Monitoring jellyfish outbreaks along Israel's Mediterranean coast using digital footprints.

With mounting global concerns about jellyfish outbreaks, monitoring their occurrence remains challenging. Tapping into the wealth of digital data that internet users share online, which includes reports of jellyfish sightings, may provide an alternative or complement to more conventional expert-based or citizen science monitoring. Here, we explore digital footprints as a data source to monitor jellyfish outbreaks along the Israeli Mediterranean coast. We compiled jellyfish sighting data for the period 2011-2022 from multiple platforms, including leading social media platforms, searches in the Google search engine, and Wikipedia page views. Employing time series analysis, cross-correlation, and various evaluation metrics for presence/absence data, we compared weekly data from three sources: digital footprints, citizen science, and traditional expert-based field monitoring. Consistent seasonal patterns emerge across datasets, with notable correlations, particularly in jellyfish abundance. The cross-correlation between digital footprint and citizen science data exceeds >0.7, with Twitter and Instagram showing the highest correlation. Citizen science data often precedes digital footprints by up to one week. Correlation with traditional, expert-based field monitoring is limited as a result of limited data availability. Digital footprints demonstrate substantial agreement with the other data sources regarding jellyfish presence/absence and major outbreaks, especially for data from Wikipedia, Twitter, and Instagram. Overall, we highlight digital footprint data as a reliable, cost-effective tool for passive monitoring of jellyfish outbreaks, which can aid characterization in data-scarce coastal regions, including retrospective assessment. Transferring and scaling up the proposed approach should consider data accessibility as well as platform relative popularity and usage in the regions under investigation.

Reconstructing historic and modern potato late blight outbreaks using text analytics.

In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the disease should be managed. The pathogen, now known as Phytophthora infestans, still continues to threaten food security globally. A wealth of untapped knowledge exists in both archival and modern documents, but is not readily available because the details are hidden in descriptive text. In this work, we (1) used text analytics of unstructured historical reports (1843-1845) to map US late blight outbreaks; (2) characterized theories on the source of the pathogen and remedies for control; and (3) created modern late blight intensity maps using Twitter feeds. The disease spread from 5 to 17 states and provinces in the US and Canada between 1843 and 1845. Crop losses, Andean sources of the pathogen, possible causes and potential treatments were discussed. Modern disease discussion on Twitter included near-global coverage and local disease observations. Topic modeling revealed general disease information, published research, and outbreak locations. The tools described will help researchers explore and map unstructured text to track and visualize pandemics.

Outbreak of lead poisoning from a civilian indoor firing range in the UK.

INTRODUCTION: Lead exposure from discharged lead dust is a recognised risk at firing ranges. We report a lead poisoning outbreak among staff and their close contacts at a UK civilian indoor 24 m firing range. METHODS: A retrospective review was undertaken of data collected on all patients at risk of lead poisoning identified either by direct referral to the Clinical Toxicology clinicians at the West Midlands Poisons Unit, or via the Trace Elements Supra-Regional Assay Service Laboratory at Sandwell hospital. RESULTS: Eighty-seven patients were identified as having possible lead exposure, either at the firing range or via close contacts. Of these, 63 patients aged between 6 months and 78 years attended for blood lead concentration (BLC) testing. The highest BLC at presentation was 11.7 µmol/L (242 µg/dL). Only nine patients reported any symptoms at presentation. Fifteen patients received lead chelation therapy with oral dimercaptosuccinic acid (or succimer) 30 mg/kg/day or intravenous sodium calcium edetate (EDTA) 75 mg/kg/day, dependent on stock availability. DISCUSSION: This report highlights the need for vigilance of lead poisoning as an occupational hazard in the UK, including at recreational facilities such as indoor firing ranges. It emphasises the importance of regulation of lead exposure in the workplace, particularly given the vague symptoms of lead poisoning, and proposes re-appraisal of UK legislation. This report also highlights potential issues surrounding stock availability of rarely used antidotes for uncommon presentations in the event of an outbreak of poisoning.

Impact of Ebola epidemics on the daily operation of existing systems in Eastern Democratic Republic of the Congo: a brief review.

AIMS: to provide insights into the recent Ebola virus disease (EVD) outbreaks on different aspects of daily life in the Democratic Republic of the Congo and propose possible solutions. METHODS: We collected information regarding the effects of EVD outbreaks on existing systems in the eastern part of the Democratic Republic of the Congo (DRC). We searched the PubMed database using the terms "impact effect Ebola outbreak system", "Management Ebola Poor Resources Settings", "Health Economic Challenges Ebola" and "Economic impact Ebola systems." Only studies focusing on epidemiology, diagnostics, sequencing, vaccination, therapeutics, ecology, work force, governance, healthcare provision and health system, and social, political, and economic aspects were considered. The search included the electronic archives of EVD outbreak reports from government and partners. RESULTS: EVD outbreaks negatively impacts the functions of countries. The disruption in activities is proportional to the magnitude of the epidemic and slows down the transport of goods, decreases the region's tourist appeal, and increases 'brain drain'. Most low- and medium-income countries, such as the DRC, do not have a long-term holistic emergency plan for unexpected situations or sufficient resources to adequately implement countermeasures against EVD outbreaks. Although the DRC has acquired sufficient expertise in diagnostics, genomic sequencing, administration of vaccines and therapeutics, clinical trials, and research activities, deployment, operation, and maintenance of these expertise and associated tools remains a concern. LIMITATIONS: Despite the data search extension, additional reports addressing issues related to social aspects of EVD outbreaks in DRC were not retrieved. CONCLUSION: National leadership has not yet taken the lead in strategic, operational, or financial aspects. Therefore, national leaders should double their efforts and awareness to encourage local fundraising, sufficient budget al.location, infrastructure construction, equipment provision, and staff training, to effectively support a holistic approach in response to outbreaks, providing effective results, and all types of research activities.

Unusual outbreaks of curly top disease in processing tomato fields in northern California in 2021 and 2022 were caused by a rare strain of beet curly top virus and facilitated by extreme weather events.

In the western United States, curly top disease (CTD) is caused by beet curly top virus (BCTV). In California, CTD causes economic loss to processing tomato production in central and southern areas but, historically, not in the north. Here, we document unusual CTD outbreaks in processing tomato fields in the northern production area in 2021 and 2022, and show that these were caused by the rare spinach curly top strain (BCTV-SpCT). These outbreaks were associated with proximity of fields to foothills and unusually hot, dry, and windy spring weather conditions, possibly by altering migrations of the beet leafhopper (BLH) vector from locations with BCTV-SpCT reservoirs. Support for this hypothesis came from the failure to observe CTD outbreaks and BLH migrations in 2023, when spring weather conditions were cool and wet. Our results show the climate-induced emergence of a rare plant virus strain to cause an economically important disease in a new crop and location.

Risk and Preventive Factors for Depressive Symptoms Among Older Chilean Adults During the SARS-CoV-2 Outbreak: A Longitudinal Study.

OBJECTIVE: To specifically examine the multiple factors related to the increase in depressive symptoms during the COVID-19 outbreak in older adults in Chile. METHOD: A longitudinal study was conducted using a dataset from a nationally representative survey cohort of Chilean older adults followed at three time points during the COVID-19 outbreak. The main outcome was depressive symptoms (Patient Health Questionnaire scale). The independent variables included: age, sex, educational level, geographic area, living alone, self-perceived health, self-reported resilience, loneliness, and social isolation. RESULTS: A total of 424 older adults were included. Female sex (ß = 0.95, 95% CI: 0.22 to 1.68) and loneliness (ß = 1.21, 95% CI: 1.05 to 1.37) were the main risk factors for an increase in depressive symptoms in older adults. In contrast, living outside the metropolitan region (ß=-0.70, 95% CI: -1.39 to -0.02), living in company (ß=-0.34, 95% CI:-1.24 to 0.56), having better self-perceived health (ß=-5.04, 95% CI:-6.33 to -3.75) and greater resilience (ß=-0.30, 95% CI: -0.38 to -0.23) were preventive factors. CONCLUSION: These results provide useful evidence to develop mental health prevention or control strategies for older adults. CLINICAL IMPLICATIONS: The findings highlight the importance of a holistic approach to health care for older adults that integrates strategies to address loneliness, foster resilience, and promote an active social life.

The utility of whole-genome sequencing to inform epidemiologic investigations of SARS-CoV-2 clusters in acute-care hospitals.

OBJECTIVE: To evaluate the utility of selective reactive whole-genome sequencing (WGS) in aiding healthcare-associated cluster investigations. DESIGN: Mixed-methods quality-improvement study. SETTING: Thes study was conducted across 8 acute-care facilities in an integrated health system. METHODS: We analyzed healthcare-associated coronavirus disease 2019 (COVID-19) clusters between May 2020 and July 2022 for which facility infection prevention and control (IPC) teams selectively requested reactive WGS to aid the epidemiologic investigation. WGS was performed with real-time results provided to IPC teams, including genetic relatedness of sequenced isolates. We conducted structured interviews with IPC teams on the informativeness of WGS for transmission investigation and prevention. RESULTS: In total, 8 IPC teams requested WGS to aid the investigation of 17 COVID-19 clusters comprising 226 cases and 116 (51%) sequenced isolates. Of these, 16 (94%) clusters had at least 1 WGS-defined transmission event. IPC teams hypothesized transmission pathways in 14 (82%) of 17 clusters and used data visualizations to characterize these pathways in 11 clusters (65%). The teams reported that in 15 clusters (88%), WGS identified a transmission pathway; the WGS-defined pathway was not one that was predicted by epidemiologic investigation in 7 clusters (41%). WGS changed the understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in 8 clusters (47%) and altered infection prevention interventions in 8 clusters (47%). CONCLUSIONS: Selectively utilizing reactive WGS helped identify cryptic SARS-CoV-2 transmission pathways and frequently changed the understanding and response to SARS-CoV-2 outbreaks. Until WGS is widely adopted, a selective reactive WGS approach may be highly impactful in response to healthcare-associated cluster investigations.

Comprehensive overview of 2022 human monkeypox outbreak and its pathology, prevention, and treatment: A strategy for disease control.

The 2022 Monkeypox virus, an evolved DNA strain originating in Africa, exhibits heightened human-to-human transmissibility and potential animal transmission. Its host remains unidentified. While its initial slow transmission rate restrained global impact, 2022 saw a surge in cases, causing widespread concern in over 103 countries by September. This virus's distinctive human-to-human transmission marks a crucial shift, demanding a prompt revaluation of containment strategies. However, the host source for this shift requires urgent research attention. Regrettably, no universal preventive or curative methods have emerged for this evolved virus. Repurposed from smallpox vaccines, only some vaccinations offer a partial defense. Solely one therapeutic drug is available. The article's essence is to provide a comprehensive grasp of the virus's epidemiology, morphology, immune invasion mechanisms, and existing preventive and treatment measures. This knowledge equips researchers to devise strategies against its spread and potential public health implications.

The Medicine Wheel: informing the management of tuberculosis outbreaks in Indigenous communities.

Many Indigenous communities in Canada experience endemic tuberculosis with superimposed periodic epidemic outbreaks. Failures in outbreak management have resulted in the "seeding" of future infection and disease. In this paper we present a model that may be used in planning, implementation and review of tuberculosis outbreak management in Cree Indigenous communities in Canada, based on the Medicine Wheel, a paradigm for holistic living. In the context of tuberculosis management, the Medicine Wheel provides a path for the establishment of respectful cross-cultural relationships, the expression of values through action, true community engagement and partnership, and the establishment of culture-based processes of transparency, accountability and change.

[Response of the government and people in pandemics in the Tang Dynasty].

It was believed that the Tang Dynasty was a historical period with relatively few pandemics and little impact in the official history records. The reasons for this and the context and the living conditions of people during pandemics should be analysed in depth. This paper examined 49 pandemic outbreaks which seriously influenced on the society of the Tang Dynasty in terms of time and space distribution, historical features, correlation with other disasters, and regional distribution. The paper also analysed the measures taken by the government to deal with pandemics, including sending physicians and herbs, compensating the people, providing prescriptions, and burying dead bodies. This paper summarised the understanding of pandemics in the Tang Dynasty, such as the will of ghosts, the karma, the astrology and the contagion between the patients. It was found that the ways for the people at that time dealt with pandemics, included praying, offering sacrifices, asking for help from Monks and Taoist, and even moving to other safe places. It was also found the dead who were properly buried could give people psychological comfort.

National and subnational governance and decision-making processes during the COVID-19 pandemic in Nigeria: an empirical analysis.

Governance of the COVID-19 pandemic required decision-makers to make and implement decisions amidst uncertainty, public pressure and time constraints. However, few studies have attempted to assess these decision-making processes empirically during health emergencies. Thus, we aimed to understand governance, defined as the process of decision-making and implementation of decisions, during the COVID-19 pandemic in Nigeria. We conducted key informant interviews and focus group discussions with national and subnational government officials, civil society organisation (CSO) members, development partners and academic experts. Our study identified several themes on governance and decision-making processes. First, Nigeria established high-level decision-making structures at the federal and state levels, providing clear and integrated multisectoral decision-making mechanism. However, due to the emergence of conflicts between government levels, there is a need to strengthen intergovernmental arrangements. Second, while decision-makers relied on input from academic experts and CSOs, additional efforts are required to engage such stakeholders in decision-making processes, especially during the early stages of health emergencies. Third, Nigeria's previous experiences responding to disease outbreaks aided the overall response, as many capacities and coordination mechanisms for cohesive action were present. Fourth, while decision-makers took a holistic view of scientific, social and economic factors for decision-making, this process was also adaptive to account for rapidly evolving information. Lastly, more efforts are needed to ensure decisions are inclusive, equitable and transparent, and improve overall public trust in governance processes. This study provides insights and identifies opportunities to enhance governance and decision-making processes in health emergency responses, aiding future pandemic preparedness efforts.

Strategies for maintaining and strengthening the health care workers during epidemics: a scoping review.

INTRODUCTION: During epidemics such as COVID-19, healthcare workers (HCWs) face several challenges, leading to a shortage and weakening of human resources. To address this issue, employing effective strategies is essential in maintaining and strengthening human resources during outbreaks. This study aimed to gather and classify strategies that could retain and strengthen human health resources during epidemics. METHODS: In this scoping review, all studies published about strategies for maintaining and strengthening HCWs in epidemics were collected from 4 international databases, including PubMed, Embase, Scopus, and Web of Science. The English language articles published after 2000 up until June 2022 recommended specific strategies regarding the research question. Then, they were analyzed and classified according to thematic analysis based on Braun and Clarke 6 phases protocols. RESULTS: In total, 9405 records were screened, of which 59 articles were included, and their full texts were reviewed. Fifty factors were identified and classified into five themes: Instruction, Protection, Supporting, Caring, and Communication. Most of the suggestions were conducted in high-income countries and related to the Supporting theme. DISCUSSION: The majority of strategies discussed in the literature addressed only one or two aspects of human resources. This study provides a holistic perspective on these issues by providing a thematic map of different strategies for strengthening and maintaining HCWs during epidemics. Considering the multidimensionality of human nature, it is suggested that policymakers and managers of health systems provide facilities that simultaneously address a wide range of needs.

Dynamic risk connectedness of crude oil price and sustainable investment in the United States: evidence from DCC-GARCH.

Sustainable investment is widely regarded as an important market-based approach to achieving inclusive green growth. To achieve the inclusive green growth objective, companies providing sustainable products must be profitable enough to attract private capital. Oil price changes can however affect the profitability of such companies. This study assesses volatility transmission between crude oil prices and sustainable investment in the USA. Using the dynamic conditional correlation-generalized autoregressive conditional heteroskedasticity (DCC-GARCH) method, daily data from September 28, 2012, to October 19, 2022, is analyzed. There are several key findings from this analysis. The risk connectedness of crude oil and sustainable investment is found to vary with time. Results further show that the risk connectedness increases in periods of important economic and geopolitical events. The greatest risk connectedness of crude oil and sustainable investment is observed during the outbreak of coronavirus disease (COVID-19). Moreover, the result shows that crude oil is the main risk transmitter, whereas, both the energy efficiency and pollution mitigation indices (i.e., sustainable investment) are risk receivers, and crude oil is constantly dominating sustainable investment. The study findings provide valuable insights for investors and policymakers alike.

Investigation of a Multistate Outbreak of Listeria monocytogenes Infections Linked to Frozen Vegetables Produced at Individually Quick-Frozen Vegetable Manufacturing Facilities.

In 2016, the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state partners investigated nine Listeria monocytogenes infections linked to frozen vegetables. The investigation began with two environmental L. monocytogenes isolates recovered from Manufacturer A, primarily a processor of frozen onions, that were a match by whole genome sequencing (WGS) to eight clinical isolates and historical onion isolates with limited collection details. Epidemiologic information, product distribution, and laboratory evidence linked suspect food items, including products sourced from Manufacturer B, also a manufacturer of frozen vegetable/fruit products, with an additional illness. The environmental isolates were obtained during investigations at Manufacturers A and B. State and federal partners interviewed ill people, analyzed shopper card data, and collected household and retail samples. Nine ill persons between 2013 and 2016 were reported in four states. Of four ill people with information available, frozen vegetable consumption was reported by three, with shopper cards confirming purchases of Manufacturer B brands. Two identified outbreak strains of L. monocytogenes (Outbreak Strain 1 and Outbreak Strain 2) were a match to environmental isolates from Manufacturer A and/or isolates from frozen vegetables recovered from open and unopened product samples sourced from Manufacturer B; the investigation resulted in extensive voluntary recalls. The close genetic relationship between isolates helped investigators determine the source of the outbreak and take steps to protect public health. This is the first known multistate outbreak of listeriosis in the United States linked to frozen vegetables and highlights the significance of sampling and WGS analyses when there is limited epidemiologic information. Additionally, this investigation emphasizes the need for further research regarding food safety risks associated with frozen foods.

An outbreak of severe coagulopathy in northern Israel among users of illicit synthetic cannabinoids adulterated with brodifacoum.

INTRODUCTION: Adulteration of illicit drugs is a well-known phenomenon that may expose consumers to unexpected adverse effects. We report a large outbreak of severe coagulopathy in northern Israel during nine months in 2021-2022 among users of synthetic cannabinoids adulterated with a long-acting anticoagulant, brodifacoum. METHODS: We performed a retrospective cohort study based on data extracted from the Israeli National Poison Information Center database and from electronic medical patient records at three participating hospitals. Confiscated drug samples and blood samples obtained at admission in a subgroup of patients were tested for the presence of long-acting anticoagulants. RESULTS: We identified 98 patients affected by the outbreak. All patients had a prolonged international normalized ratio on admission, and in 69%, the blood was non-coagulating. For patients treated in the three participating centers (n = 72), the presenting complaint was overt bleeding in 79% of patients, most commonly in the urinary (53%) and gastrointestinal tracts (50%). The most severe complications were intracranial bleeding (4%), hemothorax (3%), pericardial bleeding (1%), and four patients died. Brodifacoum was detected in all available blood samples (median concentration 207 µg/L, interquartile range 112-349 µg/L, range 45-1,118 µg/L), and the drug samples contained both brodifacoum and the synthetic cannabinoid ADB-BUTINACA. All patients were treated with high-dose phytomenadione (vitamin K1) and additionally by packed red blood cell transfusions, fresh frozen plasma, and/or 4-factor prothrombin complex concentrate when indicated. The most frequent phytomenadione (vitamin K1) dose regimen was initially 20 mg intravenously every eight hours, and at discharge, 20 mg orally three times daily. CONCLUSIONS: Outbreaks of severe coagulopathies in users of synthetic cannabinoids adulterated with a long-acting anticoagulant continue to erupt in different regions of the world. Rapid recognition of an outbreak requires a high index of suspicion when confronting young, otherwise healthy subjects with otherwise unexplained severe coagulopathy.

A community-based contact isolation strategy to reduce the spread of Ebola virus disease: an analysis of the 2018-2020 outbreak in the Democratic Republic of the Congo.

INTRODUCTION: Despite tremendous progress in the development of diagnostics, vaccines and therapeutics for Ebola virus disease (EVD), challenges remain in the implementation of holistic strategies to rapidly curtail outbreaks. We investigated the effectiveness of a community-based contact isolation strategy to limit the spread of the disease in the Democratic Republic of Congo (DRC). METHODS: We did a quasi-experimental comparison study. Eligible participants were EVD contacts registered from 12 June 2019 to 18 May 2020 in Beni and Mabalako Health Zones. Intervention group participants were isolated to specific community sites for the duration of their follow-up. Comparison group participants underwent contact tracing without isolation. The primary outcome was measured as the reproduction number (R) in the two groups. Secondary outcomes were the delay from symptom onset to isolation and case management, case fatality rate (CFR) and vaccination uptake. RESULTS: 27 324 EVD contacts were included in the study; 585 in the intervention group and 26 739 in the comparison group. The intervention group generated 32 confirmed cases (5.5%) in the first generation, while the comparison group generated 87 (0.3%). However, the 32 confirmed cases arising from the intervention contacts did not generate any additional transmission (R=0.00), whereas the 87 confirmed cases arising from the comparison group generated 99 secondary cases (R=1.14). The average delay between symptom onset and case isolation was shorter (1.3 vs 4.8 days; p<0.0001), CFR lower (12.5% vs 48.4%; p=0.0001) and postexposure vaccination uptake higher (86.0% vs 56.8%; p<0.0001) in the intervention group compared with the comparison group. A significant difference was also found between intervention and comparison groups in survival rate at the discharge of hospitalised confirmed patients (87.9% vs 47.7%, respectively; p=0.0004). CONCLUSION: The community-based contact isolation strategy used in DRC shows promise as a potentially effective approach for the rapid cessation of EVD transmission, highlighting the importance of rapidly implemented, community-oriented and trust-building control strategies.

An application of Bayesian vector heterogeneous autoregressions to study network interlinkages of the crude oil and gold, stock, and cryptocurrency markets during the COVID-19 outbreak.

We investigate fat tails and network interconnections of crude oil, gold, stock, and cryptocurrency using seven Bayesian vector heterogeneous autoregression fashions. In this paper, we incorporate parameter uncertainty by using Bayesian VAR models for estimation. To make rational investment decisions, we decompose a network of financial assets and commodity prices into various time horizons to obtain essential insight and knowledge. During the short, medium, and long run, this paper differentiates dynamically between network interlinkages between these markets. We found some noteworthy results in our study. In the first place, network interlinkages exhibit remarkable differences over time. Interlinkages between networks are increased in the short term, medium term, and long term due to transient events occurring in markets during the study period. As a result of the ongoing COVID-19 epidemic, the long-term ties within the system are significantly impacted. Additionally, based on net directional linkages, each market's role shifts (from sending to receiving shock and vice versa) before the pre-COVID-19 pandemic course, whereas they remain persistent during COVID-19. Observations of short- and medium-term trends reveal that three markets, namely, crude oil, gold, and stock, receive shocks, which are transmitted to these markets by the cryptocurrency market. In terms of long-horizon measures, the results indicate that the gold and cryptocurrency markets persist as shock transmitters. Our findings are critical since policymakers can also design appropriate policies to reduce the vulnerabilities of such markets and prevent risk spread and instability.

Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom.

Globalization of the food supply chain has created conditions favorable for emergence and spread of multidrug-resistant (MDR) foodborne pathogens. In November 2021, the UK Health Security Agency detected an outbreak of 17 cases infected with the same strain of MDR extended spectrum beta-lactamase (ESBL)-producing Shigella sonnei. Phylogenetic analysis of whole-genome sequencing data revealed the outbreak was closely related to strains of S. sonnei isolated from travelers returning to the UK from Egypt. None of the outbreak cases reported travel and all 17 cases reported eating food from a restaurant/food outlet in the week prior to symptom onset, of which 11/17 (64.7%) ate at branches of the same national restaurant franchise. All 17 cases were adults and 14/17 (82.4%) were female. Ingredient-level analyses of the meals consumed by the cases identified spring onions as the common ingredient. Food chain investigations revealed that the spring onions served at the implicated restaurants could be traced back to a single Egyptian producer. The foodborne transmission of ESBL-producing bacteria is an emerging global health concern, and concerted action from all stakeholders is required to ensure an effective response to mitigate the risks to public health.

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.

BACKGROUND: The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer. RESULTS: SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation. CONCLUSION: Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.

Imported spring onions related to the first recorded outbreak of enteroinvasive Escherichia coli in Denmark, November to December 2021.

Between November and December 2021, the first ever recorded outbreak of enteroinvasive Escherichia coli in Denmark occurred at national scale. We describe the investigation of this outbreak, which was initially recognised in early December 2021. A total of 88 cases (58 female; 30 male) with a median age of 52 years (range: 0-91) were detected by PCR-based diagnostic methods. Case ascertainment was complicated by current culture-free diagnostic procedures, with only 34 cases confirmed by culture, serotyping and whole genome sequencing. Isolates from cases grouped into two serotypes (O136:H7 and O96:H19), which was supported by whole-genome-sequence-phylogeny, also yielding two clusters. Interviews of 42 cases and traceback investigation pointed towards consumption of ready-to-eat salads as the outbreak cause. While the ready-to-eat salads comprised different vegetables, imported spring onions were the only common ingredient and thus the likely source. Environmental investigations failed to recover outbreak strains. This report highlights the value of fast typing (here O-typing) to confirm cases in an outbreak situation. Timely communication and data sharing are also important, and were facilitated by the national collaboration between relevant laboratories, the public health institute and the veterinary and food administration. High hygiene standards for imported fresh vegetables intended for ready-to-eat products are essential.