Matching Clostridioides difficile strains obtained from shoe soles of healthcare workers epidemiologically linked to patients and confirmed by whole-genome sequencing.

BACKGROUND: The source of transmission of Clostridioides difficile in healthcare institutions is frequently unknown. The aim of this prospective cohort study was to assess the association between strains cultured from patients and shoe soles of healthcare workers (HCWs), as already shown in the operating theatre, but not on general hospital wards in an acute-care institution. METHODS: We conducted a study at a university tertiary care centre in Switzerland. From October 2019 to July 2020, shoe soles of HCWs were cultured for C. difficile twice per shift while taking care of a patient infected with toxigenic C. difficile. Additional risk factors were assessed by interviewing involved HCWs. Patients' faecal samples were processed by routine microbiological methods. Similarity of the HCWs' and patients' strains was determined by whole-genome sequencing (WGS). RESULTS: A total of 103 HCWs exposed to 42 hospitalized patients participated in the study, providing 206 samples. Contamination of shoe soles with C. difficile was detected in 37 samples (17.8%) of HCWs taking care of patients infected with C. difficile. Overall, transmission was suspected by epidemiological link and matching strains demonstrated by WGS in 74%. CONCLUSIONS: HCWs' shoe soles were positive in 17.8% with C. difficile strains linked epidemiologically and confirmed by WGS to infected patients suggesting potential transmission by HCWs' shoe soles. This pilot study provides sufficient evidence to further evaluate this potential mode of healthcare-associated transmission of C. difficile by a larger clinical trial.

Impact of Magnetic Field Configuration on Heat Transport in Stellarators and Heliotrons.

We assess the magnetic field configuration in modern fusion devices by comparing experiments with the same heating power, between a stellarator and a heliotron. The key role of turbulence is evident in the optimized stellarator, while neoclassical processes largely determine the transport in the heliotron device. Gyrokinetic simulations elucidate the underlying mechanisms promoting stronger ion scale turbulence in the stellarator. Similar plasma performances in these experiments suggests that neoclassical and turbulent transport should both be optimized in next step reactor designs.

Demonstration of reduced neoclassical energy transport in Wendelstein 7-X.

Research on magnetic confinement of high-temperature plasmas has the ultimate goal of harnessing nuclear fusion for the production of electricity. Although the tokamak1 is the leading toroidal magnetic-confinement concept, it is not without shortcomings and the fusion community has therefore also pursued alternative concepts such as the stellarator. Unlike axisymmetric tokamaks, stellarators possess a three-dimensional (3D) magnetic field geometry. The availability of this additional dimension opens up an extensive configuration space for computational optimization of both the field geometry itself and the current-carrying coils that produce it. Such an optimization was undertaken in designing Wendelstein 7-X (W7-X)2, a large helical-axis advanced stellarator (HELIAS), which began operation in 2015 at Greifswald, Germany. A major drawback of 3D magnetic field geometry, however, is that it introduces a strong temperature dependence into the stellarator's non-turbulent 'neoclassical' energy transport. Indeed, such energy losses will become prohibitive in high-temperature reactor plasmas unless a strong reduction of the geometrical factor associated with this transport can be achieved; such a reduction was therefore a principal goal of the design of W7-X. In spite of the modest heating power currently available, W7-X has already been able to achieve high-temperature plasma conditions during its 2017 and 2018 experimental campaigns, producing record values of the fusion triple product for such stellarator plasmas3,4. The triple product of plasma density, ion temperature and energy confinement time is used in fusion research as a figure of merit, as it must attain a certain threshold value before net-energy-producing operation of a reactor becomes possible1,5. Here we demonstrate that such record values provide evidence for reduced neoclassical energy transport in W7-X, as the plasma profiles that produced these results could not have been obtained in stellarators lacking a comparably high level of neoclassical optimization.

Does high adherence to contact precautions lead to low in-hospital transmission of multi-drug-resistant micro-organisms in the endemic setting?

BACKGROUND: Conflicting results have been published on the impact of contact precautions (CPs) on reduction of transmission of multi-drug-resistant micro-organisms (MDROs) in the endemic setting. Ambiguous definitions coupled with low adherence partly explain these differences. AIM: We prospectively monitored the level of adherence to CPs and aimed to relate it to in-hospital transmission of MDROs. METHODS: Between January 2016 and March 2018, all patients under CPs underwent continuous monitoring of adherence to CPs by routine on-site visits on days 0, 3 and 7 after initiating CPs using a standardized checklist. The protocol included 10 interventions that were routinely checked such as CP sign at the door as well as wearing of gowns and gloves upon entry to the patient room. Patients requiring CPs were defined as colonized or infected with MDROs (meticillin-resistant Staphylococcus aureus (MRSA), non-Escherichia coli extended-spectrum beta lactamase (ESBL) Enterobacterales, vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative micro-organisms (CRGN)) as well as patients infected with respiratory viruses, norovirus, scabies and hypervirulent strains of Clostridioides difficile. FINDINGS: Overall, data from 13,756 CP records from 1378 visits of 812 patients were analysed. Adherence varied between 93% and 100% for each intervention, except for "separate space for contaminated material" with an adherence of 5.3-6.1%. The incidence of in-hospital transmission during the study period was extremely low for MRSA, VRE, non-E.coli ESBL Enterobacterales and CRGN with 0.00-0.064 cases/1000 patient days. CONCLUSION: High adherence coupled with continuous monitoring of CPs correlated with a very low in-hospital transmission rate. These results indicate that CPs are highly effective if routine monitoring of adherence is implemented.

Unexpected Mycoplasma hominis infection in two renal transplant recipients traced back to the same donor by whole-genome sequencing.

Mycoplasma hominis is a common colonizer of the lower genitourinary tract. Although its clinical relevance for causing urogenital infections in immunocompetent individuals is controversial, this bacterium has been involved in severe invasive infections in allograft recipients. In this report, we describe two cases of M. hominis infection in two young renal transplant recipients within the first month post-transplant. Although at first no epidemiological link between the two cases had been suspected, whole-genome sequencing (WGS) analysis showed that both isolates were identical, highly suggestive of an origin with the common organ donor.

Turbulence Mechanisms of Enhanced Performance Stellarator Plasmas.

We theoretically assess two mechanisms thought to be responsible for the enhanced performance observed in plasma discharges of the Wendelstein 7-X stellarator experiment fueled by pellet injection. The effects of the ambipolar radial electric field and the electron density peaking on the turbulent ion heat transport are separately evaluated using large-scale gyrokinetic simulations. The essential role of the stellarator magnetic geometry is demonstrated, by comparison with a tokamak.

Successful management of a Clostridioides difficile ribotype 027 outbreak with a lean intervention bundle.

BACKGROUND: In a 2015 point-prevalence study, Clostridioides difficile 027, a hypervirulent ribotype, was absent from healthcare institutions in Switzerland. In late 2016, we detected an outbreak of C. difficile infection (CDI) with ribotype 027 occurring across several hospitals in the same hospital network. METHODS: The first cases of CDI due to ribotype 027 triggered an outbreak investigation, including whole genome sequencing (WGS) to identify outbreak strains. FINDINGS: Twenty-eight patients with CDI caused by ribotype 027 between December 2016 and December 2017 were identified, out of which 20 were caused by a single clone. Commonalities among these patients were hospitalization in the same room or on the same ward, receiving care from the same healthcare workers, and shared toilet areas. In addition to the epidemiological links suggesting possible transmission pathways between cases, WGS confirmed the clonality of this C. difficile 027 outbreak. The outbreak was contained by isolation precautions, raising awareness among healthcare workers, harmonizing diagnostic algorithms, and switching to a sporicidal agent for environmental disinfection. Of note, neither default gowning and gloving nor hand washing with water and soap were implemented. CONCLUSION: This C. difficile 027 outbreak was recognized belatedly due to lack of screening for this ribotype in some hospitals, and was contained by a swift response with simple infection prevention measures and adapting the laboratory approach. In order to have a better understanding of C. difficile epidemiology, diagnostic approaches should be standardized, CDI declared notifiable, and longitudinal data on prevalent ribotypes collected in countries where this is not established.

Charge exchange recombination spectroscopy at Wendelstein 7-X.

The Charge Exchange Recombination Spectroscopy (CXRS) diagnostic has become a routine diagnostic on almost all major high temperature fusion experimental devices. For the optimized stellarator Wendelstein 7-X (W7-X), a highly flexible and extensive CXRS diagnostic has been built to provide high-resolution local measurements of several important plasma parameters using the recently commissioned neutral beam heating. This paper outlines the design specifics of the W7-X CXRS system and gives examples of the initial results obtained, including typical ion temperature profiles for several common heating scenarios, toroidal flow and radial electric field derived from velocity measurements, beam attenuation via beam emission spectra, and normalized impurity density profiles under some typical plasma conditions.

Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis.

Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656T (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus Auritidibacter. Auritidibacter ignavus DSM 45359T (=IMMIB L-1656T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359T by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359T had only 97.5 % similarity to that of A. ignavus IMMIB L-1656T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359T had genome of 2.53×106 bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×106 bp with DNA G+C contents of 59.3-59.52 %. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.

Complete Genome Assembly of an Auritidibacter ignavus Isolate Obtained from an Ear Infection in Switzerland and a Comparison to Global Isolates.

We present the whole-genome sequence of an isolate of Auritidibacter ignavus, associated with ear infections. This complete assembly was compared to genomes of four global isolates, which revealed a high diversity within the species.

Stakeholder evaluations of risk interventions for non-potable recycled water schemes: A case study.

Non-potable recycled water schemes can benefit sustainable urban water management through reducing demand for drinking water and mitigating environmental loadings through the provision of advanced wastewater treatment. However, scheme feasibility can be diminished by high capital and operating costs which can be elevated by perceptions of health risks and subsequently overly cautious risk reduction measures. Conversely, a failure to anticipate the risk management expectations of stakeholders can undermine scheme feasibility through insufficient demand for recycled water. The aim of this study was to explore how stakeholders' perceptions and preferences for risk management and recycled water end-uses might influence scheme design. Using a case study scheme in London, four risk management intervention scenarios and six alternative end uses were evaluated using a stochastic PROMETHEE-based method that incorporated quantitative microbial risk assessment and stakeholder criteria weights together with an attitudinal survey of stakeholders' risk perceptions. Through pair-wise criteria judgements, results showed that stakeholders prioritised health risk reductions which led to the more conservative management intervention of adding water treatment processes being ranked the highest. In contrast, responses to the attitudinal survey indicated that the stakeholders favoured maintaining the case study's existing levels of risk control but with more stakeholder engagement. The findings highlighted potential benefits of understanding risk perceptions associated with different design options and contrasting these with multi-criteria model results. Extrapolating from these findings, future research could explore potential challenges and benefits of providing flexibility in scheme designs to appeal to a wider range of stakeholder needs as well as being more adaptable to future social, environmental or economic challenges. The study concludes that contemporary risk management guidance would benefit from more explicitly outlining constructive ways to engage stakeholders in scheme evaluation.

Informing public attitudes to non-potable water reuse - The impact of message framing.

Water reuse is of increasing relevance for water-stressed regions but is often considered a contentious option. Research has shown that providing the public with information about reuse options can impact positively on its acceptability, although such impacts can be confined to specific groups. In this context, there is growing interest in understanding the impact of different forms and mechanisms of communication with the public around reuse. This contribution has investigated the use of video animations to communicate the safety of non-potable recycled water schemes. The aim of this study was to evaluate how different ways of framing messages about the safety of recycled water might impact on public attitudes. Participants were recruited in London (n = 689), UK, and randomly allocated to test and control groups, with the former being exposed to one of four video animations that used different frames to convey messages about recycled water safety. Surveys collected pre- and post-video message responses for dependent variables including the general acceptance of diverse non-potable recycled water uses, risk perceptions and trust. The findings complement existing knowledge on the impacts of different types of messaging on public attitudes to reuse schemes with important evidence for the positive impact of water safety communications framed in terms of compliance with water quality requirements. Contrarily, a positive attitudinal impact was not evident for safety message framed in terms of the selection of water treatment technology to remove contaminants nor in terms of non-potable water risks relative to other every-day risks. The results are of value to water resource planners looking to develop communication resources, as part of more comprehensive public engagement strategies, for improving perceptions of water reuse. Importantly, the findings help isolate the effects of specific message frames, and inform the debate on whether an increased understanding of risk positively or negatively influences willingness to support water reuse schemes.

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

BACKGROUND: Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS: Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS: All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS: This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.

Public responses to water reuse - Understanding the evidence.

Over the years, much research has attempted to unpack what drives public responses to water reuse, using a variety of approaches. A large amount of this work was captured by an initial review that covered research undertaken up to the early 2000s (Hartley, 2006). This paper showcases post-millennium evidence and thinking around public responses to water reuse, and highlights the novel insights and shifts in emphasis that have occurred in the field. Our analysis is structured around four broad, and highly interrelated, strands of thinking: 1) work focused on identifying the range of factors that influence public reactions to the concept of water reuse, and broadly looking for associations between different factors; 2) more specific approaches rooted in the socio-psychological modelling techniques; 3) work with a particular focus on understanding the influences of trust, risk perceptions and affective (emotional) reactions; and 4) work utilising social constructivist perspectives and socio-technical systems theory to frame responses to water reuse. Some of the most significant advancements in thinking in this field stem from the increasingly sophisticated understanding of the 'yuck factor' and the role of such pre-cognitive affective reactions. These are deeply entrenched within individuals, but are also linked with wider societal processes and social representations. Work in this area suggests that responses to reuse are situated within an overall process of technological 'legitimation'. These emerging insights should help stimulate some novel thinking around approaches to public engagement for water reuse.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

BACKGROUND: Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics. RESULTS: Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied. CONCLUSIONS: The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Impurity Transport in a Mixed-Collisionality Stellarator Plasma.

A potential threat to the performance of magnetically confined fusion plasmas is the problem of impurity accumulation, which causes the concentration of highly charged impurity ions to rise uncontrollably in the center of the plasma and spoil the energy confinement by excessive radiation. It has long been thought that the collisional transport of impurities in stellarators always leads to such an accumulation (if the electric field points inwards, which is usually the case), whereas tokamaks, being axisymmetric, can benefit from "temperature screening," i.e., an outward flux of impurities driven by the temperature gradient. Here it is shown, using analytical techniques supported by results from a new numerical code, that such screening can arise in stellarator plasmas, too, and indeed does so in one of the most relevant operating regimes, where the impurities are highly collisional while the bulk plasma is at low collisionality.