Draft genome assemblies of ciprofloxacin-resistant derivatives of Bacillus cereus strain ATCC14579

Microbiology Resource Announcements, Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

ABSTRACT Ciprofloxacin resistance in Bacillus cereus involves diverse and understudied mechanisms. Here, we present draft genome assemblies of 95 experimentally evolved strains that exhibit increased growth the presence ciprofloxacin, many containing novel mutations not previously described for this phenotype.

Language: Английский

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Kastor: a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes

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

Published: April 18, 2025

Abstract Long read sequencing technologies provide an efficient approach to generating highly contiguous and informative assemblies. However, higher relative error rates can introduce frameshifts premature stop codons that pseudogenize genes, hindering downstream analyses. We developed a software tool detects gene-fragmenting errors in draft assemblies of small genomes through comparison with curated set reference genome sequences raw information. In our presented example, detected represent less than 0.05% the genome, but when corrected reduced rate pseudogenes from 23.3 5.6% example long assemblies, comparable short demonstrate this detect assembly generated correct them de-fragment genes.

Language: Английский

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Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 13, 2023

Abstract Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- long-reads) assembly approaches. Complete allow a deeper understanding evolution genomic variation beyond single nucleotide variants (SNVs). They also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids missed or misassembled by algorithms. Here, we present Hybracter allows fast, automatic, scalable recovery near-perfect first approach. can be run either as assembler only assembler. We compared to existing automated tools diverse panel samples varying levels with manually curated ground truth reference genomes. demonstrate is more accurate faster than gold standard Unicycler. show long-reads most comparable methods accurately recovering plasmids. Data Summary developed Python Snakemake command-line software tool Linux MacOS systems. freely available under an MIT License on GitHub ( https://github.com/gbouras13/hybracter ) documentation at Read Docs https://hybracter.readthedocs.io/en/latest/ ). install via PyPI https://pypi.org/project/hybracter/ Bioconda https://anaconda.org/bioconda/hybracter A Docker/Singularity container https://quay.io/repository/gbouras13/hybracter . All code used benchmark Hybracter, including genomes, publicly https://github.com/gbouras13/hybracter_benchmarking released DOI https://zenodo.org/doi/10.5281/zenodo.10910108 Zenodo. The subsampled FASTQ files benchmarking Zenodo https://doi.org/10.5281/zenodo.10906937 super simplex ATCC reads sequenced part this study found BioProject PRJNA1042815. Hall et al. fast duplex read (prior subsampling) SRA PRJNA1087001. raw Lermaniaux PRJNA1020811. Staphylococcus aureus JKD6159 PRJNA50759. Mycobacterium tuberculosis H37R2 PRJNA836783. list BioSample accession numbers each benchmarked sample Supplementary Table 1. output Pypolca outputs https://zenodo.org/doi/10.5281/zenodo.10072192 Impact Statement genome routine vital genomics, especially identification mobile genetic elements As becomes cheaper, easier access accurate, crucial. With new widely-used both only. Additionally, it solves problems assemblers struggling plasmid from performing par methods. natively exploit parallelisation high-performance computing (HPC) clusters cloud-based environments, enabling users assemble hundreds thousands one line code. source GitHub, PyPi.

Language: Английский

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Oxford Nanopore's 2024 sequencing technology forListeria monocytogenesoutbreak detection and source attribution: progress and clone-specific challenges

Published: July 12, 2024

Abstract Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established technologies are currently challenged by Oxford Nanopore Technologies (ONT), which offers accessible cost-effective alternative enabling gap-free assemblies chromosomes plasmids. Limited accuracy has hindered its use for investigating transmission, but recent technology updates have brought significant improvements. To evaluate readiness detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters with ONT’s V14 Rapid Barcoding Kit R10.4.1 flow cells. The most accurate several tested workflows generated a median one error (SNP indel) per assembly. For 66 isolates, cgMLST profiles ONT-only were identical to those Illumina data. Eight lower quality more than 20 erroneous sites each, primarily caused methylations at the GAAGAC motif (5′-GAA G6mA C-3 / 3′-GT 4mC TTC-5′). This led inaccurate clustering, failing group persistence-associated clone that carried responsible restriction-modification system. Out 50 methylation motifs detected among only was linked substantially increased rates. Our study shows L. genomes assembled data suitable high-resolution genotyping, further improvements chemistries basecallers required reliable routine in food safety investigations.

Language: Английский

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Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance

Pathogens, Journal Year: 2024, Volume and Issue: 13(9), P. 730 - 730

Published: Aug. 28, 2024

Background. In the context of increasing antimicrobial resistance (AMR), whole-genome sequencing (WGS) bacteria is considered a highly accurate and comprehensive surveillance method for detecting tracking spread resistant pathogens. Two primary technologies exist: short-read (50–300 base pairs) long-read (thousands pairs). The former, based on Illumina platforms (ISPs), provides extensive coverage high accuracy single nucleotide polymorphisms (SNPs) small insertions/deletions, but limited by its read length. latter, such as Oxford Nanopore Technologies (ONT), enables assembly genomes, particularly those with repetitive regions structural variants, although has historically been lower. Results. We performed head-to-head comparison these techniques to sequence K. pneumoniae VS17 isolate, focusing blaNDM gene alleles in program. Discrepancies between ISP (blaNDM-4 allele identified) ONT (blaNDM-1 blaNDM-5 were observed. Conjugation assays Sanger sequencing, used gold standard, confirmed validity results. This study demonstrates importance or hybrid assemblies carbapenemase identification highlights limitations short reads duplications multiple alleles. Conclusions. this proof-of-concept study, we conclude that recent technology may outperform standard Such information crucial given rising prevalence strains producing carbapenemases, especially WGS increasingly epidemiological infection control.

Language: Английский

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Oxford Nanopore’s 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges

Journal of Clinical Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 4, 2024

ABSTRACT Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers accessible cost-effective alternative enabling gap-free assemblies chromosomes plasmids. Limited accuracy has hindered its use for investigating transmission, but recent technology updates have brought significant improvements. To evaluate readiness detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters with ONT‘s V14 Rapid Barcoding Kit R10.4.1 flow cells. The most accurate several tested workflows generated a median one error (SNP indel) per assembly. For 66 isolates, the cgMLST profiles ONT-only were identical to those Illumina data. Eight lower quality, more than 20 erroneous sites each, primarily caused methylations at GAAGAC motif (5′-GAAG 6mA C-3′/5′-GT 4mC TTC-3′). This led inaccurate clustering, failing group persistence-associated clone that carried responsible restriction–modification system. Out 50 methylation motifs detected among only was linked substantially increased rates. Our study shows L. genomes assembled data suitable high-resolution genotyping, further improvements chemistries basecallers required reliable routine in food safety investigations.

Language: Английский

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Genomic and Phenotypic Characterization of Streptomyces sirii sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil

Microorganisms, Journal Year: 2024, Volume and Issue: 12(12), P. 2628 - 2628

Published: Dec. 19, 2024

In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of Bambusa vulgaris. The designated BP-8 showed noticeable antibacterial activity. was subjected to a whole-genome analysis via polyphasic taxonomy approach, and its metabolite identified by HRLS-MS. results the physiological morphological analyses indicated that is aerobic, neutrophilic, mesophilic organism tolerant 8% NaCl can use wide range carbohydrates. It forms curly sporophores with warty surface. phylogenetic average nucleotide identity in silico DNA–DNA hybridization calculation represents type novel Streptomyces species. A comparative genome sequences closest related strains revealed presence genes encoding chemotaxonomic markers characteristic Streptomyces. compound as amicetin. Genomic mining also more than 10 biosynthetic gene clusters have not been described previously may lead discovery new valuable compounds. On basis these results, BP-8T (=VKM Ac-3066T = CCTCC AA 2024094T) proposed species sirii sp. nov.

Language: Английский

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Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Oct. 1, 2024

Language: Английский

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Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(11)

Published: Nov. 11, 2024

The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at lower cost, yet error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) duplex mode, improve data quality. Our study compares with PacBio Illumina, including hybrid data. We used

Language: Английский

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The presence of an ESBL-encoding plasmid reported during aKlebsiella pneumoniaenosocomial outbreak in the United Kingdom

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

Published: Dec. 9, 2024

Abstract The presence of extended-spectrum β-lactamase (ESBL) encoding plasmids in bacteria contributes towards rising resistance rates, mortality and healthcare costs clinical settings. An EBSL-encoding plasmid, pESBL-PH was identified during a nosocomial outbreak Klebsiella pneumoniae ST628 at United Kingdom general district hospital 2018. A plasmid from the earliest 2018 K. strain discovered assembled using both Oxford nanopore long reads illumina short reads, yielding fully closed pESBL-PH-2018. pESBL-PH-2018 queried against complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, downloaded on July 16, 2024. To identify structurally similar strict thresholds were applied: shared hash ratio > 0.9 mash similarity ≥ 0.98. This returned 61 belonging to 13 unique sequence types (STs) hosts. detected countries, dating 2012-2023, associated with range infections including bacteremia. Low numbers single nucleotide polymorphisms (SNPs) between query further confirming their relatedness. AMR region varied; interestingly IS 26 mediated-tandem amplification genes, ESBL bla CTX-M-15 two independent strains raising copy number three. Furthermore, genomic background carrying pESBL-PH-2018-like analyzed, revealing truncation chromosomal ompK36 porin gene carbapenemase carriage accessory 17.85% 26.78% chromosome available. analysis reveals widespread dissemination an ESBL-encoding resistance-encoding strains, requiring active surveillance.

Language: Английский

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