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The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies
- Source :
- Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861)
- Publication Year :
- 2022
- Publisher :
- ETH Zurich, 2022.
-
Abstract
- The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find that chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long reads during assembly graph generation (Canu). By contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.<br />Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861)<br />ISSN:0962-8436<br />ISSN:1471-2970<br />ISSN:0080-4622
- Subjects :
- assembly
antibiotic resistance
Gene Transfer, Horizontal
Sequence Analysis, DNA
General Biochemistry, Genetics and Molecular Biology
Anti-Bacterial Agents
phylogenetics
whole-genome sequencing
plasmid
long-read sequencing
Escherichia coli
Animals
Humans
General Agricultural and Biological Sciences
Genome, Bacterial
Phylogeny
Plasmids
Subjects
Details
- Language :
- English
- ISSN :
- 09628436, 14712970, and 00804622
- Database :
- OpenAIRE
- Journal :
- Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861)
- Accession number :
- edsair.doi.dedup.....88b8df6f3afcce25ec1787726438cc30
- Full Text :
- https://doi.org/10.3929/ethz-b-000568456