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http://genomemedicine.com/content/3/7/48
MEETING REPORT
Agency, UK) evaluated the annotation accuracy of five ultimately lead to the development of radical interven
popular genome annotation pipelines - RAST, FgenesB, tions to stop the spread of epidemics. Oliver Pybus
MG/ER, IGS and xBASE - using manual annotations of (Oxford University, UK) stressed that NGS should not be
Salmonella typhimurium genomes as a gold standard. restricted to bacteria by describing its application for
She reported that 50 to 80% of bacterial proteins can be RNA viruses, including common human RNA viral
identified from NGS data. Keith Jolley (University of pathogens such as HIV, influenza and hepatitis C. He
Oxford, UK) described the freely accessible Bacterial highlighted the importance of the timely development of
Isolate Genome Sequence Database (BIGSdb; http:// data analysis methods to take advantage of the
pubmlst.org/software/database/bigsdb/). exponential growth in available sequence data.
Helena Seth-Smith (Wellcome Trust Sanger Institute, It was especially refreshing to see many excellent
Hinxton, UK) discussed the application of NGS to analyze presentations from talented early-career female scien
a major cause of sexually transmitted disease, Chlamydia tists. Rebecca Gladstone (Health Protection Agency, UK)
trachomatis, which gave an insight into population gave a talk on the phenotypic and genotypic diversity of
structures and the evolution of the bacterium. Angela Streptococcus pneumoniae isolates seen during the intro
McCann (University College Cork, Ireland) presented an duction of conjugate vaccines. She emphasized that WGS
analysis of genetic diversity in Salmonella enterica, a can uncover relationships between strains that are not
pathogen in cattle and poultry disease, using paired-end detected by other methods (such as MLST). Another
Illumina reads to detect SNPs. The topology inferred remarkable young scientist, Jacqueline Chan (Centre for
from SNP analysis is consistent with epidemiological data Systems Biology, UK), outlined the use of high-through
and therefore NGS sequencing can be used as a predic put sequencing to track pathogenic bacterial infections in
tive tool at the onset of an outbreak. hospitals and the use of phage therapy as an alternative to
Genome sequencing has provided a wealth of informa antibiotics. Jennifer Gardy (British Columbia Center for
tion on the genetics and biology of the versatile bacterium Disease Control, Canada) addressed the important issue
Escherichia coli. Ulrich Dobrindt (University of Mnster, of analyzing the dynamics of tuberculosis outbreaks. She
Germany) presented his NGS analysis of E. coli popula demonstrated how a combination of epidemiologic data,
tion diversity and microevolution. This approach has the WGS and social-network analysis can be used to deter
potential to improve the typing of pathogenic E. coli mine the origins and transmission dynamics of the out
variants. Rolf Kaas (Technical University of Denmark, break. Supang Martin (Health Protection Agency, UK)
Denmark) compared nucleotide identity amongst 171 investigated the development and evolution of drug resis
E.coli strains. Kaas showed that fast- and slow-evolving tance in the pol gene of HIV-1 using phylogenetic
genes should be treated differently in the development of analysis. She demonstrated the existence of recombina
a dynamic typing method that can be used in different tion between viruses from different subpopulations, and
outbreak scenarios. discussed the complex dynamics in the development of
The hypervirulent bacterium Clostridium difficile is the drug resistance in patients undergoing treatments with
most serious cause of antibiotic-associated diarrhea, fre protease, reverse transcriptase and integrase inhibitors.
quently resulting from eradication of the normal gut flora Pimlapas Leekitcharoenphon (Technical University of
by antibiotics. Miao He (Wellcome Trust Sanger Denmark, Denmark) presented an interesting study on
Institute, UK) described the application of whole-genome genomic variation in core genes of S. enterica genomes.
sequencing (WGS) for analysis of genetic variation The core genes are conserved in most of the subspecies
among a global collection of 370 different strains of and variation within them is essential for bacterial
C. difficile. A combination of genomics data with time/ adaptation.
space and clinical data allows the identification of both
long-range transmission events between and within Future perspectives
countries and routes of transmission within hospitals. It The members of the scientific organizing committee
also makes it possible to differentiate re-lapsing disease initiated an open session in which attendees discussed
and re-infection. This topic was continued by Tim Peto which bioinformatics tools would be the best in a clinical
(John Radcliffe Hospital, UK). Peto demonstrated that environment. Participants indicated a strong demand for
WGS can provide more information than multi-locus the organization of adequate data-sharing (of reference
sequence typing (MLST). Brendan Wren (London School genomes and strains, for example), a desire to link
of Hygiene & Tropical Medicine, UK) presented a whole- relevant data types, and the need to devise standard data
genome comparison of Campylobacter jejuni, Yersinia generation and analysis protocols. Many errors have been
enterocolitica and C. difficile that can be useful for under found in GenBank records, and it was advised that
standing how bacterial pathogens transmit and evolve. researchers should provide indicators of the quality of
Understanding the mechanism of pathogenicity will assembly. As remarked by Nick Loman (University of
Solovyev and Tatarinova Genome Medicine 2011, 3:48 Page 3 of 3
http://genomemedicine.com/content/3/7/48