Patent Publication Number: US-2020283845-A1

Title: Microarray Based Multiplex Pathogen Analysis for Plants, Agriculture, Food, and Water

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This is a continuation under 35 U.S.C. § 120 of pending non-provisional application U.S. Ser. No. 15/388,561, filed Dec. 22, 2016, which claims benefit of priority under 35 U.S.C. § 119(e) of U.S. Ser. No. 62/271,371, filed Dec. 28, 2015, now abandoned, the entirety of both of which are hereby incorporated by reference. 
    
    
     TECHNICAL FIELD 
     The present disclosure is in the technical field of DNA based pathogen analysis. More particularly, the present disclosure is in the technical field of pathogen analysis on plant, agriculture, food and water material using DNA based microarray technology. 
     BACKGROUND-PRIOR ART 
     Prevailing techniques used to identify microbial pathogens rely upon established clinical microbiology monitoring. Pathogen identification is conducted using standard culture and susceptibility tests. These tests require a substantial investment of time, effort, cost as well as labile products. Further, such techniques are not ideal for testing large numbers of samples. Culture-based testing is fraught with inaccuracies which include both false positives and false negatives, as well as unreliable quantification of colony forming units (CFUs). There are issues with the presence of viable but non-culturable microorganisms which do not show up using conventional culture methods. Certain culture tests are very non-specific in terms of detecting both harmful and harmless species which diminishes the utility of the test to determine if there is a threat present in the sample being tested. 
     In response to challenges including false positives and culturing of microorganisms, DNA-based diagnostic methods such as polymerase chain reaction (PCR) amplification techniques were developed. For use of PCR, the pathogen DNA to be analyzed is extracted from the material prior to analysis, this is a time-consuming and costly step in the process. In an attempt to eliminate the preanalysis extraction step of PCR, Colony PCR was developed. Using cells directly from colonies from plates or liquid cultures, Colony PCR allows PCR!of bacterial cells without sample preparation. This technique was a partial success, as it was not as sensitive as culture which indicated a possible issue with interference of the PCR by constituents in the specimens. The possible interference issue was deemed not significant enough to invalidate the utility of the testing performed. However, such interference can be significant for highly sensitive detection of pathogens for certain types of tests. Consequently, Colony PCR did not eliminate the pre-analysis extraction step for use of PCR, especially for highly sensitive detection of pathogens. 
     It is known from the literature that 16S DNA in bacteria and the ITS2 DNA in yeast or mold can be PCR amplified, and once amplified can be analyzed to provide information about the specific bacteria or specific fungal contamination in or on plant material. Further, for certain samples such as blood, fecal matter and others, PCR may be performed on the DNA in such samples absent any extraction of the DNA. However, for blood it is known that the result of such direct PCR is prone to substantial sample to sample variation due to inhibition by blood analytes. Additionally, attempts to perform direct PCR analysis on plant matter have generally been unsuccessful, due to heavy inhibition of PCR by plant constituents. 
     Over time, additional methods and techniques were developed to improve on the challenges of timely and specific detection and identification of pathogens. Immunoassay techniques provide specific analysis, however, the technique is costly in the use of chemical consumables and has a long response time. Optical sensor technologies produce fast real-time detection, however, such sensors lack identification specificity, as they offer a generic detection capability as the pathogen is usually optically similar to its benign background. Quantitative Polymerase Chain Reaction (qPCR) technique is capable of amplification and detection of a DNA sample in less than an hour. However, qPCR is largely limited to the analysis of a single pathogen. Consequently, if many pathogens are to be analyzed concurrently, as is the case with plant, agriculture, food and water material, a relatively large number of individual tests are performed in parallel. 
     Biological microarrays have become a key mechanism in a wide range of tools used to detect and analyze DNA. Microarray-based detection combines DNA amplification with the broad screening capability of microarray technology. This results in a specific detection and improved rate of process. DNA microarrays can be fabricated with the capacity to interrogate, by hybridization, certain segments of the DNA in bacteria and eukaryotic cells such as yeast and mold. However, processing a large number of PCR reactions for downstream microarray applications is costly and requires highly skilled individuals with complex organizational support. Because of these challenges, microarray techniques have not led to the development of downstream applications. 
     We have found, that there is a need for a method of DNA based pathogen analysis that interrogates a large number of samples, uses fewer chemical and labile products, and provides faster results while maintaining accuracy, specificity and reliability. 
     SUMMARY OF EMBODIMENTS 
     Embodiments of the present disclosure for a microarray based multiplex pathogen analysis method include two steps. One step is DNA amplification of the pathogen DNA of interest. For example, PCR amplification of the sample is conducted prior to biochemical or physical extraction of the pathogen DNA. In this step, the DNA amplification reaction itself provides enrichment of the pathogen DNA(s) of interest. By bypassing the DNA extraction and purification steps, the test procedure is made markedly faster. Further, the test procedure improves sensitivity as the circumvention of DNA extraction procedures mitigates the DNA loss and DNA dilution that accompany DNA extraction. In short, the embodiments do not require pre-analysis DNA extraction nor purification because a microbial pellet obtained from the material is subjected to DNA amplification without purification, the resulting PCR-amplified material is then suitable for analysis. 
     A second step is DNA microarray analysis of highly repetitive DNA segments in the plant borne pathogens; DNA segments in bacteria or DNA segments in eukaryotic pathogens (yeast and mold), or amplification of specific sequences from unique single copy gene. The repetitive DNA segments are used primarily for highly sensitive detection of specific organisms or for unique biomarker genes or genomic sequences with significant value towards identifying pathogens or even genetic variations within the genome of the host organism (i.e., a plant). In bacteria, the highly repetitive DNA segments are the 16S rDNA gene. 
     In eukaryotes, the highly repetitive DNA segments are the Internal Transcribed Spacer—2 region, (ITS2). These two types of highly repetitive DNA are known to harbor DNA sequence changes that can be used to distinguish bacteria from each other (16S) and yeast or mold from each other (ITS2). In the present disclosure, a panel of nucleic acid probes is assembled that are capable of recognizing (by DNA hybridization) those DNA sequence changes in bacteria (within 16S), and also within the genes which encode specific pathogen genes and the corresponding sequence changes in yeast or mold (within ITS2). Therefore, subsequent to DNA amplification of non-extracted samples, the amplified 16S DNA can be interrogated on a single microarray, as a single hybridization test, thereby resolving a panel of bacteria which may be present in the plant, agriculture, food, or water specimens. Similarly, subsequent to DNA amplification of non-extracted samples, the amplified ITS2 DNA can be interrogated on a single microarray, as a single hybridization test, thereby resolving a panel of yeast and mold which may be present in the plant, agriculture, food, or water material. The embodiments of the present disclosure with a microarray component of the present disclosure allow a number of individual tests to be performed as a single multiplex test. 
     Embodiments of the present disclosure are described herein by reference to a microarray based multiplex pathogen analysis. The disclosure is not, however, limited by the #! advantages of the aforementioned embodiment. The present method may also be applied to many types of material capable of generating DNA based pathogen analysis. Further, it should be understood that the disclosed embodiments may be combined with one another. In addition, features of particular embodiments may be exchanged with features of other embodiments. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       These and other features, aspects, and advantages of the embodiments of the present disclosure will become better understood when the following detailed description is read with reference to the accompanying drawings in which like characters represent like parts throughout the drawing, wherein: 
         FIG. 1  is a graphical representation of the position of PCR primers employed within the 16S locus (all bacteria, SEQ ID NOS: 1-4) and also in the stx1 locus (pathogenic  E. coli , SEQ ID NOS: 5-8) to be used to PCR amplify unpurified bacterial contamination obtained from cannabis wash and related plant wash. These PCR primers are used to amplify and dye label DNA from such samples for bacterial analysis via microarray hybridization. 
         FIG. 2  is a graphical representation of the position of PCR primers employed within the stx2 locus (pathogenic  E. coli , SEQ ID NOS: 9-12) and also in the invA locus (all  Salmonella , SEQ ID NOS: 13-16) to be used to PCR amplify unpurified bacterial contamination obtained from cannabis wash and related plant wash. These PCR primers are used to amplify and dye label DNA from such samples for bacterial analysis via microarray hybridization. 
         FIG. 3  is a graphical representation of the position of PCR primers employed within the tuf locus (All  E. coli , SEQ ID NOS: 17-20) to be used to PCR amplify unpurified bacterial contamination obtained from cannabis wash and related plant wash. These PCR primers are used to amplify and dye label DNA from such samples for bacterial analysis via microarray hybridization. 
         FIG. 4  is a graphical representation of the position of PCR primers employed within the ITS2 locus (All yeast and mold, SEQ ID NOS: 21-24) to be used to PCR amplify unpurified yeast and mold contamination obtained from cannabis wash and related plant wash. These PCR primers are used to amplify and dye label DNA from such samples for yeast and mold analysis via microarray hybridization. 
         FIG. 5  is a graphical representation of the position of PCR primers employed within the ITS1 locus (Cannabis Plant Control, SEQ ID NOS: 25-28) to be used to PCR amplify unpurified DNA obtained from cannabis wash. These PCR primers are used to amplify and dye label DNA from such samples for DNA analysis via microarray hybridization. This PCR reaction is used to generate an internal plant host control signal, via hybridization, to be used to normalize bacterial, yeast, mold and fungal signals obtained by microarray analysis on the same microarray. 
         FIGS. 6A-6B  are Tables which list representative oligonucleotide hybridization probes employed within the 16S locus (bacteria, SEQ ID NOS: 37-79) and ITS2 locus (yeast and mold, SEQ ID NOS: 80-116) to be used to detect the PCR products obtained via amplification of unpurified bacteria, yeast, mold and fungi obtained from cannabis wash. These microarray hybridization probes are optimized to support hybridization analysis at room temperature. They are linked to microarray supports via modifications, not shown here. 
         FIG. 7  displays representative oligonucleotide sequences which are used as microarray probes in an embodiment for DNA microarray based analysis of bacterial pathogens (stx1, stx2, invA, tuf; SEQ ID NOS: 117-120, respectively) and for DNA analysis of the presence of host cannabis DNA at the ITS1 region ( Cannabis  spp, SEQ ID NO: 121). 
         FIG. 8  is a flow diagram to demonstrate the acceptance of unpurified cannabis wash or other surface sampling from cannabis (and related plant material or water sample) then to PCR amplify the raw cannabis or related plant material or water sample, then to perform microarray analysis on that material so as to interrogate the pathogen complement of those plant or water samples. 
         FIG. 9  is an image of the microarray format used to implement the hybridization probes. This representative format comprises 12 microarrays printed on a glass slide, each separated by a Teflon divider (left). Also, shown is a blow-up (right) of one such microarray for the analysis of pathogens in cannabis and related plant materials or water samples. The Teflon border about each microarray is fit to localize a 50 uL fluid sample for room temperature hybridization analysis, to be followed by washing at room temperature then microarray image scanning of the dye-labelled pathogen and host plant DNA. 
         FIGS. 10A-10B  are representative microarray hybridization data obtained from purified bacterial DNA standards ( FIG. 10A ) and purified fungal DNA standards ( FIG. 10B ). In each case, the purified bacterial DNA ( FIG. 10A ) is PCR amplified as though it were an unpurified DNA, then hybridized on the microarray via the microarray probes described above. The data show that in this microarray format, each of the bacteria can be specifically identified via room temperature hybridization and washing. Similarly, the purified fungal DNA ( FIG. 10B ) is PCR amplified as though it were an unpurified DNA, then hybridized on the microarray via the microarray probes described above. The data show that in this microarray format, each of the fungal DNAs can be specifically identified via room temperature hybridization and washing. 
         FIG. 11  is representative microarray hybridization data obtained from 5 representative raw cannabis wash samples. In each case, the raw pathogen complement of these 5 samples is PCR amplified, then hybridized on the microarray via the microarray probes described above. The data show that in this microarray format, specific bacterial, yeast, mold and fungal contaminants can be specifically identified via room temperature hybridization and washing. 
         FIG. 12  is representative microarray hybridization data obtained from a representative raw cannabis wash sample compared to a representative (raw) highly characterized, candida sample. In each case, the raw pathogen complement of each sample is PCR amplified, then hybridized on the microarray via the microarray probes described above. The data show that in this microarray format, specific fungal contaminants can be specifically identified via room temperature hybridization and washing on either raw cannabis wash or cloned fungal reference sample. 
         FIGS. 13A-13B  are graphical representations of the position of PCR primers employed in a variation of an embodiment for low level detection of Enterobacteriaceae (SEQ ID NOS: 29-32) and  Aspergillus  spp. (SEQ ID NOS: 33-36). These PCR primers are used to selectively amplify and dye label DNA from targeted organisms for analysis via microarray hybridization. 
         FIGS. 14A-14B  are graphical representations of microarray hybridization data demonstrating low level detection of  E. coli  O157:H7 and  E. coli  O111 from certified reference material consisting ofenumerated colonies of specified bacteria spiked onto  Humulus lupulus , (Hop plant). 
         FIG. 15  is a graphical representation of microarray hybridization data demonstrating low level detection of  Salmonella enterica  from certified reference material consisting of enumerated colonies of specified bacteria spiked onto  Humulus lupulus , (Hop plant). 
         FIGS. 16A-16R  are a collection of representative microarray hybridization data obtained from powdered dry food samples with no enrichment and 18 hour enrichment for comparison. The data shows that bacterial microbes were successfully detected without the need for enrichment. 
         FIG. 17A  shows diagrams for sample collection and preparation from two methods. Both the tape pull and wash method are used to process samples to provide a solution for microbial detection via microarray analysis. 
         FIG. 17B  is representative microarray hybridization data obtained from blueberry and lemon washes. Both sample types were found to be positive for fungal microbes demonstrating the use of an embodiment for recovery of yeast and mold microbes on fruit surfaces. 
         FIG. 17C  is representative microarray hybridization data obtained from blueberry and lemon tape pulls. Both the blueberry and lemon washes and tape pulls produced the same yeast and mold microbial profiles demonstrating that either method for recovering microbes from a fruit&#39;s surface may be used to obtain a useful analysis of potential pathogens. 
         FIG. 18  is representative microarray data from raw water filtrate. Microbes collected via filtration from 5 well-water samples were washed from the water filters much as the surface of plant leaves or fruit surfaces are washed and were found to contain aerobic and bile-tolerant gram negative bacteria in this embodiment. The data in  FIG. 18  demonstrates the same combination of raw sample genotyping, PCR, and microarray analysis used for cannabis and fruit washes may also be used to screen for microbial contamination in environmental water samples. 
     
    
    
     DETAILED DESCRIPTION OF SPECIFIC EMBODIMENTS 
     The present disclosure provides an improved method for DNA based pathogen analysis. The embodiments of the present disclosure contemplate the use of DNA amplification methodologies, including but not limited to loop-mediated isothermal amplification (LAMP) or polymerase chain reaction (PCR) tests that can selectively amplify the DNA complement of that plant material using unpurified plant and pathogen material. The embodiments are also based on the use of aforementioned PCR-amplified DNA as the substrate for microarray-based hybridization analysis, wherein the hybridization is made simple because the DNA probes used to interrogate the DNA of such pathogens is optimized to function at room temperature. This enables the use of the above mentioned microarray test at ambient temperature, thus bypassing the previously established requirement that testing be supported by an exogenous temperature-regulating device. 
     Turning now to the Drawings, and referring first to  FIG. 1 , an exemplar of the first PCR step is shown. As is standard, such PCR reactions are initiated by the administration of PCR Primers. Primers define the start and stopping point of the PCR based DNA amplification reaction. In this embodiment, a pair of PCR reactions is utilized to support the needed DNA amplification. In general, such PCR amplification is performed in series: a first pair of PCRs, with the suffix “P1” in  FIG. 1  are used to amplify about 1 μL of any unpurified DNA sample, such as a raw cannabis leaf wash for example. About 1 μL of the product of that first PCR reaction is used as the substrate for a second PCR reaction that is used to affix a fluorescent dye label to the DNA, so that the label may be used to detect the PCR product when it binds by hybridization to the microarray. The role of this two-step reaction is to avert the need to purify the pathogen DNA to be analyzed: the first PCR reaction, with primers “P1” is optimized to accommodate the raw starting material, while the second PCR primer pair “P2” are optimized to obtain maximal DNA yield, plus dye labeling from the product of the first reaction. Taken in the aggregate, the sum of the two reactions obviates the need to either purify or characterize the pathogen DNA of interest. 
     Two types of such two-step PCR reaction are shown in  FIG. 1 . The top section reveals at low resolution the 16SrDNA region which is amplified in an embodiment, to isolate and amplify a region which may be subsequently interrogated by hybridization. The DNA sequence of this 16S rDNA region is known to vary greatly among different bacterial species. Consequently, having amplified this region by two step PCR, that sequence variation may be interrogated by the subsequent microarray hybridization step. 
     The bottom section of  FIG. 1  displays the stx1 gene locus which is present in the most important pathogenic strains of  E coli  and which encodes Shigatoxin 1. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed bacterial samples so as to present the stx1 locus for analysis by microarray based DNA hybridization. 
     The top section of  FIG. 2  displays the stx2 gene locus which is also present in the most important pathogenic strains of  E coli  and which encodes Shigatoxin 2. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed bacterial samples so as to present the stx2 locus for analysis by microarray based DNA hybridization. 
     The bottom section of  FIG. 2  displays the invA gene locus which is present in all strains of  Salmonella  and which encodes the Invasion A gene product. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed bacterial samples so as to present the invA locus for analysis by microarray based DNA hybridization. 
       FIG. 3  displays the tuf gene locus which is present in all strains of  E coli  and which encodes the ribosomal elongation factor Tu. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed bacterial samples so as to present the tuf locus for analysis by microarray based DNA hybridization. 
       FIG. 4  displays the ITS2 region which is present in all eukaryotes, including all strains of yeast and mold and which encodes the intergenic region between ribosomal genes 5.8S and 28S. ITS2 is highly variable in sequence and that sequence variation can be used to resolve strain differences in yeast and mold. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed yeast and mold samples so as to present the ITS2 region for analysis by microarray based DNA hybridization. 
       FIG. 5  displays the ITS1 region which is present in all eukaryotes, including all plants and animals, which encodes the intergenic region between ribosomal genes 18S and 5.8S. ITS1 is highly variable in sequence among higher plants and that sequence variation can be used to identify plant species, and in many cases, animal species as well. Employing the same two-step PCR approach, we have designed a set of two PCR primer pairs which, in tandem, can be used to amplify and label unprocessed cannabis samples so as to present the ITS1 region for analysis by microarray based DNA hybridization. The identification and quantitation of the cannabis sequence variant of ITS1 is used as an internal normalization standard in the analysis of pathogens recovered from the same cannabis samples. 
       FIG. 6A  displays representative oligonucleotide sequences which are used as microarray probes in an embodiment for DNA microarray based analysis of bacterial pathogens.  FIG. 6A  lists the sequences of a number of representative oligonucleotide probe sequences that have been designed to analyze bacteria, via PCR products obtained by 2 step amplification of the 16S locus in bacteria, as described in  FIG. 1 . The sequence of those probes has been varied to accommodate the cognate sequence variation which occurs as a function of species difference among bacteria. 
       FIG. 6B  displays representative oligonucleotide sequences which are used as microarray probes in an embodiment for DNA microarray based analysis of fungal pathogens.  FIG. 6B  lists the sequence of a number of representative oligonucleotide probe sequences that have been designed to analyze fungi, via PCR products obtained by 2 step amplification of the ITS2 region in bacteria, as described in  FIG. 4 . The sequences of those probes has been varied to accommodate the cognate sequence variation which occurs as a function of species difference among fungi. 
       FIG. 7  displays representative oligonucleotide sequences which are used as microarray probes in an embodiment for DNA microarray based analysis of bacterial pathogens (stx1, stx2, invA, tuf) and for DNA analysis of the presence of host cannabis DNA at the ITS1 region ( Cannabis  spp). 
     In  FIG. 8 , we display a flow diagram to describe how an embodiment is used to analysis the bacterial pathogen or yeast and mold complement of a cannabis or related plant sample. Pathogen samples can be harvested from cannabis plant material by tape pulling if surface bound pathogen or by simple washing of the leaves or buds or stems, followed by a single multiplex “Loci Enhancement” Multiplex PCR reaction, then followed by a single multiplex “Labelling PCR”. A different pair of two step PCR reactions is used to analyze bacteria, than the pair of two step PCR reactions used to analyze yeast and mold. In all cases, the DNA of the target bacteria or yeast or mold of fungi are PCR amplified without extraction or characterization of the DNA prior to two step PCR. Subsequent to the Loci Enhancement and Labelling PCR steps, the resulting PCR product is simply diluted into binding buffer and then applied to the microarray test. The subsequent microarray steps required for analysis (hybridization and washing) are performed at lab ambient temperature. 
       FIG. 9  provides images of a representative implementation of microarrays used in an embodiment. In this implementation, all oligonucleotide probes required for bacterial analysis along with cannabis DNA controls (as in  FIG. 6A ) are fabricated into a single 144 element (12×12) microarray, along with additional bacterial probes such as those in  FIG. 7 . In this implementation, all oligonucleotide probes required for yeast and mold analysis along with cannabis DNA controls (as in  FIG. 6B ) are fabricated into a single 144 element (12×12) microarray, along with additional fungal probes such as those in  FIG. 7 . The arrays are manufactured on PTFE coated glass slides as two columns of 6 identical microarrays. Each of the 12 identical microarrays is capable of performing, depending on the oligonucleotide probes employed, a complete microarray based analysis bacterial analysis or a complete microarray based analysis of yeast and mold. Oligonucleotide probes are linked to the glass support via microfluidic printing, either piezoelectric or contact based or an equivalent. The individual microarrays are fluidically isolated from the other 11 in this case, by the hydrophobic PTFE coating, but other methods of physical isolation can be employed. 
       FIGS. 10A-10B  display representative DNA microarray analysis of an embodiment. In this case, purified bacterial DNA or purified fungal DNA has been used, to test for affinity and specificity subsequent to the two-step PCR reaction and microarray based hybridization analysis. As can be seen, the oligonucleotide probes designed to detect each of the test bacterial DNA ( FIG. 10A ) of test fungal DNA ( FIG. 10B ) have bound to the target DNA correctly via hybridization and thus have correctly detected the bacterium or yeast. 
     Representative Microarray Hybridization Data Obtained from Purified Bacterial DNA Standards 
                             PURIFIED DNA BACTERIA PANEL                                                      Aeromonas        Bacillus        Campylobactor                hydrophila        subtilus      ssp.               Low Pan Bacteria    4434    15943    38700        Control                    Medium Pan Bacteria    7893    33069    28705        Control                    High Pan Bacteria    14934    23469    32936        Control                    Low Bile tolerant gram    5364    947    867        negative                    High Bile tolerant gram    55228    339    422        negative                    Total Coliform    106    101    145          E. coli      104    121    127          E. Coli  specific gene    318    255    422          E. Coli  Stx1    106    116    158          E. Coli  Stx2    100    100    126          Enterobacteriacea      885    125    211          Salmonella /    115    99    124          Enterobacter                        Salmonella  specific    189    175    217        gene                      Aeromonas      10335    120    123          Pseudomonas      106    107    120          Pseudomonas      169    228    173          aeriginosa                        Xanthomonas      98    188    122          Listeria      117    263    144          Campylobacter      148    120    65535          Bacillus  Group 2    143    34517    121                         E. coli                    E. coli      0157:H7      Listeria  ssp.               Low Pan Bacteria    4215    1745    14140        Control                    Medium Pan Bacteria    8349    3638    35237        Control                    High Pan Bacteria    9827    4327    16726        Control                    Low Bile tolerant gram    2803    1801    817        negative                    High Bile tolerant gram    24172    14746    1482        negative                    Total Coliform    8276    9175    139          E. coli      55419    47805    151          E. Coli  specific gene    57638    57112    521          E. Coli  Stx1    134    65535    151          E. Coli  Stx2    169    52041    135          Enterobacteriacea      58323    36641    179          Salmonella /    190    160    144          Enterobacter                        Salmonella  specific    208    392    212        gene                      Aeromonas      127    139    163          Pseudomonas      130    126    133          Pseudomonas      318    1217    208          aeriginosa                        Xanthomonas      133    143    143          Listeria      136    128    24783          Campylobacter      139    153    224          Bacillus  Group 2    128    150    137                     Pseudomonas        Salmonella        Xanthomonas                aeruginosa        enterica      ssp.               Low Pan Bacteria    26431    11167    22152        Control                    Medium Pan Bacteria    39002    17682    24141        Control                    High Pan Bacteria    38682    28596    22072        Control                    Low Bile tolerant gram    4852    4453    461        negative                    High Bile tolerant gram    36337    32579    356        negative                    Total Coliform    145    204    196          E. coli      144    83    147          E. Coli  specific gene    695    641    461          E. Coli  Stx1    142    196    145          E. Coli  Stx2    147    117    132          Enterobacteriacea      375    23847    204          Salmonella /    138    37520    144          Enterobacter                        Salmonella  specific    211    8124    231        gene                      Aeromonas      142    99    146          Pseudomonas      25866    77    153          Pseudomonas      64437    135    424          aeriginosa                        Xanthomonas      221    80    41903          Listeria      144    79    131          Campylobacter      144    88    160          Bacillus  Group 2    139    81    134                    
Representative Microarray Hybridization Data Obtained from Purified Bacterial DNA Standards
 
     
       
         
           
               
            
               
                   
               
               
                 PURIFIED DNA FUNGAL PANEL 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 
                   A. 
                 
                 
                   A. 
                 
                   
                 
                   Fusarium 
                 
                 
                   Penicillium 
                 
                   
               
               
                   
                 
                   fumigatus 
                 
                 
                   flavus 
                 
                 
                   A. niger 
                 
                 spp. 
                 spp. 
                 
                   Mucor 
                 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Low Pan 
                 4269 
                 6097 
                 5252 
                 13907 
                 3929 
                 3073 
               
               
                 Fungal 
                   
                   
                   
                   
                   
                   
               
               
                 Control 
                   
                   
                   
                   
                   
                   
               
               
                 Medium 
                 27006 
                 30445 
                 19746 
                 30972 
                 30947 
                 49986 
               
               
                 Pan Fungal 
                   
                   
                   
                   
                   
                   
               
               
                 Control 
                   
                   
                   
                   
                   
                   
               
               
                 High Pan 
                 64940 
                 64679 
                 54483 
                 47268 
                 65535 
                 63932 
               
               
                 Fungal 
                   
                   
                   
                   
                   
                   
               
               
                 Control 
                   
                   
                   
                   
                   
                   
               
               
                 Negative 
                 119 
                 127 
                 151 
                 107 
                 117 
                 118 
               
               
                 control 
                   
                   
                   
                   
                   
                   
               
               
                 
                   A. 
                 
                 62018 
                 232 
                 114 
                 604 
                 126 
                 228 
               
               
                 
                   fumigatus 
                 
                   
                   
                   
                   
                   
                   
               
               
                 
                   A. flavus 
                 
                 210 
                 65535 
                 116 
                 102 
                 115 
                 128 
               
               
                 
                   A. niger 
                 
                 113 
                 235 
                 24867 
                 108 
                 115 
                 112 
               
               
                 
                   Botrytis 
                 
                 189 
                 205 
                 435 
                 101 
                 126 
                 121 
               
               
                 
                   Penicillium 
                 
                 171 
                 282 
                 121 
                 100 
                 5891 
                 316 
               
               
                 
                   F. solani 
                 
                 112 
                 131 
                 174 
                 16578 
                 113 
                 140 
               
               
                 
                   Mucor 
                 
                 118 
                 127 
                 113 
                 150 
                 113 
                 29886 
               
               
                   
               
            
           
         
       
     
       FIG. 11  displays representative DNA microarray analysis of an embodiment. In this case, 5 different unpurified raw cannabis leaf wash samples have been used, to test for affinity and specificity subsequent to the two-step PCR reaction and microarray based hybridization analysis. Both bacterial and fungal analysis has been performed on all 5 leaf wash samples, by dividing each sample into halves and subsequently processing them each for analysis of bacteria or for analysis of yeast and mold. The data of  FIG. 11  were obtained by combining the outcome of both assays. The data of  FIG. 11  show that the combination of two step PCR and microarray hybridization analysis, as described in  FIG. 8 , can be used to interrogate the pathogen complement of a routine cannabis leaf wash. It is expected, but not shown that such washing of any plant material could be performed similarly. 
       FIG. 12  displays representative DNA microarray analysis of an embodiment. In this case, (1) unpurified raw cannabis leaf wash samples was used and was compared to data obtained from a commercially-obtained homogenous vitroid culture of live  Candida , a fungus (more specifically a type of yeast) to test for affinity and specificity subsequent to the two-step PCR reaction and microarray based hybridization analysis. Both cannabis leaf wash and cultured fungal analysis have been performed by processing them each for analysis via probes specific for fungi (see  FIGS. 6B and 7 ). The data of  FIG. 12  were obtained by combining the outcome of analysis of both the leaf wash and vitroid culture samples. The data of  FIG. 12  show that the combination of two step PCR and microarray hybridization analysis, as described in  FIG. 8 , can be used to interrogate the fungal complement of a routine cannabis leaf wash as adequately as can be done with a pure (live) fungal sample. It is expected, but not shown that fungal analysis via such washing of any plant material could be performed similarly. 
       FIGS. 13A-13B  are a variation of the assay described in the top section of  FIG. 1  as shown in  FIG. 13A . This version of the assay was designed to detect the presence of very low levels of pathogenic Enterobacteriaceae. Instead of amplifying the HV3 region of the 16S rDNA loci for all bacteria, the PCR primers are specific for the family Enterobacteriaceae. Increased sensitivity is achieved by the elimination of the testing for background species of bacteria that would lead to reagent exhaustion and potentially mask the detection of low level pathogens. One CFU detection of  E. coli  and  Salmonella enterica  was demonstrated with this version of the assay as shown in  FIG. 13A .  FIG. 13B  shows a variation on the assay described in  FIG. 4 . This version of the assay replaces the universal fungal PCR primers employed in Figure. 4 with PCR primers specific for the genus  Aspergillus . As in the corresponding Enterobacteriaceae assay, increased sensitivity is achieved by eliminating the competition for amplification reagents by background species. One CFU detection of  Aspergillus niger, Aspergillus flavus  and  Aspergillus fumigatus  has been demonstrated with this version of the assay, as shown in  FIG. 13B . 
       FIGS. 14 and 15  display representative DNA microarray analysis of an embodiment: to demonstrate assay sensitivity over a range of microbial inputs. In this case, certified reference material consisting of enumerated bacterial colonies of  E. coli  O157:H7 , E. coli  O111 ( FIG. 14 ) and  Salmonella enterica  ( FIG. 15 ) were spiked as a dilution series onto a hops plant surrogate matrix then processed using the assay version described in  FIGS. 13A-13B . Hybridization results from relevant probes from  FIGS. 6A-6B  are shown. The larger numbers on the x-axis represents the total number of bacterial colony forming units (CFU) that were spiked onto each hops plant sample, whereas the smaller numbers on the x-axis represent the number of CFU&#39;s of the spiked material that were actually inputted into the assay. Only about 1/50 of the original spiked hops sample volume was actually analyzed on the microarray. Thus, the smaller numbers upon the x-axis of  FIGS. 14 &amp; 15  are exactly 1/50th that of the total (lower) values. As is seen,  FIGS. 14 and 15  both show that the microarray test of an embodiment can detect less than 1 CFU per microarray assay. The nucleic acid targets within the bacterial genomes displayed in  FIGS. 14 and 15  comprise 16S rDNA. There are multiple copies of the 16S rDNA gene in each of these bacterial organisms, which enables detection at &lt;1CFU levels. Since a colony forming unit approximates a single bacterium in many cases, the data of  FIGS. 14 and 15  demonstrate that the present microarray assay has sensitivity which approaches the ability to detect a single (or a very small number) of bacteria per assay. Similar sensitivity is expected for all bacteria and eukaryotic microbes in that it is known that they all present multiple copies of the ribosomal rDNA genes per cell. 
       FIGS. 16A-16R  display an application of an embodiment to Processed Agricultural Products. The above teaching shows, by example, that unprocessed leaf and bud samples may be washed in an aqueous water solution, to yield a water-wash containing microbial pathogens which can then be analyzed via the present combination of RSG and microarrays. If such fresh leaf and bud materials were processed by drying, grinding or other ordinary processes, rather than analyzed when fresh, and if the microbial complement of the processed sample remained intact, then the present combination of RSG and microarray analysis would be capable of recovering and analyzing the DNA complement of those microbes in the processed material: just as it has been shown to do for fresh leaf material. 
       FIGS. 16A-16R  display data from eighteen powdered dry food samples which were processed for analysis using the PathogenDx microarray assay system, as described above. For each sample which was already processed to be a powder, 10 g of sample was added to a Whirl-pak bag followed by 100 ml of the standard washing buffer to each bag. For those samples which were not yet a powder, they were ground with a pestle then processed. Each bag was manually stomached and then a 1 ml aliquot was removed as the “pre-enriched” sample for each food type. The bags were then placed in a 35° C. incubator for approximately 18 hours. After the enrichment, a 1 ml aliquot of the 18 hour incubation product was collected for each food type and labeled as the “enriched” sample. Both the pre-enriched and enriched aliquots were prepared for PCR amplifications followed by microarray analyses, exactly as described above.  FIGS. 16A-16R  comprise graphs of the raw data, for both pre-enriched and enriched samples for each of the food types are attached. There is also one graph for each of the Low, Medium, and High Total Aerobic, Bile Tolerant Gram Negative, and Total Yeast and Mold probes. Please note that the B3 marker (probes BTGN QCON3 and TABQCON3) is the positive control present at 5000 copies per reaction, which was doped into each specimen. 
     The data of  FIGS. 16A-16R  show that, for all specimens tested, the general combination of raw sample genotyping and microarray analysis, as described above, has successfully detected bacterial microbes in the processed food samples tested, with the exception of Rice Protein ( FIG. 161 ), which appears to be free of detectible bacterial contamination. It should be noted that in each case, the data obtained without any fluid phase enrichment, is as sensitive as that obtained with 18 hours of fluid phase enrichment at 37 C. Thus, the data of  FIGS. 16A-16R  show that an embodiment can detect bacterial contamination in processed foods without the need for pre-enrichment. 
       FIGS. 17A-17C  are embodiments for the analysis of fruit, embodiments for the analysis of vegetables and embodiments for the analysis of other plant matter. The above teaching shows by example that unprocessed leaf and bud samples in cannabis and hops may be washed in an aqueous water solution, to yield a water-wash containing microbial pathogens which can then be analyzed via the present combination of RSG and microarrays. If fresh leaf, flower, stem or root materials from fruit and vegetables could also be washed in a water solution in that same way (when fresh or after drying and grinding or other types or processing) ( FIG. 7A ) so that the present combination of RSG and microarray analysis would be capable of recovering and analyzing the DNA complement of those microbes in those other materials. 
     At least two methods of sample collection are possible. A simple rinsing of the fruit, exactly as described for cannabis, above. Another method of sample collection is a “tape pull”, wherein a piece of standard forensic tape is applied to the surface of the fruit, then pulled off. Upon pulling, the tape is then soaked in the standard wash buffer described above, to suspend the microbes attached to the tape. Subsequent to the tape-wash step, all other aspects of the processing and analysis (i.e. raw sample genotyping, PCR, then microarray analysis) are exactly as described above. 
     The data of  FIG. 17B  demonstrates that simple washing of the fruit and tape pull sampling of the fruit generate similar microbial data. The blueberry sample is shown to be positive for  Botrytis , as expected, since  Botrytis  is a well-known fungal contaminant on blueberries. The lemon sample is shown to be positive for  Penicillium , as expected, since  Penicillium  is a well-known fungal contaminant for lemons. 
     The data embodied in  FIG. 17C , demonstrates the use of an embodiment, for the recovery and analysis of yeast microbes on the surface of fruit (blueberries and lemons in this case), but an embodiment could be extended to other fruits and vegetables for the analysis of both bacterial and fungal contamination. 
       FIG. 18  shows embodiments for the analysis of environmental water samples/specimens. The above teaching shows by example that unprocessed leaf and bud samples in cannabis and hops may be washed in an aqueous water solution, to yield a water-wash containing microbial pathogens which can then be analyzed via the present combination of RSG and microarrays. If a water sample containing microbes were obtained from environmental sources (such as well water, or sea water, or soil runoff or the water from a community water supply) and then analyzed directly, or after ordinary water filtration to concentrate the microbial complement onto the surface of the filter, that the present combination of RSG and microarray analysis would be capable of recovering and analyzing the DNA complement of those microbes. 
     The data embodied in  FIG. 18  were obtained from 5 well-water samples (named 2H, 9D, 21, 23, 25) along with 2 samples of milliQ laboratory water (obtained via reverse osmosis) referred to as “Negative Control”. All samples were subjected to filtration on a sterile 0.4 um filter. Subsequent to filtration, the filters, with any microbial contamination that they may have captured, were then washed with the standard wash solution, exactly as described above for the washing of cannabis and fruit. Subsequent to that washing the suspended microbes in wash solution were then subjected to exactly the same combination of centrifugation (to yield a microbial pellet) then lysis and PCR of the unprocessed pellet-lysate (exactly as described above for cannabis), followed by PCR and microarray analysis: also as described for cannabis. 
     The data seen in  FIG. 18  demonstrate that microbes collected on filtrates of environmental water samples can be analyzed via the same combination of raw sample genotyping, then PCR and microarray analysis used for cannabis and fruit washes. The shaded elements of the Table in  FIG. 18  demonstrate that the 5 unprocessed well-water samples all contain aerobic bacteria (upper shaded box) and bile tolerant gram negative bacteria (lower shaded box). The presence of both classes of bacteria is expected for unprocessed (raw) well water. Thus, the data of  FIG. 18  demonstrate that an embodiment can be used for the analysis of environmentally derived water samples. 
     Embodiments for analysis of industrial washes derived from food processing. The above teaching shows by example that unprocessed leaf and bud samples in cannabis and hops may be washed in an aqueous water solution, to yield a water-wash containing microbial pathogens which can then be analyzed via the present combination of RSG and microarrays. The above data also show that environmentally-derived well water samples may be analyzed by an embodiment. Further, if a water sample containing microbes were obtained from industrial processing sources (such as the water effluent from the processing of fruit, vegetables, grain, meat) and then analyzed directly, or after ordinary water filtration to concentrate the microbial complement onto the surface of the filter, that the present combination of RSG and microarray analysis would be capable of recovering and analyzing the DNA complement of those microbes. 
     Embodiments for analysis of air filtrates. The above teaching shows by example that unprocessed leaf and bud samples in cannabis and hops may be washed in an aqueous water solution, to yield a water wash containing microbial pathogens which can then be analyzed via the present combination of RSG and microarrays. Further, if an air sample containing microbes as an aerosol or adsorbed to airborne dust were obtained by air filtration onto an ordinary air-filter (such as used in the filtration of air in an agricultural or food processing plant, or on factory floor, or in a public building or a private home) that such air-filters could then be washed with a water solution, as has been demonstrated for plant matter, to yield a microbe-containing filter eluate, such that the present combination of RSG and microarray analysis would be capable of recovering and analyzing the DNA complement of those microbes. 
     While the foregoing written description of an embodiments enables one of ordinary skill to make and use what is considered presently to be the best mode thereof, those of ordinary skill will understand and appreciate the existence of variations, combinations, and equivalents of the specific embodiment, method, and examples herein. The present disclosure should therefore not be limited by the above described embodiments, methods, and examples, but by all embodiments and methods within the scope and spirit of the present disclosure.