US 12,308,093 B2
Method and device for identifying specific region in microorganism target fragment and use thereof
Cong Ji, Shanghai (CN); Junbin Shao, Shanghai (CN); Yan Liu, Shanghai (CN); Xia Qi, Shanghai (CN); Yudan Jin, Shanghai (CN); and Qiteng Li, Shanghai (CN)
Assigned to SHANGHAI ZJ BIO-TECH CO., LTD, Shanghai (CN)
Appl. No. 17/916,214
Filed by SHANGHAI ZJ BIO-TECH CO., LTD., Shanghai (CN)
PCT Filed May 14, 2020, PCT No. PCT/CN2020/090180
§ 371(c)(1), (2) Date Sep. 30, 2022,
PCT Pub. No. WO2021/196358, PCT Pub. Date Oct. 7, 2021.
Claims priority of application No. 202010254403.4 (CN), filed on Apr. 2, 2020.
Prior Publication US 2023/0129284 A1, Apr. 27, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. G16B 30/10 (2019.01); G16B 35/20 (2019.01)
CPC G16B 30/10 (2019.02) [G16B 35/20 (2019.02)] 6 Claims
 
1. A method for identifying presence of a microorganism in a sample, comprising:
identifying a specific region in a microorganism target fragment, at least comprising:
(S100), respectively comparing the microorganism target fragment with whole genome sequences of one or more comparison strains one-to-one, and removing fragments in the microorganism target fragment of which a similarity exceeds a preset value, to obtain one or more residual fragments as first-round cut fragments T1-Tn, wherein n is an integer greater than or equal to 1; then
(S200), respectively comparing the first-round cut fragments T1-Tn with whole genome sequences of a second plurality of comparison strains, and removing subfragments of the first-round cut fragments of which a similarity exceeds the preset value, to obtain a collection of residual cut fragments as candidate specific regions of the microorganism target fragment; and then
(S300), verifying and obtaining a specific region, comprising: determining whether each candidate specific region meets the following requirements:
1) Searching in public databases to find whether there are species other than the species of the microorganism of the microorganism target fragment of which a similarity to the candidate specific region is greater than the preset value;
2) Respectively comparing the candidate specific region with whole genome sequences of the one or more comparison strains and the second plurality of comparison strains and a whole genome sequence of a host of a source strain of the microorganism target fragment, to find whether there are fragments with a similarity greater than the preset value;
if the candidate specific region does not meet the above requirements, the candidate specific region is a specific region of the microorganism target fragment; and performing a PCR amplification of the specific region to detect the microorganism.