EP0313 NOVEL TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY
DEVELOPMENT OF AN ONLINE DATABASE AND WEB APPLICATION FOR ANALYSIS OF SNP TYPING DATA OF ACINETOBACTER BAUMANNII Alexander Yu. Fedintsev
Eugene A. Sheck
Ivan V. Trushin
Andrey A. Avramenko
Institute of Antimicrobial Chemotherapy (IAC) Smolensk State Medical University (SSMU) Kirova Str. 46A, Smolensk, 214019 Russian Federation * E-mail:
[email protected]
Mikhail V. Edelstein*
26th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 9 - 12 April 2016, Amsterdam, Netherlands
Introduction and Purpose
Example screenshots of SNPTAb web application
Example diagrams constructed from SNPTAb data using PHYLOViZ visualyser Minimum spanning tree diagram of A. baumannii SNP types (nodes) coloured by type of acquired carbapenemases
Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variations in closely related microbial strains or isolates. Highly informative sets of SNPs can be selected from large datasets of DNA sequences, such as entire multi-locus sequence typing (MLST) databases or whole genome sequence (WGS) databases, and can be successfully used to type strains and identify specific clones or genetic lineages of microbial pathogens.
OXA-23-like OXA-40-like OXA-58-like OXA-23-like OXA-40-like
We previously reported the development of high-throughput SNP typing method for Acinetobacter baumannii, one of the most troublesome nosocomial pathogens (E. Sheck et al. P0079, ECCMID 2015). Our aim was to create an open-access database of A. baumannii SNP profiles and a web-based application to assist researchers in analysis of SNP-typing data and to enable instant linking of SNP profiles with the available MLST and whole-genome sequence data.
Methods The SQL database and software platform (called SNPTAb) were created to contain user-defined (open) sets of SNPs from chromosomal loci (gltA, recA, cpn60, gyrB, gdhB, rpoD, fusA, pyrG, rplB, rpoB and gpi) used in the University of Oxford and the Institute Pasteur MLST schemes. The SNPTAb database also contains individual isolates data (e.g. source, geographical origin, date of isolation, resistance to carbapenems, production of carbapenemases etc.). To allow comparison of SNP-, MLST- and genome-typing data, an automatic scheduled retrieval system of MLST allele sequences from pubMLST database (http://pubmlst.org/abaumannii/) and Acinetobacter WGSs from NCBI database (http://www.ncbi.nlm.nih.gov/genome/) was set up. This system employs a machine-learning algorithm for extracting nucleotide sequences of MLST loci from WGSs, which are deposited in SNPTAb database and are made available for instant querying of SNP-profiles.
goeBURST diagram of major A. baumannii clonal complexes by Oxford scheme. Sequence types (nodes) are coloured by matching SNP profiles
The web application was built using Angular JS 1.4.9, ASP.Net Web API 2 and Leaflet.
Results
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Database content. As of March 2016, the SNPTAb database contains SNP profiles of 580 Acinetobacter isolates. These include 505 records of 21 informative SNPs of clinical isolates collected between 2002 and 2015 in various regions of Russia, Belarus and Kazakhstan, and 75 records of 4612 SNPs (all nucleotide positions of 11 MLST loci) of international isolates imported from A. baumannii PubMLST database. The SNPTAb database is manually curated and allows input of isolate data and SNP profiles using the provided template file.
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The SNPTAb database also contains 1352 nucleotide sequences of MLST loci extracted from A. baumannii WGSs available in GenBank. These data, as well as data on nucleotide sequences of MLST alleles of established sequence types (STs) by Oxford and Pasteur schemes, are updated from respective online databases on a weekly basis.
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Web application. The SNPTAb web application (http://snptab.antibiotic.ru:3353/) is offered as a free service that provides the following functionality: ► allows user to define a set of SNP positions from any MLST loci used in the University of Oxford and the Institute Pasteur typing schemes; ► calculates the theoretical Simpson’s index of diversity for the defined SNP set with respect to the existing MLST schemes; ► accepts the input of multiple SNP profiles of isolates and finds matching or similar STs in MLST databases, genome sequences in GenBank, and isolates profiles in SNPTAb database; ► groups related SNP profiles using a defined threshold of Hamming distance; ► displays geographic distribution of isolates matching the defined SNP profiles on an interactive map; ► generates data files with SNP profiles and isolates data for external analysis using PHYLOViZ Software (http://www.phyloviz.net/) and goeBURST clustering algorithm.
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SNP Profiles: Profile_1 Profile_50 Profile_71 Profile_18 Profile_20 Profile_36 Profile_61 Profile_9 Profile_26 Profile_15 Profile_63 Profile_49 Profile_58 Profile_60 Profile_17
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Conclusions SNPTAb is an online application that allows analysis, storage and exchange of SNP typing data of A. baumannii. The functionality of the developed application can be extended in the future to include SNP sets derived from multiple genomic loci, not included in the MLST schemes, and to examine SNP profiles of other bacterial species.
