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Acinetobacter database construction method based on mass spectrometry and acinetobacter database

A construction method and database technology, applied in the field of Acinetobacter database, can solve the problems of incomplete strain information and low accuracy, and achieve the effect of comprehensive database, high accuracy, and not easy to miss false positives

Inactive Publication Date: 2021-02-05
ZHEJIANG UNIV
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Problems solved by technology

[0005] The embodiment of the present invention provides a method for constructing an Acinetobacter database based on mass spectrometry and the Acinetobacter database, so as to solve the problems of incomplete species information and low accuracy of the existing Acinetobacter mass spectrum library

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  • Acinetobacter database construction method based on mass spectrometry and acinetobacter database
  • Acinetobacter database construction method based on mass spectrometry and acinetobacter database
  • Acinetobacter database construction method based on mass spectrometry and acinetobacter database

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Embodiment 1

[0029] The embodiment of the present invention provides a method for constructing an Acinetobacter database based on mass spectrometry, comprising the following steps:

[0030] Step (1) Obtain the strains that meet the requirements and NGS sequencing:

[0031] Such as figure 1 As shown, Acinetobacter colonies were isolated, enriched and frozen to ensure that the obtained strains were 100% pure, and the strains were numbered BJ2020295; DNA was extracted from the genome, and the sequences were analyzed by Illumina Hiseq 2000. Perform pairwise ANI (fastANI) calculation on the genome of the NCBI database of the genus Anitobacter, execute the command: fastANI-q [QUERY_GENOME]–r[REFFERENCE_GENOME]-o[OUTPUT_LIFE], and use the result with the highest matching degree among the calculation results as the species identification result, The BJ2020295 strain was identified by NGS sequencing as Acinetobacterschindler, with an ANI score of 97.13; the high-throughput data of the obtained str...

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Abstract

The invention discloses an acinetobacter database construction method based on mass spectrometry and an acinetobacter database; and the acinetobacter database construction method comprises the following steps: performing separating to obtain an acinetobacter colony, and performing enrichment cryopreservation to ensure that the purity of the obtained strain is 100%; carrying out NGS sequencing on the strain to obtain a sequence, assembling the sequence, carrying out ANI calculation on the assembled sequence and an NCBI database genome of acinetobacter pairwise, and taking a result with the highest matching degree in calculation results as a species identification result; respectively extracting the strains obtained in the step 1 by adopting a direct coating method and / or an extraction method, and collecting spectrums after extraction to obtain a biological polypeptide fingerprint standard spectrum; opening micro type post-processing software by double click, creating a laboratory acinetobacter self-built library, building nodes according to the kingdom, phylum, class, order, family, genus and species sequence, selecting new acinetobacter data needing to be added, selecting high-quality map to build data, unifying the determined biological polypeptide fingerprint standard map and the name of the strain obtained by NGS sequencing, and adding into the corresponding nodes; and completing the library construction of the strain.

Description

technical field [0001] The invention relates to the technical field of mass spectrometry detection, in particular to a method for constructing an Acinetobacter database based on mass spectrometry and the Acinetobacter database. Background technique [0002] Acinetobacter bacteria belong to Proteobacteria, Gamma Proteobacteria, Pseudomonas, Moraxellaceae bacteria, are important conditional pathogens causing nosocomial infections, mainly threatening patients in the intensive care unit, causing Common infections include bloodstream infections, ventilator-associated pneumonia, urinary tract infections, meningitis, and wound infections, which are associated with high morbidity and mortality in infected patients. Infection outbreaks in many hospitals are caused by Acinetobacter, due to its high resistance in the environment and resistance to antimicrobials, making the infection difficult to control and treat, and leading to prolonged hospital stays and high hospital costs . [0...

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Application Information

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IPC IPC(8): G16B30/00G16B50/00C12Q1/6869C12Q1/04G01N27/64
CPCC12Q1/6869G01N27/64G16B30/00G16B50/00C12Q2535/122C12Q2537/165
Inventor 华孝挺俞云松张玲虹
Owner ZHEJIANG UNIV
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