Interconnecting global threats: climate change, biodiversity loss, and infectious diseases.

The concurrent pressures of rising global temperatures, rates and incidence of species decline, and emergence of infectious diseases represent an unprecedented planetary crisis. Intergovernmental reports have drawn focus to the escalating climate and biodiversity crises and the connections between them, but interactions among all three pressures have been largely overlooked. Non-linearities and dampening and reinforcing interactions among pressures make considering interconnections essential to anticipating planetary challenges. In this Review, we define and exemplify the causal pathways that link the three global pressures of climate change, biodiversity loss, and infectious disease. A literature assessment and case studies show that the mechanisms between certain pairs of pressures are better understood than others and that the full triad of interactions is rarely considered. Although challenges to evaluating these interactions-including a mismatch in scales, data availability, and methods-are substantial, current approaches would benefit from expanding scientific cultures to embrace interdisciplinarity and from integrating animal, human, and environmental perspectives. Considering the full suite of connections would be transformative for planetary health by identifying potential for co-benefits and mutually beneficial scenarios, and highlighting where a narrow focus on solutions to one pressure might aggravate another.

On-site detection of infectious disease based on CaCO3-based magnetic micromotor integrated with graphene field effect transistor.

A new detection platform based on CaCO3-based magnetic micromotor (CaCO3@Fe3O4) integrated with graphene field effect transistor (GFET) was construct and used for on-site SARS-CoV-2 coronavirus pathogen detection. The CaCO3@Fe3O4 micromotor, which was modified with anti-SARS-CoV-2 (labelled antibody, AntiE1), can self-moved in the solution containing hydrochloric acid (HCl) and effective to capture the SARS-CoV-2 coronavirus pathogens. After magnetic field separation, the capture micromotor was detected by GFET, exhibiting a good linear relationship within the range of 1 ag/mL to 100 ng/mL and low detection limit (0.39 ag/mL). Furthermore, the detection platform was also successfully applied to detection of SARS-CoV-2 coronavirus pathogens in soil solution, indicating the potential use in on-site application.

Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein.

Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.

Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences.

Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction number R and the dispersion parameter k have however mainly remained limited to the analysis of epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show that clusters of identical sequences are imprinted by the pathogen offspring distribution, and we derive an analytical formula for the distribution of the size of these clusters. We develop and evaluate an inference framework to jointly estimate the reproduction number and the dispersion parameter from the size distribution of clusters of identical sequences. We then illustrate its application across a range of epidemiological situations. Finally, we develop a hypothesis testing framework relying on clusters of identical sequences to determine whether a given pathogen genetic subpopulation is associated with increased or reduced transmissibility. Our work provides tools to estimate the reproduction number and transmission heterogeneity from pathogen sequences without building a phylogenetic tree, thus making it easily scalable to large pathogen genome datasets.

Long-term variations of urban-Rural disparities in infectious disease burden of over 8.44 million children, adolescents, and youth in China from 2013 to 2021: An observational study.

BACKGROUND: An accelerated epidemiological transition, spurred by economic development and urbanization, has led to a rapid transformation of the disease spectrum. However, this transition has resulted in a divergent change in the burden of infectious diseases between urban and rural areas. The objective of our study was to evaluate the long-term urban-rural disparities in infectious diseases among children, adolescents, and youths in China, while also examining the specific diseases driving these disparities. METHODS AND FINDINGS: This observational study examined data on 43 notifiable infectious diseases from 8,442,956 cases from individuals aged 4 to 24 years, with 4,487,043 cases in urban areas and 3,955,913 in rural areas. The data from 2013 to 2021 were obtained from China's Notifiable Infectious Disease Surveillance System. The 43 infectious diseases were categorized into 7 categories: vaccine-preventable, bacterial, gastrointestinal and enterovirus, sexually transmitted and bloodborne, vectorborne, zoonotic, and quarantinable diseases. The calculation of infectious disease incidence was stratified by urban and rural areas. We used the index of incidence rate ratio (IRR), calculated by dividing the urban incidence rate by the rural incidence rate for each disease category, to assess the urban-rural disparity. During the nine-year study period, most notifiable infectious diseases in both urban and rural areas exhibited either a decreased or stable pattern. However, a significant and progressively widening urban-rural disparity in notifiable infectious diseases was observed. Children, adolescents, and youths in urban areas experienced a higher average yearly incidence compared to their rural counterparts, with rates of 439 per 100,000 compared to 211 per 100,000, respectively (IRR: 2.078, 95% CI [2.075, 2.081]; p < 0.001). From 2013 to 2021, this disparity was primarily driven by higher incidences of pertussis (IRR: 1.782, 95% CI [1.705, 1.862]; p < 0.001) and seasonal influenza (IRR: 3.213, 95% CI [3.205, 3.220]; p < 0.001) among vaccine-preventable diseases, tuberculosis (IRR: 1.011, 95% CI [1.006, 1.015]; p < 0.001), and scarlet fever (IRR: 2.942, 95% CI [2.918, 2.966]; p < 0.001) among bacterial diseases, infectious diarrhea (IRR: 1.932, 95% CI [1.924, 1.939]; p < 0.001), and hand, foot, and mouth disease (IRR: 2.501, 95% CI [2.491, 2.510]; p < 0.001) among gastrointestinal and enterovirus diseases, dengue (IRR: 11.952, 95% CI [11.313, 12.628]; p < 0.001) among vectorborne diseases, and 4 sexually transmitted and bloodborne diseases (syphilis: IRR 1.743, 95% CI [1.731, 1.755], p < 0.001; gonorrhea: IRR 2.658, 95% CI [2.635, 2.682], p < 0.001; HIV/AIDS: IRR 2.269, 95% CI [2.239, 2.299], p < 0.001; hepatitis C: IRR 1.540, 95% CI [1.506, 1.575], p < 0.001), but was partially offset by lower incidences of most zoonotic and quarantinable diseases in urban areas (for example, brucellosis among zoonotic: IRR 0.516, 95% CI [0.498, 0.534], p < 0.001; hemorrhagic fever among quarantinable: IRR 0.930, 95% CI [0.881, 0.981], p = 0.008). Additionally, the overall urban-rural disparity was particularly pronounced in the middle (IRR: 1.704, 95% CI [1.699, 1.708]; p < 0.001) and northeastern regions (IRR: 1.713, 95% CI [1.700, 1.726]; p < 0.001) of China. A primary limitation of our study is that the incidence was calculated based on annual average population data without accounting for population mobility. CONCLUSIONS: A significant urban-rural disparity in notifiable infectious diseases among children, adolescents, and youths was evident from our study. The burden in urban areas exceeded that in rural areas by more than 2-fold, and this gap appears to be widening, particularly influenced by tuberculosis, scarlet fever, infectious diarrhea, and typhus. These findings underscore the urgent need for interventions to mitigate infectious diseases and address the growing urban-rural disparity.

[Pathological profile of S.P. Botkin infectious hospital during the siege of Leningrad (1941-1944)]. / Patologo-anatomicheskii profil' infektsionnoi bol'nitsy im. S.P. Botkina v gody blokady Leningrada (1941­1944 gg.).

The results of autopsies performed in the pathological department of the Infectious Diseases Hospital named after. S.P. Botkin during the siege of Leningrad (from September 8, 1941 to January 27, 1944). The structure of diseases of the deceased varied during different periods of the siege of Leningrad. In the first period (September-December 1941), diphtheria, dysentery, measles, typhoid fever, and scarlet fever prevailed among the diseases. The most common causes of death in the second period (April-December 1942) were typhus, dysentery, tuberculosis, lobar pneumonia, and typhoid fever. Nosological structure in the third period of the blockade (January 1943 - January 1944): tuberculosis, dysentery, cachexia, lobar pneumonia, infectious jaundice. The discrepancy between clinical and morphological diagnoses is most often noted for the following nosology: pulmonary tuberculosis, typhoid fever, pneumonia, stomach and hepatopancreatobiliary cancer, measles, influenza. The first period of the blockade was distinguished by a high specific proportion of examination of children's bodies - 51.2% of all autopsies; in subsequent periods, the specific share of autopsies of deceased adults (20-59 years) increased to 76.2%. The difference in the nosological structure and age groups of those who died during different periods of the siege of Leningrad was determined by the epidemiological situation in the city, social and living conditions and medical and organizational factors. Conducted in the pathological-anatomical department of the hospital named after. S.P. Botkin during the siege of Leningrad, pathological studies made it possible to timely establish the causes of deaths and identify the peculiarities of the course of infectious diseases against the background of cachexia. Regularly held clinical and anatomical conferences contributed to the reduction of defects in the diagnosis and treatment of infectious diseases.

Programas de optimización del uso de antimicrobianos en los servicios de urgencias españoles: Estudio PROA-URG / Antibiotic stewardship programs in the Spanish emergency services: PROA-URG Study

Introducción: Los programas de optimización de antimicrobianos (PROA) son herramientas clave en la adecuación de estos fármacos. La información disponible sobre la aplicación e indicadores para monitorizar estos programas en urgencias es limitada. El objetivo del estudio es conocer el grado de implantación de programas PROA en los servicios de urgencias, así como el uso de antimicrobianos en estas unidades. Material y métodos. Estudio multicéntrico retrospectivo. Se envió una invitación a todos los participantes del grupo de trabajo de farmacéuticos de urgencias REDFASTER-SEFH. Se utilizó un cuestionario de 21 ítems, contestado por un equipo formado por especialistas en los servicios de farmacia hospitalaria, urgencias, enfermedades infecciosas y microbiología. Resultados. 18 hospitales completaron la encuesta. Catorce (77,8%) disponían de un responsable PROA en la unidad. El valor de DDD por 1000 ingresos osciló entre 36,5 y 400,5 (mediana 100,4 [RIQ:57,2-157,3]). El grupo de carbapenémicos y macrólidos presentó una amplia variabilidad. Únicamente seis (33,3%) hospitales disponían de informe anual de resistencias específico para urocultivos y hemocultivos en urgencias. El porcentaje de multirresistentes en urocultivos fue del 12,5% y en hemocultivos del 12,2%. El porcentaje de adecuación en bacteremia de acuerdo con el resultado del hemocultivo fue del 81,0% (RIQ:74,6-85,0%), y en infección urinaria del 78,0% (RIQ:71,5-88,0%). Conclusiones. Pese a la existencia de responsables PROA, actividades formativas y guías de tratamiento en urgencias, la información sobre el uso de antimicrobianos y el perfil de resistencias en estas unidades es limitado. Futuras actividades han de ir encaminadas a mejorar la información sobre los resultados PROA propios para estas unidades. (AU)

Introduction: Antimicrobial stewardship programs (ASP) have become a key tool in the adaptation of these drugs to the health system. The information available on the application and indicators used in these programs in emergency departments is scarce. The objective of this study is to know theextent of ASP implementation in the emergency departments, as well as the use of antimicrobials in these units. Material and methods. Multicenter retrospective study. An invitation was sent to all participants of the REDFASTER-SEFH emergency pharmacist working group. A questionnaire was used consisting of 21 items, answered by a team made up of a pharmacist, emergency room specialist, infectious disease specialist and microbiologist. Results. Eighteen hospitals completed the survey. Fourteen (77.8%) had an ASP manager. The DDD value per 1000 admissions ranged between 36.5 and 400.5 (median: 100.4 [IQR:57.2-157.3]). Both carbapenem and macrolide group presented wide variability in use. Six (33.3%) hospitals had an annual report on the specific resistance profile for urine and blood cultures. The percentage of multi-drug resistant strains in urine cultures was 12.5% and in blood cultures 12.2%. The percentage of adequacy in the bacteremia treatment was 81.0% (IQR:74.6-85.0%), while in urinary tract infections was 78.0% (IQR:71.5-88.0). Conclusions: Despite the existence of ASP members in emergency services, as well as the training activity and local guidelines is common. knowledge of the use of antimicrobials and resistances is limited. Future activities must be aimed at improving information about the ASP results in these units. (AU)

Progresión temporal de la distribución de los serotipos de Streptococcus pneumoniae productores de enfermedad neumocócica invasiva en Galicia (España) y su relación con la resistencia a antibióticos (periodo 2011-2021) / Temporal progression of the distribution of Streptococcus pneumoniae serotypes causing invasive pneumococcal disease in Galicia (Spain) and its relationship with resistance to antibiotics (period 2011-2021)

Introducción: Streptococcus pneumoniae causa enfermedades graves en la población susceptible. La vacuna neumocócica conjugada (PCV) 13-valente (PCV13) se incluyó en el calendario infantil en 2011. Este estudio analiza la evolución de los serotipos de neumococo y de sus resistencias tras la PCV13. Métodos: Se incluyeron los neumococos serotipados en Galicia en 2011-2021. Se estudió la sensibilidad antibiótica siguiendo criterios EUCAST. Se analizaron los datos en 3 subperíodos: inicial (2011-2013), medio (2014-2017) y final (2018-2021). Se calcularon las prevalencias de los serotipos y el porcentaje de resistencia a los antibióticos más representativos. Resultados: Se incluyeron 2.869 aislados. Inicialmente el 42,7% presentaba tipos capsulares incluidos en la PCV13, frente al 15,4% al final. Los incluidos en la PCV20 y no en la PCV13 y PCV15 fueron el 12,5% inicialmente y el 41,3% al final. El 26,4% de los serotipos a lo largo del estudio no estaban incluidos en ninguna vacuna. La prevalencia del serotipo 8 se multiplicó casi por 8 y la del 12F se triplicó. El serotipo 19A fue el más resistente inicialmente. La resistencia de los serotipos 11A y 15A aumentó a lo largo del estudio. Conclusiones: La introducción de la PCV13 en la población infantil determinó un cambio en los serotipos de neumococo hacia los incluidos en la PCV20 y los no incluidos en ninguna vacuna. El serotipo 19A inicialmente fue el más resistente, y el 15A, no incluido en ninguna vacuna, merece un especial seguimiento. El serotipo 8, que fue el que más se incrementó, no mostró resistencia destacable.(AU)

Introduction: Streptococcus pneumoniae causes serious diseases in the susceptible population. The 13-valent pneumococci conjugate vaccine (PCV13) was included in the children's calendar in 2011. The objective of the study was to analyze the evolution of pneumococcal serotypes and their resistance after PCV13. Methods: This study included the pneumococci serotyped in Galicia in 2011-2021. Antibiotic susceptibility was analyzed following EUCAST criteria. The data was analyzed in 3 sub-periods: initial (2011-2013), middle (2014-2017) and final (2018-2021). The prevalence of serotypes and their percentage of resistance to the most representative antibiotics were calculated. Results: A total of 2.869 isolates were included. Initially, 42.7% isolates presented capsular types included in PCV13, compared to 15.4% at the end. Those included in PCV20 and not in PCV13 and PCV15 were 12.5% at baseline and 41.3% at the end; 26.4% of the isolates throughout the study had serotypes not included in any vaccine. The prevalence of serotype 8 multiplied almost by 8 and that of 12F tripled. The 19A serotype was initially the most resistant, while the resistance of serotypes 11A and 15A increased throughout the study. Conclusions: The introduction of PCV13 in the pediatric population determined a change in pneumococcal serotypes towards those included in PCV20 and those not included in any vaccine. Serotype 19A was initially the most resistant and the 15A, not included in any vaccine, deserves special follow-up. Serotype 8, which increased the most, did not show remarkable resistance.(AU)

Infección leve por SARS-CoV-2 en pacientes vulnerables: implantación de una vía clínica de tratamiento precoz / Mild SARS-CoV-2 infection in vulnerable patients: Implementation of a clinical pathway for early treatment

Introducción: El objetivo del manuscrito es describir la vía clínica de tratamiento precoz de pacientes con infección aguda por SARS-CoV-2 y evaluar los primeros resultados de su implementación. Métodos: Estudio descriptivo y retrospectivo de la implementación de una vía clínica de tratamiento en pacientes no hospitalizados (del 1 de enero al 30 de junio de 2022). Elaboración de vía clínica: sistemas de detección y derivación desde Atención Primaria, Servicio de Urgencias, especialidades médicas y sistema de detección automatizada; evaluación clínica y administración de tratamiento en hospital de día COVID-19, y seguimiento clínico posterior. Variables explicativas: demográficas, comorbilidad, estado vacunal, vías de derivación y administración de tratamiento. Variables de resultado: hospitalización y muerte a los 30 días, toxicidad grado 2-3 relacionada con el tratamiento. Resultados: Se administró tratamiento a 262 pacientes (53,4% mujeres, mediana de edad 60 años). Criterio de indicación de tratamiento: inmunosupresión (68,3%), y la combinación de edad, estado vacunal y comorbilidad en el resto. El 47,3% de los pacientes recibieron remdesivir, el 35,9% nirmatrelvir/ritonavir, el 13,4% sotrovimab y el 2,4% tratamiento combinado, con una mediana de 4 días tras el inicio de síntomas. El 6,1% de los pacientes precisó ingreso hospitalario, el 3,8% por progresión de COVID-19. Ningún paciente falleció. El 18,7% presentaron toxicidad grado 2-3: 89,8% disgeusia y sabor metálico relacionado con nirmatrelvir/ritonavir. Siete pacientes interrumpieron tratamiento por toxicidad. Conclusión: La creación e implementación de una vía clínica para pacientes no hospitalizados con infección por SARS-CoV-2 es efectiva y permite la accesibilidad temprana y la equidad de los tratamientos actualmente disponibles.(AU)

Introduction: The objective of this report is to describe the clinical pathway for early treatment of patients with acute SARS-CoV-2 infection and to evaluate the first results of its implementation. Methods: This is a descriptive and retrospective study of the implementation of a clinical pathway of treatment in outpatients (January 1 to June 30, 2022). Clinical pathway: detection and referral systems from Primary Care, Emergency services, hospital specialities and an automated detection system; clinical evaluation and treatment administration in the COVID-19 day-hospital and subsequent clinical follow-up. Explanatory variables: demographics, comorbidity, vaccination status, referral pathways and treatment administration. Outcome variables: hospitalization and death within 30 days, grade 2–3 toxicity related to treatment. Results: Treatment was administered to 262 patients (53.4% women, median age 60 years). The treatment indication criteria were immunosuppression (68.3%), and the combination of age, vaccination status and comorbidity in the rest; 47.3% of the patients received remdesivir, 35.9% nirmatrelvir/ritonavir, 13.4% sotrovimab and 2.4% combined treatment with a median of 4 days after symptom onset. Hospital admission was required for 6.1% of the patients, 3.8% related to COVID-19 progression. No patient died. Toxicity grade 2–3 toxicity was reported in 18.7%, 89.8% dysgeusia and metallic tasted related nirmatrelvir/ritonavir. Seven patients discontinued treatment due to toxicity. Conclusion: The creation and implementation of a clinical pathway for non-hospitalized patients with SARS-CoV-2 infection is effective and it allows early accessibility and equity of currently available treatments.(AU)

Executive summary: Guidelines for the diagnosis and treatment of septic arthritis in adults and children, developed by the GEIO (SEIMC), SEIP and SECOT / Resumen ejecutivo: Guía de diagnóstico y tratamiento de la artritis séptica en adultos y niños de GEIO (SEIMC), SEIP y SECOT

Infection of a native joint, commonly referred to as septic arthritis, is a medical emergency because of the risk of joint destruction and subsequent sequelae. Its diagnosis requires a high level of suspicion. These guidelines for the diagnosis and treatment of septic arthritis in children and adults are intended for use by any physician caring for patients with suspected or confirmed septic arthritis. They have been developed by a multidisciplinary panel with representatives from the Bone and Joint Infections Study Group (GEIO) belonging to the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), the Spanish Society of Paediatric Infections (SEIP) and the Spanish Society of Orthopaedic Surgery and Traumatology (SECOT), and two rheumatologists. The recommendations are based on evidence derived from a systematic literature review and, failing that, on the opinion of the experts who prepared these guidelines. A detailed description of the background, methods, summary of evidence, the rationale supporting each recommendation, and gaps in knowledge can be found online in the complete document.(AU)

La infección de una articulación nativa, generalmente denominada artritis séptica, constituye una urgencia médica por el riesgo de destrucción articular y las consecuentes secuelas. Su diagnóstico requiere un alto nivel de sospecha. Esta guía de diagnóstico y tratamiento de la artritis séptica en niños y adultos está destinada a cualquier médico que atienda pacientes con sospecha de artritis séptica o artritis séptica confirmada. La guía ha sido elaborada por un panel multidisciplinar en el que están representados el Grupo de Estudio de Infecciones Osteoarticulares (GEIO) de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), la Sociedad Española de Infectología Pediátrica (SEIP) y la Sociedad Española de Cirugía Ortopédica y Traumatología (SECOT); además han participado dos reumatólogos. Las recomendaciones se basan en la evidencia proporcionada por una revisión sistemática de la literatura y, en su defecto, en la opinión de los expertos que han elaborado la presente guía. En el texto completo online se hace una descripción detallada de los antecedentes, métodos, resumen de la evidencia, fundamentos que apoyan cada recomendación y las lagunas de conocimiento existentes.(AU)

Diagnóstico por amplificación isotérmica de ácidos nucleicos. Oportunidad para la farmacia comunitaria / Diagnosis by isothermal amplification of nucleic acids. Opportunity for community pharmacy

Esta revisión se centra en describir nuevos sistemas de diagnóstico molecular de tipo POC disponibles en el mercado que pueden implementarse fácilmente en farmacias comunitarias y tienen el potencial de ampliar la cartera de servicios farmacéuticos y hacer una contribución significativa a la mejora de la salud pública.El conocimiento de nuevas técnicas de diagnóstico molecular distintas de la PCR es relativamente desconocido. Sin embargo, las opciones disponibles son diversas y han alcanzado suficiente madurez tecnológica para su uso a gran escala. La pandemia de SARS-CoV-2 ha sacado al mercado pruebas de diagnóstico que, en algunos casos, se han utilizado exclusivamente en investigación durante décadas.La tecnología isotérmica de amplificación de ácidos nucleicos sigue evolucionando y es probable que en los próximos años seamos testigos de un aumento exponencial de su uso, así como del desarrollo de nuevas mejoras que simplifiquen y reduzcan aún más el coste de cada ensayo.Igualmente, no podemos obviar el hecho de que durante la pandemia de COVID-19, el público se ha habituado a autodiagnosticarse a través de canales de distribución masiva como las farmacias comunitarias, lo que puede abrir el sector a otras enfermedades —como las de transmisión sexual o salud animal—, el control de alimentos, la contaminación del agua y del aire (hongos) o la presencia de alérgenos.El conocimiento de estas nuevas tecnologías es esencial estrategia de vigilancia tecnológica e inteligencia competitiva del sector farmacéutico.(AU)

Surveillance for Emerging and Reemerging Pathogens Using Pathogen Agnostic Metagenomic Sequencing in the United States: A Critical Role for Federal Government Agencies.

The surveillance and identification of emerging, reemerging, and unknown infectious disease pathogens is essential to national public health preparedness and relies on fluidity, coordination, and interconnectivity between public and private pathogen surveillance systems and networks. Developing a national sentinel surveillance network with existing resources and infrastructure could increase efficiency, accelerate the identification of emerging public health threats, and support coordinated intervention strategies that reduce morbidity and mortality. However, implementing and sustaining programs to detect emerging and reemerging pathogens in humans using advanced molecular methods, such as metagenomic sequencing, requires making large investments in testing equipment and developing networks of clinicians, laboratory scientists, and bioinformaticians. In this study, we sought to gain an understanding of how federal government agencies currently support such pathogen agnostic testing of human specimens in the United States. We conducted a landscape analysis of federal agency websites for publicly accessible information on the availability and type of pathogen agnostic testing and details on flow of clinical specimens and data. The website analysis was supplemented by an expert review of results with representatives from the federal agencies. Operating divisions within the US Department of Health and Human Services and the US Department of Veterans Affairs have developed and sustained extensive clinical and research networks to obtain patient specimens and perform metagenomic sequencing. Metagenomic facilities supported by US agencies were not equally geographically distributed across the United States. Although many entities have work dedicated to metagenomics and/or support emerging infectious disease surveillance specimen collection, there was minimal formal collaboration across agencies.

Identification of Early Warning Signals of Infectious Diseases in Hospitals by Integrating Clinical Treatment and Disease Prevention.

The global incidence of infectious diseases has increased in recent years, posing a significant threat to human health. Hospitals typically serve as frontline institutions for detecting infectious diseases. However, accurately identifying warning signals of infectious diseases in a timely manner, especially emerging infectious diseases, can be challenging. Consequently, there is a pressing need to integrate treatment and disease prevention data to conduct comprehensive analyses aimed at preventing and controlling infectious diseases within hospitals. This paper examines the role of medical data in the early identification of infectious diseases, explores early warning technologies for infectious disease recognition, and assesses monitoring and early warning mechanisms for infectious diseases. We propose that hospitals adopt novel multidimensional early warning technologies to mine and analyze medical data from various systems, in compliance with national strategies to integrate clinical treatment and disease prevention. Furthermore, hospitals should establish institution-specific, clinical-based early warning models for infectious diseases to actively monitor early signals and enhance preparedness for infectious disease prevention and control.

MODELS: a six-step framework for developing an infectious disease model.

Since the COVID-19 pandemic began, a plethora of modeling studies related to COVID-19 have been released. While some models stand out due to their innovative approaches, others are flawed in their methodology. To assist novices, frontline healthcare workers, and public health policymakers in navigating the complex landscape of these models, we introduced a structured framework named MODELS. This framework is designed to detail the essential steps and considerations for creating a dependable epidemic model, offering direction to researchers engaged in epidemic modeling endeavors.