Overview

The Non-Tuberculous Mycobacteria Database (NTM-DB) is a user-friendly genomic database that consolidates extensive genomic data, MLST genotyping, clinical phenotype information, as well as drug resistance and pathogenicity genotype information. This database offers browsing, searching, analysis, and download functionalities, aiming to provide clinicians, researchers, and drug developers with an opportunity for comprehensive comprehension of non-tuberculous mycobacterial infections, thereby fostering related research and enabling more precise therapies.

Data Source

NTM-DB collected all available sequenced NTM genomes (totaling 16,083) and associate them with relevant metadata. Data sources include published literature, publicly available sequenced strains in NCBI's advance release samples, as well as strain assembly data collected from GenBank or RefSeq. The collected data encompass 178 species and 873 MLST types.

Database Usage

1. Browse

The navigation bar features a "Browse" drop-down menu with three options: "Species", "Strains", and "Genes".

1.1 Species

By clicking on "Species", users can access information on the 190 non-tuberculous mycobacteria (NTM) species (including subspecies) collected in this database, including the species name, taxonomy ID, type strain genome , representative genome , risk group , growth type , as well as the number of strains collected in NTM-DB that belong to each species.

1.1.1 Species Page

By clicking on the species name (e.g. Mycobacterium abscessus), users can access the corresponding species detail page to view additional information, including phylogeny, multilocus sequence typing (MLST), pan-genome, pan-resistom, and pan-virolom.

1.2 Strains

In the "Strains" table, users can view basic information on the 16,083 strains collected in this database, including accession, taxonomy, representative strain, sequence typing, isolation source, identified drug resistance and virulence genes, along with their corresponding mechanisms. Additionally, whether there are any drug susceptibility testing (DST) results available is also indicated. Furthermore, users can select details such as collection time, country, sequencing quality, and other information by checking the corresponding boxes located at the top of the page.

1.2.1 Strains Page

By clicking on the accession number (e.g. GCF_900454025.1), users can access the corresponding species detail page to view additional information, including resistom and virolom.

1.2.2 Drug Susceptibility Testing (DST)

To view all DST results stored in this database, users can click the "View drug susceptibility testing (DST) results" button located above the table. The DST page provides information on drug resistance phenotypes for the 598 NTM strains included in our database. Users can select which drug classes to display. In each cell, [R] represents "Resistant", [S] represents "Sensitive", [I] represents "Intermediate", numerical values represent minimum inhibitory concentration (MIC), and "-" indicates that corresponding information was not provided in the original literature.

1.3 Genes

The genes module includes two parts: drug resistance genes and virulence genes. This database contains 154 drug resistance genes and 462 virulence genes, providing information such as gene name, accession, related mechanisms and classifications for drug resistance and virulence, as well as the number of NTM species or strains in which specific genes exist.

1.3.1 Genes Page

Clicking on a gene name provides access to detailed information about the gene, as well as its prevalence in sequenced NTM genomes. Furthermore, we extract the region where the reference sequence of the gene hits from one strain of each species.

2. Multilocus Sequence Typing (MLST)

As sequence typing is of significant importance for non-tuberculous mycobacteria, the NTM-DB provides users with a module specifically designed for viewing the sequence types (STs) of all NTM species included in the database. Users can choose between "Colored by ST" or "Colored by Species" options. When hovering over a circle representing a particular ST (e.g. ST8), detailed information about that ST will be displayed. Clicking on a particular ST will take the user to the [Species Page] and highlight that ST on the MLST diagram.

3. Search

NTM-DB offers three advanced search modules on the search page, which are as follows:

(1) The "Species" module enables users to input a species name (e.g. M.abscessus) and match NTM species to obtain detailed information on the [Species Page].

(2) Similarly, under the "Strains" module, users can enter the accession number of a strain (e.g. GCF_001077755.1) to retrieve its corresponding page [Strains Page] and view detailed information about the strain.

(3) The "Genes" module is divided into drug resistance genes and virulence genes. Users can also enter a gene name (e.g. rpoB) to access its corresponding page [Genes Page] and view information about the gene. Furthermore, users can filter genes based on criteria such as resistance to specific drug class or virulence factor category (VFC).

* It is important to note that all search boxes are mutually exclusive.

4. Analysis

The Analysis page provides users with personalized analysis, including building evolutionary trees, MLST identification, and annotation of drug resistance genes and virulence genes. First, the user needs to submit a strain sequence file that meets the required format in the form on the page, and then select the desired analysis items. It should be noted that we provide users with two ways to build evolutionary trees:

(1) Selecting the number of closest nodes (representative strain of each closest species).

(2) Manually selecting the names of the desired species (multiple choices).

After making the selection and clicking submit button, the system will begin the analysis and display the evolutionary tree on the analysis results page, along with download links for drug resistance and virulence annotations. Users can download these files as needed.

5. Download

The original data, relevant information regarding virulence and drug resistance genes, MLST of each species, and personalized analysis results of NTM strains in NTM-DB are all available for download.

Contact Us

If you have any questions, suggestions or feedback about NTM-DB, please do not hesitate to contact us. Our team is dedicated to providing excellent service and support, and we will get back to you as soon as possible. You can reach us by emailing us directly at [ ntmdb@big.ac.cn ]. Thank you for your interest in NTM-DB, and we look forward to hearing from you.