News

Pharyngeal carriage of Neisseria species in the African meningitis belt

New paper from the group accepted in the Journal of Infection. This work was done as part of the MenAfriCar consortium project and investigated the influence of non pathogenic Neisseria species on the epidemiology of meningococcal infection in the African meningitis Belt.

The article is now available online: http://www.journalofinfection.com/article/S0163-4453(16)30004-4/abstract

citation: Diallo K, Trotter C, Timbine Y, Tamboura B, Sow SO, Issaka B, Dano ID, Collard J-M, Dieng M, Diallo A, Mihret A, Ali OA, Aseffa A, Quaye SL, Bugri A, Osei I, Gamougam K, Mbainadji L, Daugla DM, Gadzama G, Sambo ZB, Omotara BA, Bennett JS, Rebbetts LS, Watkins ER, Nascimento M, Woukeu A, Manigart O, Borrow R, Stuart JM, Greenwood BM, Maiden MC, Pharyngeal carriage of Neisseria species in the African meningitis belt, Journal of Infection (2016), doi: 10.1016/ j.jinf.2016.03.010.

Wellcome Trust Advanced Course: Molecular approaches to clinical microbiology in Africa

It is with great excitement that the Maiden team arrived to The Gambia for thIMG_6475e 6th edition of the Wellcome Trust Advance Course in Molecular Approaches to Clinical Microbiology in Africa hosted by Professor Martin Antonio at the MRC  The Gambia.

Carina Brehony (lab manager) has arrived first from Ireland, followed by Keith Jolley (lead bioinformaticien), Martin Maiden (professor and master mind behind the course) from Oxford and I, Kanny Diallo (Lab assistant) arriving from Mali where I am currently doing a fieldwork project. We have also met with other instructors and some participant during the travels.

IMG_6566This one week intensive course is the opportunity for 20 African microbiologists to be trained, hands-on, on different molecular techniques that can be applied to their work when they go back to their institutions. During the days the participant alternate between lab work, lectures, bioinformatics work and discussion cessions.

It is also a great networking event as participant comes from everywhere in Africa. This year we had participants from Ghana, Senegal, Mali, Nigeria, Ethiopia, Zambia, Tanzania, Cameroon, Botswana, Malawi, Kenya, South Africa and The Gambia.

IMG_6544The host country change every year, which also allow us (and the participants) to work in a different research centre in Africa. This is also an opportunity to see how things are done in other institutions. The MRC Gambia is an impressive research centre, with state of the art facilities and equipment, highly trained staff, a perfect environment to do research. There have been many highlights to this course. from being featured in the local TV journal, to  visiting the molecular diagnostic lab, Martin Maiden’s sequencing dance, the great lectures from the instructors and the many discussions we had with the participant over lunch or tea break.

The next class will be at the Malawi Liverpool Wellcome Trust; Malawi here we come  !!!

IMG_6518

BIGSdb version 1.12.0 released

BIGSdb version 1.12.0 has been released and is available for download from Sourceforge and GitHub. This is the genomics platform that runs the PubMLST databases. Since the release of version 1.11.0, we have introduced the following:

New functionality

  • Submissions of new allele, MLST profile, isolate and genome data can be made to curators via the RESTful interface.
  • Support for allele retirement so that identifier re-use can be prevented if an allele has been removed.
  • Relaxed auto allele definer CDS checks for use when designating new pseudogene alleles.
  • Support for querying by allele counts of individual loci or total number of allele designations across the genome.

Interface

The isolate querying interfaces have been merged so that browsing, querying and retrieving by lists of attributes are all combined on a single page. The principal advantage of this is that this allows the further combination of subqueries to build more complex searches. You can now, for example, paste in a list of isolate ids or any other attribute and then filter these based on provenance or allele designation/scheme criteria. Query form elements can be shown or hidden at will so that the basic form remains uncluttered and additional forms shown only when needed. This has been developed with mobile use in mind so that the query experience on phones and tablets remains positive.

Isolate querying

Combine query form elements to build complex searches

Performance improvements

  • Larger analysis jobs for the Locus Explorer, Export and Two Field Breakdown plugins are now queued and run offline.
  • Faster scheme breakdown analysis.
  • Improvements to scheme caching so that caches are (optionally) updated automatically in the background following a batch isolate upload.
  • Efficiency improvements when comparing peptide loci in Genome Comparator analyses.

Full documentation can be found at http://bigsdb.readthedocs.org/.

BIGSdb version 1.11.0 released

BIGSdb version 1.11.0 has been released and is available for download from Sourceforge and GitHub. This is the genomics platform that runs the PubMLST databases. This is a major release that provides the following:

New functionality

  • RESTful interface to facilitate access to data within BIGSdb databases by third-party tools. Authentication is supported by OAuth 1.0A to allow access to password-restricted resources.
  • Web-based data submission system that allows users to submit data (alleles, profiles, isolates) to curators via the web. The interface supports data generated by NGS tools.
  • Command line contig uploader script that allows data to be uploaded to the database outside of the web interface.

Interface

  • New icons (using Font Awesome). These are scalable vector icons that work at any resolution and allow CSS styling.

Improved account security

  • Passwords are now hashed using the bcrypt algorithm to resist brute-force attacks if the authentication database is compromised.

Performance improvements

  • Improved distribution of autotagger and autodefiner jobs between threads.
  • Support for multi-threading in MAFFT alignments.
  • Improved performance of scheme completion queries.
  • Improved contig upload performance.

Full documentation can be found at http://bigsdb.readthedocs.org/.

UK Meningococcal Carriage Study 4 wrap up meeting at Oxford Martin School June 1st

Bridge2

On June 1st, 65 delegates from all of the UK sites involved in the fourth UK Meningococcal Carriage Study met at the Oxford Martin School for a study wrap-up meeting. The eleven sites involved were: Oxford, Bristol, Glasgow, Cardiff, Stockport, Wigan, Preston, Manchester, Maidstone & Tunbridge Wells, London and Plymouth.

The meeting was a chance for all the sites and their teams to meet up and discuss the study from their site’s perspective and also discuss future plans for the project. In total, across all the sites 21,806 students aged 15-19 years of age were recruited for swabbing. This was a major achievement for the consortium. Thanks to everyone involved for your hard work and dedication!!

For more details of the study please visit the study website

4th UK Carriage Study in the news

During the all-day event for young people on March 6th at the Oxford University Museum of Natural History, part of this year’s Oxfordshire Science Festival, a team from our group and the Oxford Vaccine Group, participated in the ‘Meet the Scientists’ session and included Holly Bratcher, Carina Brehony and Kanny Diallo.
This was published in the Oxford Mail

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of genomic data

The gene-by-gene method analysis for de novo genomic data has just been published in BMC Genomics.

Whole genome sequencing technologies have rapidly expanded the number of bacterial genomes available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. The performance of our unified system for cataloguing genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. The method generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy and catalogues diversity efficiently, permitting the analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting genomic data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.

  • Bratcher HB, Corton C, et al.  A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics. 2014 December;15:1138.
  • Download PDF

Wellcome Fellowship awarded

Kanny Diallo has been awarded a Wellcome Trust Research Training Fellowship in Public Health and Tropical Medicine, to work towards a DPhil in the Maiden Lab in a joint project with Professor Samba Sow at The Centre pour les Vaccins en Développement, Bamako, Mali (CVD-Mali).  Well done Kanny!

The Centre pour les Vaccins en Développement, Bamako – See more at: http://www.menafricar.org/our-partners/african-institutions/centre-pour-les-vaccins-en-d%C3%A9veloppement#sthash.2xqPwPj6.dpuf

The Centre pour les Vaccins en Développement, Bamako – See more at: http://www.menafricar.org/our-partners/african-institutions/centre-pour-les-vaccins-en-d%C3%A9veloppement#sthash.2xqPwPj6.dpuf
The Centre pour les Vaccins en Développement, Bamako – See more at: http://www.menafricar.org/our-partners/african-institutions/centre-pour-les-vaccins-en-d%C3%A9veloppement#sthash.2xqPwPj6.dpuf
The Centre pour les Vaccins en Développement, Bamako – See more at: http://www.menafricar.org/our-partners/african-institutions/centre-pour-les-vaccins-en-d%C3%A9veloppement#sthash.2xqPwPj6.dpuf
Centre pour les Vaccins en Développement
Centre pour les Vaccins en Développement
Centre pour les Vaccins en Développement (CVD-Mal.  Well done Kanny!