Lessons Learnt from Monitoring the Etna Volcano Using an IoT Sensor Network through a Period of Intense Eruptive Activity.

This paper describes the successes and failures after 4 years of continuous operation of a network of sensors, communicating nodes, and gateways deployed on the Etna Volcano in Sicily since 2019, including a period of Etna intense volcanic activity that occurred in 2021 and resulted in over 60 paroxysms. It documents how the installation of gateways at medium altitude allowed for data collection from sensors up to the summit craters. Most of the sensors left on the volcanic edifice during winters and during this period of intense volcanic activity were destroyed, but the whole gateway infrastructure remained fully operational, allowing for a very fruitful new field campaign two years later, in August 2023. Our experience has shown that the best strategy for IoT deployment on very active and/or high-altitude volcanoes like Etna is to permanently install gateways in areas where they are protected both from meteorological and volcanic hazards, that is mainly at the foot of the volcanic edifice, and to deploy temporary sensors and communicating nodes in the more exposed areas during field trips or in the summer season.

ConnecSenS, a Versatile IoT Platform for Environment Monitoring: Bring Water to Cloud.

Climate change is having an increasingly rapid impact on ecosystems and particularly on the issue of water resources. The Internet of Things and communication technologies have now reached a level of maturity that allows sensors to be deployed more easily on sites to monitor them. The communicating node based on LoRaWAN technology presented in this article is open and allows the interfacing of numerous sensors for designing long-term environmental monitoring systems of isolated sites. The data integration in the cloud is ensured by a workflow driving the storage and indexing of data, allowing a simple and efficient use of the data for different users (scientists, administration, citizens) through specific dashboards and extractions. This article presents this infrastructure through environmental monitoring use cases related to water resources.

CEBA: A Data Lake for Data Sharing and Environmental Monitoring.

This article presents a platform for environmental data named "Environmental Cloud for the Benefit of Agriculture" (CEBA). The CEBA should fill the gap of a regional institutional platform to share, search, store and visualize heterogeneous scientific data related to the environment and agricultural researches. One of the main features of this tool is its ease of use and the accessibility of all types of data. To answer the question of data description, a scientific consensus has been established around the qualification of data with at least the information "when" (time), "where" (geographical coordinates) and "what" (metadata). The development of an on-premise solution using the data lake concept to provide a cloud service for end-users with institutional authentication and for open data access has been completed. Compared to other platforms, CEBA fully supports the management of geographic coordinates at every stage of data management. A comprehensive JavaScript Objet Notation (JSON) architecture has been designed, among other things, to facilitate multi-stage data enrichment. Data from the wireless network are queried and accessed in near real-time, using a distributed JSON-based search engine.

Antibiotic resistance profile and molecular characterization of Staphylococcus aureus strains isolated in hospitals in Kabul, Afghanistan.

The aim of this study was to investigate the molecular features and the antibiotic resistance profile of 98 clinical Staphylococcus aureus isolates collected during 6 months in two hospitals of Kabul, Afghanistan. For all isolates, antimicrobial resistance patterns were determined by the disc diffusion method (including methicillin resistance which was detected using cefoxitin). The presence of the mecA/mecC genes was detected by PCR. Strains were then extensively characterized using microarray analysis. Of the 98 S. aureus isolates, methicillin-resistant S. aureus (MRSA) prevalence was high at 66.3%. Antibiotic susceptibility testing also revealed a high resistance rate to penicillin (100%), erythromycin (66.3%), ciprofloxacin (55.1%), and cotrimoxazole (40.8%). Resistance to tobramycin was detected in 25.5%, to gentamicin in 16.3%, to chloramphenicol in 34.7%, and to doxycycline in 23.5% of the isolates. All the MRSA isolates were mecA-positive and none of them harbored mecC. Isolates were grouped into twelve clonal complexes and twenty-seven distinct clones. The most frequently detected clones were the Southwest Pacific clone (CC30-MRSA-IV PVL+) (21/65 MRSA, 32.3%), the CC22-MRSA-IV TSST-1+ clone (11/65 MRSA, 16.9%), and the Bengal Bay clone (ST772-MRSA-V PVL+) (11/65 MRSA, 16.9%). The PVL genes were found in 59.2% (46/65 MRSA and 12/33 methicillin-susceptible S. aureus, MSSA) and tst1 gene in 16.3% of isolates. This molecular study highlights the high prevalence of MRSA and the large genetic diversity of the S. aureus isolates circulating and detected in two hospitals of Kabul, with the presence of multiple virulence and antibiotic resistance genes.

Performance of the Hologic Panther Fusion® MRSA Assay for the nasal screening of methicillin-sensitive and methicillin-resistant Staphylococcus aureus carriage.

Staphylococcus aureus (SA) nasal carriage screening is usually based on either culture or molecular biology. The aim of the study was to evaluate the performance of the Panther Fusion® MRSA Assay (PF) that proposes a complete automation of the molecular screening for MSSA and MRSA carriage. Four hundred thirty-four nasal samples collected on ESwab™ were screened using PF. Results were compared with standard culture on BBL™ CHROMagar™ Staph aureus and chromID® MRSA agar. Discordant results were analyzed with additional techniques: Xpert SA Nasal Complete on GeneXpert (GX), culture on selective agar after 24 h in broth enrichment, and, if necessary, characterization of mec gene and SCCmec cassette using DNA microarray. The PF presented an overall agreement of 97.5% for SA detection and 97.9% for MRSA detection. Furthermore, 7.1% (31/434) of the samples were SA-negative in primary culture but SA-positive using PF and GX, confirming the greater sensitivity of molecular tests compared with culture. Of note, 4 out of 30 MRSA-positive samples were not detected due to an atypical SCCmec cassette, while 2 samples were falsely detected as MRSA due to co-colonization with a MSSA drop-out strain and a methicillin-resistant coagulase-negative staphylococcal strain. Considering all results, the PF instrument appears as a reliable and rapid (< 3 h) package for MSSA/MRSA nasal screening. This technology using random access capability and direct sampling of the primary container is innovative and corresponds therefore to a new step in complete molecular biology automation in bacteriology.

Septic Shock Shapes B Cell Response toward an Exhausted-like/Immunoregulatory Profile in Patients.

Septic shock is accompanied by the development of immune dysfunctions whose intensity and duration are associated with increased risk of secondary infections and mortality. Although B lymphocytes play a pivotal role in the immune response to infections, no comprehensive exploration of circulating B cell status has been performed during the immunosuppressive phase of septic shock. Thus, our aim was to extensively characterize the phenotype and function of B cells in septic shock, including IL-10 production. Circulating B lymphocyte phenotype and function were evaluated by flow cytometry on fresh whole blood and after ex vivo stimulation in adult septic shock patients sampled at day 1, 3, and 6 after the onset of shock. The circulating B cell number was reduced in septic shock patients, whereas the B cell proportion among total lymphocytes was increased. The remaining circulating B lymphocytes presented with decreased MHC class II expression and increased CD21low CD95high exhausted-like phenotype but showed no change in maturation status. Circulating B cell functions were markedly altered after sepsis with reduced ex vivo activation and proliferation capacities. Finally, B cell response after septic shock was characterized by a clear plasmacytosis and an increased IL-10 production in remaining B cells from patients after ex vivo stimulation. During the sepsis-induced immunosuppression phase, B cell response is altered and is oriented toward an exhausted-like/immunoregulatory profile. Further studies are now needed to confirm the immunoregulatory properties of B lymphocytes and evaluate their role in sepsis-induced immunosuppression.

From Sensor to Cloud: An IoT Network of Radon Outdoor Probes to Monitor Active Volcanoes.

While radon in soil gases has been identified for decades as a potential precursor of volcanic eruptions, there has been a recent interest for monitoring radon in air on active volcanoes. We present here the first network of outdoor air radon sensors that was installed successfully on Mt. Etna volcano, Sicily, Italy in September 2019. Small radon sensors designed for workers and home dosimetry were tropicalized in order to be operated continuously in harsh volcanic conditions with an autonomy of several months. Two stations have been installed on the south flank of the volcano at ~3000 m of elevation. A private network has been deployed in order to transfer the measurements from the stations directly to a server located in France, using a low-power wide-area transmission technology from Internet of Things (IoT) called LoRaWAN. Data finally feed a data lake, allowing flexibility in data management and sharing. A first analysis of the radon datasets confirms previous observations, while adding temporal information never accessed before. The observed performances confirm IoT solutions are very adapted to active volcano monitoring in terms of range, autonomy, and data loss.

How things changed during the COVID-19 pandemic's first year: A longitudinal, mixed-methods study of organisational resilience processes among healthcare workers.

COVID-19 had a huge impact on healthcare systems globally. Institutions, care teams and individuals made considerable efforts to adapt their practices. The present longitudinal, mixed-methods study examined a large sample of healthcare institution employees in Switzerland. Organisational resilience processes were assessed by identifying problematic real-world situations and evaluating how they were managed during three phases of the pandemic's first year. Results highlighted differences between resilience processes across the different types of problematic situations encountered by healthcare workers. Four configurations of organisational resilience were identified depending on teams' performance and ability to adapt over time: "learning from mistakes", "effective development", "new standards" and "hindered resilience". Resilience trajectories differed depending on professional categories, hierarchical status and the problematic situation's perceived severity. Factors promoting or impairing organisational resilience are discussed. Findings highlighted the importance of individuals', teams' and institutions' meso- and micro-level adaptations and macro-level actors' structural actions.

Adaptation of Staphylococcus aureus in a Medium Mimicking a Diabetic Foot Environment.

Staphylococcus aureus is the most prevalent pathogen isolated from diabetic foot infections (DFIs). The purpose of this study was to evaluate its behavior in an in vitro model mimicking the conditions encountered in DFI. Four clinical S. aureus strains were cultivated for 16 weeks in a specific environment based on the wound-like medium biofilm model. The adaptation of isolates was evaluated as follows: by Caenorhabditis elegans model (to evaluate virulence); by quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) (to evaluate expression of the main virulence genes); and by Biofilm Ring test® (to assess the biofilm formation). After 16 weeks, the four S. aureus had adapted their metabolism, with the development of small colony variants and the loss of ß-hemolysin expression. The in vivo nematode model suggested a decrease of virulence, confirmed by qRT-PCRs, showing a significant decrease of expression of the main staphylococcal virulence genes tested, notably the toxin-encoding genes. An increased expression of genes involved in adhesion and biofilm was noted. Our data based on an in vitro model confirm the impact of environment on the adaptation switch of S. aureus to prolonged stress environmental conditions. These results contribute to explore and characterize the virulence of S. aureus in chronic wounds.

The Impact of Nursing Staffs' Working Conditions on the Quality of Care Received by Older Adults in Long-Term Residential Care Facilities: A Systematic Review of Interventional and Observational Studies.

BACKGROUND: Little documentation exists on relationships between long-term residential care facilities (LTRCFs), staff working conditions and residents' quality of care (QoC). Supporting evidence is weak because most studies examining this employ cross-sectional designs. METHODS: Systematic searches of twelve bibliographic databases sought experimental and longitudinal studies, published up to May 2021, focusing on LTRCF nursing staff's working conditions and the QoC they provided to older adults. RESULTS: Of the 3577 articles identified, 159 were read entirely, and 11 were retained for inclusion. Higher nursing staff hours worked per resident per day (HPRD) were associated with significant reductions in pressure sores and urinary tract infections. Overall staff qualification levels and numbers of RNs had significant positive influences on QoC. CONCLUSIONS: To the best of our knowledge, this systematic review is the first to combine cohort studies with a quasi-experimental study to explore associations between LTRCF nursing staff's working conditions and older adult residents' QoC. Human factors (including HPRD, staff turnover, skill mix, staff ratios) and the specific working contribution of RNs had overwhelmingly significant influences on QoC. It seems essential that LTRCF supervisory and decision-making bodies should promote optimal working conditions for nursing staff because these have such a direct impact on residents' QoC.

Case Report: Arthroscopic "Debridement Antibiotics and Implant Retention" With Local Injection of Personalized Phage Therapy to Salvage a Relapsing Pseudomonas Aeruginosa Prosthetic Knee Infection.

Bacteriophages are viruses that specifically target bacteria. They are considered to have a high potential in patients with prosthetic joint infection (PJI), as they have a synergistic anti-biofilm activity with antibiotics. We report here the case of an 88-year-old man (63 kg) with relapsing Pseudomonas aeruginosa prosthetic knee infection. The patient had severe alteration of the general status and was bedridden with congestive heart failure. As prosthesis explantation and/or exchange was not feasible, we proposed to this patient the use of phage therapy to try to control the disease in accordance with the local ethics committee and the French National Agency for Medicines and Health Products Safety (ANSM). Three phages, targeting P. aeruginosa, were selected based on their lytic activity on the patient's strain (phagogram). Hospital pharmacist mixed extemporaneously the active phages (initial concentration 1 ml of 1 × 1010 PFU/ml for each phage) to obtain a cocktail of phages in a suspension form (final dilution 1 × 109 PFU/ml for both phages). Conventional arthroscopy was performed and 30 cc of the magistral preparation was injected through the arthroscope (PhagoDAIR procedure). The patient received intravenous ceftazidime and then oral ciprofloxacin as suppressive antimicrobial therapy. Under this treatment, the patient rapidly improved with disappearance of signs of heart failure and pain of the left knee. During the follow-up of 1 year, the local status of the left knee was normal, and its motion and walking were unpainful. The present case suggests that the PhagoDAIR procedure by arthroscopy has the potential to be used as salvage therapy for patients with P. aeruginosa relapsing PJI, in combination with suppressive antimicrobial therapy. A Phase II clinical study deserves to be performed to confirm this hypothesis.

Association of characteristics of tampon use with menstrual toxic shock syndrome in France.

BACKGROUND: Menstrual tampons are widely used in western countries. Indirect evidence suggests that tampon misuse could be associated with an increased risk of menstrual toxic shock syndrome (MTSS). The aim of this study was to determine what characteristics of tampon use are associated with increased risk of menstrual toxic shock syndrome (MTSS). METHODS: A nationwide, case-control study in France, was conducted with women that use tampons with MTSS diagnoses according to the CDC diagnostic criteria (n = 55, from January 2011, to December 2017) and a control group of women with no MTSS history (n = 126, from February to December 2017). Information regarding tampon use during a 6-month period was collected. Associations between tampon use and MTSS were assessed using logistic regression models stratified by residential area. FINDINGS: Compared to controls, women diagnosed with MTSS more frequently reported maximum tampon wear of >6 h (62% vs. 41%; P = 0.02), overnight tampon use (77% vs. 54%; P = 0.006), and neither read nor followed tampon instructions in case of reading (65% vs. 42%; P = 0.006). In univariate analysis, MTSS risk was two-fold higher with tampon use for >6 consecutive hours (odds ratio, 2.3 [95% CI, 1.2-4.5]), and three-fold higher with tampon use during sleep for >8 h (odds ratio, 3.2 [95% CI, 1.4-7.7]). In multivariate logistic regression analysis, only maximum tampon use for >6 h (odds ratio, 2.03 [95% CI, 1.04-3.98]), and neither read nor followed the tampon instructions in case of reading (odds ratio, 2.25 [95% CI, 1.15-4.39]) were independently associated with MTSS. INTERPRETATION: Our study suggests that the risk of MTSS was associated with using tampons for more than 6 h, overnight tampon use during sleep, and neither read nor followed tampon insertion instructions in case of reading. FUNDING: LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon within the programme "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR).

Phage Therapy as Adjuvant to Conservative Surgery and Antibiotics to Salvage Patients With Relapsing S. aureus Prosthetic Knee Infection.

Objectives: To report the management of three consecutive patients with relapsing Staphylococcus aureus prosthetic knee infection (PKI) for whom explantation was not feasible who received a phage therapy during a "Debridement Antibiotics and Implant Retention" (DAIR) procedure followed by suppressive antimicrobial therapy. Methods: Each case was discussed individually in our reference center and with the French National Agency (ANSM). The lytic activity of three phages targeting S. aureus, which was produced with a controlled and reproducible process, was assessed before surgery (phagogram). A hospital pharmacist extemporaneously assembled the phage cocktail (1 ml of 1 × 1010 PFU/ml for each phage) as "magistral" preparation (final dilution 1 × 109 PFU/ml), which was administered by the surgeon directly into the joint, after the DAIR procedure and joint closure (PhagoDAIR procedure). Results: Three elderly patients were treated with the PhagoDAIR procedure. Phagograms revealed a high susceptibility to at least two of the three phages. During surgery, all patients had poor local conditions including pus in contact to the implant. After a prolonged follow-up, mild discharge of synovial fluid persisted in two patients, for whom a subsequent DAIR was performed showing only mild synovial inflammation without bacterial persistence or super-infection. The outcome was finally favorable with a significant and impressive clinical improvement of the function. Conclusions: The PhagoDAIR procedure has the potential to be used as salvage for patients with relapsing S. aureus PKI, in combination with suppressive antibiotics to avoid considerable loss of function. This report provides preliminary data supporting the setup of a prospective multicentric clinical trial.

Author Correction: Complex ecological interactions of Staphylococcus aureus in tampons during menstruation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Unexpected categories at risk of S. aureus nasal carriage among hospital workers.

OBJECTIVES: Thirty percent of the general population are Staphylococcus aureus nasal carriers. It has been shown that this increases with repeated contact with patients, but it is not known whether all categories of healthcare workers are at equal risk of carriage. We aimed to explore S. aureus nasal carriage among healthcare professionals. METHODS: Prospective study conducted in two French university hospitals in 2014 and 2016. Volunteers were screened for S. aureus nasal carriage. Profession and hygiene habits were collected. Based on the results of this initial study, a second study focused on semi-skilled workers and biomedical equipment technicians (BETs) only; participants were given education on the basic rules of hygiene, then re-screened three months later. RESULTS: In the initial study, 38.8% of the 436 participants were detected as nasal carriers. There was a significant difference in nasal carriage according to professional category (p < 0.0001); the lowest was found among administrative agents (17.3%), followed by healthcare providers (37.4%), laboratory technicians (37.6%). The greatest proportion was found among semi-skilled workers and BETs (52.9%). Spa-typing ruled out the hypothesis of a single clone dissemination among colleagues. After the three-month hygiene awareness campaign, all re-screened individuals remained positive, and with their respective initial strain. CONCLUSIONS: To the best of our knowledge we report here for the first time that semi-skilled workers and BETs are specifically more at risk of S. aureus nasal colonisation. This striking finding urges hospital hygiene departments to evaluate this specific professional category and implement strategies to improve hygiene awareness.

Demographic fluctuation of community-acquired antibiotic-resistant Staphylococcus aureus lineages: potential role of flimsy antibiotic exposure.

Community-acquired (CA)- as opposed to hospital acquired- methicillin-resistant Staphylococcus aureus (MRSA) lineages arose worldwide during the 1990s. To determine which factors, including selective antibiotic pressure, govern the expansion of two major lineages of CA-MRSA, namely "USA300" in Northern America and "European ST80" in North Africa, Europe and Middle-East, we explored virulence factor expression, and fitness levels with or without antibiotics. The sampled strains were collected in a temporal window representing various steps of the epidemics, reflecting predicted changes in effective population size as inferred from whole-genome analysis. In addition to slight variations in virulence factor expression and biofilm production that might influence the ecological niches of theses lineages, competitive fitness experiments revealed that the biological cost of resistance to methicillin, fusidic acid and fluoroquinolones is totally reversed in the presence of trace amount of antibiotics. Our results suggest that low-level antibiotics exposure in human and animal environments contributed to the expansion of both European ST80 and USA300 lineages in community settings. This surge was likely driven by antibiotic (ab)use promoting the accumulation of antibiotics as environmental pollutants. The current results provide a novel link between effective population size increase of a pathogen and a selective advantage conferred by antibiotic resistance.

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation.

Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons' microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.

Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes.

Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate hypotheses regarding the host range of B. burgdorferi lineages based on population genomic data.