Search

Presents a letter to the editor about Vibrio parahaemolyticus.

Background: In the past decades, climate change has been impacting human lives and health via extreme weather and climate events and alterations in labour capacity, food security, and the prevalence and geographical distribution of infectious diseases across the globe. Climate change and health indicators (CCHIs) are workable tools designed to capture the complex set of interdependent interactions through which climate change is affecting human health. Since 2015, a novel sub-set of CCHIs, focusing on climate change impacts, exposures, and vulnerability indicators (CCIEVIs) has been developed, refined, and integrated by Working Group 1 of the "Lancet Countdown: Tracking Progress on Health and Climate Change", an international collaboration across disciplines that include climate, geography, epidemiology, occupation health, and economics. Discussion: This research in practice article is a reflective narrative documenting how we have developed CCIEVIs as a discrete set of quantifiable indicators that are updated annually to provide the most recent picture of climate change's impacts on human health. In our experience, the main challenge was to define globally relevant indicators that also have local relevance and as such can support decision making across multiple spatial scales. We found a hazard, exposure, and vulnerability framework to be effective in this regard. We here describe how we used such a framework to define CCIEVIs based on both data availability and the indicators' relevance to climate change and human health. We also report on how CCIEVIs have been improved and added to, detailing the underlying data and methods, and in doing so provide the defining quality criteria for Lancet Countdown CCIEVIs. Conclusions: Our experience shows that CCIEVIs can effectively contribute to a world-wide monitoring system that aims to track, communicate, and harness evidence on climate-induced health impacts towards effective intervention strategies. An ongoing challenge is how to improve CCIEVIs so that the description of the linkages between climate change and human health can become more and more comprehensive. [ABSTRACT FROM AUTHOR]

We report transcontinental expansion of Vibrio parahaemolyticus sequence type 36 into Lima, Peru. From national collections, we identified 7 isolates from 2 different Pacific Northwest complex lineages that surfaced during 2011-2016. Sequence type 36 is likely established in environmental reservoirs. Systematic surveillance enabled detection of these epidemic isolates. [ABSTRACT FROM AUTHOR]

There is a growing interest in the role of climate change in driving the spread of waterborne infectious diseases, such as those caused by bacterial pathogens. One particular group of pathogenic bacteria – vibrios – are a globally important cause of diseases in humans and aquatic animals. These Gram-negative bacteria, including the species Vibrio vulnificus, Vibrio parahaemolyticus and Vibrio cholerae , grow in warm, low-salinity waters, and their abundance in the natural environment mirrors ambient environmental temperatures. In a rapidly warming marine environment, there are greater numbers of human infections, and most notably outbreaks linked to extreme weather events such as heatwaves in temperate regions such as Northern Europe. Because the growth of pathogenic vibrios in the natural environment is largely dictated by temperature, we argue that this group of pathogens represents an important and tangible barometer of climate change in marine systems. We provide a number of specific examples of the impacts of climate change on this group of bacteria and their associated diseases, and discuss advanced strategies to improve our understanding of these emerging waterborne diseases through the integration of microbiological, genomic, epidemiological, climatic, and ocean sciences. [ABSTRACT FROM AUTHOR]

It is critical to gain insight into how climate change impacts evolutionary responses within climate-sensitive pathogen populations, such as increased resilience, opportunistic responses and the emergence of dominant variants from highly variable genomic backgrounds and subsequent global dispersal. This review proposes a framework to support such analysis, by combining genomic evolutionary analysis with climate time-series data in a novel spatiotemporal dataframe for use within machine learning applications, to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. Such workflows will inform accessible public health tools and early-warning systems, to aid decision-making and mitigate future human health threats. [Display omitted] • Climate change drives pathogen ecology, evolution and novel strain emergence. • Absence of tools to identify how pathogens are adapting to climate change. • Combining genomic and climate data will open analysis possibilities. • Machine learning can increase predictive capabilities of future pathogen evolution. [ABSTRACT FROM AUTHOR]

During summer 2014, a total of 89 Vibrio infections were reported in Sweden and Finland, substantially more yearly infections than previously have been reported in northern Europe. Infections were spread across most coastal counties of Sweden and Finland, but unusually, numerous infections were reported in subarctic regions; cases were reported as far north as 65°N, ≈100 miles (160 km) from the Arctic Circle. Most infections were caused by non-O1/O139 V. cholerae (70 cases, corresponding to 77% of the total, all strains were negative for the cholera toxin gene). An extreme heat wave in northern Scandinavia during summer 2014 led to unprecedented high sea surface temperatures, which appear to have been responsible for the emergence of Vibrio bacteria at these latitudes. The emergence of vibriosis in high-latitude regions requires improved diagnostic detection and clinical awareness of these emerging pathogens. [ABSTRACT FROM AUTHOR]

Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions. [ABSTRACT FROM AUTHOR]

Competing Interests: Declaration of interests Thirteen of the authors (ZA, S-CH, LJ, AM, CO, MO, JP, YP-S, DS, LB-V, MRo, MW, and HW) were compensated for their time while drafting and developing the Lancet Countdown's report. LC was supported by a grant from the National Heart, Lung, and Blood Institute of the National Institutes of Health. CD received funding from the European Research Council (FLORA, grant number 101039402). RD was supported by a grant from the High Tide Foundation and subcontracts on funds from the Wellcome Trust and US Centers for Disease Control and Prevention. GG-S received funding from the UK National Institute for Health and Care Research for the Global Health Research Group on Diet and Activity (NIHR133205, with sub-award contract number G109900-SJ1/171 with the University of Cambridge). SHG's research was supported by the National Research Foundation, Prime Minister's Office, Singapore, under its Campus for Research Excellence and Technological Enterprise programme (grant number NRF2019-THE001-0006). JJH was supported by two grants from the Wellcome Trust and a grant from the US National Science Foundation. RH, RK, and MSo acknowledge funding from Academy of Finland projects HEATCOST (grant 334798) and VFSP-WASE (grant 359421), together with EU Horizon projects FirEUrisk (grant number 101003890) and EXHAUSTION (grant number 820655). OJ was supported by grants from the National Health Medical Research Council (Heat and Health: building resilience to extreme heat in a warming world, GNT1147789); Wellcome Trust (Heat stress in ready-made garment factories in Bangladesh and the Heat inform pregnant study); and Resilience New South Wales (A new heat stress scale for general public); holds a patent for the Environmental Measurement Unit; and has received consulting fees from the National Institutes of Health. HM received funding from the Oak Foundation to support work on climate change through RealZero, is partly funded by the National Institute for Health Research's Comprehensive Biomedical Research Centre at University College London Hospitals, and received fees from Bayer Pharmaceuticals and Chiesl for sustainability consulting. JM-U was supported by grants PID2021-127107NB-I00 from Ministerio de Ciencia e Innovación (Spain) and 2021 SGR 00526 from Generalitat de Catalunya (Spain). JRo's work is supported by the Alexander von Humboldt foundation. RL, JRo, and MRo were supported by Horizon Europe through the IDAlert project (101057554) and UK Research and Innovation (reference number 10056533). RNS reports a contract with Massachusetts General Hospital. MSo and AU were supported by the Finnish Foreign Ministry project IBA-ILMA (grant number VN/13798/2023). MSp was supported by funding from the Wellcome Trust, through Our Planet Our Health (Livestock, Environment and People, award number 205212/Z/16/Z) and a Wellcome Career Development Award (Towards the full cost of diets, award number 225318/Z/22/Z). JDSh was supported by the Canadian Institutes of Health Research, the Commonwealth Fund, and the Emergency Care Research Institute and has received consulting fees from the Institute for Healthcare Research. JT was supported by the Research Council of Finland (T-Winning Spaces 2035 project), the UK Medical Research Council (PICNIC project), and the Finnish Ministry of the Environment (SEASON project). JB is employed as a consultant by the Global Climate and Health Alliance. ML received consulting fees from YarCom for advisory services and was supported by general use gifts awarded to the Center on Global Energy Policy at Columbia University, USA. JMil acknowledges consulting fees from the C40 Climate Leadership Group. CZ-C received a consultancy from the University of Alberta and was supported by contracts with her university (Universidad Peruana Cayetano Heredia), University of Leeds, WHO, and the Wellcome Trust; she was also supported by a letter of agreement between her university and the Food and Agriculture Organization's Indigenous Peoples Unit. MD was supported by the Wellcome Trust via the Complex Urban Systems for Sustainability and Health project (grants 205207/Z/16/Z and 209387/Z/17/Z). IH, S-CH, MRo, CT, and RL were supported by the Horizon Europe CATALYSE project (CATALYSE grant number 101057131, HORIZON-HLTH-2021-ENVHLTH-02, with UK Research and Innovation reference number 10041512). The work of YH, YL, DT, and QZ was supported by the National Aeronautics and Space Administration's Earth Action programme (grant number 80NSSC21K0507). AJP was supported by the Bezos Earth Fund and the Schmidt Family Foundation. ER and SD were supported by a Process-based models for climate impact attribution across sectors (PROCLIAS) grant (COST Action PROCLIAS grant CA19139), funded by European Cooperation in Science and Technology. All other authors declare no competing interests.

El Niño events, the warm phase of the El Niño Southern Oscillation, facilitate the movement of warm surface waters eastwards across the Pacific Ocean. Marine organisms transported by these waters can act as biological corridors for water-borne bacteria with attachment abilities. El Niño events have been hypothesized as driving the recent emergence of Vibrio parahaemolyticus (Vp) variants, marine bacterium causing gastroenteritis, in South America, but the lack of a robust methodological framework limited any further exploration. Here, we introduce two new analysis approaches to explore Vp dynamics in South America, which will be central to uncovering Vp dynamics in the future. Distributed non-linear lag models found that strong El Niño events increase the relative probability of Vp detection in Peru, with a 3-4-month lag time. Machine learning found that the presence of a specific gene ( vopZ ) involved in attachment to plankton in a pandemic Vp clone in South America was temporally associated with strong El Niño events, offering a possible strategy for survival over long-range dispersal, such as that offered by El Niño events. Robust surveillance of marine pathogens and methodological development are necessary to produce resolute conclusions on the effect of El Niño events on water-borne diseases.

The underlying evolutionary mechanisms driving global expansions of pathogen strains are poorly understood. Vibrio parahaemolyticus is one of only two marine pathogens where variants have emerged in distinct climates globally. The success of a Vibrio parahaemolyticus clone (VpST3) in Latin America- the first spread identified outside its endemic region of tropical Asia- provided an invaluable opportunity to investigate mechanisms of VpST3 expansion into a distinct marine climate. A global collection of VpST3 isolates and novel Latin American isolates were used for evolutionary population genomics, pangenome analysis and combined with oceanic climate data. We found a VpST3 population (LatAm-VpST3) introduced in Latin America well before the emergence of this clone in India, previously considered the onset of the VpST3 epidemic. LatAm-VpST3 underwent successful adaptation to local conditions over its evolutionary divergence from Asian VpST3 isolates, to become dominant in Latin America. Selection signatures were found in genes providing resilience to the distinct marine climate. Core genome mutations and accessory gene presences that promoted survival over long dispersals or increased environmental fitness were associated with environmental conditions. These results provide novel insights into the global expansion of this successful V. parahaemolyticus clone into regions with different climate scenarios., (© 2024. The Author(s).)

Vibrio parahaemolyticus , Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus , V. vulnificus and non-choleragenic V. cholerae , respectively. Approximately one out of five V. parahaemolyticus -positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised., Competing Interests: If you wish to access the declaration of interests of any expert contributing to an EFSA scientific assessment, please contact interestmanagement@efsa.europa.eu., (© 2024 European Food Safety Authority. EFSA Journal published by Wiley‐VCH GmbH on behalf of European Food Safety Authority.)

This study delves into the genomic features of 10 Vibrio strains collected from deep-sea hydrothermal vents in the Pacific Ocean, providing insights into their evolutionary history and ecological adaptations. Through sequencing and pan-genome analysis involving 141 Vibrio species, we found that deep-sea strains exhibit larger genomes with unique gene distributions, suggesting adaptation to the vent environment. The phylogenomic reconstruction of the investigated isolates revealed the presence of 2 main clades: The first is monophyletic, consisting exclusively of Vibrio alginolyticus, while the second forms a monophyletic clade comprising both Vibrio antiquarius and Vibrio diabolicus species, which were previously isolated from deep-sea vents. All strains carry virulence and antibiotic resistance genes related to those found in human pathogenic Vibrio species which may play a wider ecological role other than host infection in these environments. In addition, functional genomic analysis identified genes potentially related to deep-sea survival and stress response, alongside candidate genes encoding for novel antimicrobial agents. Ultimately, the pan-genome we generated represents a valuable resource for future studies investigating the taxonomy, evolution, and ecology of Vibrio species., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Globally, the diverse bacterial genus Vibrio is the most important group of bacterial pathogens found in marine and coastal waters. These bacteria can cause an array of human infections via direct exposure to seawater or through the consumption of seafoods grown and cultivated in coastal and estuarine settings. Crucially, we appear to be on the cusp of an alarming global increase in Vibrio disease. A worldwide increase in seafood consumption, the globalisation of the seafood trade, the more frequent use of coastal waters for recreational activities, and climate change all contribute to greatly increased human health risks associated with Vibrio bacteria. Coupled with a population that is increasingly susceptible to more serious infections, we are likely to see a marked increase in both reported cases and fatalities in the near future. In this Personal View, we discuss and frame this important and emerging public health issue, and provide various contemporary case studies to illustrate how the risk profiles of pathogenic Vibrio bacteria have transformed in the past two decades-particularly in response to changing climatological and meteorological drivers such as marine coastal warming and extreme weather events such as heatwaves and storms. We share various approaches to help better understand and manage risks associated with these bacteria, ranging from risk mitigation strategies to enhanced epidemiological monitoring and surveillance approaches., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Competing Interests: Declaration of interests VK and OS are staff members of the WHO Regional Office for Europe. The authors alone are responsible for the views expressed in this publication and they do not necessarily represent the decisions or policies of WHO. The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of WHO concerning the legal status of any country, territory, city, or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted and dashed lines on maps represent approximate border lines for which there might not yet be full agreement. AK and EV are staff members of the European Environment Agency. The views expressed in this article are solely those of the authors and its content does not necessarily represent the views or position of the European Environment Agency. All other authors declare no competing interests.

Competing Interests: Declaration of interests 14 of the authors (MRo, MWa, LJ, MBO'H, CO, HW, CdN, HK, PL, DS, CG, ZA, MY-G, and KRvD) were compensated for their time while drafting and developing the Lancet Countdown's report. OG was supported by the EU Horizon Grant: Climate Action To Advance Healthy Societies in Europe (Project 101057131–CATALYSE), for which there is overlap of data collection and preprocessing with the materials submitted in this report. MSp was supported by the Wellcome Trust Livestock, Environment and People (grant number 205212/Z/16/Z) and Wellcome Trust (grant number 225318/Z/22/Z). JT was supported by the Academy of Finland grants for the T-Winning (grant number 353327). CD was supported by the UK Natural Environment Research Council Independent Research Fellowship (grant number NE/N01524X/1), which ended in 2021, and by the European Research Council starting grant FLORA (grant number 101039402). OJ was supported by the NHMRC Investigator Grant entitled Heat and Health: Building resilience to extreme heat in a warming world (GNT20009507), the Wellcome Trust grant Heat stress in ready-made garment factories in Bangladesh (216059/Z/19/Z), and the Resilience New South Wales grant A new heat stress scale for general public (PJ-0000850). YL was supported by funding from the National Aeronautics and Space Administration (grant number: 80NSSC21K0507) for the wildfire population exposure and fire danger indicators. TO and IH were supported by the UK Research and Innovation Engineering and Physical Sciences Research Council Centre for Research in Energy Demand Solutions (grant number EP/R035288/1). MRo was supported by funding from IDAlert project (UK Research and Innovation project reference number 10056533). KB was supported by funding from the National Institute for Health and Care Research (NIHR) Centre on Non-communicable Diseases and Environmental Change (NIHR203247). All other authors declare no competing interests. The authors alone are responsible for the views expressed in this Commission, and they do not necessarily represent the views, decisions, or policies of the institutions with which they are affiliated.

Background: Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe the prevalence, genetic diversity, and evolutionary dynamics of HMPV., Methods: Laboratory-confirmed HMPV were characterised based on partial-coding G gene sequences with MEGA.v6.0. WGS was performed with Illumina, and evolutionary analyses with Datamonkey and Nextstrain., Results: HMPV prevalence was 2.5%, peaking in February-April and with an alternation in the predominance of HMPV-A and -B until the emergence of SARS-CoV-2, not circulating until summer and autumn-winter 2021, with a higher prevalence and with the almost only circulation of A2c 111dup . G and SH proteins were the most variable, and 70% of F protein was under negative selection. Mutation rate of HMPV genome was 6.95 × 10 -4 substitutions/site/year., Conclusion: HMPV showed a significant morbidity until the emergence of SARS-CoV-2 pandemic in 2020, not circulating again until summer and autumn 2021, with a higher prevalence and with almost the only circulation of A2c 111dup , probably due to a more efficient immune evasion mechanism. The F protein showed a very conserved nature, supporting the need for steric shielding. The tMRCA showed a recent emergence of the A2c variants carrying duplications, supporting the importance of virological surveillance., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Vibrio parahaemolyticus has been identified as an emerging human pathogen worldwide with cases undergoing a global expansion over recent decades in phase with climate change. New Zealand had remained free of outbreaks until 2019, but different outbreaks have been reported consecutively since then. To provide new insights into the recent emergence of cases associated with outbreak clones over recent years, a comparative genomic study was carried out using a selection of clinical (mostly outbreak) and environmental isolates of V. parahaemolyticus obtained in New Zealand between 1973 and 2021. Among 151 isolates of clinical ( n =60) and environmental ( n =91) origin, 47 sequence types (STs) were identified, including 31 novel STs. The population of environmental isolates generated 30 novel STs, whereas only 1 novel ST (ST2658) was identified among the population of clinical isolates. The novel clinical ST was a single-locus variant of the pandemic ST36 strain, indicating further evolution of this pandemic strain. The environmental isolates exhibited a significant genetic heterogeneity compared to the clinical isolates. The whole-genome phylogeny separated the population of clinical isolates from their environmental counterparts, clearly indicating their distant genetic relatedness. In addition to differences in ancestral profiles and genetic relatedness, these two groups of isolates exhibited a profound difference in their virulence profiles. While the entire population of clinical isolates harboured the thermostable direct haemolysin ( tdh ) and/or the thermostable-related haemolysin ( trh ), only a few isolates of environmental origin possessed the same virulence genes. In contrast to tdh and trh , adhesin-encoding genes, vpadF and MSHA, showed a significantly ( P <0.001) greater association with the environmental isolates compared to the clinical isolates. The effectors, VopQ, VPA0450 and VopS, which belong to T3SS1, were ubiquitous, being present in each isolate regardless of its origin. The effectors VopC and VopA, which belong to T3SS2, were rarely detected in any of the examined isolates. Our data indicate that the clinical and environmental isolates of V. parahaemolyticus from New Zealand differ in their population structures, ancestral profiles, genetic relatedness and virulence profiles. In addition, we identified numerous unique non-synonymous single-nucleotide polymorphisms (nsSNPs) in adhesins and effectors, exclusively associated with the clinical isolates tested, which may suggest a possible role of these mutations in the overall virulence of the clinical isolates.

Harmful marine bacteria, such as Vibrio or Aeromonas species, typically exist at low abundance in ocean environments but represent a reservoir from which epidemics can arise. Particularly, Vibrio strains and their associated infections are on the rise globally due to increasing sea surface temperature representing an emergent threat for human and animal health also being responsible for large economic losses in the aquaculture industry worldwide. New technological approaches are needed to improve strategies targeting these pathogens. This review discusses new approaches based on improved sampling strategies and novel analytical methods offering increased accuracy, high throughput, and informativeness to study and detect microbial pathogens in the marine environment. Detecting and characterizing ultra-low-abundance pathogenic strains can serve as a critical tool in risk management and outbreak prevention of diseases caused by emerging marine pathogens., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Luigi Vezzulli reports financial support was provided by Italian Ministry of University and Research (MUR)., (Copyright © 2023. Published by Elsevier Ltd.)

When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies., (© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

The Vibrionaceae is a highly diverse family of aquatic bacteria. Some members of this ubiquitous group can cause a variety of diseases in humans ranging from cholera caused by Vibrio cholerae, severe septicemia caused by Vibrio vulnificus, to acute gastroenteritis by Vibrio parahaemolyticus. Planet Earth is experiencing unprecedented changes of planetary scale associated with climate change. These environmental perturbations paired with overpopulation and pollution are increasing the distribution of pathogenic Vibrios and exacerbating the risk of causing infections. In this chapter, we discuss various aspects of Vibrio infections within the context of the twenty-first century with a major emphasis on the aforementioned pathogenic species. Overall, we believe that the twenty-first century is posed to be both one full of challenges due to the rise of these pathogens, and also a catalyst for innovative and groundbreaking discoveries., (© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

The epidemiological dynamics of V. parahaemolyticus´ infections have been characterized by the abrupt appearance of outbreaks in remote areas where these diseases had not been previously detected, without knowing the routes of entry of the pathogens in the new area. However, there are recent studies that show the link between the appearance of epidemic outbreaks of Vibrio and environmental factors such as oceanic transport of warm waters, which has provided a possible mechanism for the dispersion of Vibrio diseases globally. Despite this evidence, there is little information on the possible routes of entry and transport of infectious agents from endemic countries to the entire world. In this sense, the recent advances in genomic sequencing tools are making it possible to infer possible biogeographical patterns of diverse pathogens with relevance in public health like V. parahaemolyticus. In this chapter, we will address several general aspects about V. parahaemolyticus, including their microbiological and genetic detection, main virulence factors, and the epidemiology of genotypes involved in foodborne outbreaks globally., (© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

Competing Interests: Declaration of interests CD was supported by the UK Natural Environment Research Council (NE/R010811/1) and the UK Natural Environment Research Council Independent Research Fellowship (NE/N01524X/1) and contributes to the Sustainable and Healthy Food Systems project supported by the Wellcome Trust (205200/Z/16/Z). MD was supported by the Wellcome Trust's Complex Urban Systems for Sustainability and Health (CUSSH) project (209387/Z/17/Z). YL was supported by the US National Aeronautics and Space Administration Applied Sciences Program (80NSSC21K0507). RL was supported by a Royal Society Dorothy Hodgkin Fellowship. MSo was supported by Horizon 2020 project EXHAUSTION (820655) and Academy of Finland HEATCOST (334798). SHG and JKWL were supported by Singapore's National Research Foundation, Singapore's Prime Minister's Office, under its Campus for Research Excellence and Technological Enterprise programme. IH was supported by the UK Research and Innovation (UKRI) Engineering and Physical Sciences Research Council Centre for Research in Energy Demand Solutions (EP/R035288/1) and UKRI APEx (NE/T001887/1). JM was supported by the German Ministry for Education and Research (01LA1826A and 03SFK5J0). ML was supported by the Sloan Foundation. All other authors declare no competing interests.

Competing Interests: Declaration of interests VK and OS are staff members of the WHO Regional Office for Europe. The authors alone are responsible for the views expressed in this publication and they do not necessarily represent the decisions or policies of the World Health Organization. The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of WHO concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted and dashed lines on maps represent approximate border lines for which there may not yet be full agreement. All other authors declare no competing interests.

Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes. Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively.

Controlling foodborne diseases requires robust outbreak detection and a comprehensive understanding of outbreak dynamics. Here, by integrating large-scale phylogenomic analysis of 3,642 isolates and epidemiological data, we performed 'data-driven' outbreak detection and described the long-term outbreak dynamics of the leading seafood-associated pathogen, Vibrio parahaemolyticus, in Shenzhen, China, over a 17-year period. Contradictory to the widely accepted notion that sporadic patients and independent point-source outbreaks dominated foodborne infections, we found that 71% of isolates from patients grouped into within-1-month clusters that differed by ≤6 single nucleotide polymorphisms, indicating putative outbreaks. Furthermore, we showed that despite the long time spans between clusters, 70% of them were genomically closely related and were inferred to arise from a small number of common sources, which provides evidence that hidden persistent reservoirs generated most of the outbreaks rather than independent point-sources. Phylogeographical analysis further revealed the geographical heterogeneity of outbreaks and identified a coastal district as the potential hotspot of outbreaks and as the hub and major source of cross-district spread events. Our findings provide a comprehensive picture of the long-term spatiotemporal dynamics of foodborne outbreaks and present a different perspective on the major source of foodborne infections, which will inform the design of future disease control strategies., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Antibiotic resistance genes (ARGs) are undergoing a remarkably rapid geographic expansion in various ecosystems, including pristine environments such as Antarctica. The study of ARGs and environmental resistance genes (ERGs) mechanisms could provide a better understanding of their origin, evolution, and dissemination in these pristine environments. Here, we describe the diversity of ARGs and ERGs and the importance of mobile genetic elements as a possible mechanism for the dissemination of resistance genes in Antarctica. We analyzed five soil metagenomes from Deception Island in Antarctica. Results showed that detected ARGs are associated with mechanisms such as antibiotic efflux, antibiotic inactivation, and target alteration. On the other hand, resistance to metals, surfactants, and aromatic hydrocarbons were the dominant ERGs. The taxonomy of ARGs showed that Pseudomonas , Psychrobacter , and Staphylococcus could be key taxa for studying antibiotic resistance and environmental resistance to stress in Deception Island. In addition, results showed that ARGs are mainly associated with phage-type mobile elements suggesting a potential role in their dissemination and prevalence. Finally, these results provide valuable information regarding the ARGs and ERGs in Deception Island including the potential contribution of mobile genetic elements to the spread of ARGs and ERGs in one of the least studied Antarctic ecosystems to date.

Competing Interests: Declaration of interests We declare no competing interests.

Background: Infections caused by non-cholera Vibrio species have undergone a global expansion over the past few decades reaching new areas of the world that were previously considered adverse for these organisms. The geographical extent of the expansion has not been uniform, and some areas have shown a rapid increase in infections., Methods: We applied a new generation of models combining climate, population, and socioeconomic projections to map future scenarios of distribution and season suitability for pathogenic Vibrio. We used the Coupled Model Intercomparison Project 6 framework. Three datasets were used: Geophysical Fluid Dynamics Laboratory's CM4.0 sea surface temperature and sea surface salinity; the coastline length dataset from the World Resources Institute; and Inter-Sectoral Impact Model Intercomparison Project 2b annual global population data. Future projections were used up to the year 2100 and historical simulations from 1850 to 2014. We also project human population at risk under different shared socioeconomic pathways worldwide., Findings: Projections showed that coastal areas suitable for Vibrio could cover 38 000 km of new coastal areas by 2100 under the most unfavourable scenario with an expansion rate of season suitability in these regions of around 1 month every 30 years. Population at risk in suitable regions almost doubled from 1980 to 2020 (from 610 million to 1100 million under the scenario of medium challenges to mitigation and adaptation, shared socioeconomic pathway 2-4.5), although the increment will be more moderate in the future and stabilises after 2050 at 1300 million. Finally, we provide the first global estimate for Vibrio infections, with values around half a million of cases worldwide in 2020., Interpretation: Our projections anticipated an expansion of both the temporal and spatial disease burden for Vibrio infections, in particular at high latitudes of the northern hemisphere. However, the largest extent occurred from 1980 to 2020 and a more moderate increase is expected for the future. The most positive outcome is that the projections showed that Vibrio morbidity will remain relatively stable over the coming decades., Funding: NOAA Atlantic Oceanographic and Meteorological Laboratory and NOAA OceanWatch, and by the University of Miami's Cooperative Institute for Marine and Atmospheric Studies., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

The significance of large tropical lakes as environmental reservoirs of Vibrio cholerae in cholera endemic countries has yet to be established. By combining large scale plankton sampling, microbial culture and ultrasensitive molecular methods, namely Droplet Digital PCR (ddPCR) and targeted genomics, the presence of Vibrio cholerae was investigated in a 96,600 L volume of surface water collected on a 322 nautical mile (596 km) transect in Lake Tanganyika. V. cholerae was detected and identified in a large area of the lake. In contrast, toxigenic strains of V. cholerae O1 or O139 were not detected in plankton samples possibly in relation to environmental conditions of the lake ecosystem, namely very low salinity compared to marine brackish and coastal environments. This represents to our knowledge, the largest environmental study to determine the role of tropical lakes as a reservoir of V. cholerae., (© 2021. The Author(s).)

Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput sequencing technologies. An additional innovation introduced by these technologies was the need of developing new strategies to manage and investigate the massive amount of sequencing data generated. This situation stimulated the rapid expansion of the field of bioinformatics with the release of new tools to be applied to the downstream analysis and interpretation of sequencing data mainly generated using Illumina technology. In recent years, a third generation of sequencing technologies has been developed and have been applied in parallel and complementarily to the former sequencing strategies. In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists. Nanopore technology offers a low price, portability and fast sequencing throughput. This powerful technology has been recently tested for 16S rRNA analyses showing promising results. However, compared with previous technologies, there is a scarcity of bioinformatic tools and protocols designed specifically for the analysis of Nanopore 16S sequences. Due its notable characteristics, researchers have recently started performing assessments regarding the suitability MinION on 16S rRNA sequencing studies, and have obtained remarkable results. Here we present a review of the state-of-the-art of MinION technology applied to microbiome studies, the current possible application and main challenges for its use on 16S rRNA metabarcoding., (© 2020 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)

Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.

Antarctic have been suggested as an attractive source for antibiotics discovery and members of Streptomyces genus have historically been studied as natural producers of antimicrobial metabolites. Nonetheless, our knowledge on antibiotic-producing Streptomyces from Antarctic is very limited. In this study, the antimicrobial activity of organic extracts from Antarctic Streptomyces strains was evaluated by disk diffusion assays and minimum inhibitory concentration. The strain Streptomyces sp. So13.3 showed the greatest antibiotic activity (MIC = 15.6 μg/mL) against Gram-positive bacteria and growth reduction of Gram‒negative pathogens. The bioactive fraction in the crude extract was revealed by TLC‒bioautography at R f  = 0.78 with molecular weight between 148 and 624 m/z detected by LC-ESI-MS/MS. The strain So13.3 was taxonomically affiliated as Streptomyces fildesensis. Whole genome sequencing and analysis suggested a 9.47 Mb genome size with 42 predicted biosynthetic gene clusters (BGCs) and 56 putative clusters representing a 22% of total genome content. Interestingly, a large number of them (11 of 42 BGCs and 40 of 56 putative BGCs), did not show similarities with other known BGCs. Our results highlight the potential of the Antarctic Streptomyces strains as a promising source of novel antimicrobials, particularly the strain Streptomyces fildesensis So13.3, which first draft genome is reported in this work.

Vibrio is a genus of ubiquitous bacteria found in a wide variety of aquatic and marine habitats; of the >100 described Vibrio spp., ~12 cause infections in humans. Vibrio cholerae can cause cholera, a severe diarrhoeal disease that can be quickly fatal if untreated and is typically transmitted via contaminated water and person-to-person contact. Non-cholera Vibrio spp. (for example, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus) cause vibriosis - infections normally acquired through exposure to sea water or through consumption of raw or undercooked contaminated seafood. Non-cholera bacteria can lead to several clinical manifestations, most commonly mild, self-limiting gastroenteritis, with the exception of V. vulnificus, an opportunistic pathogen with a high mortality that causes wound infections that can rapidly lead to septicaemia. Treatment for Vibrio spp. infection largely depends on the causative pathogen: for example, rehydration therapy for V. cholerae infection and debridement of infected tissues for V. vulnificus-associated wound infections, with antibiotic therapy for severe cholera and systemic infections. Although cholera is preventable and effective oral cholera vaccines are available, outbreaks can be triggered by natural or man-made events that contaminate drinking water or compromise access to safe water and sanitation. The incidence of vibriosis is rising, perhaps owing in part to the spread of Vibrio spp. favoured by climate change and rising sea water temperature.

Galicia in northwestern Spain has been considered a hotspot for Vibrio parahaemolyticus infections. Infections abruptly emerged in 1998 and, over the next 15 years, were associated with large outbreaks caused by strains belonging to a single clone. We report a recent transition in the epidemiologic pattern in which cases throughout the region have been linked to different and unrelated strains. Global genome-wide phylogenetic analysis revealed that most of the pathogenic strains isolated from infections were associated with globally diverse isolates, indicating frequent episodic introductions from disparate and remote sources. Moreover, we identified that the 2 major switches in the epidemic dynamics of V. parahaemolyticus in the regions, the emergence of cases and an epidemiologic shift in 2015-2016, were associated with the rise of sea surface temperature in coastal areas of Galicia. This association may represent a fundamental contributing factor in the emergence of illness linked to these introduced pathogenic strains.

The detection of pathogenic Vibrio in seafood from Senegal has generated five food alerts in the European Union. To investigate the presence and abundance Vibrio cholerae and Vibrio parahaemolyticus in seafood and coastal and estuarine waters, 123 seafood samples and 52 water samples were collected during 2007-2009 from two large seafood markets in Dakar, and from different oceanic and estuarine areas of the country. V. parahaemolyticus was detected in 30.1% of seafood samples, whereas presence of V. cholerae was only found in 1.6%. In water samples, V. parahaemolyticus and V. cholerae were detected in 28.8% and 5.7% of the samples, respectively. Abundance of V. parahaemolyticus in seafood from the fishing areas ranged from <0.3 to 7.5 most probable number (MPN) per gram. In samples from markets, densities of V. parahaemolyticus showed higher values ranging from 0.61 to >110 MPN/g. Densities of V. cholerae in the two positive seafood samples reached values of 0.36 and 0.61 MPN/g, repectively. V. parahaemolyticus strains were found to possess tlh, but not tdh and trh by polymerase chain reaction, and all the strains of V. cholerae were non-O1 or non-O139. These results suggest that the prevalence of high salinities in coastal and estuarine environments of Senegal limits the occurrence of V. parahaemolyticus and V. cholerae, despite warmer temperatures prevailing in seawater environments throughout the year. Furthermore, temperature abuse driven by a deficient cold chain over the distribution and retail sales may represent a major risk due to the postharvest multiplication of these Vibrio pathogens.

Foodborne diseases and other enteric infections often occur as outbreaks and cause morbidity and mortality all over the world. In Perú, they represent a serious public health problem, and are caused by a great variety of infectious agents. For epidemiological research, a wide array of typification methods are used. One of the most important tools for the molecular subtyping of bacterial pathogens is the Pulsed Field Gel Electrophoresis (PFGE), which is a highly precise method that allows the discrimination between different bacterial isolates which are epidemiologically related. The Instituto Nacional de Salud del Perú (INS) is part of the WHO Global Foodborne Infections Network (WHO-GFN) and of the PulseNet Latin American and Caribbean Net (PN-AL & C), with whom it shares the genetic profiles of the isolated pathogenic strains, so that it is possible to compare de genotypes of similar strains found in different countries and to identify the occurrence of epidemic outbreaks in the region, strengthening the regional system of epidemiological surveillance and generating a rapid, coordinated response between the countries. We present the two last years experience including the advances in the use of these strategic tools that have allowed us to characterize genotype patterns implicated in foodborne diseases from isolates recovered in the laboratory network of Peru.