many of these aspects cannot be properly addressed yet, we describe
a number of steps and related computational tools that when
properly combined in a pipeline may support the discovery of
new, effective antigens in a bacterial group of interest.
2 Materials
Biological databases mentioned below, widely used and integrated
in reverse vaccinology pipelines, are provided in Table 1. This table
also lists free and open-source tools and software packages that can
be used along with the in silico antigen discovery process. The
utility of some of these tools in specific stages of the process is
detailed in corresponding sections of the methodology, together
with hints for their proper use. A note is also given on whether
these tools can process datasets in a high-throughput manner and
whether they can be implemented in a computational pipeline.
3 Methods
The strategy we propose here is divided into four main stages
(Fig. 1): data acquisition, a subtractive proteomic approach and
the steps of filtering and prioritizing candidates. The strategy starts
with the selection of representative genome sequences for an
organism (species) or a group of organisms and their subsequent
analysis. Subtractive proteomics along with classical reverse vaccinology is applied for screening core protein antigens conserved
across circulating strains in pathogenic species. To refine the set of
selected candidates, we finally look at proteins that are more likely
to be effective antigens by combining a set of criteria.
3.1 Selection
of Species and Strains
and Acquisition
of Complete Genome
Nucleotide/Protein
Sequences
This is one of the most important steps in the process. The strains
selected should be representative for the global pathogen population. Missing a part of this population may result in a vaccine
ineffective against some pathogen variants. When the genome of
the pathogen is very similar to that of a nonpathogenic organism
(e.g., Burkholderia pseudomallei vs. Burkholderia thailandensis,
N. meningitidis vs. Neisseria lactamica, Enterohemorrhagic Escherichia coli strains vs. nonpathogenic E. coli strains) different organisms or organism subgroups can be included in the analysis in order
to identify antigens specific for the pathogenic set. In some cases,
these antigens will be pathogenicity or virulence factors themselves,
and their immunoblocking (e.g., by a therapeutic vaccine) can be a
valid therapeutic strategy [70].
Genome sequences and annotation data for bacterial species are
available in multiple statuses according to the quality of the assembly: Complete (all chromosomes are present and gapless and there
Bacterial Pan-Proteome-Based Antigen Discovery
47
a number of steps and related computational tools that when
properly combined in a pipeline may support the discovery of
new, effective antigens in a bacterial group of interest.
2 Materials
Biological databases mentioned below, widely used and integrated
in reverse vaccinology pipelines, are provided in Table 1. This table
also lists free and open-source tools and software packages that can
be used along with the in silico antigen discovery process. The
utility of some of these tools in specific stages of the process is
detailed in corresponding sections of the methodology, together
with hints for their proper use. A note is also given on whether
these tools can process datasets in a high-throughput manner and
whether they can be implemented in a computational pipeline.
3 Methods
The strategy we propose here is divided into four main stages
(Fig. 1): data acquisition, a subtractive proteomic approach and
the steps of filtering and prioritizing candidates. The strategy starts
with the selection of representative genome sequences for an
organism (species) or a group of organisms and their subsequent
analysis. Subtractive proteomics along with classical reverse vaccinology is applied for screening core protein antigens conserved
across circulating strains in pathogenic species. To refine the set of
selected candidates, we finally look at proteins that are more likely
to be effective antigens by combining a set of criteria.
3.1 Selection
of Species and Strains
and Acquisition
of Complete Genome
Nucleotide/Protein
Sequences
This is one of the most important steps in the process. The strains
selected should be representative for the global pathogen population. Missing a part of this population may result in a vaccine
ineffective against some pathogen variants. When the genome of
the pathogen is very similar to that of a nonpathogenic organism
(e.g., Burkholderia pseudomallei vs. Burkholderia thailandensis,
N. meningitidis vs. Neisseria lactamica, Enterohemorrhagic Escherichia coli strains vs. nonpathogenic E. coli strains) different organisms or organism subgroups can be included in the analysis in order
to identify antigens specific for the pathogenic set. In some cases,
these antigens will be pathogenicity or virulence factors themselves,
and their immunoblocking (e.g., by a therapeutic vaccine) can be a
valid therapeutic strategy [70].
Genome sequences and annotation data for bacterial species are
available in multiple statuses according to the quality of the assembly: Complete (all chromosomes are present and gapless and there
Bacterial Pan-Proteome-Based Antigen Discovery
47