Genomic Analysis of ESBL-Producing Isolates

Only ESBL-E were subjected to whole-genome sequencing (WGS) as described recently (21 (link)). Subsequently, we performed multilocus sequence typing (MLST) and core genome MLST (cgMLST) if a species-specific scheme was available at https://www.cgmlst.org (22 (link)). Based on the allelic profiles of the cgMLST scheme, we constructed a neighbor-joining tree to display the clonal relationship among the ESBL-E and, if applicable, additional reference strains using Ridom SeqSphere+ software version 7 (Ridom GmbH, Münster, Germany) (23 (link)). For extraction of genomic determinants related to the ESBL phenotype, we used the AMRFinder (24 (link)) that is implemented in SeqSphere+. The genome sequences determined here were available at https://www.cgmlst.org.

Free full text: Click here

Wiethoff J.P., Sandmann S., Theiler T., Nze Nkogue C., Akomo-Okoue E.F., Varghese J., Kreidenweiss A., Mellmann A., Lell B., Adegnika A.A., Held J, & Schaumburg F. (2023). Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon. Microbiology Spectrum, 11(4), e00664-23.

Publication 2023

Ridom SeqSphere+ software version 7

Allelic Clonal Genome Phenotype Strains Tree

Corresponding Organization : University of Münster

Other organizations : University of Tübingen, German Center for Infection Research, Institut Africain d'Informatique

Top 5 similar protocols

Variable analysis

independent variables

Whole-genome sequencing (WGS) of ESBL-E strains

dependent variables

Multilocus sequence typing (MLST)
Core genome MLST (cgMLST)
Allelic profiles of the cgMLST scheme
Clonal relationship among the ESBL-E and additional reference strains
Genomic determinants related to the ESBL phenotype

control variables

Species-specific cgMLST scheme available at https://www.cgmlst.org

controls

No positive or negative controls were explicitly mentioned.

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!