATTCCGTAGCAATTGAGTTGAATTGTGTTCAAGCAATGGTGAACAA 
               
               
                   
                 Typhimurium 
                 ACATAATCCCATGATTGCTCTTG 
               
               
                   
                 ACCESSION 
                   
               
               
                   
                 CP007235 
                   
               
               
                   
               
               
                 4 
                 Forward Primer 
                 TAGGAGAAGTGTTTCGACTAAC 
               
               
                   
                 for 123 bp target 
                   
               
               
                   
                 sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 937 to 958 
                   
               
               
                   
               
               
                 5 
                 Reverse Primer 
                 CAAGAGCAATCATGGGATTATG 
               
               
                   
                 for 123 bp target 
                   
               
               
                   
                 sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 1038 to 1059 
                   
               
               
                   
               
               
                 6 
                 Probe for 123 bp 
                 TTTACAATTGAGTTGAATTGTGTTCAAGC 
               
               
                   
                 target sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 1000 to 1024 
                   
               
               
                   
                 (5′FAM-3′BkFQ) 
                   
               
               
                   
               
               
                 7 
                 Probe for 123 bp 
                 AAAAGAACACAATTCAACTCAATTGCTACG 
               
               
                   
                 target sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 995 to 1020 
                   
               
               
                   
                 (5′FAM-3′BkFQ) 
                   
               
               
                   
               
               
                 8 
                 Probe for 123 bp 
                 CAATTGAGTTGAATTGTGTTCAAGC 
               
               
                   
                 target sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 1000 to 1024 
                   
               
               
                   
                 (5′FAM-3′BkFQ) 
                   
               
               
                   
               
               
                 9 
                 Probe for 123 bp 
                 GAACACAATTCAACTCAATTGCTACG 
               
               
                   
                 target sequence 
                   
               
               
                   
                 spanning residues 
                   
               
               
                   
                 995 to 1020 
               
               
                   
               
            
           
         
       
     
     Based on a publicly available software (e.g., BLAST), SEQ ID NO:1 is conserved (e.g., 100% sequence identity) in 672  Salmonella Typhimurium  strains listed by Genbank accession number in Table 2. 
     
       
         
           
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 Strains of  Salmonella Typhimurium  in which SEQ ID NO: 1 is 100% Conserved 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 LVHC01000004.1 
                 LAPF01000001.1 
                 CTPI01000002.1 
                 CTHF01000003.1 
               
               
                 LVHA01000006.1 
                 LAPD01000063.1 
                 CTPH01000002.1 
                 CTHE01000002.1 
               
               
                 LVGZ01000004.1 
                 LAPC01000018.1 
                 CTPG01000002.1 
                 CTHD01000002.1 
               
               
                 LVGY01000004.1 
                 LAOX01000013.1 
                 CTPF01000002.1 
                 CTHC01000003.1 
               
               
                 LVGX01000005.1 
                 JZAH01000029.1 
                 CTPE01000003.1 
                 CTHB01000001.1 
               
               
                 LVGW01000004.1 
                 JZAB01000025.1 
                 CTPD01000001.1 
                 CTHA01000002.1 
               
               
                 LVGU01000047.1 
                 JYZR01000005.1 
                 CTPC01000003.1 
                 CTGZ01000002.1 
               
               
                 LVGT01000051.1 
                 JYZC01000010.1 
                 CTPB01000003.1 
                 CTGY01000002.1 
               
               
                 LVGS01000046.1 
                 JYZB01000030.1 
                 CTPA01000004.1 
                 CTGX01000005.1 
               
               
                 LVGR01000047.1 
                 JYYZ01000004.1 
                 CTOZ01000002.1 
                 CTGW01000025.1 
               
               
                 LVGQ01000013.1 
                 JYYU01000025.1 
                 CTOY01000002.1 
                 CTGV01000002.1 
               
               
                 LVGP01000004.1 
                 JYYT01000016.1 
                 CTOX01000003.1 
                 CTGU01000006.1 
               
               
                 LVGN01000006.1 
                 JYYQ01000066.1 
                 CTOW01000001.1 
                 CTGT01000002.1 
               
               
                 LVGM01000008.1 
                 JYYL01000011.1 
                 CTOV01000003.1 
                 CTGS01000002.1 
               
               
                 LVGL01000007.1 
                 JYYK01000018.1 
                 CTOU01000002.1 
                 CTGR01000004.1 
               
               
                 LVGK01000003.1 
                 JYYH01000035.1 
                 CTOT01000003.1 
                 CTGQ01000002.1 
               
               
                 LVGJ01000009.1 
                 JYYC01000006.1 
                 CTOS01000002.1 
                 CTGP01000004.1 
               
               
                 LVGI01000006.1 
                 JYYB01000003.1 
                 CTOR01000003.1 
                 CTGO01000001.1 
               
               
                 LVGH01000005.1 
                 JYYA01000024.1 
                 CTOQ01000004.1 
                 CTGN01000001.1 
               
               
                 LVGG01000006.1 
                 JYXZ01000019.1 
                 CTOP01000003.1 
                 CTGM01000002.1 
               
               
                 LVGF01000006.1 
                 JYXX01000004.1 
                 CTOO01000002.1 
                 CTGL01000004.2 
               
               
                 LVFW01000011.1 
                 JYXW01000003.1 
                 CTON01000002.1 
                 CTGK01000002.1 
               
               
                 LVFV01000011.1 
                 JYXT01000019.1 
                 CTOM01000004.1 
                 CTGJ01000035.1 
               
               
                 LVFT01000012.1 
                 JYXK01000009.1 
                 CTOL01000003.1 
                 CTGI01000004.1 
               
               
                 LVFS01000014.1 
                 JYXH01000002.1 
                 CTOK01000002.1 
                 CTGH01000004.1 
               
               
                 LVFR01000005.1 
                 JYXC01000008.1 
                 CTOJ01000001.1 
                 CTGG01000002.1 
               
               
                 LVFQ01000008.1 
                 JYWW01000034.1 
                 CTOI01000002.1 
                 CTGF01000002.1 
               
               
                 LVFP01000006.1 
                 JYWU01000014.1 
                 CTOH01000003.1 
                 CTGE01000002.1 
               
               
                 LVFO01000002.1 
                 JYWT01000009.1 
                 CTOG01000003.1 
                 CTGD01000002.1 
               
               
                 LVFN01000004.1 
                 JYWA01000003.1 
                 CTOF01000002.1 
                 CTGC01000002.1 
               
               
                 LVFM01000005.1 
                 JYVW01000007.1 
                 CTOE01000002.1 
                 CTGB01000004.1 
               
               
                 LVFL01000037.1 
                 JYVV01000004.1 
                 CTOD01000002.1 
                 CTGA01000002.1 
               
               
                 LVFK01000003.1 
                 JYVU01000035.1 
                 CTOC01000003.1 
                 CTFZ01000004.1 
               
               
                 LVFJ01000013.1 
                 JYVL01000001.1 
                 CTOB01000002.1 
                 CTFY01000002.1 
               
               
                 LVFI01000003.1 
                 JYVJ01000004.1 
                 CTOA01000004.1 
                 CTFX01000001.1 
               
               
                 LVFH01000010.1 
                 JYVG01000055.1 
                 CTNZ01000003.1 
                 CTFW01000003.1 
               
               
                 LUJG01000006.1 
                 JYVE01000037.1 
                 CTNY01000003.1 
                 CTFV01000004.1 
               
               
                 LUJF01000005.1 
                 JYUZ01000004.1 
                 CTNX01000002.1 
                 CTCJ01000002.1 
               
               
                 LUJE01000003.1 
                 JYUY01000010.1 
                 CTNW01000004.1 
                 CTCI01000003.1 
               
               
                 LUJC01000020.1 
                 JYUP01000020.1 
                 CTNV01000003.1 
                 CTGH01000003.1 
               
               
                 LUIZ01000005.1 
                 JYTX01000005.1 
                 CTNU01000002.1 
                 CTCG01000002.1 
               
               
                 LUIY01000005.1 
                 JYTW01000027.1 
                 CTNT01000002.1 
                 CTCF01000002.1 
               
               
                 LUIW01000007.1 
                 JYTU01000018.1 
                 CTNS01000003.2 
                 CTCE01000003.1 
               
               
                 LUIU01000061.1 
                 JYTT01000012.1 
                 CTNR01000001.1 
                 CTCD01000002.1 
               
               
                 UIT01000019.1 
                 JYTQ01000001.1 
                 CTNQ01000001.1 
                 CTCC01000044.1 
               
               
                 UIS01000029.1 
                 JYTP01000017.1 
                 CTNP01000002.1 
                 CTCB01000003.1 
               
               
                 LUIR01000027.1 
                 JYTL01000012.1 
                 CTNO01000002.1 
                 CTCA01000003.1 
               
               
                 LUIQ01000009.1 
                 JYTI01000010.1 
                 CTNN01000003.1 
                 CTBZ01000002.1 
               
               
                 LUIP01000019.1 
                 JYTD01000002.1 
                 CTNM01000002.1 
                 CTBY01000002.1 
               
               
                 LUIO001000023.1 
                 JYTB01000004.1 
                 CTNL01000002.1 
                 CTBX01000003.1 
               
               
                 LUIN01000035.1 
                 JYSY01000001.1 
                 CTNK01000004.1 
                 CTBW01000004.1 
               
               
                 LUIM01000025.1 
                 JYSX01000031.1 
                 CTNJ01000001.1 
                 CTBV01000003.1 
               
               
                 LUIL01000040.1 
                 JYSO01000094.1 
                 CTNI01000002.1 
                 CTBU01000002.1 
               
               
                 LUIK01000041.1 
                 JYSN01000051.1 
                 CTNH01000002.1 
                 CTBT01000001.1 
               
               
                 LUIJ01000024.1 
                 JYSM01000007.1 
                 CTNG01000036.1 
                 CTBS01000003.1 
               
               
                 LUII01000036.1 
                 JYSL01000029.1 
                 CTNF01000003.1 
                 CTBR01000004.1 
               
               
                 LUIH01000014.1 
                 JYSG01000016.1 
                 CTNE01000002.1 
                 CTBQ01000003.1 
               
               
                 LUIG01000040.1 
                 JYSB01000024.1 
                 CTND01000002.1 
                 CTBP01000005.1 
               
               
                 LUIF01000036.1 
                 JYSA01000003.1 
                 CTNC01000001.1 
                 CTBO01000002.1 
               
               
                 LUIE01000017.1 
                 JYRX01000002.1 
                 CTNB01000046.1 
                 CTBN01000003.1 
               
               
                 LUID01000024.1 
                 JYRW01000014.1 
                 CTNA01000004.1 
                 CTBM01000003.1 
               
               
                 LUIC01000116.1 
                 JYRT01000085.1 
                 CTMZ01000002.1 
                 CTBK01000003.1 
               
               
                 LUIB01000040.1 
                 JYRQ01000034.1 
                 CTMY01000004.1 
                 CTBJ01000002.1 
               
               
                 LUIA01000027.1 
                 JYRM01000039.1 
                 CTMX01000002.1 
                 CTBI01000002.1 
               
               
                 LUHZ01000025.1 
                 JYRD01000017.1 
                 CTMW01000004.1 
                 CTBH01000003.1 
               
               
                 LUHY01000038.1 
                 JYRC01000016.1 
                 CTMV01000003.1 
                 CTBF01000004.1 
               
               
                 LUHX01000025.1 
                 JYQU01000020.1 
                 CTMU01000003.1 
                 CTBE01000004.1 
               
               
                 LUHV01000033.1 
                 JYQM01000015.1 
                 CTMT01000004.1 
                 CTBC01000002.1 
               
               
                 LUHU01000040.1 
                 JYQC01000008.1 
                 CTMS01000002.1 
                 CTBB01000002.1 
               
               
                 LUHT01000028.1 
                 JYQA01000030.1 
                 CTMR01000004.1 
                 CTBA01000002.1 
               
               
                 LUHS01000024.1 
                 JYPT01000005.1 
                 CTMQ01000003.1 
                 CTAZ01000003.1 
               
               
                 LUHR01000036.1 
                 JYPP01000050.1 
                 CTMP01000002.1 
                 CTAY01000001.1 
               
               
                 LONA01000003.1 
                 JYPO01000064.1 
                 CTMO01000003.1 
                 CTAX01000001.1 
               
               
                 LKJI01000024.1 
                 JYPM01000008.1 
                 CTMN01000003.1 
                 CTAW01000001.1 
               
               
                 LKJE01000032.1 
                 JUIT01000021.1 
                 CTMM01000003.1 
                 CTAV01000002.1 
               
               
                 LKJD01000006.1 
                 JRZW01000002.1 
                 CTML01000002.1 
                 CTAU01000001.1 
               
               
                 LJJK01000144.1 
                 JRZV01000001.1 
                 CTMK01000002.1 
                 CTAT01000003.1 
               
               
                 LIOJ01000001.1 
                 JRZU01000002.1 
                 CTMJ01000003.1 
                 CTAS01000002.1 
               
               
                 LIOG01000016.1 
                 JRZT01000030.1 
                 CTMI01000002.1 
                 CTAR01000002.1 
               
               
                 LIOF01000021.1 
                 JRZS01000015.1 
                 CTMH01000003.1 
                 CTAQ01000002.1 
               
               
                 LIOB01000013.1 
                 JRZR01000010.1 
                 CTMG01000002.1 
                 CTAP01000002.1 
               
               
                 LINM01000004.1 
                 JRZQ01000006.1 
                 CTMF01000002.1 
                 CTAO01000002.1 
               
               
                 LINL01000011.1 
                 JRZO01000062.1 
                 CTME01000001.1 
                 CTAN01000001.1 
               
               
                 LINK01000002.1 
                 JRZN01000054.1 
                 CTMD01000003.1 
                 CTAM01000004.1 
               
               
                 LINJ01000020.1 
                 JRZM01000003.1 
                 CTMC01000004.1 
                 CTAL01000003.1 
               
               
                 LINF01000009.1 
                 JRZL01000059.1 
                 CTMB01000002.1 
                 CTAK01000004.1 
               
               
                 LINE01000010.1 
                 JRZK01000010.1 
                 CTMA01000002.1 
                 CTAJ01000002.1 
               
               
                 LINB01000005.1 
                 SJRZJ01000012.1 
                 CTLZ01000002.1 
                 CTAI01000002.1 
               
               
                 LIMZ01000030.1 
                 SJRZI01000017.1 
                 CTLY01000002.1 
                 CTAH01000003.1 
               
               
                 LIMV01000008.1 
                 JRZH01000001.1 
                 CTLX01000004.1 
                 CTAG01000004.1 
               
               
                 LIMU01000022.1 
                 JRYU01000004.1 
                 CTLW01000002.1 
                 CTAF01000002.1 
               
               
                 LIMT01000027.1 
                 JRYT01000009.1 
                 CTLV01000004.1 
                 CTAE01000002.1 
               
               
                 LIMN01000012.1 
                 JRGW01000022.1 
                 CTLU01000001.1 
                 CTAD01000002.1 
               
               
                 LIMM01000010.1 
                 JRGV01000045.1 
                 CTLT01000004.1 
                 CTAC01000004.1 
               
               
                 LIMH01000001.1 
                 JRGU01000009.1 
                 CTLS01000004.1 
                 CTAB01000002.1 
               
               
                 LIDY01000003.1 
                 JRGT01000034.1 
                 CTLR01000003.1 
                 CQIE01000002.1 
               
               
                 LHOM01000023.1 
                 JRGS01000001.1 
                 CTLQ01000001.1 
                 CQHW01000002.1 
               
               
                 LHOJ01000006.1 
                 JRGR01000006.1 
                 CTLP01000003.1 
                 CQHV01000002.1 
               
               
                 LHOH01000004.1 
                 JHAI01000005.1 
                 CTLO01000001.1 
                 CQHU01000002.1 
               
               
                 LHOG01000003.1 
                 JHAH01000020.1 
                 CTLN01000003.1 
                 CQHS01000002.1 
               
               
                 LHOF01000033.1 
                 JHAG01000020.1 
                 CTLM01000004.1 
                 CQHR01000002.1 
               
               
                 LHNW01000001.1 
                 JHAF01000018.1 
                 CTLL01000004.1 
                 CQHQ01000002.1 
               
               
                 LHNS01000017.1 
                 JHAE01000013.1 
                 CTLK01000002.1 
                 CQHN01000002.1 
               
               
                 LHNM01000038.1 
                 FKJD01000009.1 
                 CTLJ01000002.1 
                 CQHJ01000001.1 
               
               
                 LHNL01000010.1 
                 FKJC01000004.1 
                 CTLI01000002.1 
                 CQHI01000002.1 
               
               
                 LHNI01000015.1 
                 FKJB01000003.1 
                 CTLH01000004.1 
                 CQHH01000002.1 
               
               
                 LHNH01000007.1 
                 CYID01000003.1 
                 CTLG01000004.1 
                 CQHG01000001.1 
               
               
                 LHNG01000002.1 
                 CYIC01000003.1 
                 CTLF01000002.1 
                 CQHF01000001.1 
               
               
                 LHMT01000026.1 
                 CYIB01000003.1 
                 CTLE01000002.1 
                 CQHE01000002.1 
               
               
                 LHMS01000025.1 
                 CYIA01000002.1 
                 CTLD01000004.1 
                 CQHD01000002.1 
               
               
                 LHMA01000007.1 
                 CYHZ01000003.1 
                 CTLC01000006.1 
                 CQHC01000002.1 
               
               
                 LHLX01000009.1 
                 CYHY01000003.1 
                 CTLB01000002.1 
                 CQHB01000002.1 
               
               
                 LHLU01000004.1 
                 CYHX01000003.1 
                 CTLA01000002.1 
                 CQHA01000001.1 
               
               
                 LHLP01000001.1 
                 CYHW01000002.1 
                 CTKZ01000002.1 
                 CQGZ01000001.1 
               
               
                 LHLO01000016.1 
                 CYHV01000002.1 
                 CTKI01000002.1 
                 CQGY01000002.1 
               
               
                 LHLK01000019.1 
                 CYHU01000003.1 
                 CTKG01000001.1 
                 CQGX01000002.1 
               
               
                 LHLF01000020.1 
                 CYHT01000003.1 
                 CTKD01000002.1 
                 CQGW01000002.1 
               
               
                 LHLA01000001.1 
                 CVMK01000002.1 
                 CTKC01000002.1 
                 CQGV01000002.1 
               
               
                 LHKL01000042.1 
                 CVMH01000002.1 
                 CTKB01000004.1 
                 CQGU01000002.1 
               
               
                 LHKK01000034.1 
                 CVKN01000003.1 
                 CTKA01000003.1 
                 CQGT01000001.1 
               
               
                 LHKD01000036.1 
                 CVKM01000005.1 
                 CTJZ01000002.1 
                 CQGS01000002.1 
               
               
                 LHKC01000003.1 
                 CVKK01000004.1 
                 CTJY01000002.1 
                 CQGR01000002.1 
               
               
                 LHKA01000038.1 
                 CVKJ01000005.1 
                 CTJX01000003.1 
                 CQGQ01000002.1 
               
               
                 LHJU01000003.1 
                 CVKH01000004.1 
                 CTJW01000002.1 
                 CQGP01000002.1 
               
               
                 LHJJ01000028.1 
                 CVKC01000002.1 
                 CTJV01000003.1 
                 CQGO01000002.1 
               
               
                 LHJF01000017.1 
                 CVKA01000004.1 
                 CTJU01000005.1 
                 CQGN01000002.1 
               
               
                 LHIX01000004.1 
                 CVJW01000001.1 
                 CTJT01000002.1 
                 CQGM01000002.1 
               
               
                 LHIW01000017.1 
                 CTQZ01000003.1 
                 CTJS01000002.1 
                 CQGL01000002.1 
               
               
                 LHIR01000013.1 
                 CTQY01000002.1 
                 CTJR01000003.1 
                 CQGK01000001.1 
               
               
                 LHIQ01000047.1 
                 CTQX01000004.1 
                 CTJQ01000002.1 
                 CQGJ01000002.1 
               
               
                 LHIK01000014.1 
                 CTQU01000002.1 
                 CTJP01000002.1 
                 CQGI01000001.1 
               
               
                 LHIE01000015.1 
                 CTQT01000003.1 
                 CTJO01000004.2 
                 CQGH01000002.1 
               
               
                 LHID01000040.1 
                 CTQS01000002.1 
                 CTJN01000001.1 
                 CQGG01000002.1 
               
               
                 LHHK01000011.1 
                 CTQR01000002.1 
                 CTJM01000004.1 
                 CIJW01000002.1 
               
               
                 LHHB01000001.1 
                 CTQQ01000001.1 
                 CTJK01000003.1 
                 CIJD01000002.1 
               
               
                 LHGZ01000002.1 
                 CTQP01000002.1 
                 CTJJ01000002.1 
                 CHJY01000001.1 
               
               
                 LHGY01000001.1 
                 CTQO01000002.1 
                 CTIL01000002.1 
                 CGGH01000001.1 
               
               
                 LHGL01000047.1 
                 CTQN01000002.1 
                 CTIK01000003.1 
                 CGDA01000002.1 
               
               
                 LHGJ01000005.1 
                 CTQM01000002.1 
                 CTIJ01000003.1 
                 CGCS01000001.1 
               
               
                 LHGI01000006.1 
                 CTQL01000098.1 
                 CTII01000002.1 
                 CGCQ01000002.1 
               
               
                 LHGH01000003.1 
                 CTQK01000004.1 
                 CTIH01000002.1 
                 CGCH01000002.1 
               
               
                 LHFW01000031.1 
                 CTQJ01000002.1 
                 CTIG01000002.1 
                 CFOA01000002.1 
               
               
                 LHFV01000044.1 
                 CTQI01000001.1 
                 CTIF01000004.1 
                 CFNX01000002.1 
               
               
                 LHFU01000031.1 
                 CTQH01000001.1 
                 CTIE01000003.1 
                 CFLD01000002.1 
               
               
                 LHFT01000032.1 
                 CTQG01000002.1 
                 CTID01000002.1 
                 BAKU01000002.1 
               
               
                 LHFS01000022.1 
                 CTQF01000003.1 
                 CTIC01000002.1 
                 AYVJ01000114.1 
               
               
                 LHFP01000043.1 
                 CTQE01000004.1 
                 CTIB01000003.1 
                 AYUQ01000108.1 
               
               
                 LHFF01000013.1 
                 CTQD01000002.1 
                 CTIA01000004.1 
                 AUXR01000008.1 
               
               
                 LHEY01000021.1 
                 CTQC01000001.1 
                 CTHZ01000002.1 
                 AUXE01000003.1 
               
               
                 EHEX01000008.1 
                 CTQB01000003.1 
                 CTHY01000001.1 
                 AUVE01000003.1 
               
               
                 LHEW01000017.1 
                 CTQA01000002.1 
                 CTHX01000001.1 
                 AUVD01000043.1 
               
               
                 LHEV01000005.1 
                 CTPZ01000003.1 
                 CTHW01000001.1 
                 AUQU01000045.1 
               
               
                 LHER01000004.1 
                 CTPY01000003.1 
                 CTHV01000002.1 
                 AUQT01000034.1 
               
               
                 LHEQ01000025.1 
                 CTPX01000004.1 
                 CTHU01000002.1 
                 AUQO01000062.1 
               
               
                 LHEP01000049.1 
                 CTPW01000002.1 
                 CTHT01000004.1 
                 AUQN01000039.1 
               
               
                 LHEA01000005.1 
                 CTPV01000002.1 
                 CTHS01000002.1 
                 AUQM01000038.1 
               
               
                 LFGM01000013.1 
                 CTPU01000005.1 
                 CTHR01000002.1 
                 AOXO01000096.1 
               
               
                 LFDY01000028.1 
                 CTPT01000001.1 
                 CTHQ01000002.1 
                 AOXD01000065.1 
               
               
                 LFDW01000010.1 
                 CTPS01000002.1 
                 CTHP01000002.1 
                 AOXC01000083.1 
               
               
                 LFCC01000059.1 
                 CTPR01000003.1 
                 CTHO01000004.1 
                 AJTU01000007.1 
               
               
                 LDPA01000008.1 
                 CTPQ01000002.1 
                 CTHN01000002.1 
                 AHVA01000018.1 
               
               
                 LAPQ01000066.1 
                 CTPP01000002.1 
                 CTHM01000002.1 
                 AHUZ01000018.1 
               
               
                 LAPP01000078.1 
                 CTPO01000002.1 
                 CTHL01000002.1 
                 AHUV01000085.1 
               
               
                 LAPO01000058.1 
                 CTPN01000002.1 
                 CTHK01000002.1 
                 AHUT01000031.1 
               
               
                 LAPN01000091.1 
                 CTPM01000005.1 
                 CTHJ01000001.1 
                 AHUS01000047.1 
               
               
                 LAPM01000076.1 
                 CTPL01000004.1 
                 CTHI01000039.1 
                 AERV01000023.1 
               
               
                 LAPH01000042.1 
                 CTPK01000003.1 
                 CTHH01000002.1 
                 ABAO01000006.1 
               
               
                 LAPG01000091.1 
                 CTPJ01000002.1 
                 CTHG01000002.1 
                 LUIV01000062.1 
               
               
                   
               
            
           
         
       
     
     Also based on a publicly available software (e.g., BLAST), SEQ ID NO:1 is partially conserved (e.g., at least 99% sequence identity) in 48  Salmonella Typhimurium  strains listed by Genbank accession number in Table 3. 
     
       
         
           
               
             
               
                 TABLE 3 
               
               
                   
               
               
                 Strains of  Salmonella Typhimurium  in 
               
               
                 which SEQ ID NO: 1 is Partially Conserved 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 LVGO01000006.1 
                 LUJA01000002.1 
                 LDYH01000006.1 
                 AMEA02000013.1 
               
               
                 LVGE01000003.1 
                 LUIX01000003.1 
                 JYPX01000009.1 
                 AMDZ02000027.1 
               
               
                 LVGD01000004.1 
                 LFGR01000011.1 
                 JTED01000004.1 
                 AMDY01000216.1 
               
               
                 LVGC01000003.1 
                 LFGQ01000013.1 
                 AUQV01000023.1 
                 AMDX02000108.1 
               
               
                 LVGB01000001.1 
                 LFGP01000017.1 
                 ATWR01000084.1 
                 JRZX01000002.1 
               
               
                 LVGA01000003.1 
                 LFGN01000015.1 
                 AMEH02000182.1 
                 JRZP01000003.1 
               
               
                 LVFZ01000005.1 
                 LFDX01000009.1 
                 AMEG02000055.1 
                 AUQL01000040.1 
               
               
                 LVFY01000001.1 
                 LFCI01000010.1 
                 AMEF02000044.1 
                 LFGO01000009.1 
               
               
                 LVFX01000003.1 
                 LFCH01000028.1 
                 AMEE02000031.1 
                 LFDZ01000012.1 
               
               
                 LVFU01000005.1 
                 LFCG01000008.1 
                 AMED02000059.1 
                 LECA01000009.1 
               
               
                 LUJD01000002.1 
                 LECD01000013.1 
                 AMEC02000055.1 
                 LUHW01000058.1 
               
               
                 LUJB01000005.1 
                 LECC01000010.1 
                 AMEB02000105.1 
                 LECB01000012.1 
               
               
                   
               
            
           
         
       
     
     Based on a publicly available software (e.g., BLAST), SEQ ID NO:1 is not found in the following non- Typhimurium Salmonella  strains: 
       Salmonella _ enterica _serovar_Ohio_CFSAN001079
   Salmonella _ enterica _serovar_Newport_WA14881
   Salmonella _ enterica _serovar_Schwarzengrund_SL480
   Salmonella _ enterica _serovar_ Gallinarum _28791
   Salmonella _ enterica _serovar_Thompson_2010K1863
   Salmonella _ enterica _serovar_Kentucky_CDC191
   Salmonella _ enterica _serovar_ Typhi _BL196
   Salmonella _ enterica _serovar_ Enteritidis _P125109
   Salmonella _ enterica _serovar_Agona_72A52
   Salmonella _ enterica _serovar_Saintpaul_JO2008
   Salmonella _ enterica _serovar_Heidelberg_SL476
   Salmonella _ enterica _serovar_Virchow_ATCC51955
   Salmonella _ enterica _serovar_Paratyphi_B_SARA62
   Salmonella _ enterica _serovar_MontevideoMDA09249507
   Salmonella _ enterica _serovar_Muenchen_2009K0951
   Salmonella _ enterica _serovar_B areilly_CFSAN000197
   Salmonella _ enterica _serovar_Virchow_SL491
   Salmonella _ enterica _serovar_ Pullorum _19945
   Salmonella _ enterica _serovar_Dublin_SL1438
   Salmonella _ enterica _serovar_Stanley_060538
 
     In another embodiment, a detection method is based on the identification of residues 749-1697 of  Salmonella Typhimurium  ACCESSION CP007235 REGION: 658819 . . . 662133 (see SEQ ID NO:2 in Table 1). In another embodiment, a detection method is based on the identification of residues 755-1063 of  Salmonella Typhimurium  ACCESSION CP007235 REGION: 658819 . . . 662133 (see SEQ ID NO:3 in Table 1). In some embodiments, the detection method incorporates unlabeled primers and labeled probes for the detection of  Salmonella  Typhimurium. 
     Oligonucleotides 
     Oligonucleotides of the instant invention are set forth in SEQ ID NOs: 4-9. 
     Disclosed oligonucleotides can be used as primers for PCR amplification and as hybridization probes. Primers and probes are shown in Table 1. 
     The nucleic acid probes can contain a detectable label. In some embodiments, the probe comprises a reporter-quencher combination as employed in a double-stranded probe, a TAQMAN™ probe, a molecular beacon probe, a SCORPION™ probe, a dual hybridization probe, or an ECLIPSE™ probe. In some embodiments, a double-stranded probe comprises two completely or partially complementary strands. In some embodiments, one strand of the double-stranded probe comprises a reporter on the 5′ end and the other strand comprises a quencher on the 3′ end such that when the two strands hybridize, the reporter and quencher face each other and the quencher quenches the fluorescence emitted by the reporter. During PCR, the strands separate, allowing the reporter to fluoresce and to be detected. In some embodiments, each strand of the double-stranded probe includes a reporter at one end (e.g., the 5′ end) and a quencher at the other end (e.g., the 3′ end). When the two strands hybridize with each other, the reporter from the first strand is in close proximity with the quencher of the second strand such that fluorescence quenching occurs. During PCR, the strands separate, allowing the reporter to fluoresce and to be detected. In an embodiment, the probe is a double-stranded probe as described in U.S. Pat. No. 9,194,007, which is incorporated by reference in its entirety herein. In an embodiment, a reporter-quencher pair used in a double-stranded probe is 6-FAM and Iowa Black® FQ. 
     III. METHODS 
     The oligonucleotides can be used in a method for selectively detecting the presence of  Salmonella Typhimurium  in a sample. In an embodiment, the method begins by providing a reaction mixture comprising a suitable primer pair for amplification of residues 749-1697, or a portion thereof, of SEQ ID NO:2. In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence 95%, 97%, or 99% homologous to SEQ ID NO:2. In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence of SEQ ID NO:2 or a portion thereof. 
     In certain embodiments, the reaction mixture comprises a primer pair for amplification of residues 755-1063, or portions thereof, of SEQ ID NO:3. In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence 95%, 97%, or 99% homologous to SEQ ID NO:3. In some embodiments, the reaction mixture comprises a primer pair for amplification of a sequence of SEQ ID NO:3 or a portion thereof. In some embodiments, the primer pair for amplification of the nucleic acid region of SEQ ID NO:3 comprises SEQ ID NO:4 and SEQ ID NO:5. 
     In some embodiments, the method further comprises a probe for the nucleic acid region to be detected. In certain embodiments, the probe comprises a detectable label. In some embodiments, the probe is a single-stranded probe comprising SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or SEQ ID NO:9. In some embodiments, each probe is labeled with a reporter on one end (e.g., the 5′ end) and a quencher on the other end (e.g., the 3′ end). In some embodiments, the probe is a double-stranded probe comprising SEQ ID NO:6 and SEQ ID NO:7 (e.g., SEQ ID NO:6 can hybridize to SEQ ID NO:7) with each strand having a reporter on one end (e.g., the 5′ end) and a quencher on the other end (e.g., the 3′ end). 
     The next step of the method comprises performing PCR amplification (e.g., real-time PCR) of the nucleic acids of the sample using the reaction mixture. In some embodiments, PCR amplification is performed in partitions (e.g, droplets). Methods and compositions for partitioning a solution are described, for example, in published patent applications WO 2012/135259, WO 2014/117088, WO 2010/036352, and U.S. Pat. No. 9,156,010, the entire content of each of which is incorporated by reference herein. 
     In the last step of the method, the presence of  Salmonella Typhimurium  is selectively detected by detecting the amplified nucleic acids. In some embodiments, the detecting step comprises sequencing the amplified nucleic acids. 
     IV. KITS 
     In another aspect, kits for detecting  Salmonella Typhimurium  in a sample according to the methods described herein are provided. In some embodiments, a kit comprises a primer pair as described herein. In some embodiments, the kit further comprises probes as described herein. In some embodiments, the kit further comprises assay components including, but not limited to, a lysis reagent, a DNA polymerase, dNTPs, a buffer, a negative control, and a positive control. In some embodiments, the kit further comprises instructions for carrying out the methods described herein. 
     V. EXAMPLES 
     Example 1—Comparison of  Salmonella Typhimurium  Assay of the Instant Invention to  Salmonella  Spp. Assay 
     In this example, the  Salmonella Typhimurium  assay of the instant invention was compared to a commercially available  Salmonella  spp. Assay. In the experiment, eleven  Salmonella  serovars that are most relevant for the food industry were tested with the  Salmonella Typhimurium  assay of this disclosure and with the iQ-Check  Salmonella  spp. II Assay (Bio-Rad). The eleven  Salmonella  strains were streaked on a TCS Petri dish and allowed to grow for 24 hr at 37° C. Individual colonies were then picked, diluted in 500 μL sterile water and 5 μL were tested with each assay using the Bio-Rad CFX96 Touch™ Real-Time PCR Detection System. For the  Salmonella Typhimurium  assay, the double-stranded probe comprised SEQ ID NOs 6 and 7. Each strand of the double-stranded probe was labeled with 6-FAM on the 5′ end and Iowa Black™ FQ on the 3′end. The double-stranded probe was synthesized by Integrated DNA Technologies using phosphoramidite chemistry. Results are shown in Table 4. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Comparison of Assays 
               
            
           
           
               
               
               
            
               
                   
                 Bio-Rad iQ-Check  Salmonella  spp. II assay 
                   Salmonella Typhimurium  assay 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 Target 
                 Internal 
                   
                 Target 
                 Internal 
                   
               
               
                 Serovars 
                 Cq 
                 control Cq 
                 Result 
                 Cq 
                 control Cq 
                 Result 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Negative Ctrl 
                 N/A 
                 32.84 
                 Negative 
                 N/A 
                 32.49 
                 Negative 
               
               
                 Positive Ctrl 
                 31.72 
                 32.24 
                 Positive 
                 31.95 
                 31.78 
                 Positive 
               
               
                 
                   Typhimurium 
                 
                 19.69 
                 34.60 
                 Positive 
                 19.36 
                 33.43 
                 Positive 
               
               
                 
                   Monophasic Typhimurium 
                 
                 18.35 
                 N/A 
                 Positive 
                 18.08 
                 34.2 
                 Positive 
               
               
                 
                   Enteritidis 
                 
                 20.34 
                 32.72 
                 Positive 
                 N/A 
                 32.15 
                 Negative 
               
               
                 
                   Infantis 
                 
                 20.86 
                 32.40 
                 Positive 
                 N/A 
                 31.78 
                 Negative 
               
               
                 Virchow 
                 19.71 
                 33.28 
                 Positive 
                 N/A 
                 32 
                 Negative 
               
               
                 Hadar 
                 21,20 
                 32.29 
                 Positive 
                 N/A 
                 31.89 
                 Negative 
               
               
                 Paratyphi B Java 
                 20.24 
                 33.27 
                 Positive 
                 N/A 
                 31.91 
                 Negative 
               
               
                 Livingstone 
                 20.84 
                 33.21 
                 Positive 
                 N/A 
                 32.38 
                 Negative 
               
               
                 Kentucky 
                 18.67 
                 34.26 
                 Positive 
                 N/A 
                 32.17 
                 Negative 
               
               
                 Dublin 
                 21,24 
                 32.68 
                 Positive 
                 N/A 
                 31.99 
                 Negative 
               
               
                 Newport 
                 20.23 
                 32.67 
                 Positive 
                 N/A 
                 31.98 
                 Negative 
               
               
                   
               
            
           
         
       
     
     The results shown in Table 4 illustrate that only  typhimurium  is detected by the  Salmonella Typhimurium  assay. The results also show that the sensitivities of both assays are identical and that the  Salmonella Typhimurium  assay can be used as a primary screening assay or as a confirmatory, serotyping assay. 
     Example 2—Assay Selectivity 
     This example illustrates assay selectivity of the instant invention. One-hundred and nine  Salmonella enterica  subsp.  enterica  serovars and  Salmonella enterica  subspecies (in italics in Table 4) were tested with the  Salmonella Typhimurium  assay. The same method and probes as in Example 1 were used in this experiment. The organisms tested are shown in Table 5. 
     
       
         
           
               
             
               
                 TABLE 5 
               
               
                   
               
               
                 Selectivity 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 Abaetetuba 
               
               
                   
                 Aberdeen 
               
               
                   
                 Adelaïde 
               
               
                   
                 Agama 
               
               
                   
                 Albany 
               
               
                   
                 Anatum 
               
               
                   
                   arizonae * 
               
               
                   
                 Bambylor 
               
               
                   
                 Bareilly 
               
               
                   
                 Berta 
               
               
                   
                 Betioky 
               
               
                   
                 Blegdam 
               
               
                   
                 Blockley 
               
               
                   
                 
                   bongori 
                 
               
               
                   
                 Braenderup 
               
               
                   
                 Brandenburg 
               
               
                   
                 Bredeney 
               
               
                   
                 Budapest 
               
               
                   
                 California 
               
               
                   
                 Cerro 
               
               
                   
                 Carrau 
               
               
                   
                 Canoga 
               
               
                   
                 Crossness 
               
               
                   
                 Cubana 
               
               
                   
                 
                   Choleraesuis 
                 
               
               
                   
                   diarizonae * 
               
               
                   
                 Dalhem 
               
               
                   
                 Derby 
               
               
                   
                 Dublin 
               
               
                   
                 Emek 
               
               
                   
                 Duisberg 
               
               
                   
                 Enteritidis 
               
               
                   
                 Fischerkietz 
               
               
                   
                 Ferruch 
               
               
                   
                 Give 
               
               
                   
                 Gaminara 
               
               
                   
                 Gallinarum 
               
               
                   
                 Glostrup 
               
               
                   
                 Grumpensis 
               
               
                   
                 Grabow 
               
               
                   
                 Goldgoast 
               
               
                   
                 Havana 
               
               
                   
                 Hadar 
               
               
                   
                 Guinea 
               
               
                   
                 Havanna 
               
               
                   
                   houtenae * 
               
               
                   
                 Illinois 
               
               
                   
                 Heidelberg 
               
               
                   
                 Indiana 
               
               
                   
                   indica * 
               
               
                   
                 Inverness 
               
               
                   
                 Johannesburg 
               
               
                   
                 Infantis 
               
               
                   
                 Kentucky 
               
               
                   
                 Kirkee 
               
               
                   
                 Kottbus 
               
               
                   
                 Kedougou 
               
               
                   
                 Lomita 
               
               
                   
                 Livingstone 
               
               
                   
                 Manica 
               
               
                   
                 London 
               
               
                   
                 Miami 
               
               
                   
                 Minnesota 
               
               
                   
                 Maregrosso 
               
               
                   
                 Mbandaka 
               
               
                   
                 Muenchen 
               
               
                   
                 Montevideo 
               
               
                   
                 Moscow 
               
               
                   
                 Napoli 
               
               
                   
                 Nienstedten 
               
               
                   
                 Naestved 
               
               
                   
                 Newport 
               
               
                   
                 Nottingham 
               
               
                   
                 Oranienburg 
               
               
                   
                 Ouakam 
               
               
                   
                 Okatie 
               
               
                   
                 Ohio 
               
               
                   
                 Phoenix 
               
               
                   
                 Panama 
               
               
                   
                 Paratyphi B** 
               
               
                   
                 Paratyphi B java 
               
               
                   
                 Postdam 
               
               
                   
                 Poona 
               
               
                   
                 Puttin 
               
               
                   
                 Quentin 
               
               
                   
                 Rostock 
               
               
                   
                 Salamae 
               
               
                   
                 Rubislaw 
               
               
                   
                 Senftenberg 
               
               
                   
                 Saint Paul 
               
               
                   
                 Schwarzengrund 
               
               
                   
                 Singapore 
               
               
                   
                 Sheffield 
               
               
                   
                 Sundsvall 
               
               
                   
                 Springs 
               
               
                   
                 Strasbourg 
               
               
                   
                 Taksony 
               
               
                   
                 Tallahassee 
               
               
                   
                 Tournai 
               
               
                   
                 Tenessee 
               
               
                   
                 Thompson 
               
               
                   
                 Treforest 
               
               
                   
                 Tranoroa 
               
               
                   
                 Utrecht 
               
               
                   
                 Virchow 
               
               
                   
                 Zuerich 
               
               
                   
                 Yoruba 
               
               
                   
                 Wayne 
               
               
                   
                 Worthington 
               
               
                   
                   
               
            
           
         
       
     
     Of the organisms listed in Table 5, all but Paratyphi B were not detected with the assay. The results illustrate that the  Salmonella Typhimurium  assay is highly selective for  Salmonella  Typhimurium. 
     Example 3—Assay Exclusivity 
     This example illustrates assay exclusivity of the instant invention. Thirty-nine non- Salmonella  bacteria were tested with the  Salmonella Typhimurium  assay. The same method and probe as in Example 1 was used in this experiment. The bacteria tested are tabulated in Table 6. None of the bacteria listed in Table 6 were detected by the  Salmonella Typhimurium  assay, illustrating assay exclusivity. 
     
       
         
           
               
             
               
                 TABLE 6 
               
               
                   
               
               
                 Exclusivity 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 
                   Acinetobacter baumanii 
                 
               
               
                   
                 
                   Aeromonas hydrophila 
                 
               
               
                   
                 
                   Aeromonas hydrophila/caviae 
                 
               
               
                   
                 
                   Bacillus licheniformis 
                 
               
               
                   
                 
                   Bacillus cereus 
                 
               
               
                   
                 
                   Campylobacter jejuni 
                 
               
               
                   
                 
                   Campylobacter coli 
                 
               
               
                   
                 
                   Campylobacter lari 
                 
               
               
                   
                 
                   Campylobacter upsaliensis 
                 
               
               
                   
                 
                   Citrobacter freundii 
                 
               
               
                   
                 
                   Cronobacter sakazakii 
                 
               
               
                   
                 
                   Enterobacter cloacae 
                 
               
               
                   
                 
                   Enterobacter pyrinus 
                 
               
               
                   
                 
                   Enterobacter sakazakii 
                 
               
               
                   
                 
                   Enterobacter aerogenes 
                 
               
               
                   
                 
                   Enterobacter asburiae 
                 
               
               
                   
                 
                   Enterobacter amnigenus 
                 
               
               
                   
                 
                   Enterobacter cowanii 
                 
               
               
                   
                 
                   Enterococcus faecium 
                 
               
               
                   
                 
                   Escherichia coli 
                 
               
               
                   
                 
                   Escherichia hermanii 
                 
               
               
                   
                 
                   Hafnia alvei 
                 
               
               
                   
                 
                   Klebsiella oxytoca 
                 
               
               
                   
                 
                   Klebsiella pneumoniae 
                 
               
               
                   
                 
                   Listeria monocytogenes 
                 
               
               
                   
                 
                   Micrococcus luteus 
                 
               
               
                   
                 
                   Pantoea agglomerans 
                 
               
               
                   
                 
                   Proteus mirabilis 
                 
               
               
                   
                 
                   Pseudomonas fluorescens 
                 
               
               
                   
                 
                   Pseudomonas aeruginosa 
                 
               
               
                   
                 
                   Raoultella terrigena 
                 
               
               
                   
                 
                   Serratia marcescens 
                 
               
               
                   
                 
                   Shigella flexneri 
                 
               
               
                   
                 
                   Shigella sonnei 
                 
               
               
                   
                 
                   Staphylococcus aureus 
                 
               
               
                   
                 
                   Staphylococcus internmedius 
                 
               
               
                   
                 
                   Staphylococcus xylosus 
                 
               
               
                   
                 
                   Staphylococcus epidermidis 
                 
               
               
                   
                 
                   Yersinia enterocoloitica 
                 
               
               
                   
                   
               
            
           
         
       
     
     Example 4—Assay Specificity 
     This example illustrates assay specificity of the instant invention. Seventy-nine  Salmonella Typhimurium  serovars were tested with the  Salmonella Typhimurium  assay. The same method and probe as in Example 1 was used in this experiment. The bacteria tested are tabulated in Table 7. All of the bacteria listed in Table 7 were detected by the  Salmonella Typhimurium  assay, illustrating assay specificity. 
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Specificity 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 Antigenic 
                   
                 Primary 
                   
                 Strain number 
                 Strain number 
               
               
                 Serovar 
                 formula 
                 Comment 
                 source 
                 Origin 
                 (Bio-Rad Library) 
                 (Other Library) 
               
               
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Brine 
                 002 
                 no Anses: 38.09 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Beef meat 
                 003 
                 no Anses: 442.09 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Pork (crépine 
                 004 
                 no Anses: 447.09 
               
               
                   
                   
                   
                   
                 de porc) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Lamb with 
                 005 
                 no Anses: 591.09 
               
               
                   
                   
                   
                   
                 sauce 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Stuffed quail 
                 006 
                 no Anses: 695.09 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Culture from 
                 007 
                 no Anses: 839.09 
               
               
                   
                   
                   
                   
                 lamb feces 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Environment 
                 008 
                 no Anses: 838.09 
               
               
                   
                   
                   
                   
                 (Duck) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Culture from 
                 009 
                 no Anses: 553.11 
               
               
                   
                   
                   
                   
                 horse feces 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 White pepper 
                 010 
                 no Anses: 564.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Hoki filet with 
                 011 
                 no Anses: 708.11 
               
               
                   
                   
                   
                   
                 cream 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Pigeon viscera 
                 012 
                 no Anses: 781.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Compost 
                 013 
                 no Anses: 792.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Environmental 
                 014 
                 no Anses: 835.11 
               
               
                   
                   
                   
                   
                 (Chicken) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Streaky ham 
                 015 
                 no Anses: 840.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Whole quail 
                 016 
                 no Anses: 845.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Spareribs 
                 017 
                 no Anses: 880.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Culture from 
                 018 
                 no Anses: 886.11 
               
               
                   
                   
                   
                   
                 swine feces 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Raw milk 
                 019 
                 no Anses: 907.11 
               
               
                   
                   
                   
                   
                 (cow) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Sausage 
                 020 
                 no Anses: 976.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Tomato filling 
                 021 
                 no Anses: 977.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Stuffed 
                 022 
                 no Anses: 979.11 
               
               
                   
                   
                   
                   
                 potatoes 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Fish meal 
                 023 
                 no Anses: 985.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Pet food 
                 043 
                 no Anses: 1175.11 
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Foie gras 
                 030 
                 no Anses: 119.11 
               
               
                   
                   
                   
                   
                 (Liver) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Milk powder 
                 081 
                 ADRIA no4 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pasteurized 
                 082 
                 ADRIA no13 
               
               
                   
                   
                   
                 Development 
                 liquid egg 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pasteurized 
                 083 
                 ADRIA no206 
               
               
                   
                   
                   
                 Development 
                 liquid egg 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Egg yolk 
                 084 
                 ADRIA no472 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pasteurized 
                 085 
                 ADRIA no776 
               
               
                   
                   
                   
                 Development 
                 liquid egg 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Ready-to-eat 
                 086 
                 CIP 58.58 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Foie (Liver) 
                 087 
                 ADRIA no19 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Raw ground 
                 088 
                 ADRIA no22 
               
               
                   
                   
                   
                 Development 
                 meat 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Ready-to-eat 
                 089 
                 ADRIA no167 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Chipolatas 
                 090 
                 ADRIA no193 
               
               
                   
                   
                   
                 Development 
                 sausages 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Chipolatas 
                 091 
                 ADRIA no830 
               
               
                   
                   
                   
                 Development 
                 sausages 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Merguez 
                 092 
                 ADRIA no911 
               
               
                   
                   
                   
                 Development 
                 sausages 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Chipolatas 
                 093 
                 ADRIA no987 
               
               
                   
                   
                   
                 Development 
                 sausages 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Meat (pâté) 
                 094 
                 ADRIA no4874 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Frozen meat 
                 095 
                 A00C003 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Frozen meat 
                 096 
                 A00C004 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Frozen beef 
                 097 
                 A00C059 
               
               
                   
                   
                   
                 Development 
                 trim 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 ground beef 
                 098 
                 A00C060 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 106 
                 Ad1070 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 107 
                 ST325 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 108 
                 ST1 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 109 
                 ST394 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 110 
                 ST719 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 111 
                 ST11 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Liquid egg 
                 113 
                 JES411 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Beef trim 
                 116 
                 Ad913 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Pork 
                 118 
                 Ad1249 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 pork (crépine) 
                 119 
                 Ad1338 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 ground meat 
                 120 
                 Ad1410 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Liquid egg 
                 121 
                 Ad1484 
               
               
                   
                   
                   
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 Drinking 
                 122 
                 Ad1546 
               
               
                   
                   
                   
                 Development 
                 water from 
                   
                   
               
               
                   
                   
                   
                   
                 trough 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 ADRIA 
                 salmon with 
                 123 
                 Ad1603 
               
               
                   
                   
                   
                 Development 
                 vegetables 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:—:— 
                 non motile 
                 ADRIA 
                 Tiramisu 
                 124 
                 Ad1333 
               
               
                   
                   
                 variant 
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:—:1,2 
                 monophasic 
                 ADRIA 
                 Hen 
                 125 
                 Ad1335 
               
               
                   
                   
                 variant 
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 ADRIA 
                 Pork specialty 
                 126 
                 Ad1334 
               
               
                   
                   
                 variant 
                 Development 
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Environmental 
                 160 
                 2002LSAL00347 
               
               
                   
                   
                   
                   
                 (Quail) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Environmental 
                 161 
                 2016LSAL02607 
               
               
                   
                   
                   
                   
                 (goose) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Environmental 
                 162 
                 2009LSAL04410 
               
               
                   
                   
                 variant 
                   
                 (Pork) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:—:1,2 
                 monophasic 
                 Anses 
                 Environmental 
                 163 
                 2010LSAL01759 
               
               
                   
                   
                 variant 
                   
                 ( Gallus gallus - 
                   
                   
               
               
                   
                   
                   
                   
                 hen) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Environmental 
                 164 
                 2011LSAL04681 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Environmental 
                 165 
                 2012LSAL04635 
               
               
                   
                   
                 variant 
                   
                 (Turkey) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:1,2 
                   
                 Anses 
                 Environmental 
                 166 
                 2013LSAL00987 
               
               
                   
                   
                   
                   
                 ( Gallus gallus ) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Environmental 
                 167 
                 2014LSAL00857 
               
               
                   
                   
                 variant 
                   
                 (Bovine) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Pork meat 
                 168 
                 2011LSAL06561 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Veal meat 
                 169 
                 2012LSAL05317 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Turkey meat 
                 170 
                 2014LSAL02635 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 
                   Gallus gallus 
                 
                 171 
                 2014LSAL03913 
               
               
                   
                   
                 variant 
                   
                 meat 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 Poultry Feed 
                 172 
                 2011LSAL04983 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 cattle feed 
                 173 
                 2012LSAL03407 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 animal blood 
                 174 
                 2012LSAL03874 
               
               
                   
                   
                 variant 
                   
                 products 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 cattle feed 
                 175 
                 2015LSAL00792 
               
               
                   
                   
                 variant 
                   
                   
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 beef meat 
                 176 
                 2013LSAL02030 
               
               
                   
                   
                 variant 
                   
                 (carcass) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 pork 
                 177 
                 2015LSAL01461 
               
               
                   
                   
                 variant 
                   
                 (carcass) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 turkey 
                 178 
                 2013LSAL03886 
               
               
                   
                   
                 variant 
                   
                 (carcass) 
                   
                   
               
               
                 
                   Typhimurium 
                 
                 1,4,[5],12:i:— 
                 monophasic 
                 Anses 
                 chicken 
                 179 
                 2016LSAL00194 
               
               
                   
                   
                 variant 
                   
                 (carcass) 
               
               
                   
               
            
           
         
       
     
     It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All patents, patent applications, internet sources, and other published reference materials cited in this specification are incorporated herein by reference in their entireties. Any discrepancy between any reference material cited herein or any prior art in general and an explicit teaching of this specification is intended to be resolved in favor of the teaching in this specification. This includes any discrepancy between an art-understood definition of a word or phrase and a definition explicitly provided in this specification of the same word or phrase.