Literature DB >> 17002618

A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses.

S Platt1, B Pichon, R George, J Green.   

Abstract

Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.

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Year:  2006        PMID： 17002618     DOI： 10.1111/j.1469-0691.2006.01541.x

Source DB:  PubMed          Journal:  Clin Microbiol Infect        ISSN： 1198-743X            Impact factor:   8.067


  9 in total

1.  Molecular typing of pneumococci for investigation of linked cases of invasive pneumococcal disease.

Authors:  Bruno Pichon; Laura Moyce; Carmen Sheppard; Mary Slack; Deborah Turbitt; Richard Pebody; David A Spencer; Justin Edwards; Daniel Krahé; Robert George
Journal:  J Clin Microbiol       Date:  2010-02-17       Impact factor: 5.948

2.  Streptococcus pneumoniae isolates expressing a capsule with epitopes of both serotypes 6A and 6B.

Authors:  Carmen L Sheppard; Bruno Pichon; Robert C George; Lucinda M C Hall
Journal:  Clin Vaccine Immunol       Date:  2010-09-28

3.  Double-locus sequence typing using clfB and spa, a fast and simple method for epidemiological typing of methicillin-resistant Staphylococcus aureus.

Authors:  G Kuhn; P Francioli; D S Blanc
Journal:  J Clin Microbiol       Date:  2006-11-08       Impact factor: 5.948

4.  Temporal trends of antimicrobial resistance and clonality of invasive Streptococcus pneumoniae isolates in Finland, 2002 to 2006.

Authors:  Lotta Siira; Merja Rantala; Jari Jalava; Antti J Hakanen; Pentti Huovinen; Tarja Kaijalainen; Outi Lyytikäinen; Anni Virolainen
Journal:  Antimicrob Agents Chemother       Date:  2009-03-09       Impact factor: 5.191

Review 5.  Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar.

Authors:  K A Jolley; M C Maiden
Journal:  Euro Surveill       Date:  2013-01-24

6.  Changes in molecular epidemiology of streptococcus pneumoniae causing meningitis following introduction of pneumococcal conjugate vaccination in England and Wales.

Authors:  Bruno Pichon; Shamez N Ladhani; Mary P E Slack; Anne Segonds-Pichon; Nick J Andrews; Pauline A Waight; Elizabeth Miller; Robert George
Journal:  J Clin Microbiol       Date:  2012-12-26       Impact factor: 5.948

Review 7.  Listeria monocytogenes in foods-From culture identification to whole-genome characteristics.

Authors:  Jacek Osek; Beata Lachtara; Kinga Wieczorek
Journal:  Food Sci Nutr       Date:  2022-05-03       Impact factor: 3.553

8.  Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing.

Authors:  Hélène van Cuyck; Bruno Pichon; Philippe Leroy; Alexandra Granger-Farbos; Anthony Underwood; Bruno Soullié; Jean-Louis Koeck
Journal:  BMC Microbiol       Date:  2012-10-22       Impact factor: 3.605

9.  Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data.

Authors:  Lee S Katz; Chris R Bolen; Brian H Harcourt; Susanna Schmink; Xin Wang; Andrey Kislyuk; Robert T Taylor; Leonard W Mayer; I King Jordan
Journal:  Nucleic Acids Res       Date:  2009-05-25       Impact factor: 16.971
  9 in total

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