Multidrug-Resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016-2017.

Multidrug- and colistin-resistant Salmonella enterica serotype 4,[5],12:i:- sequence type 34 is present in Europe and Asia. Using genomic surveillance, we determined that this sequence type is also endemic to Australia. Our findings highlight the public health benefits of genome sequencing-guided surveillance for monitoring the spread of multidrug-resistant mobile genes and isolates.

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 identification requires the sub-culture of signaled blood culture broth with identification available only after colonies on solid agar have matured. MALDI-TOF MS is a reliable, rapid method for identification of the majority of clinically relevant bacteria when applied to colonies on solid media.

Computational inference of grammars for larger-than-gene structures from annotated gene sequences.

Motivation: 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.

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

Background: 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.