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Background: The urinary microbiome, or urobiome, is a novel area of research that has been gaining attention recently, as urine was thought to be sterile for years. There is limited information about the composition of the urobiome in health and disease. The urobiome may be affected by several factors and diseases such as diabetes, a disease that often leads to kidney damage. Thus, we need to understand the role of the urobiome to assess and monitor kidney disease related to diabetes over time., Methods: We conducted a systematic review to summarize knowledge about the urobiome in association with diabetes mellitus and diabetic kidney disease. The search was conducted in several electronic databases until November 2024., Results: Eighteen studies were selected including cross-sectional case-control studies, cross-sectional surveys and one prospective longitudinal study. In total, the urobiome of 1,571 people was sequenced, of which 662 people had diabetes, and of these 36 had confirmed diabetic kidney disease; 609 were healthy individuals, 179 had prediabetes or were at risk of type 2 diabetes mellitus and 121 did not have diabetes but had other comorbidities. Eight studies analysed data from females, one was focused on male data, and the other nine had mixed female-male data. Most of the studies had a small sample size, used voided midstream urine, and used 16S rRNA sequencing., Conclusion: This systematic review summarizes trends seen throughout published data available to have a first baseline knowledge of the urinary microbiome, and its microbiota, in association with diabetes including the decreased richness and α-diversity in urinary microbiota in individuals with diabetes compared to healthy controls and the decreased α-diversity with the evolution of kidney disease independently of the cause., Competing Interests: J.Ä. has served on the advisory boards for Astella, AstraZeneca, and Boehringer Ingelheim and has received lecturing fees from AstraZeneca and Novartis, all unrelated to the present work. This does not alter our adherence to PLOS ONE policies on sharing data and materials. The remaining authors declare no competing interests. There are no patents, products in development or marketed products associated with this research to declare., (Copyright: © 2025 Graells et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: Antimicrobial resistance (AMR) is a multifactorial challenge driven by a complex interplay of proximal drivers, such as the overuse and misuse of antimicrobials and the high burden of infectious diseases, and distal factors, encompassing broader societal conditions such as poverty, inadequate sanitation, and healthcare system deficiencies. However, distinguishing between proximal and distal drivers remains a conceptual challenge., Objectives: We conducted an umbrella review, aiming to systematically map current evidence about proximal and distal drivers of AMR and to investigate their relationships., Methods: Forty-seven reviews were analysed, and unique causal links were retained to construct a causality network of AMR. To distinguish between proximal and distal drivers, we calculated a 'driver distalness index (Di)', defined as an average relative position of a driver in its causal pathways to AMR., Results: The primary emphasis of the literature remained on proximal drivers, with fragmented existing evidence about distal drivers. The network analysis showed that proximal drivers of AMR are associated with risks of resistance transmission (Di = 0.49, SD = 0.14) and antibiotic use (Di = 0.58, SD = 0.2), which are worsened by intermediate drivers linked with challenges of antibiotic discovery (Di = 0.62, SD = 0.07), infection prevention (Di = 0.67, SD = 0.14) and surveillance (Di = 0.69, SD = 0.16). Distal drivers, such as living conditions, access to sanitation infrastructure, population growth and urbanisation, and gaps in policy implementation were development and governance challenges, acting as deep leverage points in the system in addressing AMR., Conclusions: Comprehensive AMR strategies aiming to address multiple chronic AMR challenges must take advantage of opportunities for upstream interventions that specifically address distal drivers., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Introduction: Antimicrobial resistance (AMR) is a challenge to modern medicine. Interventions have been applied worldwide to tackle AMR, but these actions are often not reported to peers or published, leading to important knowledge gaps about what actions are being taken. Understanding factors that influence the implementation of AMR interventions and what factors are relevant in low-middle-income countries (LMICs) and high-income countries (HICs) were the key objectives of this exploratory study, with the aim to identifying which priorities these contexts need., Methods: A questionnaire was used to explore context, characteristics, and success factors or obstacles to intervention success based on participant input. The context was analyzed using the AMR-Intervene framework, and success factors and obstacles to intervention success were identified using thematic analysis., Results: Of the 77 interventions, 57 were implemented in HICs and 17 in LMICs. Interventions took place in the animal sector, followed by the human sector. Public organizations were mainly responsible for implementation and funding. Nine themes and 32 sub-themes emerged as important for intervention success. The themes most frequently reported were 'behavior', 'capacity and resources', 'planning', and 'information'. Five sub-themes were key in all contexts ('collaboration and coordination', 'implementation', 'assessment', 'governance', and 'awareness'), two were key in LMICs ('funding and finances' and 'surveillance, antimicrobial susceptibility testing and preventive screening'), and five were key in HICs ('mandatory', 'multiple profiles', 'personnel', 'management', and 'design')., Conclusion: LMIC sub-themes showed that funding and surveillance were still key issues for interventions, while important HIC sub-themes were more specific and detailed, including mandatory enforcement, multiple profiles, and personnel needed for good management and good design. While behavior is often underrated when implementing AMR interventions, capacity and resources are usually considered, and LMICs can benefit from sub-themes captured in HICs if tailored to their contexts. The factors identified can improve the design, planning, implementation, and evaluation of interventions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Graells, Lambraki, Cousins, Léger, Henriksson, Troell, Carson, Parmley, Majowicz, Wernli and Jørgensen.)

Background: Antimicrobial Resistance (AMR) is a global problem with large health and economic consequences. Current gaps in quantitative data are a major limitation for creating models intended to simulate the drivers of AMR. As an intermediate step, expert knowledge and opinion could be utilized to fill gaps in knowledge for areas of the system where quantitative data does not yet exist or are hard to quantify. Therefore, the objective of this study was to identify quantifiable data about the current state of the factors that drive AMR and the strengths and directions of relationships between the factors from statements made by a group of experts from the One Health system that drives AMR development and transmission in a European context., Methods: This study builds upon previous work that developed a causal loop diagram of AMR using input from two workshops conducted in 2019 in Sweden with experts within the European food system context. A secondary analysis of the workshop transcripts was conducted to identify semi-quantitative data to parameterize drivers in a model of AMR., Main Findings: Participants spoke about AMR by combining their personal experiences with professional expertise within their fields. The analysis of participants' statements provided semi-quantitative data that can help inform a future of AMR emergence and transmission based on a causal loop diagram of AMR in a Swedish One Health system context., Conclusion: Using transcripts of a workshop including participants with diverse expertise across the system that drives AMR, we gained invaluable insight into the past, current, and potential future states of the major drivers of AMR, particularly where quantitative data are lacking., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: EN, TG, and DW have no declarations of interest to report. MC and IAL work for the Public Health Agency of Canada. EJP is engaged in research funded by the Canadian Institutes for Health Research, Natural Sciences and Engineering Research Council, Ontario Ministry of Agriculture, Food and Rural Affairs, the Public Health Agency of Canada, and the Canadian Safety and Security Program. She is currently President of the Board of Directors of the Centre for Coastal Health, president of the Canadian Association of Veterinary Epidemiology and Preventive Medicine, member of the Board of Directors of the McEachran Institute, member of the Advisory Council for Research Directions: One Health, and a member of the Royal Society of Canada One Health Working Group. Prior to February 2019, she was employed by the Public Health Agency of Canada. ALG is engaged in research funded by the Canadian Institutes for Health Research, Natural Sciences and Engineering Research Council, Agriculture Canada, and Canada First Research Excellence Fund. She has served as a consultant for the Ontario Secondary School Teachers Federation (OSSTF) and as an expert witness in legal proceedings related to the SARS-CoV-2 pandemic. She is currently a member of the Board of Directors for the NSERC Emerging Infectious Disease Modelling Network – OMNI network, and Advisory Board Member of the National Collaborating Centre for Infectious Diseases (NCCID). Prior to January 2014, she was employed by the Public Health Agency of Canada. PJGH is partially funded by FORMAS Inequality and the Biosphere Project (2020-00454) and partially by CGIAR Trust Fund. PJGH is a member of the Technical Committee for the BAP Vanguard Climate Action Standard and PJGH and MT act as scientific advisors to the Seafood Business for Ocean Stewardship (SeaBOS) initiative. PJGH was supported by the CGIAR Research Program on Fish Agri-Food Systems (FISH) led by WorldFish and on Climate Change, Agriculture and Food Security (CCAFS) supported by contributors to the CGIAR Trust Fund. PJGH and MT acknowledge the Kjell and Märta Beijer Foundation for supporting this work through the Beijer Institute’s Aquaculture and Sustainable Seafood programme, and the SEAWIN project funded by FORMAS (2016-00227). PJGH is partially funded by FORMAS Inequality and the Biosphere project (2020-00454). AL works for the Swiss Federal Food Safety and Veterinary Office. PSJ was also funded via an ERC starting grant: INFLUX, grant number 101039376. He holds/has held grants as principal or co-investigator, from the following agencies and foundations all related to the topics of social-ecological systems and/or AMR: Swedish Research Council FORMAS, Wallenberg Foundations, IKEA Foundation, Erling Persson Family Foundation. CAC works for Government of Canada at the Public Health Agency of Canada. In that role she has been a subject matter expert for the World Organisation for Animal Health (WOAH) and the World Health Organization (WHO). She is a member of the advisory committee for Animal Health Canada. She has previously been engaged in research funded by the Canadian Institutes for Health Research, Ontario Ministry of Agriculture, Food and Rural Affairs, and the Canadian Safety and Security Program and has been a co-topic editor for two volumes of a Frontiers in Veterinary Science, Research Topic: Antimicrobial Usage in Companion and Food Animals: Methods, Surveys and Relationships with Antimicrobial Resistance in Animals and Humans. SEM is (or has been in the last 5 years) engaged in research grants/contracts funded by the Canadian Institutes for Health Research, the Bill and Melinda Gates Foundation/UK Dept., International Development, the Natural Sciences and Engineering Research Council of Canada, Institut de recherche Robert-Sauvé en santé et en sécurité du travail, Dairy Farmers of Canada Research Funding Program, the World Health Organization, British Columbia Centre for Disease Control, Indian and Northern Affairs Canada, and Ontario Ministry of Agriculture, Food and Rural Affairs. She currently sits on the Editorial Boards of Foodborne Pathogens and Disease, and Epidemiology and Infection, and is a member of the World Health Organization’s Foodborne Disease Burden Epidemiology Reference Group, and she has served as a paid expert on behalf of the Attorney General of Canada in legal proceedings, providing evidence on the public health risks and benefits of unpasteurized milk. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2023 Cousins et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: With AMU projected to increase, South East Asia (SEA) is at high risk of experiencing disproportionate health, social, and economic burdens due to antimicrobial resistance (AMR). Our objective was to identify factors influencing AMR in SEA's food system and places for intervention by integrating the perspectives of experts from the region to inform policy and management decisions., Materials and Methods: We conducted two 6.5 h workshops and two 90-min interviews involving 18 AMR and other disciplinary experts from human, animal, and environment sectors who brainstormed the factors influencing AMR and identified leverage points (places) for intervention. Transcripts and workshop materials were coded for factors and their connections and transcribed into a causal loop diagram (CLD). Thematic analysis described AMR dynamics in SEA's food system and leverage points for intervention. The CLD and themes were confirmed via participant feedback., Results: Participants constructed a CLD of AMR in the SEA food system that contained 98 factors interlinked by 362 connections. CLD factors reflected eight sub-areas of the SEA food system (e.g., government). Seven themes [e.g., antimicrobial and pesticide use and AMR spread ( n = 40 quotes)], six "overarching factors" that impact the entire AMR system [e.g., the drive to survive ( n = 12 quotes)], and 10 places for intervention that target CLD factors ( n = 5) and overarching factors ( n = 2) emerged from workshop discussions., Conclusion: The participant derived CLD of factors influencing AMR in the SEA food system demonstrates that AMR is a product of numerous interlinked actions taken across the One Health spectrum and that finding solutions is no simple task. Developing the model enabled the identification of potentially promising leverage points across human, animal, and environment sectors that, if comprehensively targeted using multi-pronged interventions, could evoke system wide changes that mitigate AMR. Even targeting some leverage points for intervention, such as increasing investments in research and capacity building, and setting and enforcing regulations to control antimicrobial supply, demand, and use could, in turn, shift mindsets that lead to changes in more difficult to alter leverage points, such as redefining the profit-driven intent that drives system behavior in ways that transform AMU and sustainably mitigate AMR., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Lambraki, Chadag, Cousins, Graells, Léger, Henriksson, Troell, Harbarth, Wernli, Jørgensen, Carson, Parmley and Majowicz.)

Background: Antimicrobial resistance (AMR) is a growing global crisis with long-term and unpredictable health, social and economic impacts, with which climate change is likely to interact. Understanding how to govern AMR amidst evolving climatic changes is critical. Scenario planning offers a suitable approach. By envisioning alternative futures, stakeholders more effectively can identify consequences, anticipate problems, and better determine how to intervene. This study explored future worlds and actions that may successfully address AMR in a changing climate in a high-income country, using Sweden as the case., Methods: We conducted online scenario-building workshops and interviews with eight experts who explored: (1) how promising interventions ( taxation of antimicrobials at point of sale , and infection prevention measures ) could each combat AMR in 2050 in Sweden given our changing climate; and (2) actions to take starting in 2030 to ensure success in 2050. Transcripts were thematically analyzed to produce a narrative of participant validated alternative futures., Results: Recognizing AMR to be a global problem requiring global solutions, participants looked beyond Sweden to construct three alternative futures: (1) "Tax Burn Out" revealed taxation of antimicrobials as a low-impact intervention that creates inequities and thus would fail to address AMR without other interventions, such as infection prevention measures. (2) "Addressing the Basics" identified infection prevention measures as highly impactful at containing AMR in 2050 because they would contribute to achieving the Sustainable Development Goals (SDGs), which would be essential to tackling inequities underpinning AMR and climate change, and help to stabilize climate-induced mass migration and conflicts; and (3) "Siloed Nations" described a movement toward nationalism and protectionism that would derail the "Addressing the Basics" scenario, threatening health and wellbeing of all. Several urgent actions were identified to combat AMR long-term regardless which future un-folds, such as global collaboration, and a holistic approach where AMR and climate change are addressed as interlinked issues., Conclusion: Our participatory scenario planning approach enabled participants from different sectors to create shared future visions and identify urgent actions to take that hinge on global collaboration, addressing AMR and climate change together, and achieving the SDGs to combat AMR under a changing climate., Competing Interests: BM is an employee of the Swedish Pharmaceutical Industry Association, and was previously employed by Pfizer AB. He is also a shareholder of several pharmaceutical companies. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Lambraki, Cousins, Graells, Léger, Abdelrahman, Desbois, Gallagher, Staaf Larsson, Mattson, Henriksson, Troell, Søgaard Jørgensen, Wernli, Carson, Parmley and Majowicz.)

Antimicrobial resistance (AMR) affects the environment, and animal and human health. Institutions worldwide have applied various measures, some of which have reduced antimicrobial use and AMR. However, little is known about factors influencing the success of AMR interventions. To address this gap, we engaged health professionals, designers, and implementers of AMR interventions in an exploratory study to learn about their experience and factors that challenged or facilitated interventions and the context in which interventions were implemented. Based on participant input, our thematic analysis identified behaviour; institutional governance and management; and sharing and enhancing information as key factors influencing success. Important sub-themes included: correct behaviour reinforcement, financial resources, training, assessment, and awareness of AMR. Overall, interventions were located in high-income countries, the human sector, and were publicly funded and implemented. In these contexts, behaviour patterns strongly influenced success, yet are often underrated or overlooked when designing AMR interventions. Improving our understanding of what contributes to successful interventions would allow for better designs of policies that are tailored to specific contexts. Exploratory approaches can provide encouraging results in complex challenges, as made evident in our study. Remaining challenges include more engagement in this type of study by professionals and characterisation of themes that influence intervention outcomes by context.

Introduction: Antimicrobial resistance (AMR) is a global crisis that evolves from a complex system of factors. Understanding what factors interact is key to finding solutions. Our objective was to identify the factors influencing AMR in the European food system and places to intervene., Materials and Methods: We conducted two workshops involving participants with diverse perspectives to identify the factors influencing AMR and leverage points (places) to target interventions. Transcripts were open coded for factors and connections, then transcribed into Vensim 8.0.4 to develop a causal loop diagram (CLD) and compute the number of feedback loops. Thematic analysis followed to describe AMR dynamics in Europe's food system and places for intervention. The CLD and themes were confirmed via participant feedback., Results: Seventeen participants representing human, animal and agricultural sectors identified 91 CLD factors and 331 connections. Seven themes (e.g., social and economic conditions) describing AMR dynamics in Europe's food system, five 'overarching factors' that impact the entire CLD system (e.g., leadership) and fourteen places for intervention (e.g., consumer demand) emerged from workshop discussions. Most leverage points fell on highly networked feedback loops suggesting that intervening at these places may create unpredictable consequences., Conclusions: Our study produced a CLD of factors influencing AMR in Europe's food system that implicates sectors across the One Health spectrum. The high connectivity between the CLD factors described by participants and our finding that factors are connected with many feedback mechanisms underscores the complexity of the AMR problem and the challenge with finding long-term solutions. Identifying factors and feedbacks helped identify relevant leverage points in the system. Some actions, such as government's setting AMU standards may be easier to implement. These actions in turn can support multi-pronged actions that can help redefine the vision, values and goals of the system to sustainably tackle AMR., Competing Interests: I.A.L., M.C., T.G., A.L., S.H., D.W., P.S.J., and E.J.P. have no competing interests to declare. P.H. is a member of the Technical Committee for the BAP Vanguard Climate Action Standard and P.H. and M.T. act as scientific advisors to the Seafood Business for Ocean Stewardship (SeaBOS) initiative. P.H. was supported by the CGIAR Research Program on Fish Agri-Food Systems (FISH) led by WorldFish and on Climate Change, Agriculture and Food Security (CCAFS) supported by contributors to the CGIAR Trust Fund. P.H. and M.T. acknowledge the Kjell and Märta Beijer Foundation for supporting this work through the Beijer Institute’s Aquaculture and Sustainable Seafood programme, and the SEAWIN project funded by FORMAS (2016-00227). P.H. is partially funded by FORMAS Inequality and the Biosphere project (2020-00454). A.P.D. is (or has been in the last 5 years) engaged in research grants funded by the Sustainable Aquaculture Innovation Centre, UK Research and Innovation, International Veterinary Vaccinology Network, Scottish Funding Council, Great British Prawns Ltd and Benchmark Animal Health. C.A.C. works for the Government of Canada at the Public Health Agency of Canada. C.A.C. is/has been a subject matter expert for the World Organisation for Animal Health (OIE) and the World Health Organization (WHO) and has been a co-topic editor for two volumes of a Frontiers in Veterinary Science, Research Topic: Antimicrobial Usage in Companion and Food Animals: Methods, Surveys and Relationships with Antimicrobial Resistance in Animals and Humans. S.E.M. is (or has been in the last 5 years) engaged in research grants/contracts funded by the Canadian Institutes for Health Research, the Bill and Melinda Gates Foundation/UK Dept., International Development, the Natural Sciences and Engineering Research Council of Canada, Institut de recherche Robert-Sauvé en santé et en sécurité du travail, Dairy Farmers of Canada Research Funding Program, the World Health Organization, British Columbia Centre for Disease Control, Indian and Northern Affairs Canada, and Ontario Ministry of Agriculture, Food and Rural Affairs. She currently sits on the Editorial Boards of Foodborne Pathogens and Disease, and Epidemiology and Infection, and is a member of the World Health Organization’s Foodborne Disease Burden Epidemiology Reference Group, and she has served as a paid expert on behalf of the Attorney General of Canada in legal proceedings, providing evidence on the public health risks and benefits of unpasteurized milk. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Antimicrobial resistance (AMR) is among the most pressing One Health issues. While interventions and policies with various targets and goals have been implemented, evidence about factors underpinning success and failure of interventions in different sectors is lacking. The objective of this study is to identify characteristics of AMR interventions that increase their capacity to impact AMR. This study focuses on AMR interventions targeting E. coli., Methods: We used the AMR-Intervene framework to extract descriptions of the social and ecological systems of interventions to determine factors contributing to their success., Results: We identified 52 scientific publications referring to 42 unique E. coli AMR interventions. We mainly identified interventions implemented in high-income countries (36/42), at the national level (16/42), targeting primarily one sector of society (37/42) that was mainly the human sector (25/42). Interventions were primarily funded by governments (38/42). Most intervention targeted a low leverage point in the AMR system, (36/42), and aimed to change the epidemiology of AMR (14/42). Among all included publications, 55% (29/52) described at least one success factor or obstacle (29/52) and 19% (10/52) identified at least one success factor and one obstacle. Most reported success factors related to communication between the actors and stakeholders and the role of media, and stressed the importance of collaboration between disciplines and external partners. Described obstacles covered data quality, access to data and statistical analyses, and the validity of the results., Conclusions: Overall, we identified a lack of diversity regarding interventions. In addition, most published E. coli interventions were poorly described with limited evidence of the factors that contributed to the intervention success or failure. Design and reporting guidelines would help to improve reporting quality and provide a valuable tool for improving the science of AMR interventions., (© 2021. The Author(s).)

Background: Antimicrobial resistance (AMR) is an escalating global crisis with serious health, social, and economic consequences. Building social-ecological system resilience to reduce AMR and mitigate its impacts is critical., Objective: The aim of this study is to compare and assess interventions that address AMR across the One Health spectrum and determine what actions will help to build social and ecological capacity and readiness to sustainably tackle AMR., Methods: We will apply social-ecological resilience theory to AMR in an explicit One Health context using mixed methods and identify interventions that address AMR and its key pressure antimicrobial use (AMU) identified in the scientific literature and in the gray literature using a web-based survey. Intervention impacts and the factors that challenge or contribute to the success of interventions will be determined, triangulated against expert opinions in participatory workshops and complemented using quantitative time series analyses. We will then identify indicators using regression modeling, which can predict national and regional AMU or AMR dynamics across animal and human health. Together, these analyses will help to quantify the causal loop diagrams (CLDs) of AMR in the European and Southeast Asian food system contexts that are developed by diverse stakeholders in participatory workshops. Then, using these CLDs, the long-term impacts of selected interventions on AMR will be explored under alternate future scenarios via simulation modeling and participatory workshops. A publicly available learning platform housing information about interventions on AMR from a One Health perspective will be developed to help decision makers identify promising interventions for application in their jurisdictions., Results: To date, 669 interventions have been identified in the scientific literature, 891 participants received a survey invitation, and 4 expert feedback and 4 model-building workshops have been conducted. Time series analysis, regression modeling of national and regional indicators of AMR dynamics, and scenario modeling activities are anticipated to be completed by spring 2022. Ethical approval has been obtained from the University of Waterloo's Office of Research Ethics (ethics numbers 40519 and 41781)., Conclusions: This paper provides an example of how to study complex problems such as AMR, which require the integration of knowledge across sectors and disciplines to find sustainable solutions. We anticipate that our study will contribute to a better understanding of what actions to take and in what contexts to ensure long-term success in mitigating AMR and its impact and provide useful tools (eg, CLDs, simulation models, and public databases of compiled interventions) to guide management and policy decisions., International Registered Report Identifier (irrid): DERR1-10.2196/24378., (©Irene Anna Lambraki, Shannon Elizabeth Majowicz, Elizabeth Jane Parmley, Didier Wernli, Anaïs Léger, Tiscar Graells, Melanie Cousins, Stephan Harbarth, Carolee Carson, Patrik Henriksson, Max Troell, Peter Søgaard Jørgensen. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 10.06.2021.)

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance. Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species. This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.

Objectives: The aim of this study was to monitor the spread, persistence and antibiotic resistance patterns of Legionella spp. strains found in a hospital water distribution system. These environmental studies are intended to help detect the presence of antibiotic resistant strains before they infect patients., Methods: Antimicrobial surveillance tests were performed at 27 different sampling points of the water network of a large Spanish hospital over two years. Water samples were screened for Legionella according to ISO 11731:2007. Legionella spp. isolates were identified by serotyping and by mass spectrometry (MALDI-ToF). Epidemiological molecular typing was done by Pulse-Field Gel Electrophoresis (PFGE) and by Sequence-Based Typing (SBT). Antibiotic susceptibility tests were performed using disk diffusion and ETEST®., Results: Legionella spp. were recurrently isolated for 2 years. All isolates belonged the same group, L. pneumophila serogroups 2-14. Isolates were all attributed by SBT to sequence type (ST) ST328, although PFGE revealed 5 different patterns. No significant change in antibiotic susceptibility could be observed for this study period, irrespectively of the method used., Conclusion: Colonization of water systems by Legionella spp. is still occurring, although all the prevention rules were strictly followed. Antibiotic resistance monitoring may help us to find resistance in bacteria with environmental reservoirs but difficult to isolate from patients. The knowledge of the antibiotic susceptibility in environmental strains may help us to predict changes in clinical strains. This study might also help reconsidering Legionnaires' disease (LD) diagnostic methods. L. pneumophila serogroups 2-14 present all along the time of the investigation in the water distribution system can cause LD. However, they may not be detected by routine urine tests run on patients, thereby missing an ongoing LD infection., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance.Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments, and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species.This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.