Supporting the delivery of Information Management and BIM in Ireland: Learnings from Selected International Regions

The Executive Summary introduction the report recommendations for Build Digital with respect to information management and the use of BIM as a critical vehicle of innovation to unlock improved project outcomes in construction

Phytoremediation as a Tool to Remove Drivers of Antimicrobial Resistance in the Aquatic Environment

Antimicrobials, heavy metals, and biocides are ubiquitous contaminants frequently detected in water bodies across the globe. These chemicals are known as drivers of antimicrobial resistance (AMR), as these chemicals can select for resistance. Tools and processes, are therefore, needed to remove these chemicals from the environment to tackle the environmental component of AMR. Aquatic phytoremediation is a nature-inspired green solution to remove contaminants from the environment. Phytoremediation utilises macrophytes’ ability to sequester and degrade chemical pollutants in aquatic environments. In this review, we define the problem statement by highlighting the presence of AMR drivers in the aquatic environment. We also provide an in-depth review of phytoremediation to tackle chemical pollution by evaluating mechanisms for the removal and degradation of chemicals. This review identifies potential hyper-accumulators and understands how plant species and chemical composition can influence the potential for accumulation. Different pollutants accumulate to different extents in a range of aquatic macrophytes. Therefore, the combined use of floating, submerged and emergent plants would facilitate the optimum removal of AMR drivers considered in this review. A suggested configuration includes Helianthus annus around the edge of a contaminated site, followed by a belt of submerged plants (Myriophyllum aquaticum) and a bed of floating plants (e.g., Lemna species) together with the hyperaccumulator, Phragmites australis. Whilst phytoremediation offers a promising option to treat contaminated water, several critical knowledge gaps still exist. The effect of co-exposure to contaminants on the accumulation potential of plants and the fate of antibiotic-resistant genes and bacteria during the phytoremediation process are highlighted in this review. Based on this understanding, targeted areas for future research are proposed

The co-transfer of plasmid-borne colistin-resistant genes mcr-1 and mcr-3.5, the carbapenemase gene blaNDM-5 and the 16S methylase gene rmtB from Escherichia coli

We found an unusual Escherichia coli strain with resistance to colistin, carbapenem and amikacin from sewage. We therefore characterized the strain and determined the co-transfer of the resistance determinants. Whole genome sequencing was performed using both Illumina HiSeq X10 and MinION sequencers. Short and long reads were subjected to de novo hybrid assembly. Sequence type, antimicrobial resistance genes and plasmid replicons were identified from the genome sequences. Phylogenetic analysis of all IncHI2 plasmids carrying mcr-1 available in GenBank was performed based on core genes. Conjugation experiments were performed. mcr-3.5 was cloned into E. coli DH5α. The strain belonged to ST410, a type with a global distribution. Two colistin-resistant genes, mcr-1.1 and mcr-3.5, a carbapenemase gene blaNDM-5, and a 16S methylase gene rmtB were identified on different plasmids of IncHI2(ST3)/IncN, IncP, IncX3 and IncFII, respectively. All of the four plasmids were self-transmissible and mcr-1.1, mcr-3.5, blaNDM-5 and rmtB were transferred together. mcr-1-carrying IncHI2 plasmids belonged to several sequence types with ST3 and ST4 being predominant. MIC of colistin (4 μg/ml) for DH5α containing mcr-3.5 was identical to that containing the original mcr-3 variant. In conclusion, carbapenem resistance, colistin resistance and high-level aminoglycoside resistance can be transferred together even when their encoding genes are not located on the same plasmid. The co-transfer of multiple clinically-important antimicrobial resistance represents a particular challenge for clinical treatment and infection control in healthcare settings. Isolates with resistance to both carbapenem and colistin are not restricted to a given sequence type but rather are diverse in clonal background, which warrants further surveillance. The amino acid substitutions of MCR-3.5 have not altered its activity against colistin.</p

Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse <i>Escherichia coli</i> lineages

Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ~700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions. IMPORTANCE Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. Using experimental evolution with diverse E. coli lineages and a clinical multidrug resistance plasmid, we show that although plasmids drove unique evolutionary paths per lineage, there was a surprising degree of convergence in the functions targeted by mutations across lineages, dominated by metabolic functions. Remarkably, these same metabolic functions show higher evolutionary rates in MDR-lineages in nature and in some cases, like anaerobic metabolism, their expression is directly manipulated by the plasmid. Interactions with other mobile elements resident in the genomes accelerated adaptation by disrupting genes and regulatory sequences that they inserted into. Beyond their role in horizontal gene transfer, plasmids are an important selective force driving the evolution of bacterial genomes and core cellular functions

Intrinsic tuning of poly (styrene-butadiene-styrene) (SBS) based self-healing dielectric elastomer actuators with enhanced electromechanical properties

The electromechanical properties of a thermoplastic styrene-butadiene-styrene (SBS) dielectric elastomer was intrinsically tuned by chemical grafting with polar organic groups. Methyl thioglycolate (MG) reacted with the butadiene block via a one-step thiol-ene ‘click’ reaction under UV at 25°C. The MG grafting ratio reached 98.5 mol% (with respect to the butadiene alkenes present) within 20 minutes and increased the relative permittivity to 11.4 at 103 Hz, with a low tan δ. The actuation strain of the MG grafted SBS dielectric elastomer actuator was ten times larger than the SBS-based actuator, and the actuation force was four times greater than SBS. The MG grafted SBS demonstrated an ability to achieve both mechanical and electrical self-healing. The electrical breakdown strength recovered to 15% of its original value, and the strength and elongation at break recovered by 25% and 21%, respectively, after three days. The self-healing behaviour was explained by the introduction of polar MG groups that reduce viscous loss and strain relaxation. The weak CH/π bonds through the partially charged (δ+) groups adjacent to the ester of MG and the δ- centre of styrene enable polymer chains to reunite and recover properties. Intrinsic tuning can therefore enhance the electromechanical properties of dielectric elastomers and provides new actuator materials with self-healing mechanical and dielectric properties

Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in <i>Escherichia coli</i>

Multidrug-resistant Escherichia coli is a leading cause of global mortality. Transfer of plasmids carrying genes encoding beta-lactamases, carbapenamases, and colistin resistance between lineages is driving the rising rates of hard-to-treat nosocomial and community infections. Multidrug resistance (MDR) plasmid acquisition commonly causes transcriptional disruption, and while a number of studies have shown strain-specific fitness and transcriptional effects of an MDR plasmid across diverse bacterial lineages, fewer studies have compared the impacts of different MDR plasmids in a common bacterial host. As such, our ability to predict which MDR plasmids are the most likely to be maintained and spread in bacterial populations is limited. Here, we introduced eight diverse MDR plasmids encoding resistances against a range of clinically important antibiotics into E. coli K-12 MG1655 and measured their fitness costs and transcriptional impacts. The scale of the transcriptional responses varied substantially between plasmids, ranging from &gt;650 to &lt;20 chromosomal genes being differentially expressed. However, the scale of regulatory disruption did not correlate significantly with the magnitude of the plasmid fitness cost, which also varied between plasmids. The identities of differentially expressed genes differed between transconjugants, although the expression of certain metabolic genes and functions were convergently affected by multiple plasmids, including the downregulation of genes involved in L-methionine transport and metabolism. Our data show the complexity of the interaction between host genetic background and plasmid genetic background in determining the impact of MDR plasmid acquisition on E. coli.IMPORTANCE: The increase in infections that are resistant to multiple classes of antibiotics, including those isolates that carry carbapenamases, beta-lactamases, and colistin resistance genes, is of global concern. Many of these resistances are spread by conjugative plasmids. Understanding more about how an isolate responds to an incoming plasmid that encodes antibiotic resistance will provide information that could be used to predict the emergence of MDR lineages. Here, the identification of metabolic networks as being particularly sensitive to incoming plasmids suggests the possible targets for reducing plasmid transfer. </p

The coexistence of two ^blaNDM-5 genes on an IncF plasmid as revealed by nanopore sequencing

ABSTRACT In a carbapenem-resistant Escherichia coli clinical isolate of sequence type 167, two copies of bla NDM-5 were found on a 144,225-bp IncF self-transmissible plasmid of the F36:A4:B − type. Both bla NDM-5 genes were located in 11,065-bp regions flanked by two copies of IS 26 . The two regions were identical in sequence but were present at different locations on the plasmid, suggesting a duplication of the same region. This study highlights the complex genetic contexts of bla NDM-5 . </jats:p

Mapping gene-by-gene single-nucleotide variation in 8,535 <i>Mycobacterium tuberculosis</i> genomes:a resource to support potential vaccine and drug development

Tuberculosis is an infectious disease caused by the bacterium Mycobacterium tuberculosisMycobacterium bovi