Pathogen detection background microorganism judgment method and application
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A microbial and background technology, applied in the field of bioinformatics analysis, can solve problems such as fluctuations, batch false positives, background pollution, etc., and achieve high application scalability and wide-ranging effects
Active Publication Date: 2021-08-20
GZ VISION GENE TECH CO LTD +4
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This type of method can only obtain a list of potential background contamination, and use a one-size-fits-all approach to directly remove these microorganisms
However, common clinical pathogens, such as Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Stenotrophomonas maltophilia, Escherichia coli, Enterococcus faecalis, Serratia marcescens, etc., all exist at the same time Microorganisms in the background of nucleic acid extraction or reagents cannot determine whether the microorganisms in the sample are background contamination or originate from the sample itself.
[0007] The other method is to quantify by adding internal references to remove microorganisms whose relative abundance is below the threshold. This method has higher requirements f
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[0106] Example 1
[0107] A pathogen detection background microbial judgment method, such as figure 1 As shown, including the following steps:
[0108] 1. Determine the core background microorganism list.
[0109] 1.1 sample analysis.
[0110] Take the DNA sample of about 20,000 cases of MNGS sequencing in Guangzhou laboratory sequencing, according to samples, each 2000 samples are used as a data set (all of each dataset contains various types of samples, such as Alveolar lavage, sputum, cerebrospinal fluid, throat swab, blood, tissue, etc.).
[0111] First, the frequency is more than 25% in the data set, and the microorganisms in all data sets, that is, high-frequency and stably appear in the sample in the sample.
[0112] The nucleic acid extraction concentration or library concentration of these samples was then calculated, and the PEARSON correlation test of each microorganism was compared with the Spearman correlation test.
[0113] Specifically, the specific comparison seque...
Example Embodiment
[0137] Example 2
[0138] 639 cases of clinical samples were collected as a verification set, and the method of determining whether the characteristic sequence in the sample is a background sequence using the method of the method of Example 1.
[0139] According to the method of the first embodiment, it is obtained in which the Bowman does not move acne gene sequence data is analyzed, and the model is established, the ROC curve is drawn, and the result is Figure 4 As shown in the threshold 0.041, the AUC value is 0.992, the specificity is 0.942, and the sensitivity is 0.983.
[0140] The above results, the pathogenic detection method of the present invention can achieve better distinction between the samples of different source batch, and has the advantage of judging high and practicality.
[0141] It will be appreciated that the judgment method in the above embodiment is widely used, which is not subject to sample type limits, DNA or RNA, and the model is not limited to the above...
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Abstract
The invention relates to a pathogen detection background microorganism judgment method and application, and belongs to the technical field of bioinformatics analysis. The judgment method comprises the following steps of: determining a core background microorganism list: taking a plurality of biological samples, comparing gene sequence data of each microorganism to a characteristic sequence region of a corresponding microorganism, performing correlation test on nucleic acid extraction concentration or library concentration to obtain a microorganism list with negative correlation, and obtaining a core background microorganism list; determining a core background microorganism correction index CBI: taking the sum of the specific comparison sequence numbers of all microorganisms in the core background microorganism list as the CBI; and carrying out background sequence judgment: dividing the specific comparison sequence number of the microorganisms in the sample to be detected by the CBI to obtain a judgment value. By adopting the method, the background related microorganisms can be corrected according to the background microorganism index, whether the pathogenic microorganisms exist in the sample or not is judged according to the corrected quantity, and a more accurate judgment result can be obtained.
Description
technical field [0001] The invention relates to the technical field of bioinformatics analysis, in particular to a method and application for determining background microorganisms in pathogen detection. Background technique [0002] Pathogenic metagenomics (mNGS) is a high-throughput sequencing technology that does not depend on culture, directly extracts nucleic acids from clinical specimens and detects pathogens. Compared with traditional clinical laboratory detection methods, pathogenic mNGS is based on the detection of sequences at the nucleic acid level, which can break through the limitations of different pathogen types, comprehensively cover thousands of pathogens without bias, and simultaneously identify bacteria, fungi, viruses and Various types of pathogenic microorganisms such as parasites, pathogenic mNGS has gradually become an important tool in the field of clinical microbial identification. [0003] However, the accuracy of mNGS is affected by contaminants—DN...
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