A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy ofKlebsiella pneumoniaeStrains

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(7)

Published: June 14, 2022

Abstract Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, precise definition is important basic research for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication population biology epidemiological surveillance. Here, we propose a broadly applicable genomic classification nomenclature approach bacterial strains, using the prominent threat Klebsiella pneumoniae as model. Based on 629-gene core genome multilocus sequence typing (cgMLST) scheme, devised dual barcoding system that combines multilevel single linkage (MLSL) clustering life identification numbers (LINs). Phylogenetic analyses of >7,000 sequences captured structure discontinuities, were used guide 10 infraspecific genetic dissimilarity thresholds. The 7-gene (MLST) was mapped onto MLSL (threshold: 190 allelic mismatches) clonal group 43) identifiers backwards compatibility. taxonomy publicly accessible through community-curated platform (https://bigsdb.pasteur.fr/klebsiella), also enables external users’ identification. proposed strain two phylogenetically informative barcode systems provide full stability (LIN codes) nomenclatural continuity with previous (MLSL). This species-specific strategy strains should contribute unify global cross-sector collaborative knowledge emergence microevolution pathogens.

Language: Английский

---

Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2025, Volume and Issue: 75(2)

Published: Feb. 25, 2025

Two motile bacterial strains, designated as cfHf56-1 T and SW 252, were isolated from the coelomic fluid of Holothuria forskali surrounding seawater at animal sampling site, respectively. The sea cucumber was collected in Glénan archipelago (Brittany, France). Strains 252 Gram-stain-negative, non-spore-forming rod-shaped bacteria. Colonies made on marine agar plates brown color. pH temperature ranges for growth 7–8 18–30 °C, respectively, broth. major fatty acids 16 : 1 cis9 0. Phylogenetic analyses evidenced that both strains belong to a novel species genus Pseudoalteromonas . closely related type caenipelagi , byunsanensis amylolytica, with 75–78 % ANI 19–21 dDDH values. In this context, (= CIP 111854 = CECT 30642 ) is considered strain which name holothuriae sp. nov. proposed. genome characterized by size 5.1 Mbp G+C content 40.5%.

Language: Английский

---

Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2

Genome Research, Journal Year: 2023, Volume and Issue: unknown, P. gr.277655.123 - gr.277655.123

Published: July 6, 2023

A genomic sketch is a small, probabilistic representation of the set k -mers in sequencing dataset. Sketches are building blocks for large-scale analyses that consider similarities between many pairs sequences or sequence collections. While existing tools can easily compare 10,000s genomes, relevant datasets reach millions and beyond. Popular also fail to -mer multiplicities, making them less applicable quantitative settings. We describe method called Dashing 2 builds on SetSketch data structure. related HyperLogLog, but discards use leading zero count favor truncated logarithm adjustable base. Unlike HLL, perform multiplicity-aware sketching when combined with ProbMinHash method. integrates locality-sensitive hashing scale all-pairs comparisons sequences. free, open source software.

Language: Английский

---

Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex

Research in Microbiology, Journal Year: 2023, Volume and Issue: 174(7), P. 104113 - 104113

Published: Aug. 10, 2023

Language: Английский

---

A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence

Peer Community Journal, Journal Year: 2023, Volume and Issue: 3

Published: Aug. 31, 2023

Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features interpret emergence the global C. diphtheriae population framework. Methods: We developed bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) extract from genomes Corynebacteria species complex, medically relevant including tox gene presence disruption. analyzed 101 human isolates collected 2022 metropolitan overseas France (France-2022). To define background this emergence, we sequenced 379 additional (mainly France, 2018-2021) collated 870 publicly-available genomes. Results: The France-2022 comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging 10 sublineages (<500 distinct core genes). dataset 245 33.9% genomes, with predicting non-toxigenicity 16.0% these. 12% 43.6% ones, were multidrug resistant. Convergence toxigenicity penicillin erythromycin resistance was observed 2 France-2022. Phylogenetic lineages Gravis Mitis contrasted strikingly their pathogenicity-associated genes. Conclusions: This work provides a tool framework analyze revealing heterogeneities virulence features. Emerging combining first-line antimicrobial represent novel threats. epidemiology studies should be intensified globally improve understanding reemergence spatial spread.

Language: Английский

---

The pineapple reference genome: Telomere‐to‐telomere assembly, manually curated annotation, and comparative analysis

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(10), P. 2208 - 2225

Published: Aug. 7, 2024

ABSTRACT Pineapple is the third most crucial tropical fruit worldwide and available in five varieties. Genomes of different pineapple varieties have been released to date; however, none them are complete, with all exhibiting substantial gaps representing only two This significantly hinders advancement breeding efforts. In this study, we sequenced genomes three varieties: a wild variety, fiber globally cultivated edible variety. We constructed first gap‐free reference genome (Ref) for pineapple. By consolidating multiple sources evidence manually revising each gene structure annotation, identified 26,656 protein‐coding genes. The BUSCO evaluation indicated completeness 99.2%, demonstrating high quality annotations genome. Utilizing these resources, 7,209 structural variations across Approximately 30.8% genes were located within ±5 kb variations, including 30 associated anthocyanin synthesis. Further analysis functional experiments demonstrated that expression AcMYB528 aligns accumulation anthocyanins leaves, both which may be affected by 1.9‐kb insertion fragment. addition, developed Ananas Genome Database, offers data browsing, retrieval, analysis, download functions. construction database addresses lack resource databases. summary, acquired seamless high‐quality annotations, providing solid foundation genomics valuable breeding.

Language: Английский

---

Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(1)

Published: Jan. 7, 2025

Background. The Staphylococcus capitis NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood. Methods. Demographic and clinical data for 45 neonates S. 90 other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, significance was determined. 27 at 2 hospitals between 2017 2022 underwent long-read (ONT) ( n =27) short-read (Illumina) sequencing =18). These sequences compared sequenced blood culture isolates adult paediatric patients the same =6), surface swabs (found 5/150 samples), rectal (in 2/69 samples) NICU environmental samples 5/114 samples). Reads all mapped to hybrid assembly local site strain, forming complete UK reference genome, outbreak analysis comparison 826 Germany. Results. bacteraemia increased length stay sampling (median day 22 vs 12 CoNS isolated; P =0.05). A phylogeny revealed cluster comprised 25/27 3/5 superficial, 2/2 1/5 isolates. No wards belonged this cluster. Phylogenetic published confirmed that but found relatively high genomic diversity (mean pairwise distance 84.9 SNPs) an estimated molecular clock 5.1 SNPs/genome/year (95% credibility interval 4.3–5.9). presence superficial cultures did not correlate bacteraemia, both carriage identified also experienced bacteraemia. Conclusions. occurred longer admission than CoNS. Genomic confirms clinically significant infections distinct non-NICU samples. Multiple introductions , rather prolonged persistence, seen over 5 years infections.

Language: Английский

---

Early neonatal acquisition of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in Madagascar and Cambodia: clonal and plasmid-level contributions of maternal gut carriage

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Early neonatal infections caused by extended-spectrum-beta-lactamase-producing Enterobacterales (ESBL-PE) are prevalent in low- and middle-income countries, posing significant treatment challenges. This study investigated ESBL-PE colonization 499 mother-neonate pairs from Madagascar Cambodia, with stool samples collected at delivery neonates before day three. Using short- long-read sequencing, identical isolates or plasmids were identified within each pair to assess acquisition maternal source. Multinomial regression associated risk factors. Maternal gut carriage accounted for only 16.5% of acquisition, suggesting that most cases originated other sources. Primiparity wet season an increased the mother, while cesarean delivery, resuscitation, These findings challenge paradigm is primary source early colonization, highlighting need further research into alternative sources inform targeted interventions.

Language: Английский

---

Whole-genome based phylogeny and comparative genomics of Sporidiobolales and related taxa of Basidiomycetes

IMA Fungus, Journal Year: 2025, Volume and Issue: 16

Published: May 13, 2025

Language: Английский

---

RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: May 17, 2023

We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with streaming parallelization modern multi-core platforms. 113,674 complete bacterial sequences from RefSeq, 455 GB in FASTA format, can be clustered within less than 6 min 1,009,738 GenBank assembled genomes, 4.0 TB only 34 128-core workstation. results further identify 1269 redundant identical nucleotide content, the RefSeq genomes database.

Language: Английский

---