Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets.

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection-representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments-specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets. IMPORTANCE Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance-the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.

Taxonomic revision of the Australian arid zone lizards Gehyra variegata and G. montium (Squamata, Gekkonidae) with description of three new species.

The taxonomy of central Australian populations of geckos of the genus Gehyra has been uncertain since chromosomal studies carried out in the 1970s and 1980s revealed considerable heterogeneity and apparently independent patterns of morphological and karyotypic diversity. Following detailed molecular genetic studies, species boundaries in this complex have become clearer and we here re-set the boundaries of the three named species involved, G. variegata (Duméril & Bibron, 1836), G. montium Storr, 1982, and G. nana King, 1982, and describe three new species. Two of the new species, G. moritzi and G. pulingka, include populations formerly assigned to either G. montium or G. nana Storr, 1982, while the third, G. versicolor, includes all of the eastern Australian populations formerly assigned to G. variegata.

Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys.

MOTIVATION: When working with non-model organisms, few if any species-specific markers are available for phylogenetic, phylogeographic and population studies. Therefore, researchers often try to adapt markers developed in distantly related taxa, resulting in poor amplification and ascertainment bias in their target taxa. Markers can be developed de novo and anonymous nuclear loci (ANL) are proving to be a boon for researchers seeking large numbers of fast-evolving, independent loci. However, the development of ANL can be laboratory intensive and expensive. A workflow is described to identify suitable low-copy anonymous loci from high-throughput shotgun sequences, dramatically reducing the cost and time required to develop these markers and produce robust multilocus datasets. RESULTS: By successively removing repetitive and evolutionary conserved sequences from low coverage shotgun libraries, we were able to isolate thousands of potential ANL. Empirical testing of loci developed from two reptile taxa confirmed that our methodology yields markers with comparable amplification rates and nucleotide diversities to ANLs developed using other methodologies. Our approach capitalizes on next-generation sequencing technologies to enable the development of phylogenetic, phylogeographic and population markers for taxa lacking suitable genomic resources.