Retrospective genome-oriented analysis reveals low transmission rate of multidrug-resistant Pseudomonas aeruginosa from contaminated toilets at a bone marrow transplant unit.

BACKGROUND: Prevention of toilet-to-patient transmission of multidrug-resistant Pseudomonas aeruginosa (MDR PA) poses management-related challenges at many bone marrow transplant units (BMTUs). AIM: To conduct a longitudinal retrospective analysis of the toilet-to-patient transmission rate for MDR PA under existing infection control (IC) measures at a BMTU with persistent MDR PA toilet colonization. METHODS: The local IC bundle comprised: (1) patient education regarding IC; (2) routine patient screening; (3) toilet flushing volume of 9 L; (4) bromination of toilet water tanks, and (5) toilet decontamination using hydrogen peroxide. Toilet water was sampled periodically between 2016 and 2021 (minimum every three months: 26 intervals). Upon MDR PA detection, disinfection and re-sampling were repeated until ≤3 cfu/100 mL was reached. Whole-genome sequencing (WGS) was performed retrospectively on all available MDR PA isolates (90 out of 117 positive environmental samples, 10 out of 14 patients, including nine nosocomial). FINDINGS: WGS of patient isolates identified six sequence types (STs), with ST235/CT1352/FIM-1 and ST309/CT3049/no-carbapenemase being predominant (three isolates each). Environmental sampling consistently identified MDR PA ST235 (65.5% ST235/CT1352/FIM-1), showing low genetic diversity (difference of ≤29 alleles by core-genome multi-locus sequence typing (cgMLST)). This indicates that direct toilet-to-patient transmission was infrequent although MDR PA was widespread (detection on 79 occasions, detection in every toilet). Only three MDR PA patient isolates can be attributed to the ST235/CT1352/FIM-1 toilet MRD PA population over six years. CONCLUSION: Stringent targeted toilet disinfection can reduce the potential risk for MDR PA acquisition by patients.

Whole-genome sequencing reveals two prolonged simultaneous outbreaks involving Pseudomonas aeruginosa high-risk strains ST111 and ST235 with resistance to quaternary ammonium compounds.

OBJECTIVE: Water-bearing systems are known as frequent Pseudomonas aeruginosa (PA) outbreak sources. However, many older buildings continue to have sanitary facilities in high-risk departments such as the ICU. We present two simultaneous prolonged multi-drug-resistant (MDR) PA outbreaks detected at the ICU of a pulmonology hospital, which were resolved by whole-genome sequencing (WGS). METHODS: Outbreak management and investigations were initiated in August 2019 after detecting two patients with nosocomial VIM-2-positive MDR PA. The investigations involved weekly patient screenings for four months and extensive environmental sampling for 15 months. All patient and environmental isolates were collected and analysed by WGS. RESULTS: From April to September 2019, we identified 10 patients with nosocomial MDR PA, including five VIM-2-positive strains. VIM-2-positive strains were also detected in nine sink drains, two toilets, and a cleaning bucket. WGS revealed that of 16 VIM-2-positive isolates, 14 were ST111 that carried qacE, or qacEΔ1 genes, whereas 13 isolates clustered (difference of ≤11 alleles by cgMLST). OXA-2 (two toilets), and OXA-2, OXA-74, PER-1 (two patients, three toilets) qacEΔ1-positive ST235 isolates dominated among VIM-2-negative isolates. The remaining seven PA strains were ST17, ST233, ST273, ST309 and ST446. Outbreak containment was achieved by replacing U-bends, and cleaning buckets, and switching from quaternary ammonium compounds (QUATs) to oxygen-releasing disinfectant products. CONCLUSION: Comprehension and management of two simultaneous MDR PA outbreaks involving the high-risk strains ST111 and ST235 were facilitated by precise control due to identification of different outbreak sources per strain, and by the in-silico detection of high-level QUATs resistance in all isolates.

Concerning emergence of a new vancomycin-resistant Enterococcus faecium strain ST1299/CT1903/vanA at a tertiary university centre in South Germany.

BACKGROUND: vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. AIM: To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions. METHODS: At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data. FINDINGS: Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links. CONCLUSION: A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.

Patients with multi-drug-resistant organisms feel inadequately informed about their status: adverse effects of contact isolation.

BACKGROUND: Contact isolation of patients with multi-drug-resistant organisms (MDROs) is an essential element of infection prevention strategies in hospitals worldwide. However, this practice may be associated with adverse side effects on patients' health and well-being. AIM: This study was the first to assess mental health and well-being variables among isolated patients compared with non-isolated control patients in a German cohort. METHODS: We conducted a matched case-control study among N = 267 patients admitted to a tertiary care teaching hospital in Germany. Their levels of anxiety, depression, loneliness, and dissatisfaction with their hospital experience were assessed using a questionnaire. Additionally, among isolated patients, it was evaluated how well they felt informed about their MDRO status. FINDINGS: In our cohort, patients under contact isolation were significantly more dissatisfied than non-isolated control patients but did not show higher levels of anxiety, depression, and loneliness. A large proportion of patients felt insufficiently informed about their MDRO status. This lack of information was the strongest predictor of dissatisfaction among isolated patients. CONCLUSION: These findings underline the importance of adequate patient communication. It is essential for patients' well-being to receive timely, relevant, and understandable information about the background and consequences of their infection or colonisation with MDROs.

A comparative study of prevalence and spatial distribution of major Anopheline vector fauna in a hyper- and a hypomalaria endemic district of Odisha, India with special reference to onset of first wet season.

The state's retrospective findings indicate the incidence of malaria deaths, which is more during the onset of first monsoon season. Based upon this fact, our objective was to study the distribution pattern of major Anopheles vectors in two endemic districts viz. Kalahandi and Cuttack of Odisha, India that differ significantly according to malariogenic stratification, under the impact of first monsoon shower. A comparative study of vector abundance, predominance, their habitats, resting site preference, impact of abiotic rhythm (light/dark period) on vector distribution, gonotrophic status as well as sporozoite rate was established in a high and a low endemic district of Odisha, when the degree of malaria transmission elevates to its peak level Anopheles culicifacies was found to be predominant in hyperendemic Kalahandi district while Anopheles subpictus was abundant in hypo-endemic Cuttack district. Both primary vector An. culicifacies and the secondary vector An. subpictus mostly prefer CS (Cattle shed) compared to HD (Human dwelling) in Kalahandi district where as there was slight shifting of resting habitat of An. culicifacies from CS to HD in Cuttack district. Anopheles culicifacies prefers to rest on wall besides objects in Kalahandi while no such site preference was observed in Cuttack district. On the other hand, distribution of An. subpictus was highly influenced by the daily rhythm of light/dark cycle (i.e. day and night) in Cuttack. The gonotrophic condition revealed the high tendency of the predominant vectors towards endophilic resting. The sporozoite rate was 0.66% in Kalahandi and nil in Cuttack district. The proper monitoring of vector prevalence and distribution, at least during the peak transmission period can avert a perpetuated upsurge in malaria.

Perennial malaria transmission and its association with rainfall at Kalahandi district of Odisha, Eastern India: A retrospective analysis.

India contributes substantially to global malaria incidents. Vector dynamics is the significant determinant of malaria risk. Hence, knowledge on the interaction between rainfall, malaria cases and malaria vector density can be very useful for controlling malaria transmission. Kalahandi was screened for malaria cases, Anopheline vector density and their temporal relationship with rainfall. Epidemiological data was obtained from National Vector Borne Disease Control Programme, Odisha, India. Three years vector population study was carried out. Rainfall data was obtained from a database maintained by the Govt. of Odisha and was analysed using Univariate ANOVA and Pearson correlation co-efficient tests using R-prog. Malaria was found to be prevalent throughout the year attaining peak between July to August and another peak in December, amidst which the clinical malaria cases being recorded implied highest incidents in the month of July. The results estimated the seasonality of the population of An. culicifacies, An. fluviatilis and An. annularis over the region and determined the influence of rainfall on the vector population dynamics. Simple linear regression analysis suggested that at one month lag monthly rainfall (P=0.0007) was a significant meteorological factor. Rainfall seemed to be one of the best malaria predictors because of its positive correlation with proliferation of malaria cases in conjunction with An. culicifacies density making malaria a serious health issue in Kalahandi.

Perennial malaria transmission and its association with rainfall at Kalahandi district of Odisha, Eastern India: A retrospective analysis

@#India contributes substantially to global malaria incidents. Vector dynamics is the significant determinant of malaria risk. Hence, knowledge on the interaction between rainfall, malaria cases and malaria vector density can be very useful for controlling malaria transmission. Kalahandi was screened for malaria cases, Anopheline vector density and their temporal relationship with rainfall. Epidemiological data was obtained from National Vector Borne Disease Control Programme, Odisha, India. Three years vector population study was carried out. Rainfall data was obtained from a database maintained by the Govt. of Odisha and was analysed using Univariate ANOVA and Pearson correlation co-efficient tests using R-prog. Malaria was found to be prevalent throughout the year attaining peak between July to August and another peak in December, amidst which the clinical malaria cases being recorded implied highest incidents in the month of July. The results estimated the seasonality of the population of An. culicifacies, An. fluviatilis and An. annularis over the region and determined the influence of rainfall on the vector population dynamics. Simple linear regression analysis suggested that at one month lag monthly rainfall (P=0.0007) was a significant meteorological factor. Rainfall seemed to be one of the best malaria predictors because of its positive correlation with proliferation of malaria cases in conjunction with An. culicifacies density making malaria a serious health issue in Kalahandi.

A comparative study of prevalence and spatial distribution of major Anopheline vector fauna in a hyper- and a hypomalaria endemic district of Odisha, India with special reference to onset of first wet season

@#The state’s retrospective findings indicate the incidence of malaria deaths, which is more during the onset of first monsoon season. Based upon this fact, our objective was to study the distribution pattern of major Anopheles vectors in two endemic districts viz. Kalahandi and Cuttack of Odisha, India that differ significantly according to malariogenic stratification, under the impact of first monsoon shower. A comparative study of vector abundance, predominance, their habitats, resting site preference, impact of abiotic rhythm (light/dark period) on vector distribution, gonotrophic status as well as sporozoite rate was established in a high and a low endemic district of Odisha, when the degree of malaria transmission elevates to its peak level Anopheles culicifacies was found to be predominant in hyperendemic Kalahandi district while Anopheles subpictus was abundant in hypo-endemic Cuttack district. Both primary vector An. culicifacies and the secondary vector An. subpictus mostly prefer CS (Cattle shed) compared to HD (Human dwelling) in Kalahandi district where as there was slight shifting of resting habitat of An. culicifacies from CS to HD in Cuttack district. Anopheles culicifacies prefers to rest on wall besides objects in Kalahandi while no such site preference was observed in Cuttack district. On the other hand, distribution of An. subpictus was highly influenced by the daily rhythm of light/dark cycle (i.e. day and night) in Cuttack. The gonotrophic condition revealed the high tendency of the predominant vectors towards endophilic resting. The sporozoite rate was 0.66% in Kalahandi and nil in Cuttack district. The proper monitoring of vector prevalence and distribution, at least during the peak transmission period can avert a perpetuated upsurge in malaria.

Effect of antioxidants supplementation on the quality of Beetal buck semen stored at 4°C.

AIM: An experiment was designed to evaluate the role of Vitamin E and glutathione in improving the seminal parameters during hypothermic storage of liquid semen at 4°C for 72 h. MATERIALS AND METHODS: Thirty-six semen ejaculates were collected by artificial vagina from 6 bucks (Beetal) during the normal reproduction season (September to November) at weekly interval. The samples were centrifuged, and the seminal plasma was removed. The sperm pellet was diluted with Tris-based extender and divided into three groups. Group T1: Control samples without antioxidants, Group T2: Samples supplemented with tocopherol at 3 mM, and Group T3: Samples supplemented with glutathione at 1 mM. The samples were evaluated for progressive motility, percent liveability, percent abnormal spermatozoa, and acrosome integrity after liquid preservation for 0, 24, 48, and 72 h. The level of lipid peroxidation and antioxidant enzymes, namely, glutathione peroxidase (GPx) and superoxide dismutase (SOD) were estimated after liquid preservation for 0 and 72 h. RESULTS: It was observed that, after storage of semen at 4°C up to 72 h, the progressive sperm motility, percent liveability, percent abnormal spermatozoa, and percent intact acrosomes were significantly (p<0.05) higher in group T2 and T3 samples as compared to control. However, the level of lipid peroxidation in T2 and T3 groups was significantly (p<0.05) lower after 72 h of incubation at 4°C. Similarly, GPx and SOD values were significantly (p<0.05) increased in T2 and T3 groups after 72 h of storage at 4°C. CONCLUSION: Thus, it can be concluded that Vitamin E and glutathione supplementation at 3 mM and 1 mM, respectively, while preserving the semen samples at 4°C helped in maintaining the seminal parameters up to 72 h and protected the spermatozoa from oxidative damage.

The importance of international collaboration for rare diseases research: a European perspective.

Over the last two decades, important contributions were made at national, European and international levels to foster collaboration into rare diseases research. The European Union (EU) has put much effort into funding rare diseases research, encouraging national funding organizations to collaborate together in the E-Rare program, setting up European Reference Networks for rare diseases and complex conditions, and initiating the International Rare Diseases Research Consortium (IRDiRC) together with the National Institutes of Health in the USA. Co-ordination of the activities of funding agencies, academic researchers, companies, regulatory bodies, and patient advocacy organizations and partnerships with, for example, the European Research Infrastructures maximizes the collective impact of global investments in rare diseases research. This contributes to accelerating progress, for example, in faster diagnosis through enhanced discovery of causative genes, better understanding of natural history of rare diseases through creation of common registries and databases and boosting of innovative therapeutic approaches. Several examples of funded pre-clinical and clinical gene therapy projects show that integration of multinational and multidisciplinary expertize generates new knowledge and can result in multicentre gene therapy trials. International collaboration in rare diseases research is key to improve the life of people living with a rare disease.

Thermal Resistance of Transferred-Silicon-Nanomembrane Interfaces.

We report measurements of the interfacial thermal resistance between mechanically joined single crystals of silicon, the results of which are up to a factor of 5 times lower than any previously reported thermal resistances of mechanically created interfaces. Detailed characterization of the interfaces is presented, as well as a theoretical model incorporating the critical properties determining the interfacial thermal resistance in the experiments. The results demonstrate that van der Waals interfaces can have very low thermal resistance, with important implications for membrane-based micro- and nanoelectronics.

Coherently embedded Ag nanostructures in Si: 3D imaging and their application to SERS.

Surface enhanced Raman spectroscopy (SERS) has been established as a powerful tool to detect very low-concentration bio-molecules. One of the challenging problems is to have reliable and robust SERS substrate. Here, we report on a simple method to grow coherently embedded (endotaxial) silver nanostructures in silicon substrates, analyze their three-dimensional shape by scanning transmission electron microscopy tomography and demonstrate their use as a highly reproducible and stable substrate for SERS measurements. Bi-layers consisting of Ag and GeOx thin films were grown on native oxide covered silicon substrate using a physical vapor deposition method. Followed by annealing at 800°C under ambient conditions, this resulted in the formation of endotaxial Ag nanostructures of specific shape depending upon the substrate orientation. These structures are utilized for detection of Crystal Violet molecules of 5 × 10(-10) M concentrations. These are expected to be one of the highly robust, reusable and novel substrates for single molecule detection.

Changes in intracellular metabolite pools during growth of adherent MDCK cells in two different media.

In bioprocess engineering, the growth of continuous cell lines is mainly studied with respect to the changes in cell concentration, the resulting demand for substrates, and the accumulation of extracellular metabolites. The underlying metabolic process rests upon intracellular metabolite pools and their interaction with enzymes in the form of substrates, products, or allosteric effectors. Here, we quantitatively analyze time courses of 29 intracellular metabolites of adherent Madin-Darby canine kidney cells during cultivation in a serum-containing medium and a serum-free medium. The cells, which originated from the same pre-culture, showed similar overall growth behavior and only slight differences in their demand for the substrates glucose (GLC), glutamine (GLN), and glutamate (GLU). Analysis of intracellular metabolites, which mainly cover the glycolytic pathway, the citric acid cycle, and the nucleotide pools, revealed surprisingly similar dynamics for both cultivation conditions. Instead of a strong influence of the medium, we rather observed a growth phase-specific behavior in glycolysis and in the lower citric acid cycle. Furthermore, analysis of the lower part of glycolysis suggests the well-known regulation of pyruvate kinase by fructose 1,6-bisphosphate. The upper citric acid cycle (citrate, cis-aconitate, and isocitrate) is apparently uncoupled from the lower part (α-ketoglutarate, succinate, fumarate, and malate), which is in line with the characteristics of a truncated cycle. Decreased adenosine triphosphate and guanosine triphosphate pools, as well as a relatively low energy charge soon after inoculation of cells, indicate a high demand for cellular energy and the consumption of nucleotides for biosynthesis. We finally conclude that, with sufficient availability of substrates, the dynamics of GLC and GLN/GLU metabolism is influenced mainly by the cellular growth regime and regulatory function of key enzymes.

[Orphanet and its consortium: where to find expert-validated information on rare diseases]. / Orphanet et son réseau: où trouver une information validée sur les maladies rares.

There are approximately 6000 rare diseases, and 80% of them are genetic. In Europe, a disease is considered rare when it affects no more than one person in 2000. In France, two to three million people are affected, while nearly 30 million others are affected across Europe (5-8% of the whole European population). The majority of rare diseases are poorly understood by health professionals. Due to the lack of sufficient scientific and medical knowledge, many patients are misdiagnosed, which results in delays in care that can be harmful. Because many rare diseases are often associated with neurological manifestations, the neurologist in his daily practice may often encounter these complex diseases that require special care as well as a multidisciplinary approach. Orphanet is the reference portal for rare diseases. Freely accessible on the Internet, it is a non-profit service officially supported by the French Ministry of Health and the European Commission. Its mission is to keep healthcare professionals and patients informed and, by so doing, it contributes to improvements in the diagnosis and treatment of rare diseases. It is currently the only project that establishes a link between diseases and any published information concerning them, and the appropriate services for patients as well as healthcare professionals. Orphanet is currently the most comprehensive site in terms of referenced and documented data, and it has in just a few years become the global reference portal for rare diseases and orphan drugs for all audiences. Orphanet generates a million page views per month. The site is available in six languages (English, French, Spanish, Italian, German and Portuguese) and offers a range of services, including: an inventory, classification and peer-reviewed encyclopedia of rare diseases along with the associated genes (more than 2000 diseases with neurological manifestations are described); a diagnostic support tool; clinical and emergency guidelines; a directory of specialised services in 37 partner countries; an encyclopedia aimed at the general public; an inventory of orphan drugs; downloadable thematic studies and reports on such subjects as the prevalence of rare diseases, orphan drugs, aids and services for patients; and numerous links to other sources of information. Five to ten new rare diseases are described every month, which represents a major challenge for health professionals in terms of keeping their knowledge up to date. The Orphanet website content is expert-validated and updated continuously to respond in real time.

DC heating induced shape transformation of Ge structures on ultraclean Si(5 5 12) surfaces.

We report the growth of Ge nanostructures and microstructures on ultraclean, high vicinal angle silicon surfaces and show that self-assembled growth at optimum thickness of the overlayer leads to interesting shape transformations, namely from nanoparticle to trapezoidal structures, at higher thickness values. Thin films of Ge of varying thickness from 3 to 12 ML were grown under ultrahigh vacuum conditions on a Si(5 5 12) substrate while keeping the substrate at a temperature of 600 °C. The substrate heating was achieved by two methods: (i) by heating a filament under the substrate (radiative heating, RH) and (ii) by passing direct current through the samples in three directions (perpendicular, parallel and at 45° to the (110) direction of the substrate). We find irregular, more spherical-like island structures under RH conditions. The shape transformations have been found under DC heating conditions and for Ge deposition more than 8 ML thick. The longer sides of the trapezoid structures are found to be along (110) irrespective of the DC current direction. We also show the absence of such a shape transformation in the case of Ge deposition on Si(111) substrates. Scanning transmission electron microscopy measurements suggested the mixing of Ge and Si. This has been confirmed with a quantitative estimation of the intermixing using Rutherford backscattering spectrometry (RBS) measurements. The role of DC heating in the formation of aligned structures is discussed. Although the RBS simulations show the presence of a possible SiO(x) layer, under the experimental conditions of the present study, the oxide layer would not play a role in determining the formation of the various structures that were reported here.

New avian suspension cell lines provide production of influenza virus and MVA in serum-free media: studies on growth, metabolism and virus propagation.

Few suspension cells can be used for vaccine manufacturing today as they either do not meet requirements from health regulatory authorities or do not produce high virus titres. Two new avian designer cell lines (AGE1.CR and AGE1.CR.pIX) that have been adapted to grow in suspension in serum-free medium were evaluated for their potential as host cells for influenza and modified vaccinia Ankara (MVA, wild type) vaccine production. Their metabolism was studied during growth in static (T-flasks) and dynamic cultivation systems (roller bottles, stirred tank reactor, wave bioreactor). High cell concentrations up to 5.8x10(6)cells/mL were obtained with doubling times of 23h for AGE1.CR and 35h for AGE1.CR.pIX, respectively. Both viruses were produced to high titres (3.5 logHA/100 microL for influenza virus, 3.2x10(8)pfu/mL for MVA). Hence, the CR cell lines are an appropriate substrate for pharmaceutical influenza and MVA production.

Formation of aligned nanosilicide structures in a MBE-grown Au/Si(110) system: a real-time temperature-dependent TEM study.

Thin Au films (∼2 nm) were deposited on an Si(110) substrate epitaxially under ultra-high vacuum (UHV) conditions in a molecular beam epitaxy (MBE) system. Real-time in situ transmission electron microscopy (TEM) measurements were carried out at various temperatures (from room temperature to 700 °C), which shows the formation and growth of aligned gold silicide nanorod-like structures. The real-time selected-area electron diffraction patterns show the presence of silicon and unreacted gold at lower temperatures (up to 363 °C), while at higher temperatures only the signature of silicon has been observed. The diffraction analysis from room temperature cooled systems show the presence of gold silicide structures. Around 700 °C, 97% of the nanostructures were found to be aligned nanosilicide-rod-like structures with a longer side of ≈37 nm and aspect ratio of 1.38. For a high temperature annealed system (at 600 °C), selected-area diffraction (SAD) and high resolution lattice (after cooling down to room temperature) confirmed the formation of nano- Au(5)Si(2) structures. The alignment of gold silicide structures has been explained on the basis of lattice matching between the substrate silicon and silicide structures.