Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals : focus on carbapenem resistance genes and genes associated with bacteria causing hospital-acquired infections

Background: Wastewater-based monitoring represents a useful tool for antibiotic resist-ance surveillance. Aim: To investigate the prevalence and abundance of antibiotic resistance genes (ARGs) in hospital wastewater over time. Methods: Wastewater from two hospitals in Finland (HUS1 and HUS2) was monitored weekly for nine weeks (weeks 25-33) in summer 2020. A high-throughput real-time poly-merization chain reaction (HT-qPCR) system was used to detect and quantify 216 ARGs and genes associated with mobile genetic elements (MGEs), integrons, and bacteria causing hospital-acquired infections (HAIs), as well as the 16S rRNA gene. Data from HT-qPCR were analysed and visualized using a novel digital platform, ResistApp. Eight carbapenem resistance genes (blaGES, blaKPC, blaVIM, blaNDM, blaCMY, blaMOX, blaOXA48, and blaOXA51) and three genes associated with bacteria causing HAIs (Acinetobacter bau-mannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were studied. Findings: There was a significantly higher number of ARGs at both hospitals in weeks 27-30 (174-191 genes) compared to other sampling weeks (151-171 genes). Our analyses also indicated that the two hospitals, which used different amounts of antibiotics, had significantly different resistance gene profiles. Carbapenem resistance genes were more prevalent and abundant in HUS1 than HUS2. Across both hospitals, blaGES and blaVIM were the most prevalent and abundant. There was also a strong positive association between blaKPC and K. pneumoniae in HUS1 wastewater. Conclusion: Routine wastewater-based monitoring using ResistApp can provide valuable information on the prevalence and abundance of ARGs in hospitals. This helps hospitals understand the spread of antibiotic resistance in hospitals and identify potential areas for intervention. (c) 2021 The Authors. Published by Elsevier Ltd on behalf of The Healthcare Infection Society. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Peer reviewe

Phase Diagram for Charge Density Waves in a Magnetic Field

The influence of an external magnetic field on a quasi one-dimensional system with a charge density wave (CDW) instability is treated within the random phase approximation which includes both CDW and spin density wave correlations. We show that the CDW is sensitive to both orbital and Pauli effects of the field. In the case of perfect nesting, the critical temperature decreases monotonously with the field, and the wave vector of the instability starts to shift above some critical value of magnetic field. Depending on the ratio between the spin and charge coupling constants and on the direction of the applied magnetic field, the wave vector shift is either parallel ($CDW_x$ order) or perpendicular ($CDW_y$ order) to the most conducting direction. The $CDW_x$ order is a field dependent linear combination of the charge and spin density waves and is sensible only to the Pauli effect. The wave vector shift in $CDW_y$ depends on the interchain coupling, but the critical temperature does not. This order is affected by the confinement of the electronic orbits. By increasing the relative strength of the orbital effect with respect to the Pauli effect, one can destroy the $CDW_y$, establishing either a $CDW_x$, or a $CDW_0$ (corresponding to perfect nesting wave vector). We also show that by increasing the imperfect nesting parameter, one passes from the regime where the critical temperature decreases with the field to the regime where it is initially enhanced by the orbital effect and eventually suppressed by the Pauli effect. For a bad nesting, the quantized phases of the field-induced CDW appear.Comment: 30 pages (LaTeX) + 15 figure

Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil.

Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity ( nifH -amplicon sequencing), abundance (qPCR) and functional capacity (15N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg-1 day-1 and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH -harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH -harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant

Suppression of a charge density wave ground state in high magnetic fields: spin and orbital mechanisms

The charge density wave (CDW) transition temperature in the quasi-one dimensional (Q1D) organic material of (Per)$_2$Au(mnt)$_2$ is relatively low (TCDW = 12 K). Hence in a mean field BCS model, the CDW state should be completely suppressed in magnetic fields of order 30 - 40 T. To explore this possibility, the magnetoresistance of (Per)$_2$Au(mnt)$_2$ was investigated in magnetic fields to 45 T for 0.5 K < T < 12 K. For fields directed along the Q1D molecular stacking direction, TCDW decreases with field, terminating at about ~ 37 T for temperatures approaching zero. Results for this field orientation are in general agreement with theoretical predictions, including the field dependence of the magnetoresistance and the energy gap, $\Delta_{CDW}$. However, for fields tilted away from the stacking direction, orbital effects arise above 15 T that may be related to the return of un-nested Fermi surface sections that develop as the CDW state is suppressed. These findings are consistent with expectations that quasi-one dimensional metallic behavior will return outside the CDW phase boundary.Comment: 12 pages, 5 figure

Comparing the Bacterial Diversity of Acute and Chronic Dental Root Canal Infections

This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic) or chronic (asymptomatic) apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs) (at 3% divergence) belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%), Fusobacteria (17%) and Bacteroidetes (13%), while in chronic infections the dominant were Firmicutes (59%), Bacteroidetes (14%) and Actinobacteria (10%). Members of Fusobacteria were much more prevalent in acute (89%) than in chronic cases (50%). The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165) of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic). This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections

Nitrate respiration in the hydrothermal vent tubeworm Riftia pachyptila

THE vestimentiferan tubeworm Riftia pachyptila is found around hydrothermal vent areas in the deep sea. Intracellular bacterial chemoautotrophic symbionts use the oxidation of sulphide from the effluent of the vents as an energy source for CO2 fixation. They apparently provide most or all of the nutritional requirements for their gutless hosts1–5. This kind of symbiosis has since been found in many other species from various other phyla from other habitats6–9. Here we present results that the bacteria of R. pachyptila may cover a significant fraction of their respiratory needs by the use of nitrate in addition to oxygen. Nitrate is reduced to nitrite, which may be the end product (nitrate respiration)10 or it may be further reduced to nitrogen gas (denitrification)11. This metabolic trait may have an important role in the colonization of hypoxic habitats in general by animals with this kind of symbiosis

Using indirect methods to constrain symbiotic nitrogen fixation rates : a case study from an Amazonian rain forest

© The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biogeochemistry 99 (2010): 1-13, doi:10.1007/s10533-009-9392-y.Human activities have profoundly altered the global nitrogen (N) cycle. Increases in anthropogenic N have had multiple effects on the atmosphere, on terrestrial, freshwater and marine ecosystems, and even on human health. Unfortunately, methodological limitations challenge our ability to directly measure natural N inputs via biological N fixation (BNF)—the largest natural source of new N to ecosystems. This confounds efforts to quantify the extent of anthropogenic perturbation to the N cycle. To address this gap, we used a pair of indirect methods—analytical modeling and N balance—to generate independent estimates of BNF in a presumed hotspot of N fixation, a tropical rain forest site in central Rondônia in the Brazilian Amazon Basin. Our objectives were to attempt to constrain symbiotic N fixation rates in this site using indirect methods, and to assess strengths and weaknesses of this approach by looking for areas of convergence and disagreement between the estimates. This approach yielded two remarkably similar estimates of N fixation. However, when compared to a previously published bottom-up estimate, our analysis indicated much lower N inputs via symbiotic BNF in the Rondônia site than has been suggested for the tropics as a whole. This discrepancy may reflect errors associated with extrapolating bottom-up fluxes from plot-scale measures, those resulting from the indirect analyses, and/or the relatively low abundance of legumes at the Rondônia site. While indirect methods have some limitations, we suggest that until the technological challenges of directly measuring N fixation are overcome, integrated approaches that employ a combination of model-generated and empirically-derived data offer a promising way of constraining N inputs via BNF in natural ecosystems.We acknowledge and are grateful for financial support from the Andrew W. Mellon Foundation (C.C. and B.H.), the National Science Foundation (NSF DEB-0515744 to C.C. and A.T. and DEB-0315656 to C.N.), and the NASA LBA Program (NCC5-285 to C.N.)