Comprehensive Genomic Profiling of Bacterial Isolates

The BioNumerics software was used to generate a minimum spanning tree (MST) or a UPGMA hierarchical clustering as described previously [3 (link)]. The categorical coefficient was used to calculate the MST and the MST was based on in-house E. coli and K. pneumoniae wgMLST schemes. The NGS data of the K. pneumoniae and E. coli isolates were used for classical MLST and wgMLST analyses using in-house wgMLST schemes made in the SeqSphere software version 6.0.2 (Ridom). The in-house K. pneumoniae wgMLST scheme comprised 4978 genes (3471 core-genome and 1507 accessory-genome targets) using K. pneumoniae MGH 78,578 (NC_009648.1) as a reference genome. The in-house E. coli wgMLST scheme comprised 4503 genes (3199 core-genome and 1304 accessory-genome targets) using E. coli 536 (CP000247.1) as a reference genome.

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Hendrickx A.P., Landman F., de Haan A., Witteveen S., van Santen-Verheuvel M.G, & Schouls L.M. (2021). bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands. Microbial Genomics, 7(5), 000512.

Publication 2021

SeqSphere software version 6.0.2

E coli Genes Genome K pneumoniae Tree

Corresponding Organization :

Other organizations : National Institute for Public Health and the Environment

Top 5 similar protocols

Variable analysis

independent variables

The BioNumerics software was used to generate a minimum spanning tree (MST) or a UPGMA hierarchical clustering
The categorical coefficient was used to calculate the MST
The MST was based on in-house Escherichia coli and Klebsiella pneumoniae wgMLST schemes

dependent variables

The NGS data of the Klebsiella pneumoniae and Escherichia coli isolates were used for classical MLST and wgMLST analyses

control variables

The in-house Klebsiella pneumoniae wgMLST scheme comprised 4978 genes (3471 core-genome and 1507 accessory-genome targets) using Klebsiella pneumoniae MGH 78,578 (NC_009648.1) as a reference genome
The in-house Escherichia coli wgMLST scheme comprised 4503 genes (3199 core-genome and 1304 accessory-genome targets) using Escherichia coli 536 (CP000247.1) as a reference genome

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!