Domestication ofCampylobacter jejuniNCTC 11168

AbstractReference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics.Campylobacter jejunistrain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the firstCampylobacterfor which the complete genome was published (in 2000). In this study, we collected 23C. jejuniNCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37°C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change amongC. jejuniisolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.Impact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 referenceCampylobactergenomes and compare them with observable differences in common laboratory phenotypes.Data summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).All assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact:https://microreact.org/project/NCTC11168.RepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467;Table S1).The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

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Domestication of Campylobacter jejuni NCTC 11168

Microbial Genomics ◽

10.1099/mgen.0.000279 ◽

2019 ◽

Vol 5 (7) ◽

Author(s):

Ben Pascoe ◽

Lisa K. Williams ◽

Jessica K. Calland ◽

Guillaume Meric ◽

Matthew D. Hitchings ◽

...

Keyword(s):

Genetic Variation ◽

Campylobacter Jejuni ◽

Type Species ◽

Reference Strain ◽

Careful Consideration ◽

Trait Variation ◽

Content Type ◽

Link Type ◽

The Uk ◽

Reference Strains

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

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Umap and Bismap: quantifying genome and methylome mappability

10.1101/095463 ◽

2016 ◽

Cited By ~ 5

Author(s):

Mehran Karimzadeh ◽

Carl Ernst ◽

Anshul Kundaje ◽

Michael M. Hoffman

Keyword(s):

Genetic Variation ◽

Bisulfite Sequencing ◽

Cpg Islands ◽

Read Length ◽

Methylation Array ◽

Short Read ◽

Short Read Sequencing ◽

Sequencing Errors ◽

Link Type ◽

A Genome

AbstractMotivationShort-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding, and chemical modifications. Every region in a genome assembly has a property called mappability which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. At best, sequencing assays will produce misleadingly low numbers of reads in these regions. At worst, these regions have increased susceptibility to spurious mapping from reads from other regions of the genome with sequencing errors or unexpected genetic variation. Bisulfite sequencing approaches used to identify DNA methylation exacerbate these problems by introducing large numbers of reads that map to multiple regions. While many tools consider mappability during the read mapping process, subsequent analysis often loses this information. Both to correct assumptions of uniformity in downstream analysis, and to identify regions where the analysis is less reliable, it is necessary to know the mappability of both ordinary and bisulfite-converted genomes.ResultsWe introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. With a read length of 24 bp, 18.7% of the unmodified genome and 33.5% of the bisulfite-converted genome is not uniquely mappable. This complicates interpretation of functional genomics experiments using short-read sequencing, especially in regulatory regions. For example, 81% of human CpG islands overlap with regions that are not uniquely mappable. Similarly, in some ENCODE ChIP-seq datasets, up to 50% of peaks overlap with regions that are not uniquely mappable. We also explored differentially methylated regions from a case-control study and identified regions that were not uniquely mappable. In the widely used 450K methylation array, 4,230 probes are not uniquely mappable. Genome mappability is higher with longer sequencing reads, but most publicly available ChIP-seq and reduced representation bisulfite sequencing datasets have shorter reads. Therefore, uneven and low mappability remains a concern in a majority of existing data.AvailabilityA Umap and Bismap track hub for human genome assemblies GRCh37/hg19 and GRCh38/hg38, and mouse assemblies GRCm37/mm9 and GRCm38/mm10 is available at http://bismap.hoffmanlab.org for use with the UCSC and Ensembl genome browsers. We have deposited in Zenodo the current version of our software (https://doi.org/10.5281/zenodo.800648) and the mappability data used in this project (https://doi.org/10.5281/zenodo.800645). In addition, the software (https://bitbucket.org/hoffmanlab/umap) is freely available under the GNU General Public License, version 3 (GPLv3)[email protected]

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Complete genome sequence and annotation of the laboratory reference strainShigella flexneriserotype 5a M90T and genome-wide transcriptional start site determination

10.1101/595066 ◽

2019 ◽

Author(s):

Ramón Cervantes-Rivera ◽

Sophie Tronnet ◽

Andrea Puhar

Keyword(s):

Systems Biology ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Reference Strain ◽

Virulence Plasmid ◽

Link Type ◽

Genome Wide ◽

Laboratory Reference ◽

Transcriptional Start Sites

AbstractBackgroundShigellais a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans.Shigellainvades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strainS. flexneriserotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches.ResultsWe have sequenced, assembled, annotated and manually curated the full genome ofS. flexneri5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new pipeline to prepare gapless, highly accurate genome sequences. Furthermore, we have performed genome-wide analysis of transcriptional start sites and determined the length of 5’ untranslated regions (5’-UTRs) at typical culture conditions for the inoculum ofin vitroinfection experiments. We identified 6,723 primary TSS (pTSS) and 7,328 secondary TSS (sTSS). TheS. flexneri5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) to use its analysis tools inS. flexneri5a M90T genome.ConclusionsWe provide the first complete genome forS. flexneriserotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employingS. flexneriM90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation ofS. flexneri5a M90T. The hybrid pipeline that we report here combining genome sequencing with long-reads technology and polishing with RNAseq data defines a powerful strategy for genome assembly, polishing and annotation in any type of organism.

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CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

10.1101/064451 ◽

2016 ◽

Cited By ~ 2

Author(s):

Thomas R. Connor ◽

Nicholas J. Loman ◽

Simon Thompson ◽

Andy Smith ◽

Joel Southgate ◽

...

Keyword(s):

Data Storage ◽

High Throughput Sequencing ◽

Cloud Infrastructure ◽

Link Type ◽

Medical Microbiology ◽

Public Resource ◽

Technological Advances ◽

Data Files ◽

The Uk ◽

Computational Resources

AbstractThe increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.DATA SUMMARYThe paper describes a new, freely available public resource and therefore no data has been generated. The resource can be accessed at http://www.climb.ac.uk. Source code for software developed for the project can be found at http://github.com/MRC-CLIMB/I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.IMPACT STATEMENTTechnological advances mean that genome sequencing is now relatively simple, quick, and affordable. However, handling large genome datasets remains a significant challenge for many microbiologists, with substantial requirements for computational resources and expertise in data storage and analysis. This has led to fragmentary approaches to software development and data sharing that reduce the reproducibility of research and limits opportunities for bioinformatics training. Here, we describe a nationwide electronic infrastructure that has been designed to support the UK microbiology community, providing simple mechanisms for accessing large, shared, computational resources designed to meet the bioinformatic needs of microbiologists.

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AGILE: a seamless phase I/IIa platform for the rapid evaluation of candidates for COVID-19 treatment: an update to the structured summary of a study protocol for a randomised platform trial letter

Trials ◽

10.1186/s13063-021-05458-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gareth O. Griffiths ◽

Richard FitzGerald ◽

Thomas Jaki ◽

Andrea Corkhill ◽

Helen Reynolds ◽

...

Keyword(s):

Phase I ◽

Early Stage ◽

Late Phase ◽

Optimum Dose ◽

Open Label ◽

Link Type ◽

Hospitalised Patients ◽

Volunteer Study ◽

The Uk ◽

Phase Trial

Abstract Background There is an urgent unmet clinical need for the identification of novel therapeutics for the treatment of COVID-19. A number of COVID-19 late phase trial platforms have been developed to investigate (often repurposed) drugs both in the UK and globally (e.g. RECOVERY led by the University of Oxford and SOLIDARITY led by WHO). There is a pressing need to investigate novel candidates within early phase trial platforms, from which promising candidates can feed into established later phase platforms. AGILE grew from a UK-wide collaboration to undertake early stage clinical evaluation of candidates for SARS-CoV-2 infection to accelerate national and global healthcare interventions. Methods/design AGILE is a seamless phase I/IIa platform study to establish the optimum dose, determine the activity and safety of each candidate and recommend whether it should be evaluated further. Each candidate is evaluated in its own trial, either as an open label single arm healthy volunteer study or in patients, randomising between candidate and control usually in a 2:1 allocation in favour of the candidate. Each dose is assessed sequentially for safety usually in cohorts of 6 patients. Once a phase II dose has been identified, efficacy is assessed by seamlessly expanding into a larger cohort. AGILE is completely flexible in that the core design in the master protocol can be adapted for each candidate based on prior knowledge of the candidate (i.e. population, primary endpoint and sample size can be amended). This information is detailed in each candidate specific trial protocol of the master protocol. Discussion Few approved treatments for COVID-19 are available such as dexamethasone, remdesivir and tocilizumab in hospitalised patients. The AGILE platform aims to rapidly identify new efficacious and safe treatments to help end the current global COVID-19 pandemic. We currently have three candidate specific trials within this platform study that are open to recruitment. Trial registration EudraCT Number: 2020-001860-27 14 March 2020 ClinicalTrials.gov Identifier: NCT04746183 19 February 2021 ISRCTN reference: 27106947

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Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽

10.1093/genetics/157.1.283 ◽

2001 ◽

Vol 157 (1) ◽

pp. 283-294 ◽

Cited By ~ 2

Author(s):

Kristie Ashton ◽

Ana Patricia Wagoner ◽

Roland Carrillo ◽

Greg Gibson

Keyword(s):

Heart Rate ◽

Genetic Variation ◽

Recombinant Inbred Lines ◽

Model Organism ◽

Interval Mapping ◽

Activity Levels ◽

Environmental Variance ◽

Genome Wide ◽

A Genome ◽

Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

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Knowledge as a Revenue Driver, Not a Cost Centre: the LexisNexis GLP and How to Use Market Intelligence to Make Knowledge a Vital Growth Engine for Law Firms

Legal Information Management ◽

10.1017/s147266962000050x ◽

2020 ◽

Vol 20 (4) ◽

pp. 213-218

Author(s):

Christopher O'Connor

Keyword(s):

Quantitative Measure ◽

Law Firms ◽

Legal Services ◽

Market Intelligence ◽

Link Type ◽

Marketing Team ◽

Virtual Conference ◽

The Uk ◽

Individual Metrics ◽

Legal Product

AbstractThis article by the LexisNexis Segment Marketing team explains the approach, methodology and findings of the LexisNexis Gross Legal Product (GLP) report, first presented at the BIALL's Virtual Conference in June 2020. The GLP is a quantitative measure of underlying demand for legal services in the UK, comprised of 250 individual metrics which serve as proxies for legal activity. The article outlines the methodology and sources used to build the GLP; headline findings for Q2 2020 YTD; and provides suggestions for how firm leaders and knowledge professionals could use the information in their work. The GLP Q2 model found that demand for legal activity has declined by 7% since the start of 2020.

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Genetic variation in Drosophila melanogaster pathogen susceptibility

Parasitology ◽

10.1017/s0031182006009929 ◽

2006 ◽

Vol 132 (6) ◽

pp. 767-773 ◽

Cited By ~ 53

Author(s):

M. C. TINSLEY ◽

S. BLANFORD ◽

F. M. JIGGINS

Keyword(s):

Biological Control ◽

Drosophila Melanogaster ◽

Genetic Variation ◽

Model Organism ◽

Resistance Evolution ◽

Control Programmes ◽

Host Ecology ◽

Insect Pathogens ◽

Immunological Research ◽

Pathogen Exposure

Genetic variation in susceptibility to pathogens is a central concern both to evolutionary and medical biologists, and for the implementation of biological control programmes. We have investigated the extent of such variation in Drosophila melanogaster, a major model organism for immunological research. We found that within populations, different Drosophila genotypes show wide-ranging variation in their ability to survive infection with the entomopathogenic fungus Beauveria bassiana. Furthermore, striking divergence in susceptibility has occurred between genotypes from temperate and tropical African locations. We hypothesize that this may have been driven by adaptation to local differences in pathogen exposure or host ecology. Genetic variation within populations may be maintained by temporal or spatial variation in the costs and benefits of pathogen defence. Insect pathogens are employed widely as biological control agents and entomopathogenic fungi are currently being developed for reducing malaria transmission by mosquitoes. Our data highlight the need for concern about resistance evolution to these novel biopesticides in vector populations.

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Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004699 ◽

2019 ◽

Vol 71 (3) ◽

Cited By ~ 3

Author(s):

Xue Zhang ◽

Lida Zhang ◽

XiaoYan Yu ◽

Jing Zhang ◽

Yanjie Jiao ◽

...

Keyword(s):

Type Species ◽

Cow Dung ◽

Rrna Gene ◽

Content Type ◽

Mycolic Acids ◽

Link Type ◽

Pr China ◽

Taxonomic Characterization ◽

Reference Strains

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia , with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia , for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).

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Trust, efficacy and ethicacy when testing prisoners for COVID-19

International Journal of Prisoner Health ◽

10.1108/ijph-10-2020-0084 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Steve Lambert ◽

Dean Wilkinson

Keyword(s):

Large Scale ◽

Current System ◽

Epidemiological Studies ◽

Careful Consideration ◽

Power Relationships ◽

England And Wales ◽

Content Type ◽

Large Scale Testing ◽

The Uk ◽

The Impact

Purpose The outbreak of the severe acute respiratory syndrome coronavirus 2 virus and subsequent COVID-19 illness has had a major impact on all levels of society internationally. The extent of the impact of COVID-19 on prison staff and prisoners in England and Wales is unknown. Testing for COVID-19 both asymptomatic and symptomatic, as well as for antibodies, to date, has been minimal. The purpose of this paper is to explore the widespread testing of COVID-19 in prisons poses philosophical and ethical questions around trust, efficacy and ethicacy. Design/methodology/approach This paper is both descriptive, providing an overview of the widespread testing of COVID-19 in prisoners in England and Wales, and conceptual in that it discusses and argues the issues associated with large-scale testing. This paper provides a discussion, using comparative studies, of the issues associated with large-scale testing of prisoners across the prison estate in England and Wales (120 prisons). The issues identified in this paper are contextualised through the lens of COVID-19, but they are equally transferrable to epidemiological studies of any pandemic. Given the prevalence of COVID-19 globally and the lack of information about its spread in prisons, at the time of writing this paper, there is a programme of asymptomatic testing of prisoners. However, there remains a paucity of data on the spread of COVID-19 in prisons because of the progress with the ongoing testing programme. Findings The authors argue that the widespread testing of prisoners requires careful consideration of the details regarding who is included in testing, how consent is gained and how tests are administered. This paper outlines and argues the importance of considering the complex nuance of power relationships within the prison system, among prisoner officers, medical staff and prisoners and the detrimental consequences. Practical implications The widespread testing of COVID-19 presents ethical and practical challenges. Careful planning is required when considering the ethics of who should be included in COVID-19 testing, how consent will be gained, who and how tests will be administered and very practical challenges around the recording and assigning of COVID-19 test kits inside the prison. The current system for the general population requires scanning of barcodes and registration using a mobile number; these facilities are not permitted inside a prison. Originality/value This paper looks at the issues associated with mass testing of prisoners for COVID-19. According to the authors’ knowledge, there has not been any research that looks at the issues of testing either in the UK or internationally. The literature available details countries’ responses to the pandemic rather and scientific papers on the development of vaccines. Therefore, this paper is an original review of some of the practicalities that need to be addressed to ensure that testing can be as successful as possible.

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