Population genomics of Klebsiella pneumoniae

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(6), С. 344 - 359

Опубликована: Фев. 13, 2020

Язык: Английский

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Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

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

Опубликована: Ноя. 5, 2021

Command-line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command-line pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and, nonetheless, fast Bakta conducts comprehensive workflow including detection small proteins taking into account replicon metadata. The coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates precise assignment public database cross-references. Annotation are exported GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as JSON facilitating automated downstream analysis. We other rapid contemporary both targeted taxonomically broad benchmarks isolates metagenomic-assembled demonstrated outperforms terms functional annotations, categories cross-references, whilst providing comparable wall-clock runtimes. implemented Python 3 runs MacOS Linux systems. It freely available under GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version https://bakta.computational.bio.

Язык: Английский

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PLSDB: a resource of complete bacterial plasmids

Nucleic Acids Research, Год журнала: 2018, Номер 47(D1), С. D195 - D202

Опубликована: Окт. 17, 2018

Abstract The study of bacterial isolates or communities requires the analysis therein included plasmids in order to provide an extensive characterization organisms. Plasmids harboring resistance and virulence factors are especial interest as they contribute dissemination antibiotic resistance. As number newly sequenced genomes is growing a comprehensive resource required which will allow browse filter available plasmids, perform sequence analyses. Here, we present PLSDB, containing 13 789 plasmid records collected from NCBI nucleotide database. web server provides interactive view all obtained with additional meta information such characteristics, sample-related taxonomy. Moreover, data can be uploaded search for short sequences (e.g. specific genes) compare given collection determine whether sample contains one multiple known (containment analysis). freely accessible under https://ccb-microbe.cs.uni-saarland.de/plsdb/.

Язык: Английский

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Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(6)

Опубликована: Фев. 1, 2021

Significance There is great interest in understanding how antibiotic resistance disseminated by MGEs (i.e., plasmids, insertion sequences, and integrons). We have systematically investigated their interactions mediating the horizontal transfer of combining silico genomic analysis a large collection complete bacterial plasmids (14,029) genomes (12,059), then confirmed we observe nature using direct experimental approaches. showed whole picture all IS-associated patterns AMR genes across different genetic backgrounds our results highlight significant relationships between conjugative ISs shaping dissemination genes.

Язык: Английский

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Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

Nucleic Acids Research, Год журнала: 2019, Номер 48(4), С. 2000 - 2012

Опубликована: Дек. 13, 2019

CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites. In contrast to all types of systems, type IV has remained largely overlooked. Here, we describe a previously uncharted diversity gene cassettes, primarily encoded by plasmid-like elements from diverse prokaryotic taxa. Remarkably, via comprehensive analysis their CRISPR spacer content, these were found exhibit strong bias towards the targeting plasmids. Our data indicate that have diverged those host-related adopt role in mediating conflicts between Furthermore, find evidence for cross-talk certain I co-exist intracellularly, thus providing simple answer enigmatic absence adaptation modules. Collectively, our results lead expansion reclassification novel insights into biological function evolution elusive systems.

Язык: Английский

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PLSDB: advancing a comprehensive database of bacterial plasmids

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D273 - D278

Опубликована: Окт. 22, 2021

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity scale of metagenomics experiments, number reported plasmids rapidly growing as well, amassing a considerable false positives due undetected misassembles. Here, our previously published database PLSDB provides reliable resource researchers quickly compare their sequences against selected annotated previous findings. Within two years, size this has more than doubled from initial 13,789 now 34,513 entries over course eight regular updates. For update, we aggregated community feedback major changes featuring new analysis functionality well performance, quality, accessibility improvements. New filtering steps, annotations, preprocessing existing records improve quality provided data. Additionally, features implemented web-server ease user interaction allow deeper understanding custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was along python library, remote queries automated workflows. The latest release freely accessible under https://www.ccb.uni-saarland.de/plsdb.

Язык: Английский

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Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

Microbial Genomics, Год журнала: 2020, Номер 6(10)

Опубликована: Июнь 24, 2020

Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in environmental adaptation bacteria. Due to potential mobilization or conjugation capabilities, plasmids important vehicles for antimicrobial resistance genes virulence factors with huge increasing clinical implications. They therefore subject large genomic studies within scientific community worldwide. As result rapidly improving next-generation sequencing methods, quantity sequenced bacterial genomes is constantly increasing, turn raising need specialized tools (i) extract plasmid sequences from draft assemblies, (ii) derive their origin distribution, (iii) further investigate repertoire. Recently, several bioinformatic methods have emerged tackle this issue; however, combination high sensitivity specificity sequence identification rarely achieved taxon-independent manner. In addition, many software not appropriate high-throughput analyses cannot be included existing pipelines due technical design implementation. study, we investigated differences replicon distributions protein-coding on scale as new approach distinguish plasmid-borne chromosome-borne contigs. We defined computed statistical discrimination thresholds metric: distribution score (RDS), which an accuracy 96.6 %. The final performance was improved by RDS metric heuristics exploiting plasmid-specific higher-level contig characterizations. implemented workflow bioinformatics tool called Platon recruitment characterization contigs short-read assemblies. Compared PlasFlow, higher (97.5 %) more balanced predictions (F1=82.6 tested broad range taxa better equal against targeted PlasmidFinder PlaScope Escherichia coli isolates. available at: http://platon.computational.bio/ .

Язык: Английский

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A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

Nature Microbiology, Год журнала: 2022, Номер 7(12), С. 2054 - 2067

Опубликована: Ноя. 21, 2022

Abstract The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically ecologically diverse. Many species are opportunistic pathogens can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated pneumoniae clones that non-susceptible to carbapenems spread rapidly, representing a high public health burden. Here we report an analysis 3,482 genome sequences 15 sampled over 17-month period from wide range clinical, community, animal environmental settings around the Italian city Pavia. Northern Italy hotspot for hospital-acquired carbapenem thus pertinent setting examine overlap between isolates clinical non-clinical settings. We no genotypic or phenotypic evidence non-susceptibility outside environment. Although noted occasional transmission settings, our data point limited role reservoirs human acquisition spp. also provide detailed genus-wide view genomic diversity population structure, including identification new groups.

Язык: Английский

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Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges

Environmental Toxicology and Chemistry, Год журнала: 2022, Номер 41(3), С. 687 - 714

Опубликована: Фев. 22, 2022

Abstract River ecosystems are very important parts of the water cycle and an excellent habitat, food, drinking source for many organisms, including humans. Antibiotics emerging contaminants which can enter rivers from various sources. Several antibiotics their related antibiotic resistance genes (ARGs) have been detected in these by research programs could constitute a substantial problem. The presence other cofactors boost development ARGs chromosomes or mobile genetic elements natural bacteria rivers. environmental also be transferred to clinically pathogens. However, both not currently monitored national international authorities responsible controlling quality bodies. For example, they included contaminant list European Water Framework Directive US Water‐Quality Benchmarks Contaminants. Although naturally present environment, few studies focused on non‐impacted assess background ARG levels rivers, provide some useful indications future regulation legislation. study reviews associated most commonly measured primary analysis tools used assessment. In addition, factors that enhance resistance, such as effects chemical mixtures, climate change, potential coronavirus disease 2019 pandemic, discussed. Environ Toxicol Chem 2022;41:687–714. © 2022 SETAC

Язык: Английский

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Carbapenem-resistant Klebsiella pneumoniae capsular types, antibiotic resistance and virulence factors in China: a longitudinal, multi-centre study

Nature Microbiology, Год журнала: 2024, Номер 9(3), С. 814 - 829

Опубликована: Фев. 29, 2024

Abstract Epidemiological knowledge of circulating carbapenem-resistant Klebsiella pneumoniae (CRKP) is needed to develop effective strategies against this public health threat. Here we present a longitudinal analysis 1,017 CRKP isolates recovered from patients 40 hospitals across China between 2016 and 2020. Virulence gene capsule typing revealed expansion type KL64 (59.5%) alongside decreases in KL47 prevalence. Hypervirulent increased prevalence 28.2% 45.7% Phylogenetic spatiotemporal Beijing Shanghai as transmission hubs accounting for differential geographical strains China. Moderate frequency or O-antigen loss was also detected among isolates. Non-capsular were more susceptible phagocytosis, attenuated during mouse infections, but showed serum resistance biofilm formation. These findings give insight into serotype dynamics, revealing the importance monitoring shifts future development immunological infections.

Язык: Английский

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