Process for source attribution

Abstract

A computer-implemented method for source attribution of contaminants at a site.A computer-implemented method for displaying source attribution and a representation thereof for contaminants at a site.The method can be used to identify and / or control contamination at a site, for example, a food production site.

Description

[Technical field]

[0001] The present invention relates to a computer-implemented method for source attribution of contaminants at a site. The present invention also relates to a computer-implemented method for displaying the source attribution of contaminants at a site and a representation thereof. The method can be used to identify and / or manage contamination at a site, for example a food production site. [Background technology]

[0002] Identifying and managing contamination is a challenge that affects many industries. For example, in the context of the food industry, contamination of consumables can have serious downstream impacts for both the consumer and the business involved. From the consumer's perspective, food contamination can lead to consumer illness. From the business's perspective, food contamination can have both short-term and long-term negative consequences. There can be immediate or short-term impacts related to lost time and / or revenue associated with allocating resources to mitigate the contamination. Long-term revenue losses can also result from reduced consumer confidence in the quality and safety of contaminated foods.

[0003] Methods for identifying and controlling contamination may limit the impact of contamination events on both consumers and businesses. Such methods may be applicable to a wide range of industries, such as, for example, the food, forensic, and medical industries. Alternatively, such methods may be targeted to a specific industry or subset of an industry.

[0004] Efficient attribution of contaminants to sources may further minimize the impact of contamination events on both consumers and businesses. For example, in the food industry context, efficient attribution of contaminants to sources may prevent further cases of product contamination, thereby enabling businesses to prevent further cases of consumer illness.

[0005] There remains a need for methods to identify contaminants, to attribute sources of contaminants to surfaces or near surfaces on a site, and / or to control contamination events.

[0006] It is an object of the present invention to go some way to fulfilling this need and / or at least to provide a useful choice to the public and / or industry.

[0007] References herein to patents, other external documents, or other sources are generally intended to provide a context for describing features of the invention. Unless otherwise expressly stated, the reference to such external documents shall not be construed as an admission that such documents or such sources are prior art or form part of the common general knowledge in the art in any jurisdiction. Summary of the Invention

[0008] In one aspect, the present invention relates to a computer-implemented method for source attribution of contaminants at a site, the method comprising: storing in electronic memory an electronic representation of the site, the representation including respective location information for one or more surfaces within the site; receiving in an electronic memory contamination status information relating to one of the one or more surfaces; Modifying the representation to associate the location information with contamination status information for the corresponding surface; repeating the steps of receiving and modifying to generate a data set including a plurality of related contamination status information and location information; and analyzing the dataset to attribute a source of the contaminant to or near one of the one or more surfaces.

[0009] In another aspect, the present invention relates to a computer-implemented method for displaying source attribution and a representation of contaminants at a site, the method comprising: generating, receiving, or storing in electronic memory an electronic representation of the site, the representation including respective location information for one or more surfaces within the site; generating or receiving in an electronic memory contamination status information relating to one of the one or more surfaces; modifying the representation to associate or link the location information to contamination status information for the corresponding surface; and transmitting the modified representation to a display device for display to a user.

[0010] In various embodiments, the method comprises: generating or receiving an initial representation of the site, including a digital plan of the site, a 3D digital model of the site, one or more images of the site, or any combination of two or more of those; generating or receiving location information for each one or more surfaces within the site; storing the initial representation and the position information in a database; and associating or linking the initial representation with location information such that a surface of the one or more surfaces may be identified by the respective location information.

[0011] In another aspect, the present invention relates to a computer-implemented method for displaying source attribution and a representation of contaminants at a site, the method comprising: generating, receiving, or storing in electronic memory respective location information for one or more surfaces within the site; generating or receiving in an electronic memory contamination status information relating to one of the one or more surfaces; transmitting the location information and contamination status information to a remote electronic memory containing an electronic representation of the site; receiving a modified electronic representation in which the location information is associated or linked to the contamination status information for the corresponding surface; and displaying the modified electronic representation to the user.

[0012] The following embodiments may relate to any of the above aspects in any combination.

[0013] In various embodiments, the contamination status information may include nucleic acid sequence information, may be generated according to a schedule, and may be determined by a method that includes collecting two or more samples from one or more surfaces according to the schedule, and analyzing the two or more samples to determine relatedness of the two or more samples.

[0014] In various embodiments, one or more of either or both of the generating and transmitting steps may be performed using a point-of-use hardware device.

[0015] In various embodiments, contamination status information may be generated or received according to a schedule.

[0016] In various embodiments, contamination status information may include nucleic acid sequence information, amino acid sequence information, microbiological assay information, chemical assay information, or biochemical assay information, or any combination of any two or more thereof.

[0017] In various embodiments, the nucleic acid sequence information may include one or more partial or entire genome sequences or a mixed genome sequence.

[0018] In various embodiments, the nucleic acid sequence information may include ribosomal RNA sequence information, single nucleotide polymorphism (SNP) information, or metagenomic information. In various embodiments, the nucleic acid sequence information may include at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 250, 500, 750, or 1000 or more SNPs, and a useful range may be selected from any of these values ​​(e.g., 1-5, 1-10, 1-50, 1-100, 1-1000, 5-10, 5-50, 5-100, 5-1000, 10-50, 10-100, or 10-1000).

[0019] In various embodiments, the nucleic acid sequence information may be generated using a nucleic acid sequencing method, including but not limited to Sanger sequencing, whole genome sequencing (WGS), or next generation sequencing (NGS).

[0020] In various embodiments, the microbiological assay information may include mass spectrometry information.

[0021] In various embodiments, the site may be a food production site, a food handling site, a food preparation site, a food logistics site, a food consumption site, an agricultural site, an animal handling site, a health care facility, a building, a vehicle, or a structure. The site may be a site where contamination must be controlled to protect human or animal health. The site may be a site subject to regulated hygiene standards, including, but not limited to, food regulations, drug manufacturing regulations, health care facility regulations, etc.

[0022] In various embodiments, contamination status information may include information regarding nucleic acid-containing materials, including but not limited to bacteria, viruses, protozoa, plants, or animals, or any combination of any two or more thereof.

[0023] In various embodiments, the representation may include a 3D digital model, a point cloud, or one or more images of the site, or any combination thereof.

[0024] In various embodiments, the point cloud may be generated by photogrammetrically processing one or more images of the site.

[0025] In various embodiments, the point cloud may be generated by laser, radar, or sonar ranging of the site.

[0026] In various embodiments, the representation may include a unique identifier linked to one or more surfaces.

[0027] In various embodiments, the contamination status information may be determined by a method that includes collecting one or more samples from one or more surfaces and analyzing the one or more samples. In various embodiments, the one or more surfaces may include process equipment, ingredient, raw material, component, and packaging entry points, process, packing and product exit points, cleaning equipment, sanitation control points, drains and other services, personnel entry points, movement, assembly, and exit points, and personnel contact points including tools, handles, computer and control interaction points.

[0028] In various embodiments, one or more samples may be obtained according to a sampling plan.

[0029] In various embodiments, the sampling plan provides a first sampling location, a second sampling location, and an nth sampling location, each sampling location determined by one or more statistically based sampling methods.

[0030] In various embodiments, the statistically based method is simple random sampling and the method includes selecting a first random sampling location, a second random sampling location, and an nth random sampling location within the site.

[0031] In various embodiments, the statistically based method is a systematic sampling, and the method includes defining a grid within a site, selecting a first sampling location on the grid, selecting a second sampling location on the grid, and selecting an nth random location on the grid.

[0032] In various embodiments, the statistically based method may be adaptive cluster sampling, the method including randomly selecting a first set of primary sampling locations within a site, determining whether each primary sampling location contains a contaminant, and selecting a second set of secondary sampling locations, each secondary sampling location adjacent to a primary sampling location that contains a contaminant.

[0033] In various embodiments, one or more samples may be collected by swabbing, wiping, vacuuming, or blotting, or any combination thereof.

[0034] In various embodiments, analysis of one or more samples may include determining the presence of microbial contaminants using assays to identify nucleic acid or amino acid information, or microbiological, chemical, or biochemical assays, or any combination thereof.

[0035] In various embodiments, analysis of one or more samples can include determining the identity of a contaminant.

[0036] In various embodiments, the analysis of one or more samples may include determining relatedness of two or more samples.

[0037] In various embodiments, the analysis of one or more samples comprises: obtaining assay information from each of two or more samples obtained from different locations within the site; determining relevance of the samples by analyzing the assay information; Identifying potential vectors of contamination; and determining movement of contaminants within the site by comparing sample associations to the latent vectors to determine movement of contaminants within the site.

[0038] In various embodiments, the analysis of one or more samples comprises: Obtaining a first nucleic acid sequence from one or more samples; Providing a second nucleic acid sequence from a reference microorganism; Defining a sequence similarity threshold for establishing microbial identity in one or more samples; and determining whether sequence similarity between the first and second nucleic acid sequences meets a threshold value.

[0039] In various embodiments, the threshold for establishing identity can be at least about 60, 70, 80, 90, 95, or 99 percent sequence similarity.

[0040] In various embodiments, the analytical method may be repeated for 10, 100, or more than 100 nucleic acid sequences from one or more samples.

[0041] In various embodiments, the microbial identity may include genus, species, and / or strain information.

[0042] In various embodiments, the method may include determining a level of risk associated with the microbial contaminant by comparing the identity of the microbial contaminant to a database containing microbial identifiers and associated risk or hazard information, and associating the risk or hazard with the microbial contaminant.

[0043] In various embodiments, the analysis of one or more samples comprises: Obtaining a first nucleic acid sequence from a first sample; Obtaining a second nucleic acid sequence from a second sample or a reference source; and comparing a first and a second nucleic acid sequence to determine the relatedness of the samples.

[0044] In various embodiments, comparing the first and second nucleic acid sequences to determine relatedness of the samples comprises: identifying one or more SNPs between each of the first and second nucleic acid sequences; Comparing the SNPs from the first and second nucleic acid sequences to determine relatedness of the samples.

[0045] In various embodiments, the analysis of one or more samples comprises: obtaining nucleic acid sequence information from each of two or more samples obtained from different locations within the site; determining relatedness of the samples by analyzing the nucleic acid sequence information; Identifying potential vectors of contamination; and determining the movement of microbial contaminants within the site by comparing sample associations to potential vectors to determine the movement of microbial contaminants within the site.

[0046] definition The phrase "machine-readable code," as used in this specification and claims, unless the context indicates otherwise, is intended to mean any form of visual or graphical code that represents, embeds or encodes information, such as a barcode, whether a linear one-dimensional barcode or a matrix-type two-dimensional barcode such as a Quick Response (QR) code, a three-dimensional code, or any other code that can be scanned, such as by image capture and processing.

[0047] The phrases "machine-readable medium" and "computer-readable medium" shall be interpreted to include a single medium or multiple media. Examples of multiple media include centralized or distributed databases and / or associated caches. These multiple media store one or more sets of machine or computer-executable instructions. These phrases shall also be interpreted to include any medium that can store, encode, or carry a set of instructions for execution by a processor of a computing device, causing the processor to perform any one or more of the methods described herein. The machine-readable medium or computer-readable medium may also store, encode, or carry data structures used by or associated with these sets of instructions. These phrases include references to solid-state memories, optical media, and magnetic media.

[0048] The phrase "electronic memory" may include any local or remote machine-readable medium, or a combination thereof, including cloud-based memory.

[0049] As used herein, the term "comprising" means "consisting at least in part of." When interpreting each statement in this specification and claims that includes the term "comprising," there may be additional features present other than the features or features that follow the term. Related terms such as "comprise" and "comprises" should be interpreted in the same manner.

[0050] Reference to a numerical range disclosed herein (e.g., 1-10) is also intended to encompass reference to all rational numbers within that range (e.g., 1, 1.1, 2, 3, 3.9, 4, 5, 6, 6.5, 7, 8, 9, and 10) and any range of rational numbers within that range (e.g., 2-8, 1.5-5.5, and 3.1-4.7). Thus, subranges of all ranges expressly disclosed herein are also expressly disclosed herein. These are merely examples of what is specifically intended, and all possible combinations of numerical values ​​between the minimum and maximum values ​​recited are considered to be expressly set forth herein as well.

[0051] As used herein, the term "and / or" means "and" or "or," or both.

[0052] As used herein, "(s)" following a noun refers to the plural and / or singular form of the noun.

[0053] The present invention may also be broadly described as consisting of the parts, elements and features referred to or shown in the specification of this patent application, individually or collectively, and any or all combinations of any two or more of the parts, elements or features, and where a particular integer having a known equivalent in the art to which the invention pertains is described herein, such known equivalent is deemed to be incorporated herein as if it were individually set forth.

[0054] The present invention contemplates constructions in accordance with the foregoing, the following of which are given by way of example only. [Brief description of the drawings]

[0055] Preferred embodiments of the invention will now be described, by way of example only, with reference to the following drawings:

[0056] [Figure 1] 1 is a flow chart showing steps of a method according to a first aspect of the present invention; [Diagram 2] 4 is a flow chart showing steps of a method according to a second aspect of the present invention; [Diagram 3] 4 is a flow chart showing steps of a method according to a third aspect of the present invention; DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0057] In the following description, specific details are given to provide a thorough understanding of the embodiments. However, it will be understood by those skilled in the art that the embodiments may be practiced without these specific details.

[0058] It is also noted that the embodiments may be described as a process that is depicted as a flowchart, a flow diagram, a structure diagram, or a block diagram. Although a flowchart may describe operations as a sequential process, many of the operations may be performed in parallel or simultaneously. Additionally, the order of the operations may be rearranged. A process terminates when the operations are completed. A process may correspond to a method, a function, a procedure, a subroutine, a subprogram, etc., in a computer program. When a process corresponds to a function, its termination corresponds to a return of the function to the calling function or the main function.

[0059] Aspects of the systems and methods described below may be operable on any type of general-purpose computer system or computing device, including, but not limited to, a desktop, laptop, notebook, tablet, smart television, car audio or phone system, game console, or mobile device. The term "mobile device" includes, but is not limited to, point-of-use hardware devices, wireless devices, mobile phones, smartphones, mobile communication devices, user communication devices, personal digital assistants, mobile handheld computers, laptop computers, wearable electronic devices such as smart watches and head-mounted devices, e-book readers, reading devices capable of reading electronic content, and / or other types of mobile devices that are typically carried by an individual and / or have some form of communication capability (e.g., wireless, infrared, short-range radio, cellular, etc.).

[0060] Further, the embodiments may be implemented by hardware, software, firmware, middleware, microcode, or any combination thereof. When implemented in software, firmware, middleware, or microcode, the program code or code segments for performing the necessary tasks may be stored in a machine-readable medium, such as a storage medium or other storage device. A processor may perform the necessary tasks. A code segment may represent a procedure, a function, a subprogram, a program, a routine, a subroutine, a module, a software package, a class, or any combination of instructions, data structures, or program statements. A code segment may be coupled to another code segment or a hardware circuit by passing and / or receiving information, data, arguments, parameters, or memory contents. Information, arguments, parameters, data, etc. may be passed, forwarded, or transmitted via any suitable means including memory sharing, message passing, token passing, network transmission, etc.

[0061] As previously mentioned, a storage medium refers to one or more devices for storing data, including read-only memory (ROM), random access memory (RAM), magnetic disk storage media, optical storage media, flash memory devices, and / or other machine-readable media for storing information. The terms "machine-readable medium" and "computer-readable medium" include, but are not limited to, portable or non-removable storage devices, optical storage devices, and / or various other media that can store, contain, or carry instructions and / or data.

[0062] The various illustrative logic blocks, modules, circuits, elements, and / or components described in connection with the examples disclosed herein may be implemented or performed using a general purpose processor, a digital signal processor (DSP), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA) or other programmable logic component, discrete gate or transistor logic, discrete hardware components, or any combination thereof designed to perform the functions described herein. A general purpose processor may be a microprocessor, but alternatively, the processor may be any conventional processor, controller, microcontroller, circuit, and / or state machine. A processor may also be implemented as a combination of computing components, e.g., a combination of a DSP and a microprocessor, several microprocessors, one or more microprocessors in combination with a DSP core, or any other such configuration.

[0063] The methods or algorithms described in connection with the examples disclosed herein may be embodied directly in hardware, in software modules executable by a processor, or in a combination of both, in the form of a processing unit, programming instructions, or in other ways, and may be contained in a single device or distributed across multiple devices. The software modules may reside in RAM memory, flash memory, ROM memory, EPROM memory, EEPROM memory, registers, hard disk, removable disk, CD-ROM, or any other form of storage medium known in the art. The storage medium may be coupled to the processor such that the processor can read information from and write information to the storage medium. Alternatively, the storage medium may be integral to the processor.

[0064] One or more of the components and functions shown in the figures may be rearranged and / or combined into a single component or embodied in several components without departing from the invention. Additional elements or components may also be added without departing from the invention. Furthermore, the functions described herein may be implemented as a business method in software, hardware, and / or a combination thereof.

[0065] In its various aspects, the invention may be embodied by a computer-implemented process, a machine (such as an electronic device, or a general-purpose computer or other device that provides a platform on which a computer program can be run), a process executed by such a machine, or an article of manufacture. Such articles may include computer program products or digital information products having stored thereon a computer-readable storage medium containing computer program instructions or computer readable data, as well as processes and machines for making and using such products.

[0066] The present invention broadly comprises a computer-implemented method for source attribution of contaminants at a site. The methods described herein may be used, for example, for risk, problem, or event management purposes. In various embodiments, one or more of the methods described herein may provide an ongoing risk assessment of a site of interest by identifying potential sources of contamination, including repeat sources of contamination, within the site.

[0067] In various embodiments, the method includes receiving contamination status information for one of the one or more surfaces in a site. In various embodiments, the contamination status information may be generated or received according to a schedule (otherwise referred to herein as a sampling plan). Thus, the method according to the present invention may provide a real-time method of monitoring one or more contaminants at a site such that the method may form part of a regular contaminant monitoring program. In various embodiments, the schedule specifies the collection of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, or 100 or more samples to generate contamination status information for the one or more surfaces, with useful ranges being selected between any of these values ​​(e.g., 2-7, 2-10, 2-30, 2-50, or 2-100). In various embodiments, a schedule may specify at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 250, 500, 750, or 1000 or more surfaces (sampling locations) for generating contamination status information, and useful ranges may be selected between any of these values ​​(e.g., 2-7, 2-10, 2-30, 2-50, or 2-100). In various embodiments, the schedule relates to a period of at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 days, and useful ranges can be selected between any of these values ​​(e.g., 1-7, 1-14, 1-30, 1-60, 1-90, 7-14, 7-30, 7-60, or 7-90).

[0068] In various embodiments, the method may be used in the source attribution of one or more contaminants within a site. A contaminant may be any undesirable or harmful substance or organism, such as a contaminating, toxic, or poisonous substance or organism. Such substances may include substances that are undesirable or unacceptable in the context of the site, such as heavy metals, antibiotics, toxins, pesticides, herbicides, etc. at a food preparation site. Such organisms may include any organism that is undesirable or unacceptable in the context of the site, such as spoilage organisms or organisms that present a food safety risk at a food preparation site. Alternatively, or in addition, a contaminant may be any substance or organism of interest at the site, provided that the identity and / or source of the substance or organism at the site is of interest. For example, a nucleic acid sequence of interest. A contaminant may be a single substance or organism, or a mixed population of substances or organisms.

[0069] Contaminants may be industrial, agricultural, chemical or biological in nature. Examples of industrial contaminants may include, but are not limited to, volatile organic compounds (VOCs) and heavy metals. Examples of agricultural contaminants may include, but are not limited to, pesticides such as insecticides, herbicides, and / or fungicides. Examples of chemical contaminants may include, but are not limited to, solvents, and organic and / or inorganic chemical wastes. Examples of biological contaminants may include any nucleic acid-containing material, including but not limited to, microorganisms.

[0070] In various embodiments, the contaminant can be bacteria, virus, protozoa, fungus, plant or animal, or any combination of two or more thereof.Bacterial contaminant can include any bacteria of interest, including food spoilage bacteria such as Lactobacillus, Leuconostoc, Pseudomonas, Alcaligenes, Serratia, Micrococcus, Flavobacterium, Serratia, Micrococcus, Proteus, Enterobacter, Streptococcus, or any combination of two or more thereof, and / or pathogenic bacteria such as Campylobacter jejuni, Escherichia coli, Listeria monocytogenes, Salmonella, Shigella, Staphylococcus aureus, or any combination of two or more thereof.Fungal contaminant can include any fungus of interest, including food spoilage bacteria such as Aspergillus, Fusarium, Cladosporium, Alternaria, or any combination of two or more thereof. Animal contaminants may include, for example, pests or vectors, which may include, for example, rodents such as mice or rats, insects such as cockroaches or mosquitoes, parasites such as fleas, mites, bedbugs, lice, termites, or any combination of any two or more thereof.

[0071] In various embodiments, the contaminant is a microbial contaminant, e.g., a bacterium or a virus, and in various embodiments, the methods described herein may be used in source attribution of microbial contaminants at a site. In such embodiments, the contamination status information may include nucleic acid sequence information, amino acid sequence information, microbiological assay information, chemical assay information, or biochemical assay information, or any combination of any two or more thereof.

[0072] In various embodiments, the contaminant is or includes one or more nucleic acid sequences of interest, and the one or more nucleic acid sequences or nucleic acid information may include, for example, an oligonucleotide, a polynucleotide, a transposon, 10, 100, or 1000 or more contiguous nucleic acids, one or more DNA molecules, one or more RNA molecules, DNA from one or more individual genes, one or more partial or entire genome sequences, one or more partial or entire RNA transcriptomes, or one or more ribosomal RNA sequences, or other information associated with any such sequences.

[0073] The methods described herein may be used for source attribution of only one contaminant in a site. Alternatively, in various embodiments, the methods described herein may be used for source attribution of two or more contaminants in a site. In such embodiments, each of the contaminants may be the same type of contaminant selected from the group consisting of bacteria, viruses, protozoa, plants, and animals. For example, the method may be used for source attribution of two contaminants, both of which are bacteria. In various embodiments, the method may be used for source attribution of different types of contaminants. For example, one of the contaminants may be bacteria and the other may be a virus. Additionally or alternatively, the contaminant may be a mixed population of contaminants, such as a mixed population of bacteria.

[0074] In various embodiments, the methods include collecting a sample from a surface at a site and analyzing the sample to determine the presence, absence, or amount of one or more contaminants in the sample.

[0075] In various embodiments, sample analysis may include several levels of analysis. A first or higher level of analysis may include one or more methods to determine whether one or more contaminants are present on the surface. For example, if the contaminant is bacteria, the first or higher level of analysis may include plating media testing or polymerase chain reaction (PCR)-based methods. In various embodiments, samples that are positive for a contaminant may be screened to select the sample for subsequent analysis, as described herein. In various embodiments, the sample may be analyzed for suitability or need for subsequent analysis, for example, by determining the identity of the contaminant, determining the distribution of the contaminant, and / or determining the level of risk or danger posed by the contaminant. Samples may be selected based on one or more selection criteria.

[0076] The subsequent analysis may include one or more methods for determining the nature of the contaminants present, i.e., the subsequent analysis may provide additional information regarding the particular contaminants present.

[0077] In various embodiments, sample analysis may involve the use of one or more tests to determine specific information about the contaminant. The tests may be performed by sensors, where practical.

[0078] As described herein, in various embodiments, sample analysis may include determining the identity of a contaminant, determining the association of two or more samples, and / or determining the movement of a contaminant within a site.

[0079] In various embodiments, the specific information regarding the contaminant may include chemical or biochemical assay information generated regarding a single analyte or multiple analytes that comprise or are contained within the sample. The assays may include binding assays, immunoassays, colorimetric assays, photometric assays, spectrophotometric assays, transmittance assays, turbidity assays, counting assays, flow cytometry assays, imaging assays, enzyme-linked immunoassays (EIA), enzyme-linked immunosorbent assays (ELISA), microarray assays, enzyme assays, or mass spectrometry assays, or any combination of any two or more thereof. Such assay information may be used to determine the identity of the contaminant, and comparison of such assay information between samples may be used to determine relatedness of two or more samples and / or to determine the movement of the contaminant within the site. Similar assay results may indicate some degree of relatedness. It is understood that any suitable assay may be used.

[0080] In various embodiments, the specific information regarding the contaminant may include nucleic acid sequence information, such as an oligonucleotide, a polynucleotide, a transposon, a nucleic acid of 10, 100, or 1000 or more contiguous bases, one or more DNA molecules, one or more RNA molecules, DNA from one or more individual genes, one or more partial or entire genome sequences, one or more partial or entire RNA transcriptomes, or one or more ribosomal RNA sequences. In various embodiments, the nucleic acid sequence information may include one or more genes, one or more non-coding regions, or one or more fragments of a nucleic acid sequence, or other information associated with any such sequence.

[0081] In various embodiments, the specific information regarding the contaminant may include microbiological assay information. The microbiological assay information may include information regarding a single organism or a mixed population of organisms, including information generated by one or more assays, including, but not limited to, binding assays, immunoassays, colony formation assays, culture assays, colorimetric assays, photometric assays, spectrophotometric assays, transmittance assays, turbidimetric assays, counting assays, flow cytometry assays, imaging assays, enzyme-linked immunoassays (EIA), enzyme-linked immunosorbent assays (ELISA), microarray assays, enzyme assays, polymerase chain reaction (PCR) assays, or mass spectrometry assays, or any combination of any two or more thereof. Mass spectrometry may include matrix-assisted laser desorption / ionization time-of-flight mass spectrometry (MALDI-TOF) information. For example, if the contaminant is a microorganism such as bacteria, the Bruker BioTyper may be used to confirm the type of bacteria present, e.g., the genus and / or species of bacteria.

[0082] In various embodiments, the sample may be analyzed by whole genome sequencing (WGS) or next generation sequencing (NGS). In various embodiments, advanced testing, such as WGS, may be used as part of a subsequent analysis performed on the sample. That is, advanced testing may be performed after the first or higher level of testing. In various embodiments, metagenomic methods, such as shotgun metagenomic sequencing, may be used to analyze samples that contain a heterogeneous population of microbial contaminants or samples that contain microbial contaminants that cannot be cultured using conventional methods.

[0083] Advanced tests such as WGS or NGS may be able to make hypotheses or conclusions about the relationship between contaminants in a sample. For example, WGS, preferably in combination with statistical analysis, may enable connections between microorganisms in two or more samples, for example samples collected from different surfaces. Such connections may lead to the following hypotheses or conclusions: The microorganisms from two or more samples are from the same population, Microorganisms from two or more samples evolved or originated from the same population (the "population of origin"); or · Microorganisms from one of the two samples evolved or originated from the other of the two samples.

[0084] In various embodiments, the methods described herein associate location information and contamination status information of the corresponding surfaces. Thus, in various embodiments, the methods described herein can be used to attribute a source of a contaminant, such as a microorganism, collected from a first surface A to a second surface B. In such embodiments, the second surface B can include the original source or population.

[0085] Whole genome sequencing can be performed locally at the site or remotely to transmit and receive contamination status information at the site. WGS can be performed using a combination of software and associated hardware. For example, WGS can be performed using polymerase chain reaction (PCR), gel electrophoresis, pulsed field gel electrophoresis (PFGE), or next-generation sequencing using an Illumina MiSeq or associated high-throughput genetic analyzer with associated software and kit-based workflow. Other instruments and protocols for generating genomic sequence data can also be used, including next-generation sequencers such as ABI Sanger chemistry-based sequencers, Pacific Biosciences PacBio single molecule real-time (SMRT) sequencers, Ion Torrent semiconductor sequencers, Oxford Nanopore MinION, and other high-throughput approaches that will be apparent to those skilled in the art. WGS can be performed using any combination of any one or any two or more of such techniques.

[0086] Bioinformatics-based approaches can be used in combination with sequencing methods such as WGS or NGS to analyze nucleic acid sequence information. For example, bioinformatics-based approaches can be used to compare nucleic acid sequence information to determine the identity of microbial contaminants, the association of different samples of microbial contaminants, mapping the movement of microbial contaminants within a site, and / or the source of microbial contaminants. Bioinformatics approaches can be performed using personalized statistical software or proprietary software. The software can be local machine-based software, such as Illumina MiSeq integrated applications, or internet-based tools, such as sequence alignment software, such as Basic Local alignment search tool (BLAST), Illumina BaseSpace Sequence Hub Apps, or access to internet-based databases, such as the National Center for Biotechnology Information (NCBI), or specific gene or genome databases, or any combination thereof.

[0087] In various embodiments, nucleic acid information can be processed to obtain sequence data of suitable quality for further analysis.For example, sequence data processing can include demultiplexing, trimming, removing low-quality sequences, removing noise, error detection, assembly alignment, and statistical quality control, and other techniques that are obvious to those skilled in the art.Sequence data processing can be performed using personalized statistical software based on Perl, R, Python, C, Java, or similar programming environments, open license applications such as Trimmomatic (usadellab.org), or local software such as Illumina MiSeq integrated applications, or Internet-based solutions such as Illumina BaseSpace Sequence Hub Apps.

[0088] In various embodiments, the identity of the microbial contaminant can be determined by comparing the processed genomic sequence data with a known reference sequence. The reference sequence can be a full or partial genomic sequence of the target microorganism stored in an electronic database, such as NCBI, EMBL, or GenBank. In various embodiments, the identity includes the genus, species, and / or strain of the microbial contaminant.

[0089] In various embodiments, the identification of microbial contaminants isolated from locations within the site may include determining sequence similarity or homology between the processed nucleic acid sequence information (target sequence) and one or more reference sequences. Such determination may be performed using methods known in the art. Such methods may include defining overlapping short sequences of consistent length (k-mers) derived from the target sequence, associating each k-mer with sequence and taxonomic information in a reference database, and identifying the target sequence and organisms using a weighting algorithm based on the number of k-mers associated with each taxonomic unit in the reference database. The determination of sequence similarity may be performed using internet-based software such as Kraken (John Hopkins University Centre for Computational Biology). In various embodiments, the threshold for establishing the identity of a microbial contaminant can be about 60, 70, 80, 90, 95, or 99 percent sequence similarity, and a suitable range can be selected from any one of these values, such as, for example, about 60-99, 60-95, 60-90, 60-80, 60-70, 70-99, 70-95, 70-90, 70-80, 80-99, 80-95, 80-90, 90-99 or 95-99 percent.

[0090] In various embodiments, Sanger-based methods or alternative long-read next-generation WGS methods, such as PacBio SMRT sequencing, can be used to generate sample and / or reference sequences without prior knowledge.

[0091] The identity, such as genus and species, of the microbial contaminant can be used to determine the level of hazard and / or risk posed by the microbial contaminant. In various embodiments, the method includes establishing the identity of the microbial contaminant, comparing the identity of the microbial contaminant to a database of microbial identifiers and associated risk or hazard information, and associating the risk or hazard information with the microbial contaminant. The risk or hazard information may include safety-based criteria, such as hygiene, pathogenicity, virulence, or business-based criteria, such as quality or regulatory considerations.

[0092] Changes in nucleic acid information, such as single nucleotide polymorphisms (SNPs), can be used to determine the relatedness of a sample of microbial contaminant to a known reference strain or other sample of microbial contaminant. SNPs can occur anywhere in the genome, for example, within a gene or within an intergenic region. Calculation of the SNP value or number of SNPs in the nucleic acid sequence information can indicate that the sample of microbial contaminant is related to the reference strain or other sample microbial contaminant.

[0093] In various embodiments, the relatedness of a microbial contaminant sample to a reference strain may be determined by identifying SNPs in the nucleic acid sequence information of the microbial contaminant compared to the nucleic acid sequence information of the reference strain and determining the level of similarity of their sequences based on the number of SNPs, with a value of zero indicating an identical strain and higher SNP values ​​indicating some degree of dissimilarity between the sequences and therefore the strains.

[0094] In various embodiments, determining the relatedness of two or more samples of microbial contaminants may include identifying SNPs between a first nucleic acid sequence information of a first microbial contaminant and a second nucleic acid sequence information of a second microbial contaminant, and determining the similarity between the first and second nucleic acid sequence information based on the number of SNPs. For example, slight differences in SNPs between the first and second nucleic acid sequence information may indicate that the microbial contaminants are closely related. In various embodiments, the relatedness of the microbial contaminant to the reference strain may be determined. Identifying SNPs may be performed using software, such as SNIPPY (GitHub.com / tseemann).

[0095] If the microbial contaminants are determined to be related, a comparison of the SNPs of these microbial contaminants can be used to determine the length of time since the microbial contaminant populations diverged / evolved from a common ancestral population (the relative age of each population). Depending on the microorganism, it may be possible to determine the number of weeks, months, or years since the microbial contaminants diverged / evolved from a common ancestor. In various embodiments, determining the length of time it takes for a given microbial contaminant population to evolve from a common ancestor can be calculated by determining the rate of change of the SNPs of the microorganisms of interest.

[0096] The expression of genes may result in specific traits for the microbial contaminant. These traits may be related to the survival of the microbial contaminant at a specific location within the site. In various embodiments, information about these traits can be used to attribute a microbial contaminant population that exhibits a specific trait to a corresponding specific location within the site. For example, a salt tolerance trait in a microbial contaminant population can be used to attribute the microbial contaminant or its ancestor to a location that is exposed to a higher salt content.

[0097] In various embodiments, the transmission of a particular trait in a population of microbial contaminants can be used to determine relatedness between the populations. In various embodiments, the method can include identifying a trait or phenotype in the microbial contaminant, attributing the trait or phenotype to a gene in the nucleic acid sequence information of the microbial contaminant, identifying the presence of the gene in the nucleic acid sequences of other samples of the microbial contaminant, and determining relatedness based on the presence of the gene in the other samples of the microbial contaminant.

[0098] Variation in specific genes or specific regions within the genome of microbial contaminants can also be used to determine relatedness. For example, genes such as ribosomal genes can contain slowly evolving conserved regions and / or rapidly evolving regions. Slowly evolving conserved regions of such genes can be used to determine longer term transformations from ancestors such as genus and / or species, or higher taxonomic levels of identification, while fast evolving regions can be used to identify specific strains within a species.

[0099] The movement of microbial contaminants within a site may be mapped by identifying the changes in SNPs from two or more populations of microbial contaminants and the locations within the site where each population was separated over time. When a microbial contaminant population (the original population) is transferred (e.g., by a vector) from a first location to a second location, the SNPs of the transferred (second) microbial contaminant population may change over time compared to the founder population. When the second population is transferred to a third location, the SNPs of the third microbial contaminant population may change further. This results in a series of microbial contaminant populations, each with a different degree of SNP change compared to the original population. In other words, the movement of microbial contaminants may be mapped by determining the changes in SNPs of the populations and relating it to the locations where each population was separated over time. Vectors in this context may include, for example, animals (including humans and pest species), incoming goods (including manufacturing materials or parts and cleaning products), waste streams, water, air, tools (including cleaning tools), and vehicles.

[0100] In various embodiments, a method of mapping the movement of microbial contaminants includes mapping the movement of microbial contaminants by identifying SNPs in the genetic sequences of two or more microbial contaminant populations, each isolated from a different location within a site, forming an array of microbial contaminant populations by placing each population according to SNP similarity from most similar to least similar, and attributing each microbial contaminant population to the location within the site where it was isolated. For example, five samples of microbial contaminants isolated from locations A, B, C, D, and E, if placed according to SNP similarity, may be ordered as C, E, B, D, A. It may be possible to infer that the microbial contaminants have moved over time from location C to E, B, D, A, or vice versa.

[0101] Alternatively, or in addition, the extent of SNP change in multiple samples of microbial contaminants may be compared to a known reference strain to identify a sample containing the original microbial contaminant population within a site. In various embodiments, the method may include comparing the identity of SNPs in two or more samples of microbial contaminants, comparing the SNPs in each sample of microbial contaminants to the SNPs in the reference strain, determining the extent of SNP change in each sample compared to the reference strain, identifying the sample with the least SNP change, and attributing that sample as the original population.

[0102] In various embodiments, SNP analysis useful herein may include comparing a sample genome sequence to a reference genome of the same species and recording the differences. The differences may be used to determine whether the sample contaminant is composed of a single strain, multiple strains, persistent strains, transient strains, the result of a single infestation, multiple infestations, or resident within a site. The known molecular evolutionary period of SNP changes within the species of interest may be used to determine relatedness and / or clonality.

[0103] In various embodiments, the method may include multiple rounds of mapping the movement of microbial contaminant populations as described above, for example, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more. In various embodiments, different microbial contaminant samples may be used in each round. The results of multiple rounds of mapping over time may be combined to improve the accuracy or resolution of the map.

[0104] Epidemiological approaches can be used in combination with or in addition to bioinformatics approaches to increase the accuracy of source attribution. Similar samples as established by various embodiments may mean that two or more contaminations are related. Epidemiological considerations are also necessary to clarify the relationship between contaminations, establish that movement between sample locations is possible, and identify vectors. Consideration of possible vectors, such as scheduling or movement of people, equipment, raw materials, products, cleaning agents, packaging materials, movement of water, waste, air, other services, or accidental events such as breakdowns, maintenance, pests, etc. on the site, may be used to help attributing the source of contamination. Similarly, consideration of strong barriers to movement, for example in construction, scheduling, or dismissal of low-risk events, may add weight to conclusions that help attributing the source of contamination.

[0105] Thus, in various embodiments, sample analysis may include determining movement of contaminants within a site by a method that includes obtaining assay information from each of two or more samples obtained from different locations within the site, determining associations of the samples by analyzing the assay information, identifying potential vectors of contamination, and determining movement of contaminants within the site by comparing the associations of the samples to the potential vectors.

[0106] Statistical approaches can be used to assess the reliability of the obtained results. In various embodiments, statistical methods can be used to test for non-randomness of the results. In various embodiments, spatial statistics can be used because the distribution of microbial contaminant populations is not random. For example, statistical methods can be used to calculate the probability that the spread of contaminant populations around the site was not random.

[0107] It will be appreciated by those skilled in the art that performing different levels of sample analysis can be cost-effective for a company. For example, a first or higher level of analysis can include a relatively inexpensive method of determining whether one or more contaminants are present. If the first analysis does not identify any contaminants on the surface tested, the company does not need to spend additional time and money on further testing. If the first analysis identifies contaminants on the surface tested, a more targeted analysis can be performed to determine the nature, e.g., amount, of the contaminants present.

[0108] In various embodiments, one or more samples may be taken from a surface without prior knowledge of potential contaminants that may be found on the surface. In various embodiments, for example, if contamination is suspected, a company, cooperative, or individual performing the method according to the present invention may perform the method to test for the presence of a particular contaminant. It will be apparent to one skilled in the art that the type of analysis performed to determine the contamination status information of a surface will depend at least in part on whether the nature of the contaminant is known.

[0109] The site may include one or more indoor and / or outdoor surfaces. In various embodiments, the site may be a site as discussed above.

[0110] The invention will now be described in more detail with reference to the accompanying drawings, in which FIG. 1 shows a method for source attribution of pollutants at a site, the method comprising: A. storing in electronic memory an electronic representation of the site, the representation including respective location information for one or more surfaces within the site; B. receiving in an electronic memory contamination status information relating to one of the one or more surfaces; C. Modifying the representation to associate the location information with contamination status information for the corresponding surface; D. repeating the steps of receiving and modifying to generate a data set including a plurality of related contamination status information and location information; E. Analyzing the dataset to attribute a source of the contaminant to or near one of the one or more surfaces.

[0111] With continued reference to Figure 1, step A includes storing an electronic representation of the site in electronic memory. In various embodiments, the electronic memory may be stored on a storage medium as described herein.

[0112] The electronic representation may include a plan of the site, a map of the site, and / or a collection of photographs or images of the site. In various embodiments, the electronic representation includes a map of the site, where the electronic representation is created by mapping the site. The map may be two-dimensional (2D), three-dimensional (3D), or four-dimensional (4D). Mapping the site may include the use of a non-digital map that is digitized to create an electronic representation of the site. In various embodiments, digital images of the site may be used to create the electronic representation of the site. In various embodiments, both digital and non-digital images may be combined to create the electronic representation of the site. In various embodiments, the map or plan of the site may be created using any suitable computer-based method, such as computer-aided design (CAD). In various embodiments, the map or plan of the site may be created using suitable surveying tools, such as a theodolite and tape measure.

[0113] The method of mapping the site may be selected based at least in part on factors such as, for example, whether the site is an indoor site or an outdoor site. It will be understood by those skilled in the art that some methods of mapping may be applicable to both interior and exterior sites, while other methods may be limited to either interior or exterior sites. By way of example, in various embodiments, exterior sites may be mapped using drones, aircraft-based sensors, other aerial sensors, or satellite-based sensors. In various embodiments, drones and other aerial sensors may also be used to map indoor sites, particularly large indoor sites such as warehouses. Mapping may also be based on a computer-aided design (CAD) model of the site.

[0114] In various embodiments, a site, for example an indoor site or an indoor area or surface of a site, may be mapped using distance scanning technology, such as those using electromagnetic radiation (EMR) or sound, including laser, radar, or sonic scanning technology. Thus, in various embodiments, a representation of the site, such as a point cloud, stick model, vector model, or 3D digital model, may be generated by EMR or acoustic measurements of the site, such as by Light Detection and Ranging (LIDAR). Suitable distance scanning technologies are known in the art, such as laser scanners, including, for example, the FARO® Focus laser scanner from FARO® Technologies UK Ltd. Typically, distance scanners scan the site to be mapped by sending out pulses of light, radio, or sound and measuring the "time of flight", i.e., the time it takes for the signal to reflect back to the scanner. In various embodiments, the time of flight measurements may be combined with other information, such as the angle of each signal, to obtain data points (or coordinates) within a point cloud, stick model, or vector model. Such scanners may perform at least about 1, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or more scans of a particular site, with suitable ranges being, for example, about 1-10, 10-1000, 10-750, 10-500, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-850, 10-900, 10-1000, 10-1000, 10-2000, 10-300, 10-400, 10-500, 10-600, 10-700, 10-8 ...1000, 10-2000, 10-300, 10-400, 10-500, 10-600, 10-7 Any of these values ​​may be selected, such as 50, 10-250, 10-100, 10-500, 100-1000, 100-750, 100-500, 100-350, 100-250, 200-1000, 200-750, 200-500, 200-350, 250-1000, 250-750, 250-500, 250-350, 500-1000, or 500-750 scans.

[0115] In various embodiments, distance scanning technology can be used to generate a single point cloud image or model of a site. A point cloud image generated by a scanning technology, e.g., 3D laser scanning technology, is used to generate a point cloud image or model, referred to herein as a point cloud, internal point cloud image or model. A point cloud image or model is made up of data points within a site. Data points from two or more cloud point images can be combined together using computer software, e.g., FARO® Scene. In various embodiments, a point cloud image or model can include millions or billions of points per cloud. Stick and vector models can be generated and manipulated in similar manners known in the art.

[0116] In various embodiments, range scanning techniques can be used to generate two or more point cloud images or models of a site. For example, several point cloud images or models can be generated, each of which corresponds to a particular section of the site, e.g., a particular surface, group of surfaces, or room within the site. Stick and vector models can be generated and manipulated in a similar manner known in the art.

[0117] Each scan made by a laser scanner, such as a FARO® Focus laser scanner, may include millions of laser distance measurements. Such laser distance measurements may be panoramic. In various embodiments, the laser distance measurements may be combined with one or more photographs or videos, such as at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 50, 100, 125, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more photographs or videos, preferably photographs, to create an electronic representation of the site. In various embodiments, the electronic representation of the site may be panoramic.

[0118] In various embodiments, one or more photographs and / or videos of the site may be combined to create an electronic representation. Thus, in various embodiments, a point cloud may be generated by photogrammetrically processing one or more images of the site.

[0119] In various embodiments, one or more photographs and / or videos of the site can be combined with one or more distance scans, such as scans taken by a laser scanner, such as a FARO® Focus Laser Scanner, to create the electronic representation. Thus, in various embodiments, the electronic representation can include a point cloud and one or more images of the site.

[0120] The one or more photographs and / or videos may be captured using, for example, a drone, an aircraft-based sensor, other sensors including, for example, other aerial sensors, satellite-based sensors, or a camera, for example, a handheld, backpack, trolley or head-mounted, vehicle or robot-mounted camera, or a combination of any two or more thereof.

[0121] The photographs and / or videos used to create the electronic representation may be black and white and / or color photographs. In various embodiments, the photographs and / or videos, preferably the photographs, may be embedded in the electronic representation, for example, using a link. Alternatively, or in addition, in various embodiments, the photographs and / or videos may be published as a web sharing companion to the scan from the laser scanner.

[0122] In various embodiments, one or more photographs may be converted into one or more external point cloud, stick or vector models. Software for converting one or more photographs into such models is known in the art and includes, but is not limited to, Bentley Photogrammetry Imaging Software.

[0123] In various embodiments, one or more such external cloud models and one or more such internal cloud models can be combined to create an electronic representation of the site. The representation can also include conversion of the data into other digital formats, such as conversion of a point cloud into a vector model with Pointfuse software, or reformatting into a solid surface model suitable for computer-aided drafting (CAD) processing.

[0124] In various embodiments, the methods described herein include collecting one or more samples from one or more surfaces of a site. Each surface of the one or more surfaces is located at a specific location within the site. As described herein, the methods may include generating, receiving, or storing in an electronic memory an electronic representation of the site, the representation including respective location information for one or more surfaces within the site. That is, the one or more surfaces are identifiable by a location on the representation. Thus, in various embodiments, collecting a sample from one of the one or more surfaces also includes collecting information regarding the location of the surface from which the sample was collected within the site.

[0125] In various embodiments, the locations of surfaces at a site where samples are collected (sampling locations) may be determined by a sampling plan. In various embodiments, the sampling plan defines the times and / or locations where samples are collected. In various embodiments, the sampling plan may include determining a first sampling location, determining a second sampling location, determining an nth sampling location on the electronic representation of the site at a given time. In this method, 1, 2, 4, 6, 8, 10, 20, 30, 40, 50, 100, 150, 200, 400, 600, 800, or 1000 or more sampling locations may be selected and a useful range may be selected from these values ​​(e.g., 1 to 150 sampling locations).

[0126] In various embodiments, each sampling location may be determined by a statistically based sampling method, such as simple random sampling, systematic sampling, ranked set sampling, adaptive cluster sampling, or a combination of two or more thereof. In various embodiments, each sampling location may be determined by a judgment-based sampling method, for example, using expert or industry knowledge. Expert or industry knowledge may include, for example, knowledge regarding locations within the site that are likely to be contaminated. In various embodiments, the statistically based method is supplemented with a judgment-based sampling method to improve the accuracy of the statistically based method.

[0127] Location information regarding one or more surfaces within a site may be collected in a variety of ways. In various embodiments, location information may be collected manually or automatically.

[0128] In various embodiments, the location information may be collected manually by the person collecting one or more samples from the surface or by another person. For example, the person collecting the location information may mark or otherwise record on a non-digital map the location of the surface where the samples are collected. The non-digital map may then be digitized to create an electronic representation of the site as described herein. Alternatively, the person collecting the location information may mark or otherwise record on a digital map the location of the surface where the samples are collected. That is, the method may include generating, receiving, or storing in an electronic memory an electronic representation of the site, and the person collecting the samples from the surface may mark or otherwise record on the electronic representation the location of the surface where the samples are collected.

[0129] In various embodiments, the location information may be collected automatically, for example, using a local or global navigation satellite system (GNSS), such as the Global Positioning System (GPS).

[0130] The respective location information may be displayed on the representation in a number of ways. For example, a reference number may be assigned to each of the one or more surfaces. The reference number may then be displayed on the representation to indicate the location of each of the one or more surfaces within the site. Alternatively, or in addition, the respective location information may be indicated, for example, by assigning a color and / or symbol to each of the one or more surfaces. The location of each of the surfaces may then be identifiable by the color and / or symbol on the representation.

[0131] In various embodiments, the respective location information for one or more surfaces within the site may be displayed using a shape corresponding to the surface. The shape may be a 2D or 3D shape. The shape may be a line, an arrow, a pointer, a label, text, a hyperlink, an image, or any symbol. For example, in various embodiments, the electronic representation may include 3D spheres, each 3D sphere corresponding to a surface within the site. The shapes, e.g., the 3D spheres, may have a size proportional to the size of the surface. Alternatively, the shapes, e.g., the 3D spheres, may have a size that does not correlate with the size of the surface. That is, the size of the shapes may only serve to indicate the respective location of the surfaces. Software for displaying shapes on electronic representations is known in the art, and includes, but is not limited to, Veesus, FARO® Scene, and AutoCAD software.

[0132] The electronic representation may include data other than location information or contamination status information for one or more surfaces of the site, respectively. In various embodiments, the electronic representation may include or be used to display metadata. Metadata is used herein to refer to data other than location information or contamination status information for one or more surfaces of the site.

[0133] The metadata may be displayed on the electronic representation in a number of ways. For example, the metadata may be displayed on the electronic representation using, for example, colors, symbols and / or shapes, text or hyperlinks that correspond to different types of metadata. Alternatively, or in addition, the metadata may be tagged or otherwise associated with respective location information for one or more surfaces in the electronic representation. For example, the metadata may be tagged or otherwise associated with respective location information for one or more surfaces in the electronic representation using a unique identifier.

[0134] In various embodiments, the unique identifier may be associated with all or some of the data corresponding to one of the one or more surfaces in the site. In various embodiments, the electronic representation may include one or more unique identifiers linked to one or more surfaces of the site. The unique identifier may include respective location information, contamination status information, and / or metadata regarding one of the one or more surfaces in the site. The unique identifier may be associated with the sample label and the test, allowing the data to be properly correlated with the location corresponding to the surface on which the test was performed. The unique identifier may be or be associated with a machine-readable code.

[0135] The metadata may be data relating to the properties of the surface from which the sample was collected, such as shape, volume, area, or appearance, information indicating the time and / or date the sample was collected, information identifying the individual responsible for collecting the sample, information about the type of sample collected from the surface, information about the method of collecting the sample from the surface, information prescribing instructions following collection of the sample, information about the conditions of the site at the time the sample was collected, such as temperature, humidity, pH level, etc., or a combination of any two or more thereof. Other types of metadata will also be apparent to those skilled in the art.

[0136] As noted above, step B of the method of Figure 1 includes receiving in an electronic memory contamination status information relating to one of the one or more surfaces. In various embodiments, receiving in an electronic memory contamination status information includes collecting such information from one of the one or more surfaces. Such information may be collected by collecting one or more samples from one of the one or more surfaces.

[0137] It will be understood by those skilled in the art that contamination status information may be collected in many ways. The method of collecting contamination information may vary depending on factors such as the type of contamination being evaluated and / or the site being evaluated. For example, contamination status information may be collected by collecting one or more samples from one of one or more surfaces of the site. The samples may be collected, for example, by swabbing, wiping, vacuuming, or blotting. The surfaces may be sampled manually or automatically.

[0138] In various embodiments, multiple samples can be collected from each surface of one or more surfaces of a site, for example, at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more samples can be collected, for example, by swabbing, from one of the one or more surfaces, and a suitable range can be selected from any of these values, for example, 1-100, 1-50, 1-20, 1-10, 1-5, 10-100, 10-50, 10-20, 20-100, or 20-50 samples.

[0139] When multiple samples are collected from a surface, an average amount of contaminant across all samples collected from the surface may be determined, and this average may then be transmitted to electronic memory as the contaminant status information corresponding to the surface.

[0140] In various embodiments, some of the samples collected from a surface may result in contaminant amounts that are considered statistical outliers. Statistical outliers may be due to, for example, incorrect sampling or equipment malfunction. In various embodiments, the statistical outliers may be excluded from the average values ​​that are transmitted to the electronic memory as contaminant status information corresponding to the surface.

[0141] As described herein, in various embodiments, information other than location information or contamination status information may also be collected from one of the one or more surfaces of a site. Such metadata may be collected before, after, or contemporaneously with the collection of location information and contamination status information.

[0142] The electronic representation of the site is modified to associate location information, contaminant status information, and optionally metadata associated with the surfaces, corresponding surface location information, contaminant status information, and optionally metadata (step C of FIG. 1). In various embodiments, modifying the electronic representation includes updating the representation to display the contamination status information for the corresponding surfaces on the representation. When the contamination status information is displayed on the electronic representation, it is displayed in a location that corresponds to the location of the surface where the contamination status information was collected.

[0143] The contamination status information may be displayed in the electronic representation in quantitative or qualitative terms. That is, the electronic representation may indicate that a surface is contaminated, i.e. a qualitative representation. Alternatively, the electronic representation may indicate both that a surface is contaminated (a qualitative representation) and the level of contamination of the surface, i.e. a quantitative representation. Methods for indicating the level of contamination will be clear to the skilled person. Such methods may include, for example, displaying a bacterial count for a particular surface in the representation, or using a key, e.g. a series of symbols where each symbol corresponds to a different level of contamination, or a traffic light system where each color corresponds to a different level of contamination.

[0144] The qualitative descriptive key may be defined by a site administrator. Alternatively, this key may be used to indicate acceptable, moderate, and unacceptable levels of contamination as defined by industry associations and / or food safety standards. In other words, a site administrator, industry association, or food safety standard may define the contamination level that is assigned to each symbol in a series of symbols or each color in a traffic light system.

[0145] In various embodiments, the method includes repeating the receiving and correcting steps to generate a data set including a plurality of associated contamination status information and location information (step D of FIG. 1). The receiving and correcting steps can be repeated as many times as necessary. For example, the receiving and correcting steps may be repeated at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1000, 10,000 or more times, with suitable ranges being, for example, 1-10,000, 1-1000, 1-100, 1-50, 1-20, 1-10, 1-5, 5-10,000, 5-1000, 5-100, 5-50, 5 Any of these values ​​may be selected, such as ~20, 5-10, 10-10,000, 10-1000, 10-100, 10-50, 10-20, 20-10,000, 20-1000, 20-100, 20-50, 50-10,000, 50-1000, 50-100, 50-10,000, 50-1000, 50-100, 100-10,000, 100-1000, 1000-10,000, etc.

[0146] In various embodiments, the method may include continuous generation of a data set including the plurality of associated contamination status information and location information. In various embodiments, the electronic representation may be continuously updated, e.g., in real time, with the plurality of associated contamination status information and location information. In such embodiments, the steps of receiving and modifying may be repeated indefinitely such that the electronic representation is continuously updated, preferably in real time.

[0147] Following step D, the data set is analyzed to attribute a source of the contaminant to or near one of the one or more surfaces of step E of FIG. 1. The concept of source attribution described herein includes correlating the contamination status information with location information. In various embodiments, the concept of source attribution described herein also includes analysis of multiple contamination status information and location information to attribute a source of the contaminant to or near one of the one or more surfaces. That is, the method may enable identifying the original source or origin of the contaminant within the site.

[0148] Analysis of the dataset to attribute a source of contaminants to at or near one of the one or more surfaces of the site may be performed manually or automatically. Manual source attribution may include analysis of the dataset by a user. The user may then form a hypothesis or conclusion about the original source of the contaminants based on associated location patterns and the contamination status information of the electronic representation. Alternatively, software may be used to analyze the dataset and attribute a source of the contaminants to at or near one of the one or more surfaces.

[0149] Figure 2 shows a method according to a second aspect of the invention. Figure 2 shows the steps of a method for displaying source attributions and representations of pollutants at a site, the method comprising: A. generating, receiving, or storing in electronic memory an electronic representation of a site, the representation including respective location information for one or more surfaces within the site; B. generating or receiving in electronic memory contamination status information for one of the one or more surfaces; C. Modifying the representation to relate or link the location information to contamination status information for the corresponding surface; D. Sending the modified representation to a display device for display to a user.

[0150] As shown in step A of Figure 2, an electronic representation of the site may be generated, received, or stored in electronic memory. In various embodiments, the method may include generating and storing the electronic representation in electronic memory. In other embodiments, the method may include receiving and storing the electronic representation in electronic memory.

[0151] Generating the electronic representation may include generating one or more than point cloud images or models of the site, as described herein. As described herein, the one or more point cloud images may be generated using photographs, videos, and / or scans of the site, e.g., scans obtained using 3D laser scanning technology. Also as described herein, the one or more point cloud images or models may include one or more interior point cloud images or models, and / or one or more exterior point cloud images or models. Methods for generating interior and exterior point cloud models are described herein with reference to FIG. 1, and it will be understood by those skilled in the art that such methods are also applicable to the method of FIG. 2.

[0152] In various embodiments, the electronic representation may be an initial representation of the site. That is, the electronic representation may include respective location information for one or more surfaces within the site. In various embodiments, the initial representation may not include contaminant status information. The initial representation may include a plan of the site, a 3D model of the site, or one or more images of the site, or any combination of any two or more thereof. The initial representation may be stored in a storage medium as described herein. In various embodiments, the initial representation may be stored in a database, for example, a database stored in a storage medium as described herein.

[0153] The electronic representation may be generated by a company, cooperative, or individual performing the inventive methods described herein. Alternatively, in various embodiments, the electronic representation may be generated by a third party. In such embodiments, the third party may provide access to the electronic representation to another company, cooperative, or individual, such that the electronic representation may be received by the company, cooperative, or individual performing the inventive methods.

[0154] A company, cooperative, or individual performing the method of the present invention may store one or more copies of the electronic or initial representation in electronic memory. When multiple copies of the electronic or initial representation are stored in electronic memory, each copy may be stored on the same or different computers. In various embodiments, all or some of the copies may be stored in a network such that changes to one copy are made across all copies in the network.

[0155] As shown in step B of FIG. 2, the method may include generating or receiving in an electronic memory contamination status information regarding the surface.

[0156] The process of generating the contamination status information may include converting the raw (quantitative) measurements of the contaminants in the sample into a qualitative representation that is displayed to the user. For example, as described herein, the contaminants may be bacteria. The raw (quantitative) measurements of the contaminants may include a bacterial count expressed in colony forming units (cfu) of a sample taken on one of the one or more surfaces of the site. In contrast, the qualitative representation may include, for example, a series of symbols corresponding to different levels of contamination, or a key such as a traffic light system corresponding to different levels of contamination as described herein.

[0157] In various embodiments, the raw (quantitative) measurement of a contaminant, e.g., the number of bacteria in a sample, may be displayed in the electronic representation. Alternatively, the raw (quantitative) measurement may be converted to a qualitative representation, and the qualitative representation may then be displayed in the electronic representation.

[0158] As described herein with reference to FIG. 1, the qualitative delineation keys may be defined by site administrators. Alternatively, the keys may be used to indicate various levels of contamination as defined by industry associations and / or food safety standards. For example, an industry association may determine that bacterial counts of hygiene indicator organisms are 10 2 Less than cfu represents an acceptable level of contamination and corresponds to the green light on the traffic light system. 10 2 ~10 5 cfu represents a medium level of pollution and corresponds to the yellow light on the traffic light system. 10 5 Exceeding cfu indicates an unacceptable level of contamination and corresponds to the red colour of the key using the traffic light system.

[0159] It will be understood by those skilled in the art that the qualitative description key may include any number of levels. For example, in various embodiments, the key may include at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more levels, and suitable ranges may be selected from any of these values, such as, for example, 1-10, 2-10, 3-10, 4-10, 5-10, 6-10, 7-10, 8-10, 9-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-8, 2-6, or 2-4 levels.

[0160] In various embodiments, the contamination status information may be depicted in ways other than using a key including symbols or colors. For example, as described herein in various embodiments, respective location information for one or more surfaces within a site may be displayed using a shape corresponding to the surface. The shapes may be 2D or 3D shapes. For example, in various embodiments, the electronic representation may include 3D spheres, each 3D sphere corresponding to a surface within the site. In such embodiments, the shapes, e.g., the 3D spheres, may have a size proportional to the contamination status of the surface.

[0161] In various embodiments, the generation of the contamination status information may be performed by a third party, i.e., the generation of the contamination status information may be performed by a party other than the company, cooperative, or individual performing the method of the present invention. In such an embodiment, the third party may provide access to the contamination status information to other companies, cooperatives, or individuals, such that the contamination status information is received by the company, cooperative, or individual performing the method according to the present invention. The third party may be a company dealing in pest or microbial control, contamination, and / or management.

[0162] Once the contamination status information is generated or received in electronic memory, the electronic representation is modified to associate or link the location information to the contamination status information of the corresponding surface (step C of FIG. 2). As described herein, in various embodiments, modifying the electronic representation includes updating the representation to display the contamination status information of the corresponding surface on the representation. When the contamination status information is displayed on the electronic representation, it is displayed in a location that corresponds to the location of the surface where the contamination status information was collected. The modified representation is then transmitted to a display device for display to a user (step D of FIG. 2).

[0163] The modified representation may be displayed on any suitable display device, such as any suitable general-purpose computer system or computing device, including, but not limited to, a desktop, laptop, notebook, tablet, smart television, game console, or mobile device described herein. Preferably, the modified representation is displayed on a desktop, laptop, notebook, tablet, smart television, or mobile device.

[0164] Figure 3 illustrates a further method according to an embodiment of the present invention. Figure 3 illustrates method steps for displaying source attributions and representations of contaminants at a site, the method comprising: A. generating, receiving, or storing in electronic memory respective location information for one or more surfaces within a site; B. generating or receiving in electronic memory contamination status information for one of the one or more surfaces; C. transmitting location and contamination status information to a remote electronic memory containing an electronic representation of the site; D. Receiving a modified electronic representation in which the location information is associated or linked to the contamination status information for the corresponding surface; E. Displaying the modified electronic representation to the user.

[0165] An example of a method for collecting location information is described in detail with reference to FIG. 1 and is also applicable to the method illustrated in FIG.

[0166] As shown in step A of Figure 3, location information regarding one or more surfaces of the site may be generated, received, or stored. In various embodiments, the method may include generating and storing location information regarding one or more surfaces of the site. In other embodiments, the method may include receiving and storing location information regarding one or more surfaces of the site.

[0167] Generating the location information may include collecting the location information as described herein. The location information may be generated by a company, cooperative, or individual performing the method according to the present invention as described herein. For example, as described above, the location information may be collected by the person collecting one or more samples from the surface or by another person. Alternatively, in various embodiments, the location information may be generated by a third party. In such embodiments, the third party may provide access to the location information to other companies, cooperatives, or individuals so that the location information is received by the company, cooperative, or individual performing the method according to the present invention. In various embodiments, the location information may be stored in an electronic memory.

[0168] In various embodiments, the method includes generating or receiving in an electronic memory contamination status information for one of the one or more surfaces (see step B of FIG. 3). In various embodiments, the location information and contamination status information may be transmitted to a remote electronic memory containing an electronic representation of the site (see step C of FIG. 3). Methods of generating and receiving location information and / or contamination status information, as well as methods of generating an electronic representation of a site, are described in detail herein with reference to FIG. 1 or 2. Such description also applies to the method of FIG. 3.

[0169] The transmission of the location information and contamination status information to a remote electronic memory depends on factors such as, for example, how the information was collected, who collected the information, and how the information was stored. In various embodiments, the transmission of the location information and / or status information may include transmission from a remote storage facility, such as a cloud-based storage facility or the Internet, to a device used to perform a computer-implemented method of source attribution according to the present invention. In various embodiments, the transmission of the location information and / or status information may include transmission from a first device on which the information is stored to a second device. In such an embodiment, the second device may be a device used to perform a computer-implemented method according to the present invention. The transmission may be wired or wireless, by any suitable protocol and over any suitable medium, including a combination of protocols and media. Examples of wireless transmission may include one or more of Wifi, Bluetooth, radio frequency (RF), infrared, and the like. The transmission may be over one or any combination of networks, including a local area network, a wide area network, a cellular network, an intranet, the Internet, the Internet, and the like.

[0170] As described above with reference to Figures 1 and 2, in various embodiments, the location information and the contamination status information are associated or linked. The electronic representation of the site can be updated based on the associated or linked location information and contamination status information to generate a revised electronic representation of the site. The revised electronic representation can be generated by a company, cooperative or individual performing a method according to the invention. Alternatively, the revised electronic representation can be generated by a third party, i.e., a party not performing a method according to the invention.

[0171] The electronic representation and the modified electronic representation of the site may be generated on the same or different devices, e.g., different computers. In various embodiments, the electronic representation and / or the modified electronic representation may be stored locally, e.g., on in-house, on-premise, or local storage hardware, or remotely, e.g., in a cloud-based storage facility or on the Internet. For example, the electronic representation and the modified electronic representation may be generated on the same device and stored locally on that device.

[0172] In various embodiments, the electronic representation and / or the modified electronic representation may be generated on the same or different devices, and the electronic representation and the modified electronic representation may be stored on a storage medium as described herein. In various embodiments, the electronic representation and / or the modified electronic representation may be stored remotely, such as, for example, in a cloud-based storage facility or on the Internet.

[0173] In various embodiments, one or more of the generating and / or transmitting steps are performed using a point-of-use hardware device, such as a handheld device. The point-of-use hardware device may be, for example, a notebook, tablet or mobile device, preferably a tablet or mobile device.

[0174] In various embodiments, the modified electronic representation may be received, for example from a storage medium, on a device used to implement a computer-implemented method of origin attribution according to the present invention (see step D of FIG. 3).

[0175] In various embodiments, the modified electronic representation may be displayed to a user. As described herein, the modified representation may be displayed on any suitable display device, such as any suitable general-purpose computer system or computing device, including, but not limited to, a desktop, laptop, notebook, tablet, smart television, game console, or mobile device as described herein. Preferably, the modified representation is displayed on a desktop, laptop, notebook, tablet, smart television, or mobile device.

[0176] A user may be able to interact with the electronic representation and / or the modified electronic representation. For example, a user may be able to add comments to various portions of the representation. Such comments may become part of the metadata associated with one of the one or more surfaces on which the comment is made.

[0177] The inventors believe that the methods described herein have the potential to provide rapid and transparent resolution of problems related to source attribution in many industries.

[0178] In various embodiments, the methods described herein can be used to monitor contamination at a site. Contaminant status information and source attribution information generated according to the methods described herein can be used to: Providing confidence in the safety and quality of products from the site, such as food from a food preparation site; · Providing evidence to consumers and / or regulatory authorities regarding the safety and quality of products from the site; positively linking or positively discounting the link between a contaminant found at one location, e.g. on a surface, and a contaminant at another location, e.g. on a product; Monitoring the site for contamination events over a period of time to establish a history of events at the site; Providing data for modelling future contamination events at specific sites and / or specific surfaces within a site; and / or ·Implementing new control activities or additional safety measures, such as targeted cleaning, for sites and / or surfaces within sites that show a high potential for contamination based on event history.

[0179] It will be appreciated by those skilled in the art that various embodiments or features of the present invention, such as the site, contaminant, surface properties, methods of generating, receiving or storing electronic representations, methods of mapping, methods of collecting contamination status information, and methods of displaying such information in an electronic representation, described with reference to any one of Figures 1-3, may also be applied to the methods shown in any one of the other figures. EXAMPLES

[0180] Example 1 The process described is used to operate a sanitation control plan at sites where contamination must be strictly controlled to protect human or animal health. A computer-based 2D floor plan map of the site is derived from architectural plans and photo surveys, and all surfaces of concern associated with the potential for contamination, including microbial contamination, are displayed on the map. Surfaces of interest include entry points for process equipment, ingredients, raw materials, components, and packaging, process, packing and product exit points, cleaning equipment, sanitation control points, drains and other services, personnel entry points, movement, assembly, and exit points, and personnel contact points including tools, handles, computer and control interaction points.

[0181] The plan includes a predefined weekly schedule that specifies the location, surface, and sampling type information to be collected for each surface for each contaminant of interest, such as microbial contaminants. The weekly schedule is developed taking into account likely points of contamination, such as preferred niches of microorganisms informed by literature, by previous detection, and also includes randomly selected surfaces within the site.

[0182] The daily schedule of sampling tasks is developed from the weekly schedule and contains all the sampling tasks necessary to complete the sampling schedule for that day. The daily schedule is distributed as a paper and / or electronic checklist for operators to take to site to guide and record sampling.

[0183] Samples for analysis, such as microbiological analysis, are taken according to standard operating procedures and sent to the testing site for analysis. Depending on the microorganism of interest, specific sampling kits, such as swabs and point-of-use swabs, and point-of-use testing devices are used. Contaminant identification analysis is performed using rapid tests, such as rapid PCR-based tests, using primers specific for the microorganism of interest and following the standard operating procedures for the test.

[0184] The results of both positive and negative testing are recorded by overlaying a respective icon and link to expanded sampling and testing information onto the mapped surface, so that the map displays a representation of the ongoing swabs and test results taking place within the site, and is continually updated as results become available.

[0185] The maps and overlaid results are analyzed periodically, e.g., weekly. The accumulation of test results over an extended period of time, e.g., a shift, a week, a month, or a period relevant to the site, such as the production season to date, is analyzed to highlight areas of high and low occurrence, respectively, for each contaminant of interest. Results are indexed, where possible, to activity within the site, e.g., product scheduling or maintenance activity, to reveal patterns of activity relative to the test results.

[0186] Taking into account the incidence and contamination risk posed by each surface and location, a remediation management plan is developed that includes actions such as specific cleaning programs, maintenance tasks or enhanced testing monitoring.

[0187] Example 2 In response to a contamination event, such as microbial contamination at a site where contamination must be tightly controlled to protect human or animal health, the process described is used to identify the source, track movement from the source, and develop remediation control actions. A computer-based representation of the site is created as a point cloud model of the facility compiled from multiple 3D laser scans using appropriate scanner software. All surfaces within the 3D model are considered candidates for sampling.

[0188] Using the 3D model as a guide, a surface sampling plan is developed, taking into account known niches of contaminants such as microorganisms of interest, vector routes of ingredients, products, services, personnel, etc., knowledge of previous detection locations, and using statistical sampling considerations such as randomized grid-based sample selection, and random selection from otherwise equivalent surfaces. The number of surfaces to be sampled is scaled according to the site. A sampling task sheet is developed from the sampling plan, contains all sampling tasks required to complete the sampling plan, and is deployed as a checklist in paper and / or portable electronic format for operators to take to the site to guide and record sampling.

[0189] A sampling schedule is created and the sampling outlined in the sampling plan is repeated after set time intervals, for example after one month, or after a given intervention. The sampling plan site is executed.

[0190] All samples are transported directly to the testing site after sampling. If available, historical samples are added to the sample pool to further extend the time period of samples under investigation. The first test is to separate the contaminant of interest, such as the microorganism of interest, from the background microbiota using a specific enrichment technique for that contaminant.

[0191] For microbial contaminants, candidate colonies from each enrichment step are analyzed using a MALDI-TOF-MS type microbial identification instrument and identified at least to the genus level. DNA from selected colonies of interest is extracted using standard laboratory processes, checked for compliance with quality indicators, and sent to a next-generation whole genome sequencing and bioinformatics pipeline to at least decompress, trim, clean, and assemble into FASTA-formatted genome sequences for subsequent analysis. Sequences are analyzed with (1) WGS-based species identification software to confirm species, strain, and subtype identification, if applicable, and (2) SNP analysis, in which the genome sequence of the sample is compared to a closely related reference genome of the same species and the number of differences is tabulated. Output from the SNP analysis is used to create a table of relatedness (closeness) between isolates based on the number of SNPs between each sample and all other samples. Using clustering analysis, the SNP data are used to determine whether the population of the species of interest consists of single or multiple clusters of similar isolates, and whether subpopulations appear to be transient, single or multiple infestations, or present within the facility. Known molecular evolutionary periods of SNP change within a species of interest are used to define clonality, and overlaying SNP proximity on a map of facilities is used to track the paths of clonal isolates within a site in 3D.

[0192] By scheduling repeated sampling exercises over an extended period of time, combined with connecting samples based on association and surface location, epidemiological considerations can be applied to identify sources, transport mechanisms, and potential product contamination pathways for target species. A database containing microbial identifiers and associated contamination risk or hazard information can be used to link risks associated with surfaces and potential microbial contaminants.

[0193] 3D mapping of all results and risk scores allows rapid communication of results in 3D format. Remedial control actions, such as maintenance, surface modification, vector flow modification, and cleaning schedule changes, are considered to remove contamination, address the source, and / or prevent migration of target species, with further scheduled surface swabbing activities used to evaluate the effectiveness of control interventions. Collected data is reused to add to or create routine sanitation plans, as exemplified in Example 1.

[0194] The foregoing description of the invention includes preferred forms thereof. Modifications can be made thereto without departing from the scope of the invention, which is defined by the appended claims.

Claims

1. 1. A computer-implemented method for source attribution of a contaminant at a site, the method comprising: storing an electronic representation of the site in an electronic memory, the representation including respective location information for one or more surfaces within the site; receiving in said electronic memory contamination status information relating to a surface of said one or more surfaces; modifying said representation to relate said location information to said contamination status information of a corresponding surface; repeating the steps of receiving and modifying to generate a data set including a plurality of related contamination status information and location information; analyzing the dataset to attribute the source of the contaminant to or near one of the one or more surfaces; the contamination status information comprises nucleic acid sequence information and is generated according to a schedule and is determined by a method comprising collecting two or more samples from the one or more surfaces according to the schedule, and analyzing the two or more samples to determine relatedness of the two or more samples; The analysis of the two or more samples comprises: (i) obtaining assay information from each of two or more samples obtained from different locations within the site; determining said relevance of said sample by analyzing said assay information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; (ii) Obtaining a first nucleic acid sequence from one or more samples; providing a second nucleic acid sequence from a reference microorganism; Defining a sequence similarity threshold for establishing microbial identity in the one or more samples; and determining whether the sequence similarity between the first and second nucleic acid sequences satisfies the threshold; (iii) Obtaining a first nucleic acid sequence from a first sample; Obtaining a second nucleic acid sequence from a second sample or a reference source; and comparing said first and second nucleic acid sequences to determine said relatedness of said samples; or (iv) obtaining nucleic acid sequence information from each of two or more samples obtained from different locations within the site; determining said relatedness of said samples by analyzing said nucleic acid sequence information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; determining the movement of contaminants within the site by a method comprising: analyzing the two or more samples includes determining the presence of one or more microbial contaminants; A computer-implemented method, wherein the source of the contaminant is determined by mapping the movement of one or more microbial contaminants by identifying one or more single nucleotide polymorphism (SNP) variations from two or more populations of microbial contaminants and the location within the site where each population was separated over time.

2. 1. A computer-implemented method for displaying source attribution and representations of contaminants at a site, the method comprising: generating, receiving, or storing in an electronic memory an electronic representation of the site, the representation including respective location information for one or more surfaces within the site; generating or receiving in said electronic memory contamination status information relating to one of said one or more surfaces; modifying said representation to relate or link said location information to said contamination status information of a corresponding surface; transmitting the modified representation to a display device for display to a user; the contamination status information comprises nucleic acid sequence information and is generated according to a schedule and is determined by a method comprising collecting two or more samples from the one or more surfaces according to the schedule, and analyzing the two or more samples to determine relatedness of the two or more samples; The analysis of the two or more samples comprises: (i) obtaining assay information from each of two or more samples obtained from different locations within the site; determining said relevance of said sample by analyzing said assay information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; (ii) Obtaining a first nucleic acid sequence from one or more samples; providing a second nucleic acid sequence from a reference microorganism; Defining a sequence similarity threshold for establishing microbial identity in the one or more samples; and determining whether the sequence similarity between the first and second nucleic acid sequences satisfies the threshold; (iii) Obtaining a first nucleic acid sequence from a first sample; Obtaining a second nucleic acid sequence from a second sample or a reference source; and comparing said first and second nucleic acid sequences to determine said relatedness of said samples; or (iv) obtaining nucleic acid sequence information from each of two or more samples obtained from different locations within the site; determining said relatedness of said samples by analyzing said nucleic acid sequence information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; determining the movement of contaminants within the site by a method comprising: analyzing the two or more samples includes determining the presence of one or more microbial contaminants; A computer-implemented method, wherein the source of the contaminant is determined by mapping the movement of one or more microbial contaminants by identifying one or more single nucleotide polymorphism (SNP) variations from two or more populations of microbial contaminants and the location within the site where each population was separated over time.

3. generating or receiving an initial representation of the site, including a digital plan of the site, a 3D digital model of the site, or one or more images of the site, or any combination of two or more thereof; generating or receiving location information for each one or more surfaces within said site; storing said initial representation and said position information in a database; and associating or linking the initial representation with location information such that a surface of the one or more surfaces may be identified by the respective location information.

4. 1. A computer-implemented method for displaying source attribution and representations of contaminants at a site, the method comprising: generating, receiving, or storing in electronic memory respective location information for one or more surfaces within said site; generating or receiving in said electronic memory contamination status information relating to one of said one or more surfaces; transmitting said location information and said contamination status information to a remote electronic memory containing an electronic representation of said site; receiving a modified electronic representation in which the location information is associated or linked to the contamination status information of the surface to which the location information corresponds; displaying the modified electronic representation to a user; the contamination status information comprises nucleic acid sequence information and is generated according to a schedule and is determined by a method comprising collecting two or more samples from the one or more surfaces according to the schedule, and analyzing the two or more samples to determine relatedness of the two or more samples; The analysis of the two or more samples comprises: (i) obtaining assay information from each of two or more samples obtained from different locations within the site; determining said relevance of said sample by analyzing said assay information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; (ii) Obtaining a first nucleic acid sequence from one or more samples; providing a second nucleic acid sequence from a reference microorganism; Defining a sequence similarity threshold for establishing microbial identity in the one or more samples; and determining whether the sequence similarity between the first and second nucleic acid sequences satisfies the threshold; (iii) Obtaining a first nucleic acid sequence from a first sample; Obtaining a second nucleic acid sequence from a second sample or a reference source; and comparing said first and second nucleic acid sequences to determine said relatedness of said samples; or (iv) obtaining nucleic acid sequence information from each of two or more samples obtained from different locations within the site; determining said relatedness of said samples by analyzing said nucleic acid sequence information; Identifying potential vectors of contamination; and comparing the associations of the samples to the latent vectors; determining the movement of contaminants within the site by a method comprising: analyzing the two or more samples includes determining the presence of one or more microbial contaminants; A computer-implemented method, wherein the source of the contaminant is determined by mapping the movement of one or more microbial contaminants by identifying one or more single nucleotide polymorphism (SNP) variations from two or more populations of microbial contaminants and the location within the site where each population was separated over time.

5. 5. The computer-implemented method of claim 4, wherein one or more of the generating and / or transmitting steps are performed using a point-of-use hardware device.

6. 6. The computer-implemented method of claim 1, wherein the contamination status information further comprises amino acid sequence information, microbiological assay information, chemical assay information, or biochemical assay information, or any combination of any two or more thereof.

7. The computer-implemented method of claim 6 , wherein the nucleic acid sequence information comprises one or more partial or entire genome sequences or mixed genome sequences.

8. The computer-implemented method of claim 6 or 7, wherein the nucleic acid sequence information comprises ribosomal RNA sequence information, single nucleotide polymorphism (SNP) information, or metagenomic information.

9. 9. The computer-implemented method of claim 7 or 8, wherein the nucleic acid sequence information is generated using a nucleic acid sequencing method, including but not limited to Sanger sequencing, whole genome sequencing (WGS), or next generation sequencing (NGS).

10. The computer-implemented method of claim 6 , wherein the microbiological assay information comprises mass spectrometry information.

11. 11. The computer-implemented method of any one of claims 1 to 10, wherein the site is a food production site, a food handling site, a food preparation site, a food logistics site, a food consumption site, an agricultural site, an animal handling site, a medical facility, a building, a vehicle, or a structure.

12. 12. The computer-implemented method of any one of claims 6 to 11, wherein the contamination status information comprises information regarding nucleic acid-containing material, including but not limited to bacteria, viruses, protozoa, plants, or animals, or any combination of any two or more thereof.

13. The computer-implemented method of any one of claims 1 to 12, wherein the representation comprises a 3D digital model, a point cloud, or one or more images of the site, or any combination thereof.

14. 14. The computer-implemented method of claim 13, wherein the point cloud is generated by photogrammetrically processing the one or more images of the site.

15. The computer-implemented method of claim 13 , wherein the point cloud is generated by laser, radar, or sonar ranging of the site.

16. The computer-implemented method of any preceding claim, wherein the representation includes a unique identifier linked to the one or more surfaces.

17. The computer-implemented method of any preceding claim, wherein the two or more samples are obtained according to a sampling plan.

18. 20. The computer-implemented method of claim 17, wherein the sampling plan provides a first sampling location, a second sampling location, and an nth sampling location, each sampling location determined by one or more statistically based sampling methods.

19. 20. The computer-implemented method of claim 18, wherein the statistically based method is simple random sampling, the method including selecting a first random sampling location, a second random sampling location, and an nth random sampling location within the site.

20. 20. The computer-implemented method of claim 18, wherein the statistically based method is a systematic sampling, the method including: defining a grid within the site; selecting a first sampling location on the grid; selecting a second sampling location on the grid; and selecting an nth random location on the grid.

21. 20. The computer-implemented method of claim 18, wherein the statistically based method is adaptive cluster sampling and includes randomly selecting, within the site, a first set of primary sampling locations, determining whether each primary sampling location contains a contaminant, and selecting a second set of secondary sampling locations, each secondary sampling location adjacent to a primary sampling location that contains a contaminant.

22. The computer-implemented method of any one of claims 1 to 21, wherein the two or more samples are collected by swabbing, wiping, vacuuming, or blotting, or any combination thereof.

23. 23. The computer-implemented method of any one of claims 1 to 22, wherein analyzing the two or more samples comprises determining the presence of a microbial contaminant using an assay to identify nucleic acid or amino acid information, or a microbiological assay, a chemical assay, or a biochemical assay, or any combination thereof.

24. The computer-implemented method of any one of claims 1 to 23, wherein analyzing the two or more samples comprises determining an identity of a contaminant.

25. The computer-implemented method of any one of claims 1 to 24, wherein the analysis of the two or more samples comprises determining the relatedness of two or more samples.

26. The analysis of the two or more samples comprises: obtaining assay information from each of two or more samples obtained from different locations within the site; determining the relevance of the sample by analyzing the assay information; Identifying potential vectors of contamination; and determining movement of the contaminants within the site by comparing the associations of the samples to the potential vectors.

27. The analysis of the two or more samples comprises: Obtaining a first nucleic acid sequence from one or more samples; Providing a second nucleic acid sequence from a reference microorganism; defining a sequence similarity threshold for establishing microbial identity in the one or more samples; and determining whether the sequence similarity between the first and second nucleic acid sequences satisfies the threshold.

28. 28. The computer-implemented method of claim 27, wherein the threshold for establishing identity is at least about 60, 70, 80, 90, 95, or 99 percent sequence similarity.

29. 29. The computer-implemented method of claim 27 or claim 28, wherein the method is repeated for 10, 100, or more than 100 nucleic acid sequences from the two or more samples.

30. The computer-implemented method of any one of claims 27 to 29, wherein the microbial identity comprises genus, species and / or strain information.

31. 31. The computer-implemented method of any one of claims 27 to 30, further comprising determining a level of risk associated with the microbial contaminant by comparing the identity of the microbial contaminant to a database containing microbial identifiers and associated risk or hazard information, and associating a risk or hazard with the microbial contaminant.

32. The analysis of the two or more samples comprises: Obtaining a first nucleic acid sequence from a first sample; Obtaining a second nucleic acid sequence from a second sample or a reference source; and comparing the first and second nucleic acid sequences to determine the relatedness of the samples.

33. Comparing the first and second nucleic acid sequences to determine the relatedness of the samples comprises: identifying one or more SNPs between each of the first and second nucleic acid sequences; and comparing the SNPs from the first and second nucleic acid sequences to determine the relatedness of the samples.

34. The analysis of the two or more samples comprises: obtaining nucleic acid sequence information from each of two or more samples obtained from different locations within the site; determining the relatedness of the samples by analyzing the nucleic acid sequence information; Identifying potential vectors of contamination; and determining the movement of microbial contaminants within the site by comparing the associations of the samples to the potential vectors.

Images