Fast hierarchical Bayesian analysis of population structure

Nucleic Acids Research, Год журнала: 2019, Номер 47(11), С. 5539 - 5549

Опубликована: Апрель 29, 2019

We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit Dirichlet process mixture model (DPM) for multilocus genotype data. Our efficient model-based approach is able cluster datasets 10-100 times larger than existing methods, which we demonstrate by analyzing alignment of over 110 000 sequences HIV-1 pol genes. also provide method partitioning hierarchy in order maximize DPM marginal likelihood, allowing us split phylogenetic trees into clades and subclades using population genomic model. Extensive tests on simulated data as well diverse set real bacterial viral show that fastbaps provides comparable or improved solutions previous while being significantly faster. The made freely available under open source MIT licence easy use R package at https://github.com/gtonkinhill/fastbaps.

Язык: Английский

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Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

The Lancet Infectious Diseases, Год журнала: 2019, Номер 19(7), С. 759 - 769

Опубликована: Июнь 10, 2019

Invasive pneumococcal disease remains an important health priority owing to increasing incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) analysing 20 027 isolates collected worldwide and from published genomic data. In this study, we aimed investigate the lineages behind predominant serotypes, mechanism of serotype replacement in disease, as well major contributing invasive post-vaccine era their antibiotic resistant traits.

Язык: Английский

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International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

EBioMedicine, Год журнала: 2019, Номер 43, С. 338 - 346

Опубликована: Апрель 16, 2019

Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study serotype, antibiotic resistance and invasiveness, in context genetic background.Our dataset 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), South (5%). These 20,027 genomes were clustered into lineages using PopPUNK, named Global Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype sequence type, predicted sensitivity. then measured invasiveness odds ratios that relating prevalence disease carriage.The collections (n = 20,027) 621 GPSCs. Thirty-five GPSCs observed >100 isolates, subsequently classed as dominant-GPSCs. In 22/35 (63%) dominant-GPSCs both non-vaccine serotypes years up until, including, first year introduction. Penicillin multidrug higher (p < .05) subset (14/35, 9/35 respectively), an increasing number classes was associated increased recombination (R2 0.27 p .0001). 28/35 dominant-GPSCs, country isolation significant predictor its antibiogram (mean misclassification error 0.28, SD ± 0.13). detected six backgrounds, when compared other backgrounds expressing same serotype. Up 1.6-fold changes ratio observed.We define can be assigned any aid international comparisons. Existing most preclude removal these vaccines; leaving potential for replacement. A resistance, and/or serotype-independent invasiveness.

Язык: Английский

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PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

GigaScience, Год журнала: 2019, Номер 8(10)

Опубликована: Окт. 1, 2019

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and genetic basis adaptation. Advances in whole genome sequencing technologies have led to a vast expansion amount genomes deposited public databases. There pressing need software solutions which are able cluster, catalogue characterise genes, or other features, increasingly large genomic datasets.Here we present pangenomics toolbox, PIRATE (Pangenome Iterative Refinement Threshold Evaluation), identifies classifies orthologous gene families pangenomes over wide range sequence similarity thresholds. builds upon recent scalable developments allow rapid interrogation thousands isolates. clusters (or annotated features) amino acid nucleotide identity thresholds uses clustering information rapidly identify paralogous putative fission/fusion events. Furthermore, orders pangenome using directed graph, provides measure allelic variation, estimates divergence each family.We demonstrate that scales linearly with both number samples computation resources, allowing analysis datasets, compares favorably popular tools. robust framework analysing pangenomes, from largely clonal panmictic species.

Язык: Английский

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Minimal standards for the description of new genera and species of rhizobia and agrobacteria

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2019, Номер 69(7), С. 1852 - 1863

Опубликована: Май 29, 2019

Herein the members of Subcommittee on Taxonomy Rhizobia and Agrobacteria International Committee Systematics Prokaryotes review recent developments in rhizobial agrobacterial taxonomy propose updated minimal standards for description new species (and genera) these groups. The essential requirements (minimal standards) a are (1) genome sequence at least proposed type strain (2) evidence differentiation from other based comparisons. It is also recommended that (3) genetic variation within documented with data several clearly different strains (4) phenotypic features described, their relevant set representative strains. Furthermore, it encouraged information provided (5) nodulation or pathogenicity phenotypes, as appropriate, gene sequences. These guidelines supplement current rules general bacterial taxonomy, which require (6) name conforms to Code Nomenclature Prokaryotes, (7) validation by publication either directly Journal Systematic Evolutionary Microbiology list when published elsewhere, (8) deposition two international culture collections separate countries.

Язык: Английский

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Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Nature Genetics, Год журнала: 2019, Номер 51(6), С. 1035 - 1043

Опубликована: Май 27, 2019

Язык: Английский

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A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation

Cell Host & Microbe, Год журнала: 2019, Номер 27(1), С. 140 - 153.e9

Опубликована: Дек. 17, 2019

Язык: Английский

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Typing methods based on whole genome sequencing data

One Health Outlook, Год журнала: 2020, Номер 2(1)

Опубликована: Фев. 18, 2020

Abstract Whole genome sequencing (WGS) of foodborne pathogens has become an effective method for investigating the information contained in sequence bacterial pathogens. In addition, its highly discriminative power enables comparison genetic relatedness between bacteria even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (human, veterinary, food, environment) investigation disease outbreaks, source attribution, improved risk characterization models. order to extract relevant from large quantity complex data produced by WGS, host bioinformatics tools been developed, allowing users analyze interpret data, starting simple gene-searches phylogenetic studies. Depending research question, complexity dataset their skill set, can choose great variety analysis data. review, we describe approaches phylogenomic studies outbreak give overview selected based Despite efforts last years, harmonization standardization typing are still urgently needed allow easy laboratories, moving towards one health surveillance system

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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Invasive pneumococcal disease 3 years after introduction of a reduced 1 + 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a prospective national observational surveillance study

The Lancet Infectious Diseases, Год журнала: 2024, Номер 24(5), С. 546 - 556

Опубликована: Фев. 2, 2024

BackgroundThe UK transition from a 2 + 1 to infant immunisation schedule with the 13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided start of COVID-19 pandemic. We describe epidemiology invasive disease (IPD) in England over 6 financial years (April March 31) between 2017–18 and 2022–23.MethodsWe used prospective national surveillance data, including serotyping whole-genome sequencing isolates, analyse IPD trends by age year. compared breakthrough infections failure rates 2022–23 among children eligible for cohorts 2019–20. assessed genomic changes time comparing Global Pneumococcal Sequencing Clusters multilocus sequence types PCV13 serotypes causing IPD.FindingsThere were 4598 laboratory-confirmed cases 2022–23, 3025 2021–22, 1240 2020–21, 5316 incidence was 14% lower than 2019–20 (incidence rate ratio [IRR] 0·86, 95% CI 0·81–0·91; p<0·001). 34% higher (aged <15 years) (378 vs 292 cases; IRR 1·34, 1·08–1·68; p=0·009) 17% adults 15 older; 4220 5024; 0·83, 0·78–0·88; The proportion PCV13-type increased 19·4% (95% 18·2–20·4; 957 4947) 29·7% (28·3–31·0; 1283 4326) mainly due serotype 3, but also 19F, 19A, 4, alongside decrease non-PCV13 8, 12F, 9N. increase 19F driven clonal expansion previously circulating strains, whereas 4 newer strains (ie, 801 15603). Breakthrough similar (1·07 per 100 000 person-years) (0·76 person-years; 1·42, 0·78–2·49; p=0·20) schedules.InterpretationOverall, after removal pandemic restrictions, not significantly different who received schedule. post-pandemic childhood especially will require close monitoring.FundingNone.

Язык: Английский

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