High-throughput short sequence typing schemes for pseudomonas aeruginosa and stenotrophomonas maltophilia pure culture and environmental DNA

ABSTRACT: Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Supplementary files

&lt;p&gt;&lt;strong&gt;Bourdin, Benoit et al., 2024 (Disinfection of sink drains to reduce a source of opportunistic pathogens): Supplemental Material&lt;/strong&gt;&lt;/p&gt

Supplementary files

&lt;p&gt;&lt;strong&gt;Bourdin et al., 2024 (Ecology of three opportunistic pathogens in NICU sinks): Supplemental Material&lt;/strong&gt;&lt;/p&gt

Les tiers-lieux en France : quelle place pour les zones hors métropole ?

L’article vise à expliquer la concentration relative des tiers-lieux par zone d’emploi (ZE) sur le territoire français. La recherche internationale s’est focalisée sur les métropoles alors que la cartographie montre que les tiers-lieux y pèsent relativement moins qu’ailleurs. On formule l’hypothèse que les tiers-lieux sont proportionnellement plus nombreux dans les ZE en difficulté économique et/ou enclavées où ils répondent aux besoins spécifiques de nouveaux travailleurs indépendants. Nous réalisons une analyse typologique afin de mettre en évidence dans quelle mesure les caractéristiques territoriales expliquent la localisation des tiers-lieux. Nous montrons que les tiers-lieux ne sont pas exclusivement un phénomène métropolitain et mettons en évidence l’existence de plusieurs France, qu’on interprète à partir d’héritages historiques de longue durée dans une perspective théorique évolutionniste.The article aims to explain the relative concentration of third places by travel-to-work area (TTWA) in France. The literature focuses on metropolises, whereas our mapping shows that third places weigh relatively less in large metro areas than elsewhere, challenging the dominant discourse. We hypothesize that third places are proportionally more numerous in economically depressed and/or landlocked TTWAs where they meet the specific needs of new self-employed workers. We carry out a typological analysis in order to highlight the extent to which spatial features explain the location of third places. We demonstrate that third places are not exclusively a metropolitan phenomenon and stress strong variations within France, which are interpreted from long-term historical legacies in an evolutionary theoretical perspective

Has the geography of collaborative spaces been affected by the pandemic? France as a case study

International audienceThis study investigates the potential devolution of collaborative spaces (CSs) to rural areas during the COVID-19 pandemic and explores the factors driving this shift. Using a geolocalised database of French CSs and employing a spatial Durbin model, we found that the pandemic may have driven CS distribution towards less densely populated regions. Our study highlights the impact of the pandemic on economic landscapes and spatial patterns of shared workspaces, with implications for place-based policies and regional development. The results suggest that supporting CSs in remote areas with longer commuting times and distances can address the urban–rural divide, fostering territorial resilience in the post-pandemic era

Les tiers-lieux en France : quelle place pour les zones hors métropole ?

The article aims to explain the relative concentration of third places by travel-to-work area (TTWA) in France. The literature focuses on metropolises, whereas our mapping shows that third places weigh relatively less in large metro areas than elsewhere, challenging the dominant discourse. We hypothesize that third places are proportionally more numerous in economically depressed and/or landlocked TTWAs where they meet the specific needs of new self-employed workers. We carry out a typological analysis in order to highlight the extent to which spatial features explain the location of third places. We demonstrate that third places are not exclusively a metropolitan phenomenon and stress strong variations within France, which are interpreted from long-term historical legacies in an evolutionary theoretical perspective

A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA

Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole-genome sequencing (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness among patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens. Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within bssA, gabR, and dhaM) distinguished strains with a high level of efficiency. This HiSST scheme was applied to an epidemiological survey of S. marcescens in a neonatal intensive care unit (NICU). In a first case study, a strain responsible for an outbreak in the NICU was found in a sink drain of this unit, by using HiSST scheme and confirmed by WGS. The HiSST scheme was also applied to environmental DNA extracted from sink-environment samples. Diversity of S. marcescens was modest, with 11, 6, and 4 different sequence types (ST) of gabR, bssA, and dhaM loci among 19 sink drains, respectively. Epidemiological relationships among sinks were inferred on the basis of pairwise comparisons of ST profiles. Further research aimed at relating ST distribution patterns to environmental features encompassing sink location, utilization, and microbial diversity is needed to improve the surveillance and management of opportunistic pathogens. IMPORTANCE Serratia marcescens is an important opportunistic human pathogen, often multidrug resistant and involved in outbreaks of nosocomial infections in neonatal intensive care units. Here, we propose a quick and user-friendly method to select the best typing scheme for nosocomial outbreaks in relating environmental and clinical sources. This method, named high-throughput short sequence typing (HiSST), allows to distinguish strains and to explore the diversity profile of nonculturable S. marcescens. The application of HiSST profile analysis for environmental DNA offers new possibilities to track opportunistic pathogens, identify their origin, and relate their distribution pattern with environmental features encompassing sink location, utilization, and microbial diversity. Adaptation of the method to other opportunistic pathogens is expected to improve knowledge regarding their ecology, which is of significant interest for epidemiological risk assessment and elaborate outbreak mitigation strategies