The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.

Titanium (Ti) has been the most widely used orthopedic implant in the past decades. However, their inert surface often leads to insufficient osteointegration of Ti implant. To solve this issue, two bioactive Mg(OH)2 films were developed on Ti surfaces using hydrothermal treatment (Ti-M1# and Ti-M2#). The Mg(OH)2 films showed nano-flake structures: sheets on Ti-M1# with a thickness of 14.7 ± 0.7 nm and a length of 131.5 ± 2.9 nm, and on Ti-M2# with a thickness of 13.4 ± 2.2 nm and a length of 56.9 ± 5.6 nm. Both films worked as Mg ions releasing platforms. With the gradual degradation of Mg(OH)2 films, weakly alkaline microenvironments will be established surrounding the modified implants. Benefiting from the sustained release of Mg ions, nanostructures, and weakly alkaline microenvironments, the as-prepared nano-Mg(OH)2 coated Ti showed better in vitro and in vivo osteogenesis. Notably, Ti-M2# showed better osteogenesis than Ti-M1#, which can be ascribed to its smaller nanostructure. Moreover, whole genome expression analysis was applied to study the osteogenic mechanism of nano-Mg(OH)2 films. For both coated samples, most of the genes related to ECM-receptor interaction, focal adhesion, and TGF-β pathways were upregulated, indicating that these signaling pathways were activated, leading to better osteogenesis. Furthermore, cells cultured on Ti-M2# showed markedly upregulated BMP-4 gene expression, suggesting that the nanostructure with Mg ion release ability can better activate BMP-4 related signaling pathways, resulting in better osteogenesis. Nano-Mg(OH)2 films demonstrated a superior osteogenesis and are promising surface modification strategy for orthopedic applications.

Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome. We identified the whole genome study approaches and sorted them according to the omics technology types (genomics, proteomics, and so on) and hierarchy. Thirty-four studies from over 90 publications were sorted into 10 omics groups: DNA level, transcriptomics, proteomics, interactomics, metabolomics, epigenomics, miRNomics/ncRNomics, phenomics, environmental omics, and pharmacogenomics. We suggest here modifications of terminology for study approaches, which share the same acronyms such as EWAS for epigenome-wide association and environment-wide association studies, and MWAS for methylome-wide association and metabolome-wide association studies. Taken together, our study presented here provides the first systematic review and analyses of whole genome approaches and presents a baseline for further controlled terminology development, with a view to a new taxonomy for omics and multi-omics studies in the future. Finally, we call for greater dialogue and collaboration across diverse omics knowledge domains and applications, for example, across plants, animals, clinical medicine, and ecology.