Which ARGs are in the sample?
What is the abundance of ARGs?
Which strains do ARGs come from?
Which movable elements carry ARGs?
Where are ARGslocated? Chromosome or Plasmid? What are the differences in ARGs different treatments and different backgrounds?
Antibiotic resistance genes (ARGs) are a new type of persistent environmental pollutants. Plasmids, integrons, and transposons that carry ARGs in bacteria can undergo horizontal gene transfer between strains. long-term existence in the environment. [1]complete DNA sequence was obtained by Nanopore sequencing technology, and the distribution and sequence of ARGs in environmental microorganisms were studied through bioinformatics analysis, so as to further explore their functions and mechanisms.
Obtained after analysis —
the identification results of ARGs in the target samples
ARGs abundance in each sample
Species information of ARGs annotated
antibiotic resistance gene clusters
antibiotic resistance gene location
[1]Knapp CW , Engemann CA , Hanson ML , et al. Indirect Evidence of Transposon-Mediated Selection of Antibiotic Resistance Genes in Aquatic Systems at Low-Level Oxytetracycline Exposures[J]. Environmental ence & Technology, 2008, 42(14) : 5348-5353.
Paper recommendation
Che Y , Xia Y , Liu L , et al., Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing[J]. Microbiome, 2019, 7(1).
Sukhum K V , Diorio-Toth L , Dantas G. Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance[J]. Clinical Pharmacology & Therapeutics, 2019, 106(3).
Leggett et al., Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens[J]. Nature Microbiology. 2019.
common problem
1. What is ARG?
A: Antibiotic resistance genes (antibiotic resistance genes), some antibiotic-resistant microorganisms carry ARGs, which are widely spread through horizontal mobile layers such as viruses and bacteria, causing genetic pollution and food safety issues, which is one of the most concerned environmental pollution issues at present .
2. What is an ARG cluster? What’sthe meaning?
A: A single Read is annotated to multiple resistance genes at the same time, which is called a gene-cluster. this product identifies 5 or more ARG reads.
3. What database is used for ARG identification?
A: The SARG 2.0 database. It mainly integrates the resistance genome data of ARG sequences in NCBI-NR, CARD (resistance gene database) and ARDB (resistance gene database) data, including 24 ARG types and 1208 resistance subtypes.
4. Are ARDB and CARD the same database?
Answer: No. ARDB is the first database to integrate drug resistance genes in various microorganisms, but it has been no longer maintained and updated since 2009. The CARD database contains all the resistance information in the ARDB database, and a data sharing platform based on volunteer contributions has been built, which can be updated in real time to ensure the validity of the data.
5. The large database cannot guarantee that all ARGs can be identified in the results?
A: The identification result is related to the situation of the sample. ARGs with high abundance in the sample can be identified.
Classic Case
• English title: Mobile antibiotic resistanceome in wastewater treatment plants revealed by Nanopore metagenomic sequencing
• Published journal: Microbiome
• Impact factor: 11.607
• Published year: 2019
Results: This study made full use of the advantages of Nanopore sequencing, long-read length and real-time sequencing, combined with Illumina sequencing, and developed a set of analysis workflows based on high-throughput sequencing for resistance gene genetic background analysis and host identification. Nanopore has greatly promoted the study of multi-drug resistance-binding plasmids. The analysis process not only gave us new insights into the mobile resistance genome of sewage treatment systems, but also provided an important reference for further analysis of the generation and transmission mechanisms of drug-resistant strains .
1. Plasmids and integrative binding elements carrying resistance genes dominate the resistance genome in wastewater treatment systems
2. Identification of broad-spectrum sustainable resistance genes by mobile originals and host tracking
3. Rapid identification of potential resistance genes in wastewater treatment systems Drug pathogenic flora
4. Genotype-phenotype association analysis reveals the important contribution of plasmids to multidrug-resistant strains
5. Multidrug-resistant gene clusters carried by plasmids