Peptoclostridium
(Clostridium) difficile (commonly
nicknamed “Cdiff”) is a spore-forming bacterium that causes serious
healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were
responsible for more than 29,000 deaths in 20111. Antibiotic resistance and recurrent
infections are common problems in treating Cdiff infections.
The BioCyc collection currently contains twelve Clostridium/Peptoclostridium difficile databases; all of them can be easily
accessed from a new home page, http://cdifficile.biocyc.org/. We chose the database for a strain
commonly used in the laboratory, Peptoclostridium
difficile 630, for a pilot project to update the genome annotation and to add
literature curation.
The genome of P.
difficile 630 was first sequenced in 2006, and was re-annotated in
2011. Genome sequences of several
additional strains have become available since then. Using the Pathway Tools software, we initially imported an
updated genome annotation from RefSeq into the existing “tier 3” P. difficile 630 database. We then added further annotation
updates that had been captured in the MicroScope database at the Pasteur
Institute.
Following the annotation update, we reviewed the
complement of metabolic pathways that had been automatically imported into the
database when it was built by PathoLogic. It is generally easier to delete a pathway that should not be
present in a database than to find and import or newly create a pathway that
should be present. By design,
PathoLogic therefore over-predicts the occurrence of pathways. Thus, much of the review work resulted
in deletion of metabolic pathways that are not in fact present in P. difficile 630. For further improvements to the
metabolic pathway complement that is present in the database, we encourage and
appreciate the advice of experts in the field.
The annotation updates described above led to an increase
from 45 to 136 genes that had been labeled with an “Evidence 1a/1b” note, i.e.,
“Function experimentally demonstrated in the studied strain/species”. This set of genes provided an
attractive target for initial literature curation. We therefore reviewed the publications cited in the genome
annotations, complemented by our own literature searches in PubMed. This resulted in the addition of
experimental evidence codes to 67 proteins and addition of a total of 80 GO
terms to 41 individual proteins in the database that is currently available as
part of the BioCyc collection. In
addition, we summarized the experimental literature for proteins with known
function and added all appropriate literature references that were found in
PubMed.
Exciting
Developments in Cdiff Research
A method for reliably creating targeted knockout
mutations was recently used for a high-throughput screen to define all
essential genes and genes involved in sporulation2. The work was done with strain R20291
and could therefore not be directly incorporated into the database for strain
630. We have generated a BioCyc SmartTable
that lists all genes that were unambiguously identified as essential:
http://cdifficile.biocyc.org/group?id=biocyc13-1553-3652814396
http://cdifficile.biocyc.org/group?id=biocyc13-1553-3652814396
After the release of our current version of BioCyc, a
publication on genome resequencing of P.
difficile 630 appeared3. This new version of the genome has not yet been incorporated into
BioCyc.
What’s in a
Name?
Clostridium
difficile has recently been reclassified
and renamed to Peptoclostridium difficile4. It will not be easy, and may prove to
be impossible, to change the habitual usage of its long-established name by the
community. So why was this necessary? After all, “Clostridium difficile” is already a mouthful, as evidenced by the
invention of the “Cdiff” moniker; and “Peptoclostridium
difficile” clearly does not make the pronunciation of the name any easier.
The classification of an organism into a particular
genus or species should imply a certain amount of relatedness, both in
evolutionary and phenotypic terms. It turns out that organisms that historically carry the genus name Clostridium are very diverse. Phylogenetic trees based on 16S rRNA
and conserved proteins (e.g. ribosomal proteins) have enabled improved
classification within this group. To better represent the diversity of organisms, distinguishing between
the “true” Clostridium genus and more
distantly related organisms within the family Clostridiaceae, certain groups of organisms received new genus
names. The new “Pepto” prefix derives
from the Greek for “digestion” or “able to digest”. Maybe everyone can get used to “Pdiff”?
References:
1
Lessa et al. (2015), N Engl J Med 372:825-34, PMID 25714160
2 Dembek et al. (2015),
MBio 6(2):e02383, PMID 25714712
3 Riedel et al.
(2015), Genome Announc 3(2):e00276-15, PMID 25858846
4
Yutin and Galperin (2013), Environ Microbiol 15(10):2631-41, PMID 23834245
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