Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(5)

Published: May 8, 2024

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. They also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance 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.

Language: Английский

---

Haemophilus influenzae Type b Meningitis in Infants, New York, New York, USA, 2022–2023

Emerging infectious diseases, Journal Year: 2025, Volume and Issue: 31(3)

Published: Feb. 21, 2025

Two unvaccinated infants residing in the same borough of New York, USA, had Haemophilus influenzae type b meningitis develop 1 year apart. Whole-genome sequencing and phylogenetic analysis revealed isolates shared a previously undescribed multilocus sequence were more closely related to each other than sequenced strains.

Language: Английский

---

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

eLife, Journal Year: 2024, Volume and Issue: 13

Published: May 20, 2024

Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive benchmarking variant accuracy genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models both simplex (single-strand) duplex (dual-strand) read types across 14 diverse species. Our findings reveal that deep learning-based callers, particularly Clair3 DeepVariant, significantly outperform traditional methods even exceed Illumina sequencing, especially when applied to ONT’s super-high model. superior performance attributed its ability overcome Illumina’s errors, which often arise from difficulties aligning reads repetitive variant-dense genomic regions. Moreover, use high-performing callers with data mitigates errors homopolymers. also investigated impact depth on calling, demonstrating 10× super-accuracy can achieve precision recall comparable to, or better than, full-depth sequencing. These results underscore potential combined advanced algorithms, replace short-read resource-limited settings.

Language: Английский

---

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

eLife, Journal Year: 2024, Volume and Issue: 13

Published: Oct. 10, 2024

Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, construction phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive benchmarking variant accuracy genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models both simplex (single-strand) duplex (dual-strand) read types across 14 diverse species. Our findings reveal that deep learning-based callers, particularly Clair3 DeepVariant, significantly outperform traditional methods even exceed Illumina sequencing, especially when applied to ONT’s super-high model. superior performance attributed its ability overcome Illumina’s errors, which often arise from difficulties aligning reads repetitive variant-dense genomic regions. Moreover, use high-performing callers with data mitigates errors homopolymers. also investigated impact depth on calling, demonstrating 10× super-accuracy can achieve precision recall comparable to, or better than, full-depth sequencing. These results underscore potential combined advanced algorithms, replace short-read resource-limited settings.

Language: Английский

---

Complete genome sequence of a Mycobacterium bovis strain associated with a bovine tuberculosis outbreak on a cattle farm in Saskatchewan, Canada

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

Published: Jan. 8, 2025

ABSTRACT Bovine tuberculosis is an important zoonotic infectious disease that presents a risk to human health, livestock, and wildlife. We report the complete genome sequence of new Mycobacterium bovis strain caused bovine outbreak on cattle farm in Saskatchewan, Canada, 2023.

Language: Английский

---

Clonal expansion of chromosome-borne CTX-M-55 extended-spectrum β-lactamase-producing Salmonella enterica serovar Agona, Taiwan

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: March 19, 2025

ABSTRACT We investigated emerging multidrug-resistant (MDR) Salmonella enterica serovar Agona in Taiwan. These MDR strains commonly harbored the efflux pump activator gene ramAp and up to 15 resistance genes, including aac (3)-IId , aadA22 aph(3')-Ia aph (6)-Id arr-2 bla CTX-M-55 LAP-2 TEM-1 dfrA14 floR lnu(F ), qnrS13 sul2 sul3 tet(A within IncHI2-IncHI2A plasmids or diverse chromosomal genomic islands (RGIs). newly comprised 44.9% 74.4% of S . isolates collected 2023 2024, respectively. Through analysis insertion sites, we identified 11 distinct RGIs. Strains containing RGI_SA11 became predominant, comprising 59.2% 2024. IMPORTANCE The emergence clonal expansion represent a growing public health concern. This study identifies significant shift mechanisms, driven by chromosomally integrated (RGIs), which likely originated from IncHI2–IncHI2A plasmids. integration antimicrobial genes enhances evolutionary fitness these strains, facilitating their persistence dissemination both human animal populations. findings underscore urgent need for enhanced surveillance, targeted interventions, global stewardship curb spread pathogens safeguard health.

Language: Английский

---

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(3)

Published: March 21, 2025

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential use in clinical diagnostics, but thorough validation required address accuracy concerns ensure reliable reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta ) the assembly of Oxford data used it investigate reproducibility results under consistent conditions. We benchmark dataset five bacterial reference strains generated eight technical replicates same DNA using Ligation Rapid Barcoding kits together with Flongle MinION flow cells. assessed by measuring discrepancies such as substitution insertion/deletion errors, analysing plasmid recovery examining genetic markers clustering information. compared genome assemblies without short-read polishing. Our show average 99.999955% nanopore-only 99.999996% when short reads were The genomic highly read following areas: identification antimicrobial resistance virulence, classical MLST, taxonomic classification, completeness contamination analysis. Interestingly, information from core SNP MLST analyses also assemblies, pairwise differences up two allele SNPs across replicates. After polishing reads, cgMLST 0 cgSNP 0–1 These highlight advances nanopore

Language: Английский

---

Complete genome sequence of the environmental Burkholderia pseudomallei strain 22-10884_313#20 from Guadeloupe, French West Indies

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

Published: March 28, 2025

ABSTRACT Burkholderia pseudomallei is the causative agent of melioidosis. Here, we present complete genome sequence strain 22-10884_313#20 , isolated from a soil sample in Guadeloupe (French West Indies).

Language: Английский

---

Complete genome sequence of two Hominenteromicrobium mulieris strains CIP 112194 and CIP 112527, isolated from a human fecal sample

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

Published: April 7, 2025

ABSTRACT The human gut microbiota is dominated by obligately anaerobic bacteria. A method based on species-targeted sorting using flow cytometry under conditions has been performed to analyze the microbiome. This report describes complete genome sequences of two Hominenteromicrobium mulieris strains CIP 112194 and 112527 that were isolated from feces a healthy adult France. volunteer young having vegetarian diet.

Language: Английский

---

Complete genome sequence of the type strain Piscinibacterium candidicorallinum LMG 29480

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

Published: April 7, 2025

ABSTRACT Piscinibacterium candidicorallinum LMG 29480 is a motile gram-stain-negative bacterium able to reduce nitrate and accumulate poly-β-hydroxybutyrate storage granules. Here, we report the complete genome sequence (3,829,664 bp, 65.16 mol% G+C content), which may prove useful in future taxonomic comparisons efforts assess role of nutrient cycling.

Language: Английский

---