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Meeting abstract
Reconstructing the virulome of the human pathogen Streptococcus
pyogenes using NMPDR subsystems-based annotation
Ramy K Aziz*
1,2
and Leslie K Mcneil
3
Address:
1
Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt,
2
Computation Institute, University
of Chicago, Chicago, IL, USA and
3
National Center for Supercomputing Applications, University of Illinois, Urbana, IL, USA
Email: Ramy K Aziz* - ramy.aziz@salmonella.org
* Corresponding author
Background
The increasing number of published complete microbial
genomes has revolutionized biological sciences and is
driving a paradigm shift in microbiology. While this
genomic revolution has made the reconstruction of an
organism's metabolism from genomic data achievable,
predicting the pathogenic potential of host-associated
microbes is still in its early stages; hence, developing inno-
vative bioinformatics tools that integrate microbiologists'
expertise and experimental laboratory data with sequence
data remains a necessity. For this purpose, the NIH-
funded National Microbial Pathogen Data Resource
(NMPDR, http://www.nmpdr.org) was established as a
bioinformatics resource center for specific bacterial path-
ogens, including staphylococci, streptococci, and sexually
transmitted bacteria [1]. Genomes in NMPDR are anno-
tated by the recently developed subsystems annotation
technology [2,3], available from the SEED environment
http://theseed.uchicago.edu/FIG/index.cgi. This technol-
ogy relies on analyzing genes in their chromosomal con-
text and combines the accuracy of human curation with
the speed of automated propagation [2].
Methods and results
In this study, we apply the subsystems annotation tech-
nology to reconstruct the virulome of the human patho-
gen Streptococcus pyogenes that claims 500,000 lives every
year [4], and causes a wide range of diseases that affect
sequenced streptococcal serotypes, and highlight the
impact of prophages and highly recombinatorial genomic
segments, including the newly discovered pilus locus [6],
on streptococcal strain emergence and diversification [7].
Our analysis defines the core and dispensable elements of
the streptococcal virulome, which includes – in addition
to the ancestral, species-specific virulence proteins – the
phage-encoded toxins and their pseudogenes. Finally, we
use comparative analysis of streptococcal subsystems in
context of actual transcriptome data to gain insight into
the complex gene regulatory networks that control viru-
lence.
References
1. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards
RA, Gerdes S, Hwang K, Kubal M, et al.: The National Microbial
Pathogen Database Resource (NMPDR): a genomics plat-
form based on subsystem annotation. Nucleic Acids Res
2007:D347-353.
2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,
Formsma K, Gerdes S, Glass EM, Kubal M, et al.: The RAST Server:
rapid annotations using subsystems technology. BMC Genom-
ics 2008, 9:75.
3. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY,
Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al.: The
subsystems approach to genome annotation and its use in
the project to annotate 1000 genomes. Nucleic Acids Res 2005,
33(17):5691-5702.
4. Carapetis JR, Steer AC, Mulholland EK, Weber M: The global bur-
den of group A streptococcal diseases. Lancet Infect Dis 2005,
5(11):685-694.
5. Cunningham MW: Pathogenesis of group A streptococcal
infections. Clin Microbiol Rev 2000, 13(3):470-511.
from UT-ORNL-KBRIN Bioinformatics Summit 2009
Pikeville, TN, USA. 20–22 March 2009
Published: 25 June 2009
BMC Bioinformatics 2009, 10(Suppl 7):A7 doi:10.1186/1471-2105-10-S7-A7
<supplement> <title> <p>UT-ORNL-KBRIN Bioinformatics Summit 2009</p> </title> <editor>Eric C Rouchka and Julia Krushkal</editor> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/pdf/1471-2105-10-S7-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1471-2105-10-S7-info.pdf</url> </supplement>
This abstract is available from: http://www.biomedcentral.com/1471-2105/10/S7/A7
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adults and children [5]. In particular, we use NMPDR
tools for pathogenomic comparison of the fully
6. Bessen DE, Kalia A: Genomic localization of a T serotype locus
to a recombinatorial zone encoding extracellular matrix-

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binding proteins in Streptococcus pyogenes. Infect Immun 2002,
70(3):1159-1167.
7. Aziz RK, Kotb M: Rise and persistence of global M1T1 clone of
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