Abstract
BackgroundIdentification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data.ResultsRaw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale.ConclusionsIn comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.
Highlights
Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing
Size reduction of probe database To improve the performance of Reads2Type, we reduced the size of the probe database via three consecutive steps, which consisted in removing 1) all the 16S rRNA probes that were unique to Enterobacteriaceae, as these have low species identification accuracy, 2) the duplicates that resulted from chopping conserved regions of different strains, and 3) the consecutive probes
The Enterobacteriaceae species prediction accuracy is higher for the case of gyrase subunit B (gyrB) genes than 16S and dnaJ genes; gyrB was selected as the marker genes for unique probes
Summary
Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. Healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Identification of bacteria is important for making accurate clinical diagnoses and for narrowing down the list of potential antibiotics that may be used against the pathogens, and for quickly initiating a medical therapy for treating the patient. WGS has recently started showing its potential as a cost-effective and rapid solution for medical diagnostics and outbreak prevention. Via WGS one can identify species and strain [3, 4] and antibiotic resistance gene [5], as well as make predictions of pathogenicity [6] and identification of novel genes. The issue to be faced will be how to handle and analyze the large amounts of sequencing data to produce useful biological and epidemiological information, for example regarding the identity of pathogens
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