Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data DOI Creative Commons
Bhavya Papudeshi, Michael J. Roach, Vijini Mallawaarachchi

et al.

Bioinformatics Advances, Journal Year: 2024, Volume and Issue: 5(1)

Published: Dec. 26, 2024

Abstract Motivation Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive time-consuming, hindering rapid clinical deployment. Results We developed Sphae, an automated bioinformatics pipeline designed streamline the therapeutic of in under 10 minutes. Using Snakemake workflow manager, Sphae integrates tools quality control, assembly, genome assessment, annotation tailored specifically biology. automates detection key markers, including virulence factors, resistance genes, lysogeny indicators such as integrase, recombinase, transposase, which could preclude use. Among 65 sequences analyzed, 28 showed potential, 8 failed due low sequencing depth, 22 contained prophage or virulent 23 had multiple genomes. This produces report assess safety suitability quickly. scalable portable, facilitating efficient deployment across most high-performance computing cloud platforms, accelerating evaluation process. Availability implementation source code freely available at https://github.com/linsalrob/sphae, with installation supported Conda, PyPi, Docker containers.

Language: Английский

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies DOI Creative Commons
George Bouras, Louise M. Judd, Robert A. Edwards

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(6)

Published: June 4, 2024

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing usually required for perfection. However, the effect of depth on performance not well understood. Here, we introduce Pypolca (with default and careful parameters) Polypolish v0.6.0 a new parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default Polypolish-careful commonly false-positive errors at low read depth; (2) most benefit occurs by 25× (3) almost never introduces any (4) Pypolca-careful single effective polisher. Overall, recommend following strategies: alone when very (<5×), (5–25×), sufficient (>25×).

Language: Английский

Citations

20
Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies DOI Creative Commons
Nicole A. Lerminiaux, Ken Fakharuddin,

Michael R. Mulvey

et al.

Canadian Journal of Microbiology, Journal Year: 2024, Volume and Issue: 70(5), P. 178 - 189

Published: Feb. 14, 2024

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read that can bridge repetitive problematic regions. Oxford Nanopore Technologies (ONT) produce platforms they continually improving their technology to obtain higher quality read is approaching the obtained such as Illumina. As these innovations continue, we evaluated how much ONT coverage produced by Rapid Barcoding Kit v14 (SQK-RBK114) necessary generate high-quality hybrid long-read-only for panel carbapenemase-producing Enterobacterales bacterial isolates. We found 30× sufficient if Illumina available, more (at least 100× recommended assemblies. polishing still single nucleotide variants (SNVs) INDELs in also examined antimicrobial resistance genes could be accurately identified data, Flye regardless detected >96% at 100% identity length. Overall, an optimal strategy (i.e., plasmid characterization AMR detection) but finer-scale analyses SNV) benefit data.

Language: Английский

Citations

18
How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies DOI Creative Commons
George Bouras, Louise M. Judd, Robert A. Edwards

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 10, 2024

Abstract It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing still required for perfection. However, the effect of depth on performance not well understood. Here, we introduce Pypolca (with default and careful parameters) Polypolish v0.6.0 a new parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default Polypolish-careful commonly false-positive errors at low depth; (2) most benefit occurs by 25× (3) never introduces any (4) Pypolca-careful single effective polisher. Overall, recommend following strategies: alone when very (<5×), (5–25×), sufficient (>25×). Data Summary open-source freely available Bioconda, PyPI, GitHub ( github.com/gbouras13/pypolca ). Bioconda github.com/rrwick/Polypolish All code data reproduce analyses figures are github.com/gbouras13/depth_vs_polishing_analysis . FASTQ sequencing reads BioProject PRJNA1042815 A detailed list accessions can be found in Table S1.

Language: Английский

Citations

12
Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection DOI Creative Commons
Bert Bogaerts,

Julien Van Braekel,

Alexander Van Uffelen

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 8, 2025

The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for analysis methods bioinformatics expertise, which can be bottleneck many laboratories. At Sciensano, Belgian national institute, an intuitive user-friendly tool portal was implemented using Galaxy, open-source platform workflow creation. Galaxy @Sciensano instance is available to both internal external scientists offers wide range tools provided by community, complemented over 50 custom pipelines developed in-house. selection currently focused primarily on WGS generated Illumina microbial pathogen typing, characterization outbreak detection, but it also addresses specific use cases other types. Our includes several custom-developed 'push-button' pipelines, are stand-alone that perform complete bacterial isolates based generate interactive HTML output reports with key findings. These include quality control, de novo assembly, sequence antimicrobial resistance prediction relevant species-specific assays. They tailored pathogens active genomic surveillance programs, relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. Mycobacterium tuberculosis. utilize internationally recognized databases PubMLST, EnteroBase, NCBI National Database Antibiotic Resistant Organisms, automatically synchronized regular basis ensure up-to-date results. Many these part routine activities reference centers laboratories, some them under ISO accreditation. This resource publicly noncommercial at https://galaxy.sciensano.be/ help laboratories establish reliable, traceable reproducible analyses encountered settings.

Language: Английский

Citations

0
Bacterial genome sequences of uncharacterized Chitinophaga species isolated from the International Space Station DOI Open Access
Christian L. Castro, Oliver Schwengers,

Sarah Stahl-Rommel

et al.

Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: 13(6)

Published: April 23, 2024

We report four

Language: Английский

Citations

0
Hibiscus acid and hydroxycitric acid dimethyl esters from Hibiscus flowers induce production of dithiolopyrrolone antibiotics by Streptomyces Strain MBN2-2 DOI Creative Commons

Felaine Anne Sumang,

Alan C. Ward, Jeff Errington

et al.

Natural Products and Bioprospecting, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 3, 2024

Plants and microbes are closely associated with each other in their ecological niches. Much has been studied about plant-microbe interactions, but little is known the effect of phytochemicals on at molecular level. To access products cryptic biosynthetic gene clusters bacteria, we incorporated an organic extract hibiscus flowers into culture media different Actinobacteria isolated from plant rhizospheres. This approach led to production broad-spectrum dithiolopyrrolone (DTP) antibiotics, thiolutin (1) aureothricin (2), by Streptomyces sp. MBN2-2. The compounds responsible for triggering these two DTPs were found be acid dimethyl ester (3) hydroxycitric 1,3-dimethyl (4). It was subsequently that addition either Fe2+ or Fe3+ induced 1 2. Chrome Azurol S (CAS) assay revealed 3 4 can chelate iron, therefore, mechanism leading appears related changes iron concentration levels. work supports idea used activate microbial further understand interactions.

Language: Английский

Citations

0
Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data DOI Creative Commons
Bhavya Papudeshi, Michael J. Roach, Vijini Mallawaarachchi

et al.

Bioinformatics Advances, Journal Year: 2024, Volume and Issue: 5(1)

Published: Dec. 26, 2024

Abstract Motivation Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive time-consuming, hindering rapid clinical deployment. Results We developed Sphae, an automated bioinformatics pipeline designed streamline the therapeutic of in under 10 minutes. Using Snakemake workflow manager, Sphae integrates tools quality control, assembly, genome assessment, annotation tailored specifically biology. automates detection key markers, including virulence factors, resistance genes, lysogeny indicators such as integrase, recombinase, transposase, which could preclude use. Among 65 sequences analyzed, 28 showed potential, 8 failed due low sequencing depth, 22 contained prophage or virulent 23 had multiple genomes. This produces report assess safety suitability quickly. scalable portable, facilitating efficient deployment across most high-performance computing cloud platforms, accelerating evaluation process. Availability implementation source code freely available at https://github.com/linsalrob/sphae, with installation supported Conda, PyPi, Docker containers.

Language: Английский

Citations

0