NDLI: Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data

Content Provider	Springer Nature : BioMed Central
Author	Mai, Guoqin Chen, Jiayi Zhang, Min Zhang, Wanyue Luo, Yuting Dai, Ying
Abstract	Background Pathogenic microorganisms can cause infections, allergies, diarrhoea, tumours, other diseases, and even death. Therefore, the detection of pathogenic microorganisms is important. Methods In this study, a bioinformatics pipeline was developed. First, a comprehensive and penetrating reference database of nucleic acids from pathogenic microorganisms was constructed, and sequence alignment analysis was performed via nanopore sequencing of metagenomic data collected from 40 patients with lower respiratory tract infection symptoms. The similarity, abundance, and matching length of the sequences were integrated to obtain a comprehensive parameter, all_ratio, which can be used to identify pathogenic microorganisms effectively. Results Compared with two previous methods, i.e., pathogen identification via microbiological culture or a previously reported metagenomic pipeline, pathogens were detected in 23 out of the 40 samples using our method, with the same results as those of the previous two methods. In five samples, pathogens such as Streptococcus pneumoniae and Granulicatella adiacens that had not been detected via the previous two methods were detected using our method. Pathogens such as Streptococcus pneumoniae and Neisseria flavescens were detected in 12 samples via our method, in contrast to the results of the previous two methods. Therefore, it is presumed that the individuals from whom these samples were obtained may have been infected with two or more pathogenic microorganisms. Conclusions This study shows that our method can efficiently identify pathogenic microorganisms and even detect pathogenic microorganisms in samples that cannot be detected via other methods, thus supplementing existing methods.
Related Links	https://bmcinfectdis.biomedcentral.com/counter/pdf/10.1186/s12879-025-10559-5.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712334
DOI	10.1186/s12879-025-10559-5
Journal	BMC Infectious Diseases
Issue Number	1
Volume Number	25
Language	English
Publisher	BioMed Central
Publisher Date	2025-02-07
Access Restriction	Open
Subject Keyword	Infectious Diseases Parasitology Medical Microbiology Tropical Medicine Internal Medicine Pathogenic microorganism Detection method Nanopore sequencing data All_ratio Lower respiratory tract infection Similarity Abundance
Content Type	Text
Resource Type	Article
Subject	Infectious Diseases
Journal Impact Factor	3.4/2023
5-Year Journal Impact Factor	3.3/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Clinical application of targeted nanopore sequencing in pathogen detection in patients with sepsis

Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study

Incidence of lower respiratory tract infection and associated viruses in a birth cohort in the Philippines

Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012

Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report

Risk of infections in bronchiectasis during disease-modifying treatment and biologics for rheumatic diseases

Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing

Molecular characterization of Pseudomonas sp. isolated from lower respiratory tract infection in HIV and non-HIV population by 16S rDNA and ARDRA

The Diagnostic Value of Metagenomic Next–Generation Sequencing in Lower Respiratory Tract Infection

Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data

Similar Documents

Clinical application of targeted nanopore sequencing in pathogen detection in patients with sepsis

Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study

Incidence of lower respiratory tract infection and associated viruses in a birth cohort in the Philippines

Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012

Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report

Risk of infections in bronchiectasis during disease-modifying treatment and biologics for rheumatic diseases

Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing

Molecular characterization of Pseudomonas sp. isolated from lower respiratory tract infection in HIV and non-HIV population by 16S rDNA and ARDRA

The Diagnostic Value of Metagenomic Next–Generation Sequencing in Lower Respiratory Tract Infection

Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data