rapid-identification-gram-negative-bacteria-from-blood-culture-broth

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional ...

Westmead hospital

Gene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The algorithm was applied to the discovery of gene cassettes associated with integrons. The discovery and annotation of antibiotic resistance genes in such cassettes is essential for effective monitoring of antibiotic resistance patterns and formulation of public health antibiotic prescription policies.

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar.

Larger than gene structures (LGS) are DNA segments that include at least one gene and often other segments such as inverted repeats and gene promoters. Mobile genetic elements (MGE) such as integrons are LGS that play an important role in horizontal gene transfer, primarily in Gram-negative organisms. Known LGS have a profound effect on organism virulence, antibiotic resistance and other properties of the organism due to the number of genes involved. Expert-compiled grammars have been shown to be an effective computational representation of LGS, well suited to automating annotation, and supporting de novo gene discovery. However, development of LGS grammars by experts is labour intensive and restricted to known LGS. Objectives: This study uses computational grammar inference methods to automate LGS discovery. We compare the ability of six algorithms to infer LGS grammars from DNA sequences annotated with genes and other short sequences. We compared the predictive power of learned grammars against an expert-developed grammar for gene cassette arrays found in Class 1, 2 and 3 integrons, which are modular LGS containing up to 9 of about 240 cassette types.

Article	Year
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. BMC bioinformatics\| PubMed ID: 19735578	2009
Computational inference of grammars for larger-than-gene structures from annotated gene sequences. Bioinformatics (Oxford, England)\| PubMed ID: 21258064	2011
The simultaneous detection and differentiation of Staphylococcus species in blood cultures using fluorescence in situ hybridization: a comment. Medical principles and practice : international journal of the Kuwait University, Health Science Centre\| PubMed ID: 21577005	2011

Jon R. Iredell

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