Large-scale chicken farm epidemic disease risk assessment method and system

Abstract

The invention provides a large-scale chicken farm epidemic disease risk assessment method and system, and the method comprises the steps: setting a plurality of sampling points in a large-scale chicken farm, and collecting a corresponding microorganism sample at each sampling point; performing sample treatment and metagenome sequencing analysis on the microorganism sample to obtain pathogenic species and abundance information results corresponding to each sampling point; constructing a sampling point influence matrix, and determining a sampling point weight based on the sampling point influence matrix; determining the pathogen species and the pathogen nucleic acid abundance in the abundance information result, and performing assignment scoring on the corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score; and determining a final risk score based on the sampling point weight and the pathogen score, and performing epidemic disease risk assessment of the large-scale chicken farm based on the final risk score. According to the method, the accuracy of risk assessment can be improved, a farm is helped to identify and assess potential epidemic disease risks, and targeted measures are taken to prevent epidemic diseases in the bud.

Description

TECHNICAL FIELD

[0001] The present application belongs to the technical field of poultry epidemic prevention and control, and particularly relates to a large-scale chicken farm epidemic risk assessment method and system. BACKGROUND

[0002] Poultry farms are facing various infectious disease risks. The spread of epidemics not only affects the health and production efficiency of poultry, but also can have a profound impact on public health safety and economic development. In recent years, the frequent occurrence of avian influenza, chicken mycoplasma disease and other epidemics has brought huge economic losses to the breeding industry and has a serious impact on the stable supply of poultry and egg food and food safety. Environmental factors play an important role in the spread of animal diseases. Conducting environmental disease risk assessment can provide a scientific basis for disease prevention and control. Through an effective risk assessment system, the farm can identify potential disease threats in advance and take necessary preventive measures. For high-risk pathogens, take measures to strengthen immunity, quickly control the epidemic, and reduce the risk to the minimum; for pathogens without risk, stop immunization, and apply the immune potential of animals to respond to high-risk pathogens, so as to carry out healthy breeding in the most economical and efficient way and produce better economic and social benefits.

[0003] For the poultry disease risk assessment in the prior art, it is usually determined according to the state of poultry, ignoring the influence of the environment, thereby leading to inaccurate actual disease risk assessment and affecting the disease prevention and control. SUMMARY

[0004] In order to solve the above technical problems, the present application provides a large-scale chicken farm epidemic risk assessment method and system to solve the technical problems proposed in the prior art.

[0005] In a first aspect, the embodiments of the present application provide the following technical solutions. A large-scale chicken farm epidemic risk assessment method comprises the following steps: A plurality of sampling points are arranged in the large-scale chicken farm, and corresponding microbial samples are collected at each sampling point; The microbial samples are subjected to sample processing and metagenomic sequencing to obtain pathogen species and abundance information results corresponding to each sampling point; A sampling point influence matrix is constructed, and a sampling point weight is determined based on the sampling point influence matrix; The pathogen nucleic acid abundance in the pathogen species and abundance information results is determined, and a corresponding pathogen is scored based on the pathogen nucleic acid abundance to obtain a pathogen score; A final risk score is determined based on the sampling point weight and the pathogen score, and a large-scale chicken farm epidemic risk assessment is performed based on the final risk score.

[0006] Compared with the prior art, the beneficial effects of the present application are: firstly, a plurality of sampling points are arranged in the large-scale chicken farm, and corresponding microbial samples are collected at each sampling point; then the microbial samples are subjected to sample processing and metagenomic sequencing to obtain pathogen species and abundance information results corresponding to each sampling point; then a sampling point influence matrix is constructed, and the sampling point weight is determined based on the sampling point influence matrix; then the pathogen nucleic acid abundance in the pathogen species and abundance information results is determined, and each pathogen is scored based on the pathogen nucleic acid abundance, to obtain a pathogen score; then the final risk score is determined based on the sampling point weight and the pathogen score, and the disease risk assessment of the large-scale chicken farm is carried out based on the final risk score. In the process of disease risk assessment, the influence of the environment is fully considered, and appropriate weights are given to each environment to improve the accuracy of risk assessment, help the farm identify and assess potential disease risks, and take targeted measures to prevent diseases.

[0007] Preferably, the sampling points include biological sampling points, in-shed environment sampling points, out-of-shed environment sampling points, non-breeding environment sampling points in the field area, and peripheral environment sampling points in the field area, and the microbial samples include chicken biological samples, in-shed samples, out-of-shed samples in the field area, non-breeding area samples in the field area, and peripheral samples in the field area.

[0008] Preferably, the step of collecting corresponding microbial samples at each sampling point comprises: Randomly selecting chicken samples according to a preset proportion of the feeding amount, and collecting samples in the form of whole blood, cleft swabs, and cloaca swabs to obtain chicken biological samples; Sampling according to the coverage rate of chicken feeding stalls, uniformly selecting a plurality of ground sampling points in the shed to collect cotton swab samples, and using an air / aerosol sampler to perform air sampling three times in the morning, noon, and evening to obtain in-shed samples; Collecting wall corner cotton swab samples at intervals of 20 meters along the shed periphery to obtain out-of-shed samples in the field area; Collecting ground, building, or tree surface cotton swab samples at intervals of 50 meters along the edge of the breeding area to obtain non-breeding area samples in the field area; Collecting road surface or building surface cotton swab samples at intervals of 100 meters along the periphery of the breeding area to obtain peripheral samples in the field area.

[0009] Preferably, the step of subjecting the microbial samples to sample processing and metagenomic sequencing to obtain pathogen species and abundance information results corresponding to each sampling point comprises: Selecting a number of microbial samples, extracting chicken biological samples from the microbial samples, performing metagenomic sequencing on the chicken biological samples according to sample types using multiple individual mixed samples, extracting a house sample, a field area outside the house sample, a field area non-raising area sample, and a field area peripheral sample from the microbial samples, performing metagenomic sequencing on the house sample, the field area outside the house sample, the field area non-raising area sample, and the field area peripheral sample according to sample types using multiple similar samples combined into mixed samples, to obtain pathogen species and abundance information results.

[0010] Preferably, the step of constructing a sampling point influence matrix based on the sampling point influence matrix to determine the sampling point weight comprises: determining the mutual influence score of each microbial sample based on an expert evaluation method, and determining the influence ratio between each microbial sample based on the mutual influence score . ; In the formula, respectively represent the mutual influence score of the first microbial sample; determining the influence matrix based on the influence ratio . ; In the formula, represents the influence ratio between the first microbial sample and the second microbial sample, represents the eigenvalue; converting the influence matrix into a determinant form and determining the maximum value of the eigenvalue based on the maximum value of the eigenvalue determining the homogeneous equation: ; In the formula, is the eigenvector; solving the homogeneous equation to obtain the eigenvector , and determining the sampling point weight based on the eigenvector.

[0011] Preferably, the step of assigning a score to the corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score specifically comprises: If the pathogen nucleic acid abundance of the pathogen enters the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is assigned a score of 100, if the pathogen nucleic acid abundance of the pathogen does not enter the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is assigned a score of 50, and if the pathogen is not detected, the pathogen is assigned a score of 0, to obtain a pathogen score.

[0012] Preferably, the step of determining a final risk score based on the sampling point weight and the pathogen score, and performing the epidemic risk assessment of the large-scale chicken farm based on the final risk score is specifically as follows: The pathogen score corresponding to the pathogen is multiplied by the corresponding sampling point weight and accumulated to obtain a final risk score. If the final risk score is greater than a preset score and the corresponding pathogen is included in a target directory, the pathogen is a high-risk pathogen. If the final risk score is greater than the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is 0 and the corresponding pathogen is included in the target directory, the pathogen is a low-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen.

[0013] In a second aspect, the embodiments of the present application provide the following technical solutions. An epidemic risk assessment system for a large-scale chicken farm comprises: A collection module is configured to set a plurality of sampling points in the large-scale chicken farm and collect corresponding microbial samples at each sampling point. A sequencing module is configured to perform sample processing and metagenomic sequencing on the microbial samples to obtain pathogen species and abundance information of samples corresponding to each sampling point. A matrix module is configured to construct a sampling point influence matrix and determine sampling point weights based on the sampling point influence matrix. A scoring module is configured to determine pathogen nucleic acid abundance in the pathogen species and abundance information, assign scores to corresponding pathogens based on the pathogen nucleic acid abundance, and obtain pathogen scores. An assessment module is configured to determine a final risk score based on the sampling point weight and the pathogen score, and perform the epidemic risk assessment of the large-scale chicken farm based on the final risk score.

[0014] In a third aspect, the embodiments of the present application provide the following technical solutions. A computer device comprises a memory, a processor, and a computer program stored on the memory and executable on the processor. The processor executes the computer program to implement the epidemic risk assessment method for a large-scale chicken farm.

[0015] In a fourth aspect, the embodiments of the present application provide the following technical solutions. A computer readable storage medium stores a computer program. The computer program is executable on a processor to implement the epidemic risk assessment method for a large-scale chicken farm. BRIEF DESCRIPTION OF DRAWINGS

[0016] To more clearly illustrate the technical solutions in the embodiments of the present invention, the drawings used in the description of the embodiments or the prior art will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0017] Figure 1 A flowchart of a method for assessing the disease risk of large-scale chicken farms provided in an embodiment of the present invention; Figure 2 Krona plot of species and percentage abundance in chicken biological samples provided in this embodiment of the invention; Figure 3 Krona plot of species and percentage abundance in enclosure samples provided in this embodiment of the invention; Figure 4 Krona plot showing species and percentage abundance in samples outside enclosures within the field, provided in this embodiment of the invention; Figure 5 Krona plot of species and percentage abundance in samples from non-breeding areas within the farm provided in this embodiment of the invention; Figure 6 Krona plot of species and percentage abundance in samples from the periphery of the field provided in this embodiment of the invention; Figure 7 This is a structural block diagram of a large-scale chicken farm disease risk assessment system provided in an embodiment of the present invention; Figure 8 This is a schematic diagram of the hardware structure of a computer device provided in an embodiment of the present invention. Detailed Implementation

[0018] Embodiments of the present invention are described in detail below, examples of which are illustrated in the accompanying drawings, wherein the same or similar reference numerals denote the same or similar elements or elements having the same or similar functions throughout. The embodiments described below with reference to the accompanying drawings are exemplary and intended to explain embodiments of the present invention, and should not be construed as limiting the present invention.

[0019] Example 1 In Embodiment 1 of the present invention, as Figure 1 As shown, a method for assessing disease risk in large-scale chicken farms includes: S1. Set up several sampling points in the large-scale chicken farm and collect corresponding microbial samples at each sampling point; The sampling points include biological sampling points, cage internal environment sampling points, cage peripheral environment sampling points, field non-breeding environment sampling points and field peripheral environment sampling points, and the microbial samples include chicken biological samples, cage internal samples, field cage external samples, field non-breeding area samples and field peripheral samples.

[0020] For actual conditions, the collected data is analyzed to identify the main risk factors affecting the occurrence of the epidemic. The risk factors can be biological factors (such as viral load, host population), environmental factors (such as temperature, humidity), management factors (such as feeding density, hygiene management), etc., but the contribution of environmental factors and management factors to the risk will also be directly or indirectly reflected in the biological factors, so the present application only considers the biological factors.

[0021] The step S1 includes: S11, randomly sampling chicken samples according to a preset proportion of feeding amount, collecting samples in the form of whole blood, cleft palate swabs and cloaca swabs to obtain chicken biological samples; Specifically, randomly sampling according to a proportion of 0.5-1.0% of the feeding amount, whole blood, cleft palate swabs and cloaca swabs, each 1, to obtain chicken biological samples.

[0022] S12, sampling according to the coverage rate of chicken feeding stalls, uniformly selecting several ground sampling points in the cage to collect cotton swab samples, and using an air / aerosol sampler to perform air sampling three times in the morning, noon and evening to obtain cage internal samples; Specifically, sampling according to a stall coverage rate of 50%, uniformly selecting 3-4 ground sampling points in the cage to collect cotton swab samples; air sampling three times in the morning, noon and evening, using an air / aerosol sampler, each sampling time being not less than 10 minutes, to obtain cage internal samples.

[0023] S13, collecting wall corner cotton swab samples at intervals of 20 meters along the cage periphery to obtain field cage external samples.

[0024] S14, collecting ground, building or tree surface cotton swab samples at intervals of 50 meters along the edge in contact with the breeding area to obtain field non-breeding area samples.

[0025] S15, collecting road surface or building surface cotton swab samples at intervals of 100 meters along the periphery of the breeding area to obtain field peripheral samples.

[0026] S2, performing sample processing and metagenomic sequencing on the microbial samples to obtain pathogen species and abundance information results corresponding to each sampling point; The step S2 specifically includes: A number of microbial samples were selected, and chicken biological samples were extracted from the microbial samples. Metagenomic sequencing was performed on the chicken biological samples using multiple individual mixed samples according to sample type. Samples from inside the coop, outside the coop, non-feeding area, and perimeter of the coop were extracted from the microbial samples. Metagenomic sequencing was performed on the samples from inside the coop, outside the coop, non-feeding area, and perimeter of the coop using multiple samples of the same type according to sample type to obtain pathogen species and abundance information.

[0027] Specifically, step S2 is mainly used for DNA / RNA extraction and quality assessment of the collected samples, library construction and high-throughput sequencing, and analysis of sequencing results such as quality control, host removal, metagenomic annotation, and assessment of microbial species and abundance. One second-generation high-throughput sequencing chip is used for each assessment, and 32 nucleic acid samples are measured. The sample allocation is as follows: (1) 12 chicken biological samples, including 3 cleft palate swabs, 3 blood samples, and 6 cloacal swabs. For each type of sample, a mixed sample of multiple individuals is used for testing. (2) 20 environmental samples, including 5 samples inside the farm pens, 5 samples outside the farm pens, 5 samples from the non-feeding area of ​​the farm, and 5 samples from the periphery of the farm. For each type of sample, a mixed sample of multiple samples of the same type is used for testing.

[0028] S3. Construct the sampling point influence matrix, and determine the sampling point weights based on the sampling point influence matrix; Step S3 includes: S31. Determine the mutual influence score for each microbial sample based on the expert evaluation method, and determine the influence ratio between each microbial sample based on the mutual influence score. : ; In the formula, They represent the first Interaction score of individual microbial samples; Specifically, the impact ratio mainly reflects the importance of the samples collected at the sampling points to the epidemic. A higher impact ratio indicates greater importance. Compare The more important it is.

[0029] S32. Determine the influence matrix based on the influence ratio. : ; In the formula, Indicates the first The microbial sample and the first The influence ratio between individual microbial samples Represents the eigenvalue.

[0030] S33, converting the influence matrix into a determinant form and determining a maximum value of eigenvalues , based on the maximum value of eigenvalues determining a homogeneous equation: ; wherein, is an eigenvector.

[0031] S34, solving the homogeneous equation to obtain an eigenvector , and determining a sampling point weight based on the eigenvector .

[0032] S4, determining pathogen nucleic acid abundance in the pathogen species and abundance information result, assigning a score to a corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score; wherein, the step S4 is specifically: If the pathogen nucleic acid abundance of the pathogen enters the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is assigned a score of 100, if the pathogen nucleic acid abundance of the pathogen does not enter the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is assigned a score of 50, and if the pathogen is not detected, the pathogen is assigned a score of 0, to obtain a pathogen score.

[0033] In the present application, the species and percentage abundance krona graph of the chicken biological sample is as shown in Figure 2 The top 20 microorganisms in the abundance ranking of the chicken biological sample are shown in Table 1 as follows: Table 1

[0034] Among them, the meaning of the first letter of the species: kingdom-k, door-p, class-c, order-o, family-f, genus-g, species-s.

[0035] The pathogen score of the pathogen in the chicken biological sample is shown in Table 2 as follows: Table 2

[0036] In the present application, the species and percentage abundance krona graph of the sample in the shed is as shown in Figure 3 The top 20 microorganisms in the abundance ranking of the sample in the shed are shown in Table 3 as follows: Table 3

[0037] The pathogen score of the pathogen in the sample in the shed is shown in Table 4 as follows: Table 4

[0038] In this application, the species and percentage abundance of samples outside the enclosures within the site are shown in the Krona diagram. Figure 4 As shown in Table 5, the top 20 most abundant microorganisms in the samples taken from outside the enclosures within the farm area are listed below: Table 5

[0039] The pathogen scores of the pathogens in the samples taken from outside the enclosures within the field area are shown in Table 6: Table 6

[0040] In this application, the species and percentage abundance of samples from non-breeding areas within the site are shown in the krona diagram. Figure 5 As shown in Table 7, the top 20 most abundant microorganisms in samples from non-breeding areas within the farm are listed below: Table 7

[0041] The pathogen scores of pathogens in samples from non-breeding areas within the farm are shown in Table 8. Table 8

[0042] In this application, the species and percentage abundance of samples from the periphery of the site are shown in the Krona diagram. Figure 6 As shown in Table 9, the top 20 most abundant microorganisms in the samples from the periphery of the field are listed below: Table 9

[0043] The pathogen scores of the pathogens in the samples within the enclosure are shown in Table 10: Table 10

[0044] S5. Determine the final risk score based on the sampling point weights and the pathogen score, and conduct a disease risk assessment for large-scale chicken farms based on the final risk score. Step S5 specifically involves: The pathogen score corresponding to the pathogen is multiplied by the corresponding sampling point weight and accumulated to obtain the final risk score. If the final risk score is greater than the preset score and the corresponding pathogen is included in the target directory, the pathogen is a high-risk pathogen. If the final risk score is greater than the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is 0 and the corresponding pathogen is included in the target directory, the pathogen is a low-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen.

[0045] Specifically, the final risk score is calculated as follows: Assuming a pathogen score of 100, 50, 50, 0, and 0 in chicken biological samples, samples inside the coop, samples outside the coop, samples outside the farm area, and samples outside the farm area, respectively, then the corresponding final score is equal to (100 × ... +50× +50× +0× +0× The preset score is 30 points. The target directory here is the "List of Class I, II, and III Animal Diseases". Based on the above, high-risk pathogens include avian leukosis and Mycoplasma gallisepticum. Farms are advised to focus on the prevention and control of these diseases, strengthening immunization and testing. Medium-risk pathogens are listed, including Newcastle disease, avian adenovirus disease, infectious bronchitis, and infectious bursal disease. Farms are advised to continue prevention and control measures. Low-risk pathogens are listed in the "List of Class I, II, and III Animal Diseases". For other chicken-related pathogens besides the high-risk and medium-risk pathogens listed above, farms are advised to consider reducing prevention and control levels, such as reducing the current number of immunizations. Additionally, parasites such as *Protozoa*, *Toxoplasma gondii*, and *Leishmania huxleyi*, as well as opportunistic pathogens such as *Streptococcus pneumoniae*, *Staphylococcus aureus*, and *Vibrio parahaemolyticus*, are among the most abundant and pathogenic to animals in the test results. These pathogens pose a potential threat to animals, and their prevention and control require close attention.

[0046] The method for assessing disease risk in large-scale chicken farms provided in Embodiment 1 of this invention firstly involves setting up several sampling points within the large-scale chicken farm and collecting corresponding microbial samples at each sampling point. Then, the microbial samples are processed and metagenomically sequenced to obtain pathogen species and abundance information for each sampling point. Next, a sampling point influence matrix is ​​constructed, and the weights of the sampling points are determined based on this matrix. Then, the abundance of pathogen nucleic acids in the pathogen species and abundance information is determined, and each pathogen is assigned a score based on its nucleic acid abundance to obtain a pathogen score. Finally, a final risk score is determined based on the sampling point weights and pathogen scores. Based on this final risk score, a disease risk assessment is conducted for the large-scale chicken farm. This invention fully considers the impact of the environment during the disease risk assessment process and assigns corresponding weights to each environmental element to improve the accuracy of the risk assessment, helping farms identify and assess potential disease risks and take targeted measures to prevent diseases before they occur.

[0047] Example 2 like Figure 2 As shown, in Embodiment 2 of the present invention, a disease risk assessment system for large-scale chicken farms is provided, the system comprising: The collection module 1 is used to set up several sampling points in a large-scale chicken farm and collect corresponding microbial samples at each sampling point; Sequencing module 2 is used to process and perform metagenomic sequencing on the microbial samples to obtain pathogen species and abundance information for each sampling point. Matrix module 3 is used to construct the sampling point influence matrix and determine the sampling point weights based on the sampling point influence matrix; Scoring module 4 is used to determine the abundance of pathogen nucleic acid in the pathogen species and abundance information results, and to assign a score to the corresponding pathogen based on the abundance of pathogen nucleic acid to obtain the pathogen score; Assessment module 5 is used to determine the final risk score based on the sampling point weights and the pathogen score, and to conduct disease risk assessment for large-scale chicken farms based on the final risk score. The acquisition module 1 includes: The first collection submodule is used to randomly select chicken samples according to a preset ratio of the number of chickens raised, and to collect samples by means of whole blood, cleft palate swabs and cloacal swabs to obtain chicken biological samples. The second sampling submodule is used to sample according to the coverage of chicken pen. Several ground sampling points are evenly selected in the pen to collect cotton swab samples. Air samples are collected three times a day, in the morning, noon and evening, using an air / aerosol sampler to obtain samples from inside the pen. The third collection submodule is used to collect cotton swab samples from the corners of the walls at 20-meter intervals along the perimeter of the enclosure to obtain samples outside the enclosures in the field area; The fourth collecting sub-module is configured to collect cotton swab samples from the ground, buildings or tree surfaces every 50 meters along the edge in contact with the breeding area to obtain non-breeding area samples in the field area; The fifth collecting sub-module is configured to collect cotton swab samples from the road surface or building surface every 100 meters along the periphery of the breeding area to obtain periphery samples in the field area.

[0048] The sequencing module 2 is specifically configured to: select a plurality of microbial samples, extract chicken biological samples from the microbial samples, perform metagenomic sequencing on the chicken biological samples according to sample types by using a plurality of individual mixed samples, extract a shed-in sample, a field area shed-out sample, a field area non-breeding area sample and a field area periphery sample from the microbial samples, perform metagenomic sequencing on the shed-in sample, the field area shed-out sample, the field area non-breeding area sample and the field area periphery sample according to sample types by using a plurality of similar samples combined into mixed samples, and obtain pathogen species and abundance information results.

[0049] The matrix module 3 includes: The first matrix sub-module is configured to determine a mutual influence score of each microbial sample based on an expert evaluation method, and determine an influence ratio between each microbial sample based on the mutual influence score . ; In the formula, and respectively represent the mutual influence score of the i-th microbial sample and the j-th microbial sample; The second matrix sub-module is configured to determine an influence matrix based on the influence ratio . ; In the formula, represents the influence ratio between the i-th microbial sample and the j-th microbial sample, represents an eigenvalue; The third matrix sub-module is configured to convert the influence matrix into a determinant form and determine a maximum value of the eigenvalue , determine a homogeneous equation based on the maximum value of the eigenvalue : ; In the formula, is an eigenvector; The fourth matrix sub-module is configured to solve the homogeneous equation to obtain the eigenvector , and determine a sampling point weight based on the eigenvector .

[0050] ​​​​​​The scoring module 4 is specifically configured to: If the pathogenic nucleic acid abundance of the pathogen enters the top 20 of the pathogenic nucleic acid abundance ranking, the pathogen is assigned a score of 100, if the pathogenic nucleic acid abundance of the pathogen does not enter the top 20 of the pathogenic nucleic acid abundance ranking, the pathogen is assigned a score of 50, and if the pathogen is not detected, the pathogen is assigned a score of 0, to obtain a pathogen score.

[0051] The evaluation module 5 is specifically configured to: The corresponding pathogen score corresponding to the corresponding pathogen is multiplied by the corresponding sampling point weight and accumulated to obtain a final risk score, if the final risk score is greater than a preset score and the corresponding pathogen is included in the target directory, the pathogen is a high-risk pathogen, if the final risk score is greater than the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen, if the final risk score is between 0 and the preset score and the corresponding pathogen is included in the target directory, the pathogen is a medium-risk pathogen, if the final risk score is 0 and the corresponding pathogen is included in the target directory, the pathogen is a low-risk pathogen, and if the final risk score is between 0 and the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen.

[0052] In some embodiments of the present application, the present application provides the following technical solutions, a computer, comprising a memory 102, a processor 101 and a computer program stored on the memory 102 and executable on the processor 101, the processor 101 executes the computer program to realize the scale chicken farm disease risk assessment method as described above.

[0053] Specifically, the above-mentioned processor 101 can include a central processing unit (CPU), or a specific integrated circuit (Application Specific Integrated Circuit, referred to as ASIC), or can be configured to implement one or more integrated circuits of the embodiments of the present application.

[0054] The memory 102 can include mass storage for data or instructions. By way of example, and not limitation, the memory 102 can include a Hard Disk Drive (HDD), a floppy disk drive, a Solid State Drive (SSD), a flash drive, a Compact Disc Read Only Memory (CD-ROM), a Digital Versatile Disk (DVD), a Blu-ray disk, a magnetic tape, or a Universal Serial Bus (USB) drive, or a combination of two or more of these. Storage memory 102, where appropriate, can include removable or non-removable (or fixed) media. Storage memory 102 can be internal or external to data processing system, where appropriate. In particular embodiments, storage memory 102 is nonvolatile memory. In particular embodiments, storage memory 102 includes Read-Only Memory (ROM) and Random Access Memory (RAM). Where appropriate, this ROM can be mask- programmed ROM, Programmable Read-Only Memory (PROM), Erasable Programmable Read-Only Memory (EPROM), Electrically Erasable Programmable Read-Only Memory (EEPROM), Electrically Alterable Read-Only Memory (EAROM), or FLASH memory, or a combination of two or more of these. Where appropriate, this RAM can be Static Random-Access Memory (SRAM) or Dynamic Random-Access Memory (DRAM), which can be Fast Page Mode Dynamic Random-Access Memory (FPMDRAM), Extended Data Output Dynamic Random-Access Memory (EDODRAM), Extended Data Output Dynamic

[0055] The memory 102 can be used to store or buffer various data files needed for processing and / or communication, and possible computer program instructions executed by the processor 101.

[0056] The processor 101 realizes the above-mentioned large-scale chicken farm epidemic risk assessment method by reading and executing the computer program instructions stored in the memory 102.

[0057] In some embodiments, the computer can also include a communication interface 103 and a bus 100. As shown, the processor 101, the memory 102, and the communication interface 103 are connected through the bus 100 and complete communication with each other. Figure 3

[0058] The communication interface 103 is used to realize the communication between the modules, devices, units and / or equipment in the embodiments of the present application. The communication interface 103 can also realize data communication with other components, such as external devices, image / data acquisition devices, databases, external storage, image / data processing workstations, etc.

[0059] ​Bus 100 includes hardware, software, or both, to couple components of the computer device to each other and to couple components to other components in the environment. Bus 100 includes, but is not limited to, at least one of the following: a data bus, an address bus, a control bus, an expansion bus, a local bus, etc. By way of example and not limitation, bus 100 can include an Accelerated Graphics Port (AGP) or other graphics bus, an Extended Industry Standard Architecture (EISA) bus, a Front Side Bus (FSB), a Hyper Transport (HT) interconnect, an Industry Standard Architecture (ISA) bus, an InfiniBand interconnect, a Low Pin Count (LPC) bus, a memory bus, a Micro Channel Architecture (MCA) bus, a Peripheral Component Interconnect (PCI) bus, a PCI-Express (PCI-X) bus, a Serial Advanced Technology Attachment (SATA) bus, a Video Electronics Standards Association Local Bus (VLB) bus, or another suitable bus or combination of two or more of these. Where appropriate, bus 100 can include one or more buses. Although the present embodiments describe and show a particular bus, the present embodiments contemplate any suitable bus or interconnect.

[0060] The computer can execute the large-scale chicken farm epidemic risk assessment method according to the large-scale chicken farm epidemic risk assessment system, thereby realizing the large-scale chicken farm epidemic risk assessment.

[0061] In some embodiments of the present application, in combination with the large-scale chicken farm epidemic risk assessment method described above, the present embodiments provide the following technical solutions: a storage medium, the storage medium has a computer program stored thereon, and the computer program is executed by a processor to realize the large-scale chicken farm epidemic risk assessment method described above.

[0062] Those skilled in the art will appreciate that the logic and / or steps represented in the flow diagrams, or otherwise described herein, can be embodied in

[0063] More specific examples (a non-exhaustive list) of the computer-readable medium include the following: an electrical connection (electronic) having one or more wires, a portable computer diskette (magnetic), a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), an optical fiber, and a portable compact disc read-only memory (CDROM). Additionally, the computer-readable medium can also be paper or another suitable medium upon which the program is printed, as the program can be electronically captured, for example, via an optical scanner, then compiled, interpreted, or otherwise processed, and stored in a computer memory in a form that is then employable by a computer.

[0064] It should be understood that aspects of the application can be implemented in hardware, software, firmware or combinations thereof. In the above embodiments, various steps or methods can be implemented in software or firmware that is stored in memory and executed by a suitable instruction execution system. For example, if implemented in hardware, as in another embodiment, any of the following technologies, known in the art, or combinations thereof, can be employed: discrete logic circuitry having logic gates for implementing logic functions upon an application of data signals, application specific integrated circuits having appropriate combinational logic gates, programmable gate arrays (PGA), field programmable gate arrays (FPGA), and the like.

[0065] The technical features of the above-described embodiments can be combined in any manner, and in order to make the description concise, not all possible combinations of the technical features in the above-described embodiments are described, however, as long as the combinations of the technical features do not contradict each other, they should be considered to be within the scope of the present specification.

[0066] The above embodiments only express several implementation manners of the present application, and the description is more specific and detailed, but it should not be understood as a limitation on the scope of the patent. It should be noted that for ordinary skilled persons in the art, without departing from the concept of the present application, several modifications and improvements can be made, which are within the scope of protection of the present application. Therefore, the protection scope of the patent of the present application should be subject to the appended claims.

Claims

1. A method for assessing the risk of disease in a large-scale chicken farm, characterized by, The method comprises the following steps: a plurality of sampling points are arranged in the large-scale chicken farm, and a corresponding microbial sample is collected at each sampling point; sample processing and metagenomic sequencing are performed on the microbial sample to obtain pathogen species and abundance information results corresponding to each sampling point; a sampling point influence matrix is constructed, and sampling point weights are determined based on the sampling point influence matrix; pathogen nucleic acid abundance in the pathogen species and abundance information results is determined, and a corresponding pathogen is scored based on the pathogen nucleic acid abundance to obtain a pathogen score; a final risk score is determined based on the sampling point weights and the pathogen score, and an epidemic risk assessment of the large-scale chicken farm is performed based on the final risk score.

2. The method of claim 1, wherein the method further comprises: The sampling points include biological sampling points, in-shed environmental sampling points, out-of-shed environmental sampling points, non-breeding environmental sampling points in the field area, and peripheral environmental sampling points in the field area. The microbial samples include chicken biological samples, in-shed samples, out-of-shed samples in the field area, non-breeding area samples in the field area, and peripheral samples in the field area.

3. The method for assessing disease risk in large-scale chicken farms according to claim 2, characterized in that, The step of collecting a corresponding microbial sample at each sampling point comprises the following steps: chicken samples are randomly selected according to a preset proportion of the feeding amount, and whole blood, palate swabs, and cloaca swabs are used to collect samples to obtain chicken biological samples; sampling is performed according to the coverage rate of chicken feeding pens, a plurality of ground sampling points are uniformly selected in the shed to collect cotton swab samples, and air sampling is performed three times in the morning, at noon, and at night using an air / aerosol sampler to obtain in-shed samples; wall corner cotton swab samples are collected every 20 meters along the shed periphery to obtain out-of-shed samples in the field area; ground, building, or tree surface cotton swab samples are collected every 50 meters along the edge of the breeding area to obtain non-breeding area samples in the field area; road surface or building surface cotton swab samples are collected every 100 meters along the periphery of the breeding area to obtain peripheral samples in the field area.

4. The method of claim 1, wherein the method further comprises: The step of performing sample processing and metagenomic sequencing on the microbial sample to obtain pathogen species and abundance information results corresponding to each sampling point comprises the following steps: a plurality of microbial samples are selected, chicken biological samples are extracted from the microbial samples, a plurality of individual mixed samples are used for metagenomic sequencing of the chicken biological samples according to sample types, in-shed samples, out-of-shed samples in the field area, non-breeding area samples in the field area, and peripheral samples in the field area are extracted from the microbial samples, and a plurality of similar samples are combined into a mixed sample for metagenomic sequencing of the in-shed samples, the out-of-shed samples in the field area, the non-breeding area samples in the field area, and the peripheral samples in the field area according to sample types to obtain pathogen species and abundance information results.

5. The method of claim 1, wherein the step of determining the risk of disease outbreak in the poultry farm is performed by using a risk assessment model. The step of constructing a sampling point influence matrix and determining sampling point weights based on the sampling point influence matrix comprises the following steps: determining a score of mutual influence for each microbial sample based on expert evaluation, determining a ratio of influence between each microbial sample based on the score of mutual influence : ； wherein respectively represent the cross-influence score of the i-th microorganism sample; determining an influence matrix based on the influence ratios : ； wherein represents the influence ratio between the first microorganism sample and the second microorganism sample, represents the eigenvalue; converting the influence matrix into determinant form and determining a maximum value of eigenvalues based on the maximum value of eigenvalues determining a homogeneous equation: ； In the formula, is a feature vector; solving the homogeneous equation to obtain an eigenvector , and determining a sampling point weight based on the eigenvector.

6. The method of claim 1, wherein the step of determining the risk of disease outbreak in the poultry farm is performed by using a risk assessment model. The step of scoring a corresponding pathogen based on the pathogen nucleic acid abundance to obtain a pathogen score comprises the following steps: if the pathogen nucleic acid abundance of a pathogen enters the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is scored 100, if the pathogen nucleic acid abundance of a pathogen does not enter the top 20 of the pathogen nucleic acid abundance ranking, the pathogen is scored 50, and if the pathogen is not detected, the pathogen is scored 0 to obtain a pathogen score.

7. The method for assessing disease risk in large-scale chicken farms according to claim 1, characterized in that, The step of determining a final risk score based on the sampling point weight and the pathogen score, and performing the epidemic risk assessment of the large-scale chicken farm based on the final risk score, specifically comprises: The pathogen score corresponding to the corresponding pathogen is multiplied by the corresponding sampling point weight and accumulated to obtain a final risk score. If the final risk score is greater than a preset score and the corresponding pathogen is included in a target directory, the pathogen is a high-risk pathogen. If the final risk score is greater than the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is included in the target directory, the pathogen is a medium-risk pathogen. If the final risk score is 0 and the corresponding pathogen is included in the target directory, the pathogen is a low-risk pathogen. If the final risk score is between 0 and the preset score and the corresponding pathogen is not included in the target directory, the pathogen is a medium-risk pathogen.

8. A system for assessing disease risk in a large-scale chicken farm, characterized by, Comprise: The acquisition module is used for setting a plurality of sampling points in the large-scale chicken farm, and collecting corresponding microbial samples at each sampling point; The sequencing module is used for sample processing and metagenomic sequencing of the microbial samples to obtain pathogen species and abundance information results corresponding to each sampling point; The matrix module is used for constructing a sampling point influence matrix and determining a sampling point weight based on the sampling point influence matrix; The scoring module is used for determining pathogen nucleic acid abundance in the pathogen species and abundance information results, and assigning scores to corresponding pathogens based on the pathogen nucleic acid abundance to obtain pathogen scores; The evaluation module is used for determining a final risk score based on the sampling point weight and the pathogen score, and performing the epidemic risk assessment of the large-scale chicken farm based on the final risk score.

9. A computer device comprising a memory, a processor, and a computer program stored on the memory and executable on the processor, characterized in that, The processor executes the computer program to realize the large-scale chicken farm epidemic risk assessment method of any one of claims 1 to 7.

10. A computer-readable storage medium, characterized in that, The computer readable storage medium stores a computer program, and the computer program is executed by the processor to realize the large-scale chicken farm epidemic risk assessment method of any one of claims 1 to 7.

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