Parallelverlage im geteilten Deutschland

Seemann, Anna-Maria

doi:10.1515/9783110543421

Cited by 2 publications

(2 citation statements)

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“…Contigs were classified as chromosomal if they could be typed with mlst 49 (v. 2.23.0) using default parameters (see runMlst.sh). Contigs were classified as plasmid if they could be typed with either Abricate 45 (v. 1.0.1) and the PlasmidFinder database 18 (as of 28/02/2023) using default parameters except --db plasmidfinder (see runPlasmidFinder.sh), or with MOB-Typer 50 (v. 3.1.4) using default parameters (see runMobTyper.sh).…”

Section: Methodsmentioning

confidence: 99%

Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons

Matlock,

Shaw,

Stoesser

2024

Preprint

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Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites (attI x attC or attC x attC). Integrons are genetic elements able to capture, excise, and shuffle these cassettes, providing 'adaptation on demand', and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene blaGES-5, an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all NCBI contigs containing blaGES-5 (n = 431), we developed a pangenome graph-based workflow to characterise and cluster the diversity of blaGES-5-associated integrons. We demonstrate that blaGES-5-associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in P. aeruginosa ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS110 disrupted attC sites, which might immobilise the gene cassettes and explain the conserved integron structure despite the presence of intI1 integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and 'shuffling' of integrons on plasmids.

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Section: Methodsmentioning

confidence: 99%

Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons

Matlock,

Shaw,

Stoesser

2024

Preprint

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“…mlst (24) takes de novo assemblies as input on the command line and uses BLASTn to align sequences to alleles. It is very fast and searches all databases on pubMLST to automatically detect the organism, then calculates the ST.…”

Section: Software Overviewmentioning

confidence: 99%

Comparison Of Multi-locus Sequence Typing software For next generation sequencing data

Page

Alikhan

Carleton³

et al. 2017

Preprint

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Multi-locus sequence typing (MLST) is a widely used method for categorising bacteria. Increasingly MLST is being performed using next generation sequencing data by reference labs and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared six of these applications against real and simulated data and present results on: 1. the accuracy of each method against traditional typing methods, 2. the performance on real outbreak datasets, 3. in the impact of contamination and varying depth of coverage, and 4. the computational resource requirements.DATA SUMMARYSimulated reads for datasets testing coverage and mixed samples have been deposited in Figshare; DOI: https://doi.org/10.6084/m9.figshare.4602301.vlOutbreak databases are available from Github; url - https://github.com/WGS-standards-and-analysis/datasetsDocker containers used to run each of the applications are available from Github; url – https://tinyurl.com/z7ks2ftAccession numbers for the data used in this paper are available in the Supplementary material.We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ☒IMPACT STATEMENTSequence typing is rapidly transitioning from traditional sequencing methods to using whole genome sequencing. A number of in silico prediction methods have been developed on an ad hoc basis and aim to replicate Multi-locus sequence typing (MLST). This is the first study to comprehensively evaluate multiple MLST software applications on real validated datasets and on common simulated difficult cases. It will give researchers a clearer understanding of the accuracy, limitations and computational performance of the methods they use, and will assist future researchers to choose the most appropriate method for their experimental goals.

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Parallelverlage im geteilten Deutschland

Cited by 2 publications

References 0 publications

Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons

Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons

Comparison Of Multi-locus Sequence Typing software For next generation sequencing data

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Parallelverlage im geteilten Deutschland

Cited by 2 publications

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Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons

Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons

Comparison Of Multi-locus Sequence Typing software For next generation sequencing data

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Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons

Global genomic epidemiology ofbla_GES-5carbapenemase-associated integrons