Ignite Creation Date:
2024-10-26 @ 3:38 PM
Last Modification Date:
2024-10-26 @ 3:38 PM
Study NCT ID:
NCT06566898
Status:
RECRUITING
Last Update Posted:
None
First Post:
2024-08-18
Brief Title:
Monitoring of Antimicrobial Resistance Based on Metagenomics Analyses in Pneumonia Patients
Sponsor:
None
Organization:
None
Study Overview
Official Title:
Monitoring of Antimicrobial Resistance Based on Metagenomics Analyses in Pneumonia Patients a Genomic Epidemiology Study
Status:
RECRUITING
Status Verified Date:
2024-08
Last Known Status:
None
Delayed Posting:
No
If Stopped, Why?:
Not Stopped
Has Expanded Access:
No
If Expanded Access, NCT#:
N/A
Has Expanded Access, NCT# Status:
N/A
Acronym:
None
Brief Summary:
Monitoring of antimicrobial resistance AMR based on metagenomics analyses in pneumonia patients is critical for optimizing clinical diagnosis and treatment and improving clinical prognosis This study is designed to ask the following key questions
1 What is the microbiome maps of patients with severe pneumonia and mild pneumonia
2 How many pathogen resistance genes are carrying in severe pneumonia and mild pneumonia
3 What is the genetic diversity of key pathogens detected in severe pneumonia and mild pneumonia during 2019-2025
1 What is the microbiome maps of patients with severe pneumonia and mild pneumonia
2 How many pathogen resistance genes are carrying in severe pneumonia and mild pneumonia
3 What is the genetic diversity of key pathogens detected in severe pneumonia and mild pneumonia during 2019-2025
Detailed Description:
This is a historical prospective obsevational study Patients diagnosed with severe and mild pneumonia are recruited continously from four hospitals Shanghai General Hospital Wuxi Peoples Hospital Affiliated to Nanjing Medical University Wuhan Union Hospital and Huanggang Central Hospital in China during March 2019 to March 2025
Next-generation sequencing Metagenomics and metatranscriptomic libraries undergo next-generation sequencing using the Illumina Novaseq 6000 platform
Microbiome analysis using KneadData v0100 reference from the human genome GRCH38 reference database to filter out the quality control of illumina sequencing data in Virosaurus download virus genome data sets for reference bowtie2 v2341 genome coverage 30 depth 1X was used to locate and analyze the post-host sequence and then the samtools idxstats command was used to calculate the classification and relative abundance of viruses Meanwhile in order to obtain the annotation information of bacteria at the species level PhyloFlash v34 was used to calculate read counts for 16S rRNA genes in the SILVA database selecting similarity greater than or equal to 98 as a threshold Using eukaryotic pathogen genome database EUPATHDB46 as reference bowtie2 and samtools were used for qualitative and quantitative analysis of fungal pathogens
The criteria for determining the cause of respiratory infection are 1 existing species known to be associated with human disease ICD-10 2 previously unidentified potential novel pathogens only DNA and RNA viruses whose genera or families have previously been shown to infect mammals and 3 possible symbiotic bacteria not included
Analysis of AMR by comparing the sequence similarity between the sequencing fragments and known drug resistance genes the detection content can determine whether drug resistance genes exist and suggest drug resistance caused by modification inactivation repression and other drug resistance genes
Drug resistance genes detection genes related to drug resistance recorded in CARD Comprehensive Antibiotic Resistance Database and ARG-ANNOT database In this assay only functional genes with drug resistance activities such as modification inactivation and repression as well as pathway and target changes caused by some point mutations were reported
Genetic diversity was computed as the mean pairwise genetic distance within a group Maximum likelihood phylogenetic trees were constructed using RaxML with a general time-reversible nucleotide substitution model and 1000 bootstraps The genetic distance between sequences was calculated using MEGAX with a bootstrap method for variance estimation
Next-generation sequencing Metagenomics and metatranscriptomic libraries undergo next-generation sequencing using the Illumina Novaseq 6000 platform
Microbiome analysis using KneadData v0100 reference from the human genome GRCH38 reference database to filter out the quality control of illumina sequencing data in Virosaurus download virus genome data sets for reference bowtie2 v2341 genome coverage 30 depth 1X was used to locate and analyze the post-host sequence and then the samtools idxstats command was used to calculate the classification and relative abundance of viruses Meanwhile in order to obtain the annotation information of bacteria at the species level PhyloFlash v34 was used to calculate read counts for 16S rRNA genes in the SILVA database selecting similarity greater than or equal to 98 as a threshold Using eukaryotic pathogen genome database EUPATHDB46 as reference bowtie2 and samtools were used for qualitative and quantitative analysis of fungal pathogens
The criteria for determining the cause of respiratory infection are 1 existing species known to be associated with human disease ICD-10 2 previously unidentified potential novel pathogens only DNA and RNA viruses whose genera or families have previously been shown to infect mammals and 3 possible symbiotic bacteria not included
Analysis of AMR by comparing the sequence similarity between the sequencing fragments and known drug resistance genes the detection content can determine whether drug resistance genes exist and suggest drug resistance caused by modification inactivation repression and other drug resistance genes
Drug resistance genes detection genes related to drug resistance recorded in CARD Comprehensive Antibiotic Resistance Database and ARG-ANNOT database In this assay only functional genes with drug resistance activities such as modification inactivation and repression as well as pathway and target changes caused by some point mutations were reported
Genetic diversity was computed as the mean pairwise genetic distance within a group Maximum likelihood phylogenetic trees were constructed using RaxML with a general time-reversible nucleotide substitution model and 1000 bootstraps The genetic distance between sequences was calculated using MEGAX with a bootstrap method for variance estimation
Study Oversight
Has Oversight DMC:
None
Is a FDA Regulated Drug?:
None
Is a FDA Regulated Device?:
None
Is an Unapproved Device?:
None
Is a PPSD?:
None
Is a US Export?:
None
Is an FDA AA801 Violation?:
None