Frequently Asked Questions:

1. How are the antimicrobial resistance and virulence genes predicted in BacWGSTdb?


2. What is the major difference between the SNP and MLST strategy?


3. Which MLST scheme should I follow, cgMLST or wgMLST?


4. How can I choose reference genomes for SNP strategy?


5. Which threshold should I follow for either SNP or MLST strategy?


6. Which software/tools are used for the phylogenetic analysis in BacWGSTdb?


7. Which 7-gene MLST schemes are used in BacWGSTdb?


8. How can I change the colour of each nodes in GrapeTree for representing different properties?


9. Why the Grapetree displays nothing?


10. How long does BacWGSTdb take to perform the phylogenetic analysis in BROWSE?


11. How long does BacWGSTdb take to process bacterial genomes in TOOLS?

 

 


  How are the antimicrobial resistance and virulence genes predicted in BacWGSTdb?
Prediction of antimicrobial resistance and virulence genes are established by BLAST search the user uploaded genomes against ResFinder and VFDB. BLAST threshold: nucleotide identity: 90%; length coverage: 90%.
 

 

  What is the major difference between the SNP and MLST strategy?
Currently the WGS-based bacterial typing mainly includes two strategies: SNP (sequence-based) and MLST (allele-based). The SNP approach compares single nucleotide differences between isolates in comparison to the reference genome, which can be used to investigate the clonal relationship between highly similar isolates (e.g. collected from outbreaks of hospital or foodborne infectious diseases). The MLST approach is an extension of conventional 7-gene MLST that expands the range of genes to whole genome scale, which is often used as a solution to middle/long-term evolutionary history of bacterial pathogens. The MLST approach can be further divided into core-genome-based MLST (cgMLST) and whole-genome-based MLST (wgMLST).
 

 

  Which MLST scheme should I follow, cgMLST or wgMLST?
The cgMLST scheme covers the core genome-related genes/loci that are conserved within a species. The wgMLST scheme is an extension of cgMLST and encompasses not only core genome genes/loci but also accessory genes/loci. The wgMLST scheme offers higher resolution than cgMLST and is more appropriate for typing closely related strains.
 

 

  How can I choose reference genomes for SNP strategy?

By SNP strategy, the reference genome is required to be highly related to the compared isolates in order for calling phylogenetically informative SNPs. Thus the reference genome and the query genome must belong to the same clonal complex (differ by two alleles at most).

If users have no idea of which sequence type (ST) their query genome belongs to, please use the single genome analysis in the TOOLS page.

Or please turn to the function 'Search best reference genome for SNP strategy' in OVERVIEW page if users just wonder which reference genome is specified in BacWGSTdb for each ST.
 

 

  Which threshold should I follow for either SNP or MLST strategy?
It depends on users' purpose. For identification of an outbreak event, there is no consensus on how similar or closely related two bacterial isolates must be to establish that they originate from the same outbreak. The number of allele differences may vary with multiple factors such as the mutation frequency and lifecycle of the bacterium, and the time-frame of sampling (longer infection time possibly leads to more allele variants).
 

 

  Which tools are used for the phylogenetic analysis in BacWGSTdb?
For SNP strategy, the phylogenetic tree is generated by Clearcut and displayed as Scalable Vector Graphics (SVG) in the web browser using TreeVector. For MLST strategy, the phylogenetic tree is generated and visualized by Grapetree.
 

 

  Which 7-gene MLST schemes are used in BacWGSTdb?

Please refer to PubMLST database for further information. It's noted that A. baumannii and E. coli own more than one public MLST scheme. Here in BacWGSTdb, the Oxford MLST scheme of A. baumannii and Achtman MLST scheme of E. coli are used.

Note that the species Bacillus anthracis, Mycobacterium tuberculosis and Yersinia pestis are monomorphic and does not have a 7-gene MLST scheme.
 

 

  How can I change the colour of each nodes in GrapeTree for representing different properties?
Please turn to the menu at the left side of Grapetree window and manipulate as follows: Tree Layout - Node Style - Colour By, which will allow users to change the node colour by different properties, i.e. ST, Host, Disease, Isolation source, Country/state, Collection year.
 

 

  Why the Grapetree displays nothing?
The most common cause is that Grapetree is not supported by your web browser. Please use Microsoft Edge, Firefox, Chrome or Safari because these browsers work successfully in BacWGSTdb. A far less common cause is the entirely identical MLST profile of the analyzed isolates. In this case, please turn to wgMLST instead of cgMLST or choose a more related threshold to include more remote isolates for comparison.
 

 

  How long does BacWGSTdb take to perform the phylogenetic analysis in BROWSE?
Basically, it will take just a few seconds if you select less than 100 isolates. However, the waiting time will be exponentially longer if users select hundreds of isolates.
 

 

  How long does BacWGSTdb take to process bacterial genomes in TOOLS?
It depends on the selected species, strategy and threshold. Most of analyses in BacWGSTdb will take 1~3 minutes. However, for wgMLST strategy upon E. coli and S. enterica, the waiting time can be 5~10 minutes.