Investigating seasonal patterns in enteric infections: a systematic review of time series methods.

Foodborne and waterborne gastrointestinal infections and their associated outbreaks are preventable, yet still result in significant morbidity, mortality and revenue loss. Many enteric infections demonstrate seasonality, or annual systematic periodic fluctuations in incidence, associated with climatic and environmental factors. Public health professionals use statistical methods and time series models to describe, compare, explain and predict seasonal patterns. However, descriptions and estimates of seasonal features, such as peak timing, depend on how researchers define seasonality for research purposes and how they apply time series methods. In this review, we outline the advantages and limitations of common methods for estimating seasonal peak timing. We provide recommendations improving reporting requirements for disease surveillance systems. Greater attention to how seasonality is defined, modelled, interpreted and reported is necessary to promote reproducible research and strengthen proactive and targeted public health policies, intervention strategies and preparedness plans to dampen the intensity and impacts of seasonal illnesses.

Global seasonal and pandemic patterns in influenza: An application of longitudinal study designs.

The confluence of growing analytic capacities and global surveillance systems for seasonal infections has created new opportunities to further develop statistical methodology and advance the understanding of the global disease dynamics. We developed a framework to characterise the seasonality of infectious diseases for publicly available global health surveillance data. Specifically, we aimed to estimate the seasonal characteristics and their uncertainty using mixed effects models with harmonic components and the δ-method and develop multi-panel visualisations to present complex interplay of seasonal peaks across geographic locations. We compiled a set of 2 422 weekly time series of 14 reported outcomes for 173 Member States from the World Health Organization's (WHO) international influenza virological surveillance system, FluNet, from 02 January 1995 through 20 June 2021. We produced an analecta of data visualisations to describe global travelling waves of influenza while addressing issues of data completeness and credibility. Our results offer directions for further improvements in data collection, reporting, analysis and development of statistical methodology and predictive approaches.

Incorporating calendar effects to predict influenza seasonality in Milwaukee, Wisconsin.

Social outings can trigger influenza transmission, especially in children and elderly. In contrast, school closures are associated with reduced influenza incidence in school-aged children. While influenza surveillance modelling studies typically account for holidays and mass gatherings, age-specific effects of school breaks, sporting events and commonly celebrated observances are not fully explored. We examined the impact of school holidays, social events and religious observances for six age groups (all ages, ⩽4, 5-24, 25-44, 45-64, ⩾65 years) on four influenza outcomes (tests, positives, influenza A and influenza B) as reported by the City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin from 2004 to 2009. We characterised holiday effects by analysing average weekly counts in negative binomial regression models controlling for weather and seasonal incidence fluctuations. We estimated age-specific annual peak timing and compared influenza outcomes before, during and after school breaks. During the 118 university holiday weeks, average weekly tests were lower than in 140 school term weeks (5.93 vs. 11.99 cases/week, P < 0.005). The dampening of tests during Winter Break was evident in all ages and in those 5-24 years (RR = 0.31; 95% CI 0.22-0.41 vs. RR = 0.14; 95% CI 0.09-0.22, respectively). A significant increase in tests was observed during Spring Break in 45-64 years old adults (RR = 2.12; 95% CI 1.14-3.96). Milwaukee Public Schools holiday breaks showed similar amplification and dampening effects. Overall, calendar effects depend on the proximity and alignment of an individual holiday to age-specific and influenza outcome-specific peak timing. Better quantification of individual holiday effects, tailored to specific age groups, should improve influenza prevention measures.

Usability of existing global and national data for flood related vulnerability assessment in Indonesia.

Public climatic data are rapidly growing in volume and complexity at global and national scales but these data remain underutilized for vulnerability assessment. We aim to explore how flood records from Dartmouth Flood Observatory, a global flood monitoring database, can be linked with a national disaster database maintained by the Indonesian National Board for Disaster Management, to aid local vulnerability assessment in Indonesia. We focused on physical damage to structures and agricultural crops from flooding and examined spatiotemporal patterns of a vulnerability metric derived from principal component analysis. We identified the most vulnerable areas based on emerging hot spot analysis and detected sporadic hotspots (i.e. on again then off again) of flooding in Jakarta and West Java. Using our derived metric, we identified oscillating cold spots (i.e. a cold spot that was previously a hot spot) of vulnerability in Banten, Jakarta, West Java, and Central Java. The detection of nonhomogeneous spatiotemporal trends in flooding and vulnerability demonstrate potential usability of public climate data and help to outline directions for novel research.

Household Flood Severity and Migration Extent in Central Java: Analysis of the Indonesian Family Life Survey.

Central Java, Indonesia, is prone to river and coastal flooding due to climate changes and geological factors. Migration is one possible adaptation to flooding, but research is limited due to lack of longitudinal spatially granular datasets on migration and metrics to identify flood-affected households. The available literature indicates social and economic barriers may limit mobility from flood prone areas. The Indonesian Family Life Survey (IFLS) provides self-reported data on household experiences with natural disasters among 1501 Central Java households followed over two waves (2007 and 2014). We examined how the severity of flooding, defined by household-level impacts captured by the IFLS (death, injury, financial loss, or relocation of a household member), influenced the extent of household movement in Central Java using a generalized ordered logit/partial proportional odds model. Households severely impacted by floods had 75% lower odds of moving farther away compared to those that did not experience floods. The most severely impacted households may be staying within flood-affected areas in Central Java. Public health, nutrition, and economic surveys should include modules focused on household experiences, impacts, and adaptations to facilitate the study of how climate changes are impacting these outcomes.

Exploring Risk Factors of Recall-Associated Foodborne Disease Outbreaks in the United States, 2009-2019.

Earlier identification and removal of contaminated food products is crucial in reducing economic burdens of foodborne outbreaks. Recalls are a safety measure that is deployed to prevent foodborne illnesses. However, few studies have examined temporal trends in recalls or compared risk factors between non-recall and recall outbreaks in the United States, due to disparate and often incomplete surveillance records in publicly reported data. We demonstrated the usability of the electronic Foodborne Outbreak Reporting System (eFORS) and National Outbreak Reporting System (NORS) for describing temporal trends and outbreak risk factors of food recalls in 1998−2019. We examined monthly trends between surveillance systems by using segmented time-series analyses. We compared the risk factors (e.g., multistate outbreak, contamination supply chain stage, pathogen etiology, and food products) of recalls and non-recalls by using logistic regression models. Out of 22,972 outbreaks, 305 (1.3%) resulted in recalls and 9378 (41%) had missing recall information. However, outbreaks with missing recall information decreased at an accelerating rate of ~25%/month in 2004−2009 and at a decelerating rate of ~13%/month after the transition from eFORS to NORS in 2009−2019. Irrespective of the contaminant etiology, multistate outbreaks according to the residence of ill persons had odds 11.00−13.50 times (7.00, 21.60) that of single-state outbreaks resulting in a recall (p < 0.001) when controlling for all risk factors. Electronic reporting has improved the availability of food recall data, yet retrospective investigations of historical records are needed. The investigation of recalls enhances public health professionals' understanding of their annual financial burden and improves outbreak prediction analytics to reduce the likelihood and severity of recalls.

Evaluating Completeness of Foodborne Outbreak Reporting in the United States, 1998-2019.

Public health agencies routinely collect time-referenced records to describe and compare foodborne outbreak characteristics. Few studies provide comprehensive metadata to inform researchers of data limitations prior to conducting statistical modeling. We described the completeness of 103 variables for 22,792 outbreaks publicly reported by the United States Centers for Disease Control and Prevention's (US CDC's) electronic Foodborne Outbreak Reporting System (eFORS) and National Outbreak Reporting System (NORS). We compared monthly trends of completeness during eFORS (1998−2008) and NORS (2009−2019) reporting periods using segmented time series analyses adjusted for seasonality. We quantified the overall, annual, and monthly completeness as the percentage of outbreaks with blank records per our study period, calendar year, and study month, respectively. We found that outbreaks of unknown genus (n = 7401), Norovirus (n = 6414), Salmonella (n = 2872), Clostridium (n = 944), and multiple genera (n = 779) accounted for 80.77% of all outbreaks. However, crude completeness ranged from 46.06% to 60.19% across the 103 variables assessed. Variables with the lowest crude completeness (ranging 3.32−6.98%) included pathogen, specimen etiological testing, and secondary transmission traceback information. Variables with low (<35%) average monthly completeness during eFORS increased by 0.33−0.40%/month after transitioning to NORS, most likely due to the expansion of surveillance capacity and coverage within the new reporting system. Examining completeness metrics in outbreak surveillance systems provides essential information on the availability of data for public reuse. These metadata offer important insights for public health statisticians and modelers to precisely monitor and track the geographic spread, event duration, and illness intensity of foodborne outbreaks.

Dynamic mapping of cholera outbreak during the Yemeni Civil War, 2016-2019.

Widespread destruction from the Yemeni Civil War (2014-present) triggered the world's largest cholera outbreak. We compiled a comprehensive health dataset and created dynamic maps to demonstrate spatiotemporal changes in cholera infections and war conflicts. We aligned and merged daily, weekly, and monthly epidemiological bulletins of confirmed cholera infections and daily conflict events and fatality records to create a dataset of weekly time series for Yemen at the governorate level (subnational regions administered by governors) from 4 January 2016 through 29 December 2019. We demonstrated the use of dynamic mapping for tracing the onset and spread of infection and manmade factors that amplify the outbreak. We report curated data and visualization techniques to further uncover associations between infectious disease outbreaks and risk factors and to better coordinate humanitarian aid and relief efforts during complex emergencies.

Critical Periods, Critical Time Points and Day-of-the-Week Effects in COVID-19 Surveillance Data: An Example in Middlesex County, Massachusetts, USA.

Critical temporal changes such as weekly fluctuations in surveillance systems often reflect changes in laboratory testing capacity, access to testing or healthcare facilities, or testing preferences. Many studies have noted but few have described day-of-the-week (DoW) effects in SARS-CoV-2 surveillance over the major waves of the novel coronavirus 2019 pandemic (COVID-19). We examined DoW effects by non-pharmaceutical intervention phases adjusting for wave-specific signatures using the John Hopkins University's (JHU's) Center for Systems Science and Engineering (CSSE) COVID-19 data repository from 2 March 2020 through 7 November 2021 in Middlesex County, Massachusetts, USA. We cross-referenced JHU's data with Massachusetts Department of Public Health (MDPH) COVID-19 records to reconcile inconsistent reporting. We created a calendar of statewide non-pharmaceutical intervention phases and defined the critical periods and timepoints of outbreak signatures for reported tests, cases, and deaths using Kolmogorov-Zurbenko adaptive filters. We determined that daily death counts had no DoW effects; tests were twice as likely to be reported on weekdays than weekends with decreasing effect sizes across intervention phases. Cases were also twice as likely to be reported on Tuesdays-Fridays (RR = 1.90-2.69 [95%CI: 1.38-4.08]) in the most stringent phases and half as likely to be reported on Mondays and Tuesdays (RR = 0.51-0.93 [0.44, 0.97]) in less stringent phases compared to Sundays; indicating temporal changes in laboratory testing practices and use of healthcare facilities. Understanding the DoW effects in daily surveillance records is valuable to better anticipate fluctuations in SARS-CoV-2 testing and manage appropriate workflow. We encourage health authorities to establish standardized reporting protocols.

Food and Nutrition Systems Dashboards: A Systematic Review.

The rapid expansion of food and nutrition information requires new ways of data sharing and dissemination. Interactive platforms integrating data portals and visualization dashboards have been effectively utilized to describe, monitor, and track information related to food and nutrition; however, a comprehensive evaluation of emerging interactive systems is lacking. We conducted a systematic review on publicly available dashboards using a set of 48 evaluation metrics for data integrity, completeness, granularity, visualization quality, and interactivity based on 4 major principles: evidence, efficiency, emphasis, and ethics. We evaluated 13 dashboards, summarized their characteristics, strengths, and limitations, and provided guidelines for developing nutrition dashboards. We applied mixed effects models to summarize evaluation results adjusted for interrater variability. The proposed metrics and evaluation principles help to improve data standardization and harmonization, dashboard performance and usability, broaden information and knowledge sharing among researchers, practitioners, and decision makers in the field of food and nutrition, and accelerate data literacy and communication.

Completeness of open access FluNet influenza surveillance data for Pan-America in 2005-2019.

For several decades, the World Health Organization has collected, maintained, and distributed invaluable country-specific disease surveillance data that allow experts to develop new analytical tools for disease tracking and forecasting. To capture the extent of available data within these sources, we proposed a completeness metric based on the effective time series length. Using FluNet records for 29 Pan-American countries from 2005 to 2019, we explored whether completeness was associated with health expenditure indicators adjusting for surveillance system heterogeneity. We observed steady improvements in completeness by 4.2-6.3% annually, especially after the A(H1N1)-2009 pandemic, when 24 countries reached > 95% completeness. Doubling in decadal health expenditure per capita was associated with ~ 7% increase in overall completeness. The proposed metric could navigate experts in assessing open access data quality and quantity for conducting credible statistical analyses, estimating disease trends, and developing outbreak forecasting systems.

Providing Food and Nutrition Services during the COVID-19 Surge at the Javits New York Medical Station.

Military field hospitals typically provide essential medical care in combat zones. In recent years, the United States (US) Army has deployed these facilities to assist domestic humanitarian emergency and natural disaster response efforts. As part of the nation's whole-of-government approach to the coronavirus disease (COVID-19) pandemic, directed by the Federal Emergency Management Agency and the Department of Health and Human Services, during New York City's (NYC) initial surge of COVID-19, from 26 March to 1 May 2020, the US Army erected the Javits New York Medical Station (JNYMS) field hospital to support the city's overwhelmed healthcare system. The JNYMS tasked a nutrition operations team (NuOp) to provide patient meals and clinical nutrition evaluations to convalescent COVID-19 patients. However, few guidelines were available for conducting emergency nutrition and dietary response efforts prior to the field hospital's opening. In this case study, we summarize the experiences of the NuOp at the JNYMS field hospital, to disseminate the best practices for future field hospital deployments. We then explain the challenges in service performance, due to information, personnel, supply, and equipment shortages. We conclude by describing the nutrition service protocols that have been implemented to overcome these challenges, including creating a standardized recordkeeping system for patient nutrition information, developing a meal tracking system to forecast meal requirements with food service contractors, and establishing a training and staffing model for military-to-civilian command transition. We highlight the need for a standardized humanitarian emergency nutrition service response framework and propose a Nutrition Response Toolkit for Humanitarian Crises, which offers low-cost, easily adaptable operational protocols for implementation in future field hospital deployments.

Signatures of Cholera Outbreak during the Yemeni Civil War, 2016-2019.

The Global Task Force on Cholera Control (GTFCC) created a strategy for early outbreak detection, hotspot identification, and resource mobilization coordination in response to the Yemeni cholera epidemic. This strategy requires a systematic approach for defining and classifying outbreak signatures, or the profile of an epidemic curve and its features. We used publicly available data to quantify outbreak features of the ongoing cholera epidemic in Yemen and clustered governorates using an adaptive time series methodology. We characterized outbreak signatures and identified clusters using a weekly time series of cholera rates in 20 Yemeni governorates and nationally from 4 September 2016 through 29 December 2019 as reported by the World Health Organization (WHO). We quantified critical points and periods using Kolmogorov-Zurbenko adaptive filter methodology. We assigned governorates into six clusters sharing similar outbreak signatures, according to similarities in critical points, critical periods, and the magnitude of peak rates. We identified four national outbreak waves beginning on 12 September 2016, 6 March 2017, 28 May 2018, and 28 January 2019. Among six identified clusters, we classified a core regional hotspot in Sana'a, Sana'a City, and Al-Hudaydah-the expected origin of the national outbreak. The five additional clusters differed in Wave 2 and Wave 3 peak frequency, timing, magnitude, and geographic location. As of 29 December 2019, no governorates had returned to pre-Wave 1 levels. The detected similarity in outbreak signatures suggests potentially shared environmental and human-made drivers of infection; the heterogeneity in outbreak signatures implies the potential traveling waves outwards from the core regional hotspot that could be governed by factors that deserve further investigation.

Seasonal synchronization of foodborne outbreaks in the United States, 1996-2017.

Modern food systems represent complex dynamic networks vulnerable to foodborne infectious outbreaks difficult to track and control. Seasonal co-occurrences (alignment of seasonal peaks) and synchronization (similarity of seasonal patterns) of infections are noted, yet rarely explored due to their complexity and methodological limitations. We proposed a systematic approach to evaluate the co-occurrence of seasonal peaks using a combination of L-moments, seasonality characteristics such as the timing (phase) and intensity (amplitude) of peaks, and three metrics of serial, phase-phase, and phase-amplitude synchronization. We used public records on counts of nine foodborne infections abstracted from CDC's FoodNet Fast online platform for the US and ten representative states from 1996 to 2017 (264 months). Based on annualized and trend-adjusted Negative Binomial Harmonic Regression (NBHR) models augmented with the δ-method, we determined that seasonal peaks of Campylobacter, Salmonella, and Shiga toxin-producing Escherichia Coli (STEC) were tightly clustered in late-July at the national and state levels. Phase-phase synchronization was observed between Cryptosporidium and Shigella, Listeria, and Salmonella (ρ = 0.51, 0.51, 0.46; p < 0.04). Later peak timing of STEC was associated with greater amplitude nationally (ρ = 0.50, p = 0.02) indicating phase-amplitude synchronization. Understanding of disease seasonal synchronization is essential for developing reliable outbreak forecasts and informing stakeholders on mitigation and preventive measures.

An analecta of visualizations for foodborne illness trends and seasonality.

Disease surveillance systems worldwide face increasing pressure to maintain and distribute data in usable formats supplemented with effective visualizations to enable actionable policy and programming responses. Annual reports and interactive portals provide access to surveillance data and visualizations depicting temporal trends and seasonal patterns of diseases. Analyses and visuals are typically limited to reporting the annual time series and the month with the highest number of cases per year. Yet, detecting potential disease outbreaks and supporting public health interventions requires detailed spatiotemporal comparisons to characterize spatiotemporal patterns of illness across diseases and locations. The Centers for Disease Control and Prevention's (CDC) FoodNet Fast provides population-based foodborne-disease surveillance records and visualizations for select counties across the US. We offer suggestions on how current FoodNet Fast data organization and visual analytics can be improved to facilitate data interpretation, decision-making, and communication of features related to trend and seasonality. The resulting compilation, or analecta, of 436 visualizations of records and codes are openly available online.