Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 20, 2024
ABSTRACT The Gram-negative bacterium Vibrio harveyi is a serious shrimp pathogen. Here, we present the genome sequence of TUMSAT-2019, which was isolated from kuruma ( Penaeus japonicus ) that originated farm in Okinawa Prefecture. assembly totaled 5.7 Mbp, consisting two chromosomes with no plasmid.
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: June 8, 2024
Abstract While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPEs) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes including the carbapenemase gene bla KPC-2 . The pQEB1 lineage is concerning due to its conferral multi-drug resistance, host range apparent transmissibility, potential for acquiring further genes. Representatives were found in three sequence types (STs) Citrobacter freundii , two STs Enterobacter cloacae species Klebsiella Hosts isolated 11 different patients who stayed various wards throughout hospital complex over a 13-month period January 2023 February 2024. At present, only representatives GenBank carried by hormaechei blood sample QE 2016 pneumoniae urine University Hospitals Coventry Warwickshire (UHCW) May 2023. UHCW had been treated QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison complete sequences. We structural variants defined molecular events responsible them. These have included IS 26 -mediated inversions acquisitions multiple insertion sequences transposons, carriers mercury or arsenic that particular inversion variant strongly associated with Liver speciality after appearing November 2023, but specialities January/February That has so far seen five bacterial hosts six patients, consistent recent ongoing inter-host inter-patient transmission this setting.
Language: Английский
Citations
2
Systematic and Applied Microbiology, Journal Year: 2024, Volume and Issue: 47(6), P. 126560 - 126560
Published: Nov. 1, 2024
Language: Английский
Citations
1
Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: 13(6)
Published: April 23, 2024
We report four
Language: Английский
Citations
0
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
Microbiological Research, Journal Year: 2024, Volume and Issue: 288, P. 127867 - 127867
Published: Aug. 14, 2024
Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance Enterobacterales isolates shows genus is second Klebsiella terms frequency carbapenem resistance. taxonomy confusing standard identification methods largely inaccurate or insufficient. There currently 27 named total 46 taxa distinguishable via average nucleotide identity (ANI) calculation between pairs genomic sequences. Here we describe an strain, ECC3473, isolated from wastewater Australian hospital whose could not be determined by nor ribosomal RNA gene multi-locus typing.
Language: Английский
Citations
0
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
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 2, 2024
Abstract Summary Accurate genome size estimation is an important component of genomic analyses, though existing tools are primarily optimised for short-read data. We present LRGE, a novel tool that uses read-to-read overlap information to estimate in reference-free manner. LRGE calculates per-read estimates by analysing the expected number overlaps each read, considering read lengths and minimum threshold. The final taken as median these estimates, ensuring robustness outliers such reads with no overlaps. Additionally, provides confidence range estimate. outperforms k -mer-based methods both accuracy computational efficiency produces comparable those from assembly-based approaches, like Raven, while using significantly less resources. validate on large, diverse bacterial dataset confirm it generalises eukaryotic datasets. Availability implementation Our method, ( L ong R ead-based G enome E stimation overlaps), implemented Rust available precompiled binary most architectures, Bioconda package, prebuilt container image, crates.io package lrge ) or library liblrge ). source code at https://github.com/mbhall88/lrge under MIT license.
Language: Английский
Citations
0
Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 12, 2024
The important human pathogen
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 18, 2024
Abstract Objectives Vibrio cholerae remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of V. isolates from Côte d’Ivoire, Ghana, Zambia and South Africa to assess genomic diversity, AMR profiles, virulence, demonstrating the utility WGS for enhanced surveillance within PulseNet network. Methods We analysed clinical environmental sources (2010–2024) using Oxford Nanopore hybracter assembly. Phylogenetic analysis, multilocus sequence typing (MLST), virulence gene detection were performed Terra, Pathogenwatch, Cloud Infrastructure Microbial Bioinformatics (CLMB) platforms, comparisons against 88 global reference genomes broader context. Results Of 79 high-quality assemblies, 67 confirmed as , serogroup O1 accounting majority (43/67, 67%). ST69 accounted 60% (40/67) isolates, eight types identified overall. Thirty-seven formed novel sub-clades AFR12 AFR15 lineages, suggesting local clonal expansions. analysis revealed high trimethoprim (96%) quinolones (83%), while azithromycin, rifampicin, tetracycline remained low (≤7%). A proportion (41/43, 95%) harboured genes at least three antibiotic classes. Conclusions highlights genetic diversity prevalence African expanding clades region. The widespread raises concerns treatment efficacy, although azithromycin remain viable options. enables precise identification species genotyping, reinforcing Africa’s pivotal role advancing enabling timely responses cholera outbreaks. Data summary All supporting data protocols have been provided article or supplementary files. ONT reads deposited under BioProject accession PRJNA1192988, spp. assemblies shared via figshare (Foster-Nyarko, Ebenezer (2024). Genomic Diversity Antimicrobial Resistance Isolates Africa: Initiative Using Sequencing Enhance Surveillance. figshare. Dataset. https://doi.org/10.6084/m9.figshare.27941376.v1 ). Individual numbers these Biosample IDs are File S2, available online version this article. genome included our also S3 . Impact statement Cholera challenge disproportionately affecting region due ongoing transmission emergence (AMR). demonstrates Technology (ONT) providing high-resolution insights into dynamics, profiles across Africa. By generating analysing sequences, we sublineages, rates genes, traits critical pathogenesis. These findings contribute deeper understanding epidemiology evolution informing targeted intervention strategies. Furthermore, growing posed by among including key therapeutic antibiotics, such trimethoprim, which could undermine current protocols. Despite this, absence rifampicin suggests drugs may options, offering avenue preserving efficacy. research underscores importance sustained surveillance, capacity building, regional collaboration mitigate impact other foodborne pathogens. leveraging technologies training initiatives, genomics workshop, provides framework strengthening capacities detect, monitor, respond outbreaks spread AMR. efforts align Union CDC’s strategic priorities on security AMR, contributing improved systems control continent.
Language: Английский
Citations
0
Microbiology Resource Announcements, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 20, 2024
ABSTRACT The Gram-negative bacterium Vibrio harveyi is a serious shrimp pathogen. Here, we present the genome sequence of TUMSAT-2019, which was isolated from kuruma ( Penaeus japonicus ) that originated farm in Okinawa Prefecture. assembly totaled 5.7 Mbp, consisting two chromosomes with no plasmid.
Language: Английский
Citations
0