Background: Increasingly sophisticated next-gen technologies have altered the manner in which bacterial and viral pathogens are characterized and have enabled improved phenotype-to-genotype linking. As such, genomes and phenomes can be generated at a rate that vastly outpaces the application of these datasets to medical countermeasure development. In order to manage the vast amount of data produced by such efforts, CRPµTIC has been developed. CRPµTIC is an information management system for the organization, storage, retrieval and display of microbial information from high-throughput phenotypic and genotypic characterization of biodefense pathogens and their near neighbors. This information is integrated with other pertinent strain information that can be used for product development.
Methods and Results: CRPµTIC is both a web-resident database and a low-common denominator process easily adapted by laboratories and enables the capture and central storage of data. CRPµTIC is based on open source software (e.g., PostgreSQL), is portable and has a full complement of strain and assay data administration functions with role-based access to maintain data integrity. CRPµTIC captures key assay- and strain-related data in simple user interfaces, and appends the more detailed instrument-level source files for user download. The various data types include: sample metadata (organism ID, clinical, temporal, geographical and acquisition information); microbiological and biochemical characterization data; genomic data such as PCR, optical mapping, and whole genome sequencing; and finally data on various CRP products developed using these strains. The data are organized in a modular structure (Microbial Data Index (MDI), Microbial Metadata, Analytical Data, and CRP Products) through which the user can quickly navigate and identify records of interest by filtering on strain names and other identifiers (e.g., country of collection). Results can be sorted in various ways, including level of strain characterization. The unique feature of CRPµTIC is that all the information and products pertaining to a given organism are traceable to a single, well characterized microbial source stored in a repository, the Unified Culture Collection (UCC). UCC represents well-characterized microbes accessioned from geographically and temporally divergent sources that are subsequently characterized using a variety of technologies. The data organized in CRPµTIC can be output in the form of an MDI with hyperlinks to the specific analytical data pages that provide additional information on specific assay results. CRPµTIC currently contains over 1400 assay results, over 1300 organisms, over 1000 CRP products and has over 30 assay data types.
Conclusions: CRPµTIC serves as an end-to-end information management solution for microbes - from isolation of an organism all the way to product development. Although CRPµTIC does not offer analytical tools, the user can download the primary data and perform secondary analyses using their own analytical tools to answer specific queries of their interest. Also, the framework of CRPµTIC is easily adaptable to new assay types and is portable to different hosting platforms. CRPµTIC is intended to serve agencies across the USG as a reliable source of information about CRP reference materials and assays for the development of medical countermeasures including diagnostics and therapeutics.
CRPµTIC: Critical Reagents Program Microbial Threat Information CenterA Solution for Organization, Storage, Retrieval and Display of Microbial Data
Tyler Barrus1, Kristin L. Jones2, Danielle Montoya1, Jane Tang1, Mark Wolcott3, Walter Berger1, Michael A. Smith2 , Shanmuga Sozhamannan2
1Noblis, 3150 Fairview Park Drive South, Falls Church, VA 22042-4504, USA | 2Critical Reagents Program, Medical Countermeasure Systems, 1564 Freedman Drive, Fort Detrick, MD 21702-5041, USA | 3United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5041, USA
Abstract Concept
NoblisMr. Walter [email protected](703) 610-2509noblis.org
CRPMs. Kristin JonesDr. Shanmuga [email protected](301) 619-2277http://www.jpeocbd.osd.mil/packs/Default.aspx?pg=1220
Stats Contact
0
50
100
150
200
250
300
350
Other
Lacto
bacillu
s
Enteroc
occu
s
Arenav
irus
Neisse
ria
Coxiell
a
Ebolavir
us
Streptoc
occu
s
Flaviv
irus
Orthop
oxvir
us
Alphavir
us
Clostrid
ium
Pasteu
rella
Staphy
lococ
cus
Esche
richia
Influe
nza v
irus
Brucella
Yersi
nia
Burkho
lderia
Franc
isella
Bacillu
s0
50
100
150
200
250
300
350
Whole
Genom
e Seq
uenc
ing (W
GS) - Viru
s
Whole
Genom
e Seq
uenc
ing (W
GS) - Bac
teria
Vitek 2
(Sus
ceptib
ility)
Vitek 2
(Iden
tifica
tion)
Standard
PCR
Real T
ime (
Quanti
tative
) PCR
Purity
Phage
Susce
ptibility
Phage
Search
Tool
(PHAST)
Optical
Map
Multiple
Loci
VNTR Ana
lysis
(MLV
A)
MAGPIX (Immun
oass
ay)
Fatty
Acid M
ethyl
Ester (F
AME)
Electro
chem
ilumine
scen
ce (E
CL)
Colony
Morp
holog
y and
Grow
th
Cell Stai
ns
Canon
ical S
NPs (ca
nSNPs)
Biolog
(Phe
notyp
ic Micr
oarra
y)
Biolog
(Orga
nism Id
entifi
catio
n)
Bioche
mical Te
sts
Antibiot
ic Sus
ceptib
ility (M
IC)
16s R
NA Seque
ncing
Number of Strains by Genus Number of Strains by Analytical Data Type
SFAF 2015, Santa Fe, NM
Number of AnalyticalData Types by Genus
Number of Productsby Group
0
100
200
300
400
500
Others
Alphavir
us
Esche
richia
Brucella
Yersi
nia
Burkho
lderia
Franc
isella
Bacillu
s0
50
100
150
200
250
300
350
Polymera
se C
hain
Reacti
ons (
PCR)
Later
al Flo
w Immun
oass
ays (
LFI)
Genom
ics (G
EN)
Electro
chem
ilumine
scen
ce (E
CL)
Antige
ns (A
G)
Antibod
ies (A
B)
BSL 3
UnknownBSL 4
BSL 2BSL 1
Applications