Bacterial defense systems exhibit synergistic anti-phage activity

Cell Host & Microbe, Год журнала: 2024, Номер 32(4), С. 557 - 572.e6

Опубликована: Фев. 22, 2024

Bacterial defense against phage predation involves diverse systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 in 42,925 bacterial genomes identified numerous instances of non-random co-occurrence negative association. For several pairs significantly co-occurring Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III ietAS systems, while tmn exhibits synergy Gabija, Septu I, PrrC. co-opts the sensory switch ATPase domain, enhancing Some system that are negatively associated E. show co-occur other taxa, demonstrating immune repertoires largely shaped by selection for resistance host-specific phages rather than epistasis. Collectively, these findings compatibility between allowing bacteria to adopt flexible strategies defense.

Язык: Английский

---

Listeria cossartiae sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2021, Номер 71(5)

Опубликована: Май 17, 2021

A total of 27

Язык: Английский

---

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS

Genes, Год журнала: 2021, Номер 12(5), С. 644 - 644

Опубликована: Апрель 26, 2021

Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance many microorganisms. An increasing number laboratories are currently in transition phase from classical methods towards next generation sequencing, generating unprecedented amounts data. Since the precision downstream analyses depends significantly on quality raw data generated sequencing instrument, comprehensive, meaningful primary control is indispensable. Here, we present AQUAMIS, Snakemake workflow an extensive assembly Illumina data, allowing to automatize initial analysis their whole-genome AQUAMIS performs all steps sequence analysis, consisting read trimming, (QC), taxonomic classification, de-novo assembly, reference identification, QC contamination both level. The results visualized interactive HTML report including species-specific thresholds, non-bioinformaticians assess experiments at glance. All also available as standard-compliant JSON file, facilitating easy exchange. We have applied analyze ~13,000 isolates well ~1000 in-silico contaminated datasets, proving workflow’s ability perform high throughput routine environments reliably predict contaminations. found that intergenus intragenus contaminations can be detected most accurately using combination different metrics within AQUAMIS.

Язык: Английский

---

RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning

Microbial Genomics, Год журнала: 2021, Номер 7(11)

Опубликована: Ноя. 30, 2021

Antimicrobial-resistance (AMR) genes in bacteria are often carried on plasmids and these can transfer AMR between bacteria. For molecular epidemiology purposes risk assessment, it is important to know whether the located highly transferable or more stable chromosomes. However, draft whole-genome sequences fragmented, making difficult discriminate plasmid chromosomal contigs. Current methods that predict from genome rely single features, like k-mer composition, circularity of DNA molecule, copy number sequence identity replication genes, all which have their drawbacks, especially when faced with large single-copy plasmids, carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination multiple including composition databases marker proteins, likely source contig chromosomal. The RFPlasmid supports models for 17 different bacterial taxa, Campylobacter, Escherichia coli Salmonella, has taxon agnostic model metagenomic assemblies unsupported organisms. available both as standalone via web interface.

Язык: Английский

---

Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods

Scientific Reports, Год журнала: 2022, Номер 12(1)

Опубликована: Фев. 4, 2022

Abstract Lactiplantibacillus plantarum is one of the most diverse species lactic acid bacteria found in various habitats. The aim this work was to perform preliminary phenotypic and genomic characterization two novel potentially probiotic L. strains isolated from Indian foods, viz., dhokla batter jaggery. Both were bile tolerant, utilized sugars, adhered intestinal epithelial cells, produced exopolysaccharides folate, susceptible for tetracycline, erythromycin, chloramphenicol, did not cause hemolysis, exhibited antimicrobial plant phenolics metabolizing activities. genetic determinants tolerance, cell-adhesion, bacteriocins production, riboflavin folate biosynthesis, polyphenols utilization, exopolysaccharide production both strains. One contained a large number unique genes while other had simultaneous presence glucansucrase fructansucrase which rare trait plantarum. Comparative genome analysis 149 highlighted high variation cell-adhesion sugar metabolism regions some properties relatively conserved. This highlights our along with technically important features

Язык: Английский

---

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer

Nucleic Acids Research, Год журнала: 2023, Номер 51(15), С. e83 - e83

Опубликована: Июнь 27, 2023

Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) the main source for discovering new today. However, NGS assembly programs tend return contigs, making plasmid detection difficult. This problem particularly grave metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools contig still suffer from some limitations. In particular, alignment-based miss diverged while learning-based often have lower precision. this work, we develop tool PLASMe capitalizes on strength alignment and methods. Closely related can be easily identified using component predicted order-specific Transformer models. By encoding sequences as language defined protein cluster-based token set, learn importance proteins correlation through positionally embedding attention mechanism. We compared other detecting complete plasmids, assembled CAMI2 simulated data. achieved highest F1-score. After validating data with known labels, also tested it real plasmidome The examination commonly used marker genes shows exhibits more reliable performance than tools.

Язык: Английский

---

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

BMC Genomics, Год журнала: 2023, Номер 24(1)

Опубликована: Май 12, 2023

Abstract Background Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis , Brucella species Francisella tularensis. Whole genome sequencing (WGS) has paved way genetic marker detection high-resolution genotyping. While tasks are established Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read yet be evaluated with little genomic variations between strains. In this study, three independent runs were performed using Illumina, ONT flow cell version 9.4.1, 10.4 six each Ba. Br. suis F. Data from alone, alone two hybrid assembly approaches compared. Results As previously shown, produces ultra-long reads, while short reads higher accuracy. Flow improved accuracy over 9.4.1. The correct (sub-)species inferred all tested technologies, individually. Moreover, sets markers virulence, almost identical respective species. long allowed assemble not only chromosomes near closure, but also virulence plasmids . Assemblies based on nanopore data both assemblies correctly detected canonical (sub-)clades tularensis well multilocus sequence types For tularensis, genotyping core-genome MLST (cgMLST) Single-Nucleotide-Polymorphism (cgSNP) typing produced comparable results versions. anthracis, similar methods. However, suis, yielded larger differences comparing Conclusions summary, combining might feasible suis. ongoing improvement technology subsequent analysis may facilitate stable genomes future.

Язык: Английский

---

Airborne antibiotic resistome and microbiome in pharmaceutical factories

Environment International, Год журнала: 2024, Номер 186, С. 108639 - 108639

Опубликована: Апрель 1, 2024

Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission an important but under-appreciated pathway for spread antibiotic genes (ARGs) in environment. Previous research has shown pharmaceutical factories a major source ARGs resistant bacteria (ARB) surrounding receiving water soil environments. Pharmaceutical are hotspots resistance, atmospheric its environmental risk remain more concerns. Here, we conducted metagenomic investigation into microbiome resistome three China. Soil (average: 38.45 %) wastewater 28.53 were contributors resistome. (vanR/vanS, blaOXA, CfxA) conferring critically clinically used antibiotics identified air samples. The treatment area had significantly higher relative abundances 0.64 copies/16 s rRNA). Approximately 28.2 % detected found associated with plasmids, this increased about 50 area. We have compiled list high-risk factories. Moreover, A total 1,043 viral operational taxonomic units linked 47 family-group taxa. Different CRISPR-Cas immune systems been bacterial hosts response phage infection. Similarly, abundance 2451.70 PPM) was Our data provide insights gene profiles (bacterial non-bacterial) reveal potential role horizontal transfer ARGs, implications human animal health.

Язык: Английский

---

Evolution of a vascular plant pathogen is associated with the loss of CRISPR-Cas and an increase in genome plasticity and virulence genes

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

---

Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland

Microbial Genomics, Год журнала: 2025, Номер 11(3)

Опубликована: Март 19, 2025

Hypervirulent Klebsiella pneumoniae (hv Kp ) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination hypervirulence and carbapenem resistance can result in severe difficult-to-treat This retrospective study aimed to investigate the spread hv sequence type 23 (ST23) Ireland convergence hypervirulent (hv) antimicrobial genotypes. Short-read sequences (PE300) for 90 K. ST23 isolates were generated by Galway Reference Laboratory Services (GRLS). Isolates from screening swabs ( n =59), infections =18), non-invasive sites =12) hospital environment =1). virulence content assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) Platon (v1.6). vivo was murine model. All genotypically 88/90 having maximal score 5 including carriage key genes. Eighty-two per cent (74/90) carried carbapenemase gene bla OXA-48 / OXA-181 NDM-1 ), 42% genes 3 or more classes. Core genomic delineation revealed be clonal similar profiles. Two distinct clusters Irish detected consisting 82/90 isolates. infection demonstrated virulence. An established clone is circulating within causing both colonization patients. lack reliable methods makes its detection control healthcare setting challenging.

Язык: Английский

---