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The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

The challenges and problems of managing good biosecurity are wide‐ranging and multifactorial with many compounding factors to pre‐dispose farmed stocks to an increased risk of infection with consequential stock losses. Many challenges are anthropogenic in origin and may be the result of the physical location (site) and/or the poor design of the production facility (i.e., water re‐use; lack of zoning based on biosecurity risk, etc.) as well as from inappropriate decisions and practices made once the site is in production (i.e., pushing the system for increased biomass production). There is a need for better regulation and health legislation across aquaculture—an industry that embraces the culture of >500 species. In the absence of regulatory frameworks and culture guidelines, it is difficult for farmers to apply certain measures such as maximum stocking densities and maximum allowed biomass, conduct disease surveillance and regular health checks, and report diseases to relevant authorities for advice. In this review, we have identified several issues which are continuing to challenge the design and implementation of efficient and effective biosecurity strategies and protocols at all levels, requiring attention over the coming decade. They are, not in any order of priority: (a) healthy seed, (b) emergency preparedness and response, (c) diagnostics, (d) microbial management at the production level, (e) disease and pathogen surveillance, (f) trade in aquatic species, (g) policies and regulatory framework, (h) welfare, (i) research and technology development, (j) antimicrobial resistance, (k) non‐conventional ways of pathogen transfer, and (l) Progressive Management Pathway.

Understanding the regional pathogen landscape and surveillance of emerging pathogens is key to mitigating epidemics. Challenges lie in resource-scarce settings, where outbreaks are likely to emerge, but where laboratory diagnostics and bioinformatics capacity are limited. Using metagenomic next-generation sequencing (mNGS), we identified a variety of vector-borne, zoonotic, and emerging pathogens responsible for undifferentiated fevers in a periurban population in Cambodia. From March 2019 to October 2020, we enrolled 464 febrile patients (and 23 afebrile persons) aged 6 mo to 65 y presenting to a large periurban hospital in Cambodia. We collected sera and prepared sequencing libraries from extracted pathogen RNA for unbiased metagenomic sequencing and subsequent bioinformatic analysis on the global cloud-based platform, CZID (“IDseq”). We employed multivariable regression models to evaluate pathogen risk factors associated with undifferentiated febrile illness. mNGS identified vector-borne pathogens as the largest clinical category with dengue virus (124 of 489) as the most abundant pathogen. Underappreciated zoonotic pathogens, such as Plasmodium knowlesi, leptospirosis, and coinfecting HIV were also detected. Early detection of chikungunya virus presaged a larger national outbreak of more than 6,000 cases. Pathogen-agnostic mNGS investigation of febrile persons in resource-scarce Southeast Asia is feasible and revealing of a diverse pathogen landscape. Coordinated and ongoing mNGS pathogen surveillance can better identify the breadth of endemic, zoonotic, or emerging pathogens and deployment of rapid public health response.

Tick-borne diseases in humans and animals have increased prevalence across the United States. To understand risk factors underlying tick-borne diseases it is useful to conduct regular surveillance and monitoring of ticks and the pathogens they carry, in a sustained and effective manner. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, this study aims to summarize the previously used methods for active surveillance of ticks and tick-borne pathogens, identify the existing knowledge gaps in ongoing surveillance, and highlight and guide the mechanisms required to inform those gaps for more effective and sustainable future surveillance efforts. After screening 2,500 unique studies between 1944 and 2018, we found 646 articles that performed active surveillance of hard ticks and/or their associated tick-borne pathogens of public health importance within the United States. An additional 103 articles were included for the 2019 to 2023 period. Active surveillance has been performed in ∼42% of the counties (1944 to 2018) and ∼23% of the counties (2019 to 2023) within the contiguous US, and states with the most coverage are in the Northeast, Upper Midwest, and along the West coast. The most reported tick was Ixodes scapularis (195 studies) and most commonly reported pathogen was Borrelia burgdorferi (143 studies). Overall, surveillance efforts have increased and become more diversified, and methods of tick and tick-borne pathogens testing have undergone changes, but those efforts are mainly concentrated in focal regions of a county. Future surveillance efforts should follow Centers for Disease Control and Prevention guidelines and target areas of United States with scarce reports of active surveillance and build collaborations and resources to increase surveillance. Graphical Abstract Graphical abstract of the main results of this systematic review study.

We analyzed body lice collected from persons experiencing homelessness in Winnipeg, Manitoba, Canada, during 2020-2021 to confirm vector species and ecotype and to identify louseborne pathogens. Of 556 lice analyzed from 7 persons, 17 louse pools (218 lice) from 1 person were positive for the louseborne bacterium Bartonella quintana.

Background Acute respiratory infections are caused by a diverse range of pathogens. The study aims to elucidate the epidemic characteristics of acute respiratory pathogens in Guangdong Province during the first year after the COVID-19 pandemic. Methods We collected sentinel surveillance data of 12 respiratory pathogens from multi-pathogen surveillance among acute respiratory infections from August 2023 to July 2024 in Guangdong Province, China. We also collected surveillance data on hospitalized pneumonia as a supplementary. We calculated the test positivity for each pathogen and performed pairwise correlation analysis. Results Multi-pathogen surveillance revealed that over half of acute respiratory infections tested positive for at least one pathogen. The most commonly detected pathogens were influenza virus (19.70%, 3,211/16,296), Streptococcus pneumoniae (10.99%, 1,343/12,215), and rhinovirus/enteroviruses (8.66%, 1,411/16,296). In the autumn and winter of 2023, the test positivity of influenza virus surpassed 20% starting in October, indicating that the winter epidemic period arrived earlier than that in the pre-COVID-19 pandemic period (typically December or later). The overall positivity was highest in the 0–14 age group (60.07%, 4,797/7,903), and pathogen distribution varied significantly across age groups. Correlation analysis revealed significant positive correlations between rhinovirus/enteroviruses and other pathogens, such as respiratory syncytial virus. Hospitalized pneumonia surveillance showed the proportion of Mycoplasma pneumoniae infections increased to 17.08% (3,707/21,701) in 2023, surpassing the pre-pandemic average of 10.52%. Conclusions After the COVID-19 pandemic, we observed different characterization of the pathogen causing acute respiratory infections in Guangdong Province. The activity of influenza and Mycoplasma pneumoniae initially exhibited shifts compared to the pre-pandemic period. Pathogen distribution varied significantly across age groups, highlighting high-risk populations for specific pathogens. Continuous multi-pathogen surveillance is essential for understanding their epidemiological characteristics and formulating effective prevention and control measures, including vaccination strategies, clinical interventions.

Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici ( Pst ), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

Respiratory pathogen surveillance dashboards surged during the COVID-19 pandemic and have remained widely used tools for real-time data visualization in public health. While these dashboards offer timely, actionable insights for monitoring trends and decision-making, their rapid expansion has also highlighted persistent challenges related to governance, data accessibility, standardization, and sustainability. To explore these issues in depth, the Center of Excellence for Respiratory Pathogens (CERP) hosted a two-day workshop in Lyon, France. Experts representing a range of respiratory pathogen surveillance initiatives convened to share experiences, highlight successes, and discuss ongoing challenges. Key themes included the need for improved data quality, transparency, and standardization; sustainable IT infrastructure and staffing; greater access to underlying data; and alignment between dashboard objectives and user needs. Participants emphasized that broader governance and collaboration challenges strongly impact dashboard performance and interoperability. This report summarizes the valuable insights and subsequent actionable recommendations that emerged from the workshop, offering guidance to both developers and users of respiratory pathogen (or disease burden) dashboards. It aims to support the development of a more integrated, effective, and sustainable global respiratory surveillance ecosystem.

Early detection protocols for the oak wilt fungal pathogen (Bretziella fagacearum) are crucial for forest health practitioners on the boundaries of the growing disease front. Established protocols use oak wilt-specific primers and gel electrophoresis to amplify and detect oak wilt among DNA extracted from nitidulid vectors. However, these protocols are prone to inconclusive results due to the presence of off-target amplification products similar in size to positive control bands. Using sequence-adapted oak wilt primers, we employed a metabarcoding amplicon sequencing approach that resolved inconclusive results and validated true oak wilt positives. We found that these off-target amplification products are co-occurring taxa from natural forest and beetle microbiomes, further necessitating a sequencing approach for early surveillance of oak wilt.

Genomic data on the foodborne pathogen Listeria monocytogenes from Central America are scarce. We analyzed 92 isolates collected during 2009-2019 from different regions in Costa Rica, compared those to publicly available genomes, and identified unrecognized outbreaks. Our findings suggest mandatory reporting of listeriosis in Costa Rica would improve pathogen surveillance.