Review of methods for space-time disease surveillance

Patterns of animal rabies in the Nizhny Novgorod region of Russia (2012-2022): the analysis of risk factors

Introduction

Animal rabies is a viral disease that poses a significant threat to domestic and wild animal populations, with devastating consequences for animal health and human life. Understanding and assessing the risk factors associated with the transmission and persistence of the rabies virus in wild and domestic animal populations is crucial for developing effective strategies to control and mitigate cases. Studies of the spatial and temporal distribution of rabies cases in the Nizhny Novgorod region during 2012-2022 provided epidemiological evidence of the circulation of infection between animals in the presence of vaccination. Among the wild animals in the area, red foxes play a major role in the spread of rabies, accounting for 96.4% of all wild animal cases.

Methods

We used spatiotemporal cluster analysis and a negative binomial regression algorithm to study the relationships between animal rabies burden by municipality and a series of environmental and sociodemographic factors.

Results

The spatiotemporal cluster analysis suggests the concentration of wild animal rabies cases in the areas of high fox population density and insufficient vaccination rates. The regression models showed satisfactory performance in explaining the observed distribution of rabies in different animals (R 2 = 0.71, 0.76, and 0.79 in the models for wild, domestic and all animals respectively), with rabies vaccination coverage and fox population density being among the main risk factors.

Conclusion

We believe that this study can provide valuable information for a better understanding of the geographical and temporal patterns of rabies distribution in different animal species, and will provide a basis for the development of density-dependent planning of vaccination campaigns.

Impacts of climate change on water-related mosquito-borne diseases in temperate regions: A systematic review of literature and meta-analysis

Mosquito-borne diseases are a known tropical phenomenon. This review was conducted to assess the mecha-nisms through which climate change impacts mosquito-borne diseases in temperate regions. Articles were searched from PubMed, Scopus, Web of Science, and Embase databases. Identification criteria were scope (climate change and mosquito-borne diseases), region (temperate), article type (peer-reviewed), publication language (English), and publication years (since 2015). The WWH (who, what, how) framework was applied to develop the research question and thematic analyses identified the mechanisms through which climate change affects mosquito-borne diseases. While temperature ranges for disease transmission vary per mosquito species, all are viable for temperate regions, particularly given projected temperature increases. Zika, chikungunya, and dengue transmission occurs between 18-34 °C (peak at 26-29 °C). West Nile virus establishment occurs at monthly average temperatures between 14-34.3 °C (peak at 23.7-25 °C). Malaria establishment occurs when the consecutive average daily temperatures are above 16 °C until the sum is above 210 °C. The identified mechanisms through which climate change affects the transmission of mosquito-borne diseases in temperate regions include: changes in the development of vectors and pathogens; changes in mosquito habitats; extended transmission seasons; changes in geographic spread; changes in abundance and behaviors of hosts; reduced abundance of mosquito predators; interruptions to control operations; and influence on other non-climate factors. Process and stochastic approaches as well as dynamic and spatial models exist to predict mosquito population dynamics, disease transmission, and climate favorability. Future projections based on the observed relations between climate factors and mosquito-borne diseases suggest that mosquito-borne disease expansion is likely to occur in temperate regions due to climate change. While West Nile virus is already established in some temperate regions, Zika, dengue, chikungunya, and malaria are also likely to become established over time. Moving forward, more research is required to model future risks by incorporating climate, environmental, sociodemographic, and mosquito-related factors under changing climates.

An Approach to Identifying Spatial Variability in Observed Infectious Disease Spread in a Prospective Time-Space Series with Applications to COVID-19 and Dengue Incidence

Most of the growing prospective analytic methods in space-time disease surveillance and intended functions of disease surveillance systems focus on earlier detection of disease outbreaks, disease clusters, or increased incidence. The spread of the virus such as SARS-CoV-2 has not been spatially and temporally uniform in an outbreak. With the identification of an infectious disease outbreak, recognizing and evaluating anomalies (excess and decline) of disease incidence spread at the time of occurrence during the course of an outbreak is a logical next step. We propose and formulate a hypergeometric probability model that investigates anomalies of infectious disease incidence spread at the time of occurrence in the timeline for many geographically described populations (e.g., hospitals, towns, counties) in an ongoing daily monitoring process. It is structured to determine whether the incidence grows or declines more rapidly in a region on the single current day or the most recent few days compared to the occurrence of the incidence during the previous few days relative to elsewhere in the surveillance period. The new method uses a time-varying baseline risk model, accounting for regularly (e.g., daily) updated information on disease incidence at the time of occurrence, and evaluates the probability of the deviation of particular frequencies to be attributed to sampling fluctuations, accounting for the unequal variances of the rates due to different population bases in geographical units. We attempt to present and illustrate a new model to advance the investigation of anomalies of infectious disease incidence spread by analyzing subsamples of spatiotemporal disease surveillance data from Taiwan on dengue and COVID-19 incidence which are mosquito-borne and contagious infectious diseases, respectively. Efficient R programs for computation are available to implement the two approximate formulae of the hypergeometric probability model for large numbers of events.

Spatiotemporal variations of "triple-demic" outbreaks of respiratory infections in the United States in the post-COVID-19 era

BACKGROUND

The US confronted a "triple-demic" of influenza, respiratory syncytial virus (RSV), and COVID-19 in the winter of 2022, leading to increased respiratory infections and a higher demand for medical supplies. It is urgent to analyze these epidemics and their spatial-temporal co-occurrence, identifying hotspots and informing public health strategies.

METHODS

We employed retrospective and prospective space-time scan statistics to assess the situations of COVID-19, influenza, and RSV in 51 US states from October 2021 to February 2022, and from October 2022 to February 2023, respectively. This enabled monitoring of spatiotemporal variations for each epidemic individually and collectively.

RESULTS

Compared to winter 2021, COVID-19 cases decreased while influenza and RSV infections significantly increased in winter 2022. We found a high-risk cluster of influenza and COVID-19 (not all three) in winter 2021. In late November 2022, a large high-risk cluster of triple-demic emerged in the central US. The number of states at high risk for multiple epidemics increased from 15 in October 2022 to 21 in January 2023.

CONCLUSIONS

Our study offers a novel spatiotemporal approach that combines both univariate and multivariate surveillance, as well as retrospective and prospective analyses. This approach offers a more comprehensive and timely understanding of how the co-occurrence of COVID-19, influenza, and RSV impacts various regions within the United States. Our findings assist in tailor-made strategies to mitigate the effects of these respiratory infections.

Epidemic Characteristics, Spatiotemporal Pattern, and Risk Factors of Other Infectious Diarrhea in Fujian Province From 2005 to 2021: Retrospective Analysis

BACKGROUND

Other infectious diarrhea (OID) continues to pose a significant public health threat to all age groups in Fujian Province. There is a need for an in-depth analysis to understand the epidemiological pattern of OID and its associated risk factors in the region.

OBJECTIVE

In this study, we aimed to describe the overall epidemic characteristics and spatiotemporal pattern of OID in Fujian Province from 2005 to 2021 and explore the linkage between sociodemographic and environmental factors and the occurrence of OID within the study area.

METHODS

Notification data for OID in Fujian were extracted from the China Information System for Disease Control and Prevention. The spatiotemporal pattern of OID was analyzed using Moran index and Kulldorff scan statistics. The seasonality of and short-term impact of meteorological factors on OID were examined using an additive decomposition model and a generalized additive model. Geographical weighted regression and generalized linear mixed model were used to identify potential risk factors.

RESULTS

A total of 388,636 OID cases were recorded in Fujian Province from January 2005 to December 2021, with an average annual incidence of 60.3 (SD 16.7) per 100,000 population. Children aged <2 years accounted for 50.7% (196,905/388,636) of all cases. There was a steady increase in OID from 2005 to 2017 and a clear seasonal shift in OID cases from autumn to winter and spring between 2005 and 2020. Higher maximum temperature, atmospheric pressure, humidity, and precipitation were linked to a higher number of deseasonalized OID cases. The spatial and temporal aggregations were concentrated in Zhangzhou City and Xiamen City for 17 study years. Furthermore, the clustered areas exhibited a dynamic spreading trend, expanding from the southernmost Fujian to the southeast and then southward over time. Factors such as densely populated areas with a large <1-year-old population, less economically developed areas, and higher pollution levels contributed to OID cases in Fujian Province.

CONCLUSIONS

This study revealed a distinct distribution of OID incidence across different population groups, seasons, and regions in Fujian Province. Zhangzhou City and Xiamen City were identified as the major hot spots for OID. Therefore, prevention and control efforts should prioritize these specific hot spots and highly susceptible groups.

Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions

Disease surveillance systems provide early warnings of disease outbreaks before they become public health emergencies. However, pandemics containment would be challenging due to the complex immunity landscape created by multiple variants. Genomic surveillance is critical for detecting novel variants with diverse characteristics and importation/emergence times. Yet, a systematic study incorporating genomic monitoring, situation assessment, and intervention strategies is lacking in the literature. We formulate an integrated computational modeling framework to study a realistic course of action based on sequencing, analysis, and response. We study the effects of the second variant's importation time, its infectiousness advantage and, its cross-infection on the novel variant's detection time, and the resulting intervention scenarios to contain epidemics driven by two-variants dynamics. Our results illustrate the limitation in the intervention's effectiveness due to the variants' competing dynamics and provide the following insights: i) There is a set of importation times that yields the worst detection time for the second variant, which depends on the first variant's basic reproductive number; ii) When the second variant is imported relatively early with respect to the first variant, the cross-infection level does not impact the detection time of the second variant. We found that depending on the target metric, the best outcomes are attained under different interventions' regimes. Our results emphasize the importance of sustained enforcement of Non-Pharmaceutical Interventions on preventing epidemic resurgence due to importation/emergence of novel variants. We also discuss how our methods can be used to study when a novel variant emerges within a population.

Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis

The SARS-CoV-2 pandemic has been characterized by the repeated emergence of genetically distinct virus variants of increased transmissibility and immune evasion compared to pre-existing lineages. In many countries, their containment required the intervention of public health authorities and the imposition of control measures. While the primary role of testing is to identify infection, target treatment, and limit spread (through isolation and contact tracing), a secondary benefit is in terms of surveillance and the early detection of new variants. Here we study the spatial invasion and early spread of the Alpha, Delta and Omicron (BA.1 and BA.2) variants in England from September 2020 to February 2022 using the random neighbourhood covering (RaNCover) method. This is a statistical technique for the detection of aberrations in spatial point processes, which we tailored here to community PCR (polymerase-chain-reaction) test data where the TaqPath kit provides a proxy measure of the switch between variants. Retrospectively, RaNCover detected the earliest signals associated with the four novel variants that led to large infection waves in England. With suitable data our method therefore has the potential to rapidly detect outbreaks of future SARS-CoV-2 variants, thus helping to inform targeted public health interventions.

Sporadic Shiga Toxin-Producing Escherichia coli-Associated Pediatric Hemolytic Uremic Syndrome, France, 2012-2021

Shiga toxin-producing Escherichia coli-associated pediatric hemolytic uremic syndrome (STEC-HUS) remains an important public health risk in France. Cases are primarily sporadic, and geographic heterogeneity has been observed in crude incidence rates. We conducted a retrospective study of 1,255 sporadic pediatric STEC-HUS cases reported during 2012-2021 to describe spatiotemporal dynamics and geographic patterns of higher STEC-HUS risk. Annual case notifications ranged from 109 to 163. Most cases (n = 780 [62%]) were in children <3 years of age. STEC serogroups O26, O80, and O157 accounted for 78% (559/717) of cases with serogroup data. We identified 13 significant space-time clusters and 3 major geographic zones of interest; areas of southeastern France were included in >5 annual space-time clusters. The results of this study have numerous implications for outbreak detection and investigation and research perspectives to improve knowledge of environmental risk factors associated with geographic disparities in STEC-HUS in France.

Enhanced cluster detection and noise reduction for geospatial time series data of COVID-19

Spatial-temporal analysis of the COVID-19 cases is critical to find its transmitting behaviour and to detect the possible emerging clusters. Poisson's prospective space-time analysis has been successfully implemented for cluster detection of geospatial time series data. However, its accuracy, number of clusters, and processing time are still a major problem for detecting small-sized clusters. The aim of this research is to improve the accuracy of cluster detection of COVID-19 at the county level in the U.S.A. by detecting small-sized clusters and reducing the noisy data. The proposed system consists of the Poisson prospective space-time analysis along with Enhanced cluster detection and noise reduction algorithm (ECDeNR) to improve the number of clusters and decrease the processing time. The results of accuracy, processing time, number of clusters, and relative risk are obtained by using different COVID-19 datasets in SaTScan. The proposed system increases the average number of clusters by 7 and the average relative risk by 9.19. Also, it provides a cluster detection accuracy of 91.35% against the current accuracy of 83.32%. It also gives a processing time of 5.69 minutes against the current processing time of 7.36 minutes on average. The proposed system focuses on improving the accuracy, number of clusters, and relative risk and reducing the processing time of the cluster detection by using ECDeNR algorithm. This study solves the issues of detecting the small-sized clusters at the early stage and enhances the overall cluster detection accuracy while decreasing the processing time.

Knowledge, attitude and practice (KAP) of smallholder farmers on foot-and-mouth disease in Cattle in West Kazakhstan

BACKGROUND

This study was performed to assess the knowledge, attitudes and practices (KAPs) of farmers and veterinary professionals towards foot-and-mouth disease (FMD) in the area studied.

METHODS

The study was based on a comprehensive questionnaire administered through face-to-face interviews. Between January and May 2022, 543 households and 27 animal health practitioners (AHP) were visited in 4 provinces of the West Kazakhstan region to assess their KAPs towards FMD.

RESULTS

A large proportion of herd owners (84%) had known the name of the disease, and nearly a half (48) of respondents had heard of FMD cases on farms in the neighbourhood. Oral mucosa lesions were the most consistent with clinical sign characteristic of FMD among farmers (31.4%), followed by hoof blisters (27.6%) and excessive salivation (18.6%). Farmers reported that new animal introduction was potentially the main factor associated with FMD occurrence in their herds. Over half of farmers (54%) interviewed prefer not to purchase livestock from unknown or potentially epidemiologically disadvantaged areas.

CONCLUSION

All AHPs (27) reported that in their zone of veterinary responsibilities, vaccination against FMD is not practised because the area investigated possesses FMD-free status. However, in the past few years, numerous FMD outbreaks have been detected throughout the region. For this reason, immediate actions need to be taken to prevent further FMD occurrences by giving the region a status of an FMD-free zone with vaccination. The current study demonstrated that inadequate quarantine controls of imported animals, absence of regular vaccination and unrestricted animal movement within the country were the primary obstacles in controlling and preventing FMD in the investigated area.

Space-time cluster detection techniques for infectious diseases: A systematic review

BACKGROUND

Public health organizations have increasingly harnessed geospatial technologies for disease surveillance, health services allocation, and targeting place-based health promotion initiatives.

METHODS

We conducted a systematic review around the theme of space-time clustering detection techniques for infectious diseases using PubMed, Web of Science, and Scopus. Two reviewers independently determined inclusion and exclusion.

RESULTS

Of 2,887 articles identified, 354 studies met inclusion criteria, the majority of which were application papers. Studies of airborne diseases were dominant, followed by vector-borne diseases. Most research used aggregated data instead of point data, and a significant proportion of articles used a repetition of a spatial clustering method, instead of using a "true" space-time detection approach, potentially leading to the detection of false positives. Noticeably, most articles did not make their data available, limiting replicability.

CONCLUSION

This review underlines recent trends in the application of space-time clustering methods to the field of infectious disease, with a rapid increase during the COVID-19 pandemic.

An Offenders-Offenses Shared Component Spatial Model for Identifying Shared and Specific Hotspots of Offenders and Offenses: A Case Study of Juvenile Delinquents and Violent Crimes in the Greater Toronto Area

Objectives

We attempted to apply the Bayesian shared component spatial modeling (SCSM) for the identification of hotspots from two (offenders and offenses) instead of one (offenders or offenses) variables and developed three risk surfaces for (1) common or shared by both offenders and offenses; (2) specific to offenders, and (3) specific to offenses.

Methods

We applied SCSM to examine the joint spatial distributions of juvenile delinquents (offenders) and violent crime (offenses) in the York Region of the Greater Toronto Area at the dissemination area level. The spatial autocorrelation, overdispersion, and latent covariates were adjusted by spatially structured and unstructured random effect terms in the model. We mapped the posterior means of the estimated shared and specific risks for identifying the three risk surfaces and types of hotspots.

Results

Results suggest that about 50% and 25% of the relative risks of juvenile delinquents and violent crimes, respectively, could be explained by the shared component of offenders and offenses. The spatially structured terms attributed to 48% and 24% of total variations of the delinquents and violent crimes, respectively. Contrastingly, the unstructured random covariates influenced 3% of total variations of the juvenile delinquents and 51% for violent crimes.

Conclusions

The Bayesian SCSM presented in this study identifies shared and specific hotspots of juvenile delinquents and violent crime. The method can be applied to other kinds of offenders and offenses and provide new insights into the clusters of high risks that are due to both offenders and offenses or due to offenders or offenses only.

Mathematical modeling in perspective of vector-borne viral infections: a review

Background

Viral diseases are highly widespread infections caused by viruses. These viruses are passing from one human to other humans through a certain medium. The medium might be mosquito, animal, reservoir and food, etc. Here, the population of both human and mosquito vectors are important.

Main body of the abstract

The main objectives are here to introduce the historical perspective of mathematical modeling, enable the mathematical modeler to understand the basic mathematical theory behind this and present a systematic review on mathematical modeling for four vector-borne viral diseases using the deterministic approach. Furthermore, we also introduced other mathematical techniques to deal with vector-borne diseases. Mathematical models could help forecast the infectious population of humans and vectors during the outbreak.

Short conclusion

This study will be helpful for mathematical modelers in vector-borne diseases and ready-made material in the review for future advancement in the subject. This study will not only benefit vector-borne conditions but will enable ideas for other illnesses.

The role of geographic information system and global positioning system in dementia care and research: a scoping review

Background

Geographic Information System (GIS) and Global Positioning System (GPS), vital tools for supporting public health research, provide a framework to collect, analyze and visualize the interaction between different levels of the health care system. The extent to which GIS and GPS applications have been used in dementia care and research is not yet investigated. This scoping review aims to elaborate on the role and types of GIS and GPS applications in dementia care and research.

Methods

A scoping review was conducted based on Arksey and O’Malley’s framework. All published articles in peer-reviewed journals were searched in PubMed, Scopus, and Web of Science, subject to involving at least one GIS/GPS approach focused on dementia. Eligible studies were reviewed, grouped, and synthesized to identify GIS and GPS applications. The PRISMA standard was used to report the study.

Results

Ninety-two studies met our inclusion criteria, and their data were extracted. Six types of GIS/GPS applications had been reported in dementia literature including mapping and surveillance (n = 59), data preparation (n = 26), dementia care provision (n = 18), basic research (n = 18), contextual and risk factor analysis (n = 4), and planning (n = 1). Thematic mapping and GPS were most frequently used techniques in the dementia field.

Conclusions

Even though the applications of GIS/GPS methodologies in dementia care and research are growing, there is limited research on GIS/GPS utilization in dementia care, risk factor analysis, and dementia policy planning. GIS and GPS are space-based systems, so they have a strong capacity for developing innovative research based on spatial analysis in the area of dementia. The existing research has been summarized in this review which could help researchers to know the GIS/GPS capabilities in dementia research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12942-022-00308-1.

Variance partitioning in spatio-temporal disease mapping models

Bayesian disease mapping, yet if undeniably useful to describe variation in risk over time and space, comes with the hurdle of prior elicitation on hard-to-interpret random effect precision parameters. We introduce a reparametrized version of the popular spatio-temporal interaction models, based on Kronecker product intrinsic Gaussian Markov random fields, that we name the variance partitioning model. The variance partitioning model includes a mixing parameter that balances the contribution of the main and interaction effects to the total (generalized) variance and enhances interpretability. The use of a penalized complexity prior on the mixing parameter aids in coding prior information in an intuitive way. We illustrate the advantages of the variance partitioning model using two case studies.

Comparing transmission potential networks based on social network surveys, close contacts and environmental overlap in rural Madagascar

Social and spatial network analysis is an important approach for investigating infectious disease transmission, especially for pathogens transmitted directly between individuals or via environmental reservoirs. Given the diversity of ways to construct networks, however, it remains unclear how well networks constructed from different data types effectively capture transmission potential. We used empirical networks from a population in rural Madagascar to compare social network survey and spatial data-based networks of the same individuals. Close contact and environmental pathogen transmission pathways were modelled with the spatial data. We found that naming social partners during the surveys predicted higher close-contact rates and the proportion of environmental overlap on the spatial data-based networks. The spatial networks captured many strong and weak connections that were missed using social network surveys alone. Across networks, we found weak correlations among centrality measures (a proxy for superspreading potential). We conclude that social network surveys provide important scaffolding for understanding disease transmission pathways but miss contact-specific heterogeneities revealed by spatial data. Our analyses also highlight that the superspreading potential of individuals may vary across transmission modes. We provide detailed methods to construct networks for close-contact transmission pathogens when not all individuals simultaneously wear GPS trackers.

A Systematic Review of Spatial and Spatio-temporal Analyses in Public Health Research in Korea

OBJECTIVES

Despite its advantages, it is not yet common practice in Korea for researchers to investigate disease associations using spatio-temporal analyses. In this study, we aimed to review health-related epidemiological research using spatio-temporal analyses and to observe methodological trends.

METHODS

Health-related studies that applied spatial or spatio-temporal methods were identified using 2 international databases (PubMed and Embase) and 4 Korean academic databases (KoreaMed, NDSL, DBpia, and RISS). Two reviewers extracted data to review the included studies. A search for relevant keywords yielded 5919 studies.

RESULTS

Of the studies that were initially found, 150 were ultimately included based on the eligibility criteria. In terms of the research topic, 5 categories with 11 subcategories were identified: chronic diseases (n=31, 20.7%), infectious diseases (n=27, 18.0%), health-related topics (including service utilization, equity, and behavior) (n=47, 31.3%), mental health (n=15, 10.0%), and cancer (n=7, 4.7%). Compared to the period between 2000 and 2010, more studies published between 2011 and 2020 were found to use 2 or more spatial analysis techniques (35.6% of included studies), and the number of studies on mapping increased 6-fold.

CONCLUSIONS

Further spatio-temporal analysis-related studies with point data are needed to provide insights and evidence to support policy decision-making for the prevention and control of infectious and chronic diseases using advances in spatial techniques.

Spatiotemporal Dynamics of Sporadic Shiga Toxin-Producing Escherichia coli Enteritis, Ireland, 2013-2017

The Republic of Ireland regularly reports the highest annual crude incidence rates of Shiga toxin–producing Escherichia coli (STEC) enteritis in the European Union, ≈10 times the average. We investigated spatiotemporal patterns of STEC enteritis in Ireland using multiple statistical tools. Overall, we georeferenced 2,755 cases of infection during January 2013–December 2017; we found >1 case notified in 2,340 (12.6%) of 18,641 Census Small Areas. We encountered the highest case numbers in children 0–5 years of age (n = 1,101, 39.6%) and associated with serogroups O26 (n = 800, 29%) and O157 (n = 638, 23.2%). Overall, we identified 17 space-time clusters, ranging from 2 (2014) to 5 (2017) clusters of sporadic infection per year; we detected recurrent clustering in 3 distinct geographic regions in the west and mid-west, all of which are primarily rural. Our findings can be used to enable targeted epidemiologic intervention and surveillance.

Knowledge, Attitudes, and Practices (KAPs) of Farmers on Foot and Mouth Disease in Cattle in Baghlan Province, Afghanistan: A Descriptive Study

Simple Summary

Foot and mouth disease (FMD) affects the productivity and health of several animals species, including cattle. In Afghanistan, cattle represent a valuable source of food security and play a vital role in the rural economy. Using a questionnaire-based approach, we evaluated the self-reported knowledge, attitudes, and practices of various stakeholders involved in the cattle industry and veterinary management of animal health in a northern province of Afghanistan. The study pointed to several aspects that could be translated into practical management options to add value to FMD management in the cattle industry in Afghanistan.

Abstract

This study was performed to investigate the knowledge, attitudes, and practices (KAPs) of farmers, animal traders, and veterinary professionals on FMD in Baghlan province, Afghanistan. Four structured questionnaires were administered to the respondents. Almost half (48.5%) of the farmers had heard of the occurrence of FMD in their neighbourhood or knew the name of the disease. The majority of farmers could recognise the clinical signs of FMD in their animals (salivation, 85.9%; tongue ulcers, 78.8%; gum lesions, 78.2%; hoof lesions, 76.8%). Most farmers stated that the “introduction of new animals” was the primary cause of FMD appearing on their farms and to control the spread of the disease, over half of the farmers (56%) preferred not to buy cattle from unknown or potentially infected sources. Animal traders’ knowledge was limited to recognising some clinical signs of the disease such as: salivation, and lesions in the mouth and on the feet. No animals were directly imported by the traders from outside Afghanistan. Over half of the local veterinary professionals (65%) kept record books of the animal diseases seen and/or treatment plans undertaken, and 80% of them reported the occurrence of FMD to the provincial, regional, and central veterinary authorities. No regular vaccination programme against FMD was implemented in the province. Poor import controls and quarantine were considered to be the main barriers to the control of FMD in the study area and the surrounding provinces. It can be concluded that, despite relatively good knowledge about FMD in the study area, there are gaps in farmers’ and traders’ knowledge that need to be addressed to overcome the burden of the disease in the province. These should focus on strengthening interprovincial quarantine measures and implementation of regular vaccination campaigns against the circulating FMDV within the area.

Understanding the Differential Impact of Vegetation Measures on Modeling the Association between Vegetation and Psychotic and Non-Psychotic Disorders in Toronto, Canada

Considerable debate exists on whether exposure to vegetation cover is associated with better mental health outcomes. Past studies could not accurately capture people's exposure to surrounding vegetation and heavily relied on non-spatial models, where the spatial autocorrelation and latent covariates could not be adjusted. Therefore, a suite of five different vegetation measures was used to separately analyze the association between vegetation cover and the number of psychotic and non-psychotic disorder cases in the neighborhoods of Toronto, Canada. Three satellite-based and two area-based vegetation measures were used to analyze these associations using Poisson lognormal models under a Bayesian framework. Healthy vegetation cover was found to be negatively associated with both psychotic and non-psychotic disorders. Results suggest that the satellite-based indices, which can measure both the density and health of vegetation cover and are also adjusted for urban and environmental perturbations, could be better alternatives to simple ratio- and area-based measures for understanding the effect of vegetation on mental health. A strong dominance of spatially structured latent covariates was found in the models, highlighting the importance of adopting a spatial approach. This study can provide critical guidelines for selecting appropriate vegetation measures and developing spatial models for future population-based epidemiological research.

Comparing malaria early detection methods in a declining transmission setting in northwestern Ethiopia

Background

Despite remarkable progress in the reduction of malaria incidence, this disease remains a public health threat to a significant portion of the world’s population. Surveillance, combined with early detection algorithms, can be an effective intervention strategy to inform timely public health responses to potential outbreaks. Our main objective was to compare the potential for detecting malaria outbreaks by selected event detection methods.

Methods

We used historical surveillance data with weekly counts of confirmed Plasmodium falciparum (including mixed) cases from the Amhara region of Ethiopia, where there was a resurgence of malaria in 2019 following several years of declining cases. We evaluated three methods for early detection of the 2019 malaria events: 1) the Centers for Disease Prevention and Control (CDC) Early Aberration Reporting System (EARS), 2) methods based on weekly statistical thresholds, including the WHO and Cullen methods, and 3) the Farrington methods.

Results

All of the methods evaluated performed better than a naïve random alarm generator. We also found distinct trade-offs between the percent of events detected and the percent of true positive alarms. CDC EARS and weekly statistical threshold methods had high event sensitivities (80–100% CDC; 57–100% weekly statistical) and low to moderate alarm specificities (25–40% CDC; 16–61% weekly statistical). Farrington variants had a wide range of scores (20–100% sensitivities; 16–100% specificities) and could achieve various balances between sensitivity and specificity.

Conclusions

Of the methods tested, we found that the Farrington improved method was most effective at maximizing both the percent of events detected and true positive alarms for our dataset (> 70% sensitivity and > 70% specificity). This method uses statistical models to establish thresholds while controlling for seasonality and multi-year trends, and we suggest that it and other model-based approaches should be considered more broadly for malaria early detection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-021-10850-5.

Detecting space-time clusters of COVID-19 in Brazil: mortality, inequality, socioeconomic vulnerability, and the relative risk of the disease in Brazilian municipalities

The first case of COVID-19 in South America occurred in Brazil on February 25, 2020. By July 20, 2020, there were 2,118,646 confirmed cases and 80,120 confirmed deaths. To assist with the development of preventive measures and targeted interventions to combat the pandemic in Brazil, we present a geographic study to detect "active" and "emerging" space-time clusters of COVID-19. We document the relationship between relative risk of COVID-19 and mortality, inequality, socioeconomic vulnerability variables. We used the prospective space-time scan statistic to detect daily COVID-19 clusters and examine the relative risk between February 25-June 7, 2020, and February 25-July 20, 2020, in 5570 Brazilian municipalities. We apply a Generalized Linear Model (GLM) to assess whether mortality rate, GINI index, and social inequality are predictors for the relative risk of each cluster. We detected 7 "active" clusters in the first time period, being one in the north, two in the northeast, two in the southeast, one in the south, and one in the capital of Brazil. In the second period, we found 9 clusters with RR > 1 located in all Brazilian regions. The results obtained through the GLM showed that there is a significant positive correlation between the predictor variables in relation to the relative risk of COVID-19. Given the presence of spatial autocorrelation in the GLM residuals, a spatial lag model was conducted that revealed that spatial effects, and both GINI index and mortality rate were strong predictors in the increase in COVID-19 relative risk in Brazil. Our research can be utilized to improve COVID-19 response and planning in all Brazilian states. The results from this study are particularly salient to public health, as they can guide targeted intervention measures, lowering the magnitude and spread of COVID-19. They can also improve resource allocation such as tests and vaccines (when available) by informing key public health officials about the highest risk areas of COVID-19.

A Bayesian mixture modeling approach for public health surveillance

Spatial monitoring of trends in health data plays an important part of public health surveillance. Most commonly, it is used to understand the etiology of a public health issue, to assess the impact of an intervention, or to provide detection of unusual behavior. In this article, we present a Bayesian mixture model for public health surveillance, which is able to provide estimates of the disease risk in space and time, and also to detect areas with unusual behavior. The model is designed to deal with a range of spatial and temporal patterns in the data, and with time series of different lengths. We carry out a simulation study to assess the performance of the model under different scenarios, and we compare it against a recently proposed Bayesian model for short time series. Finally, the proposed model is used for surveillance of road traffic accidents data in England over the years 2005-2015.

Urban Fire Dynamics and Its Association with Urban Growth: Evidence from Nanjing, China

Many Chinese cities currently are facing increased urban fire risks particularly at places such as urban villages, high-rise buildings and large warehouses. Using a unique historical fire incident dataset (2002–2013), this paper is intended to explore the urban fire dynamics and its association with urban growth in Nanjing, China, with a geographical information system (GIS)-based spatial analytics and remote sensing (RS) techniques. A new method is proposed to define a range of fire hot spots characterizing different phases of fire incident evolution, which are compared with the urban growth in the same periods. The results suggest that the fire events have been largely concentrated in the city proper and meanwhile expanding towards the suburbs, which has a similar temporal trend to the growth of population and urban land at the city level particularly since 2008. Most intensifying and persistent fire hot spots are found in the central districts, which have limited urban expansion but high population densities. Most new hot spots are located in the suburban districts, which have seen both rapid population growth and urban expansion in recent years. However, the analysis at a finer spatial scale (500 m × 500 m) shows no evidences of an explicit connection between the locations of new fire hot spots and recently developed urban land. The findings can inform future urban and emergency planning with respect to the deployment of fire and rescue resources, ultimately improving urban fire safety.

Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection

Genetic clustering is a popular method for characterizing variation in transmission rates for rapidly evolving viruses, and could potentially be used to detect outbreaks in 'near real time'. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here, we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analysed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B pol sequences from Seattle (n = 1,653) and Middle Tennessee, USA (n = 2,779), and northern Alberta, Canada (n = 809). Under varying TN93 thresholds, we fit two models to the distributions of new cases relative to clusters of known cases: 1, a null model that assumes cluster growth is strictly proportional to cluster size, i.e. no variation in transmission rates among individuals; and 2, a weighted model that incorporates individual-level covariates, such as recency of diagnosis. The optimal threshold maximizes the difference in information loss between models, where covariates are used most effectively. Optimal TN93 thresholds varied substantially between data sets, e.g. 0.0104 in Alberta and 0.016 in Seattle and Tennessee, such that the optimum for one population would potentially misdirect prevention efforts in another. For a given population, the range of thresholds where the weighted model conferred greater predictive accuracy tended to be narrow (±0.005 units), and the optimal threshold tended to be stable over time. Our framework also indicated that variation in the recency of HIV diagnosis among clusters was significantly more predictive of new cases than sample collection dates (ΔAIC > 50). These results suggest that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications, especially when translating methods between settings of low-level and generalized epidemics. Our framework not only enables investigators to calibrate a clustering method to a specific public health setting, but also provides a variable selection procedure to evaluate different predictive models of cluster growth.

Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models

It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness.

Disease-causing microorganisms, including viruses, bacteria, protozoa and fungi, form complex communities within animals and plants. These microorganisms can coexist harmoniously or even beneficially, or they may competitively interact for host resources. Well-studied examples include interactions between viruses and bacteria in the respiratory tract. Whilst ecological studies have revealed that some pathogens do interact within their hosts, identifying interactions from available population scale data from health authorities is challenging. This is exacerbated by a lack of large-scale data describing the infection patterns of multiple pathogens within single populations over long time frames. Furthermore, methods for evaluating whether infection frequencies of different pathogens fluctuate together or not over time cannot readily account for alternative explanations. For example, human pathogens may have related seasonal patterns depending on the age groups they infect and the weather conditions they survive in, and not because they are interacting. We developed a robust statistical framework to identify pathogen-pathogen interactions from population scale diagnostic data. This framework serves as a crucial step in identifying such important interactions and will guide new studies to elucidate their underpinning mechanisms. This will have important consequences for public health preparedness and the design of effective disease control interventions.

Space-time dynamics of a triple epidemic: dengue, chikungunya and Zika clusters in the city of Rio de Janeiro

Dengue, an arboviral disease transmitted by Aedes mosquitoes, has been endemic in Brazil for decades. However, vector-control strategies have not led to a significant reduction in the disease burden and have not been sufficient to prevent chikungunya and Zika entry and establishment in the country. In Rio de Janeiro city, the first Zika and chikungunya epidemics were detected between 2015 and 2016, coinciding with a dengue epidemic. Understanding the behaviour of these diseases in a triple epidemic scenario is a necessary step for devising better interventions for prevention and outbreak response. We applied scan statistics analysis to detect spatio-temporal clustering for each disease separately and for all three simultaneously. In general, clusters were not detected in the same locations and time periods, possibly owing to competition between viruses for host resources, depletion of susceptible population, different introduction times and change in behaviour of the human population (e.g. intensified vector-control activities in response to increasing cases of a particular arbovirus). Simultaneous clusters of the three diseases usually included neighbourhoods with high population density and low socioeconomic status, particularly in the North region of the city. The use of space–time cluster detection can guide intensive interventions to high-risk locations in a timely manner, to improve clinical diagnosis and management, and pinpoint vector-control measures.

Surveillance of animal diseases through implementation of a Bayesian spatio-temporal model: A simulation example with neurological syndromes in horses and West Nile Virus

A potentially sensitive way to detect disease outbreaks is syndromic surveillance, i.e. monitoring the number of syndromes reported in the population of interest, comparing it to the baseline rate, and drawing conclusions about outbreaks using statistical methods. A decision maker may use the results to take disease control actions or to initiate enhanced epidemiological investigations. In addition to the total count of syndromes there are often additional pieces of information to consider when assessing the probability of an outbreak. This includes clustering of syndromes in space and time as well as historical data on the occurrence of syndromes, seasonality of the disease, etc. In this paper, we show how Bayesian theory for syndromic surveillance applies to the occurrence of neurological syndromes in horses in France. Neurological syndromes in horses may be connected e.g. to West Nile Virus (WNV), a zoonotic disease of growing concern for public health in Europe. A Bayesian method for spatio-temporal cluster detection of syndromes and for determining the probability of an outbreak is presented. It is shown how surveillance can be performed simultaneously for a specific class of diseases (WNV or diseases similar to WNV in terms of the information available to the system) and a non-specific class of diseases (not similar to WNV in terms of the information available to the system). We also discuss some new extensions to the spatio-temporal models and the computational algorithms involved. It is shown step-by-step how data from historical WNV outbreaks and surveillance data for neurological syndromes can be used for model construction. The model is implemented using a Gibbs sampling procedure, and its sensitivity and specificity is evaluated. Finally, it is illustrated how predictive modelling of syndromes can be useful for decision making in animal health surveillance.

Geographic patterns of poor HIV/AIDS care continuum in District of Columbia

Background

Concurrent with the UNAIDS 90-90-90 and NHAS plans, the District of Columbia (DC) launched its 90/90/90/50 plan (Plan) in 2015. The Plan proposes that by 2020, 90% of all DC residents will know their HIV status; 90% of residents living with HIV will be in sustained treatment; 90% of those in treatment will reach “Viral Suppression” and DC will achieve 50% reduction of new HIV cases. To achieve these goals targeted prevention strategies are imperative for areas where the relative risk (RR) of not being linked to care (NL), not retained in any care (NRC) and low viral suppression (NVSP) are highest in the District. These outcomes are denoted in this study as poor outcomes of HIV care continuum. This study applies the Bayesian model for RR for area specific random effects to identify the census tracts with poor HIV care continuum outcomes for DC.

Methods

This analysis was conducted using cases diagnosed from 2010 to 2015 and reported to the surveillance system from the District of Columbia Department of Health (DC DOH), HIV/AIDS, Hepatitis, STD and TB Administration. The jurisdictions of the District of Columbia is divided into 179 census tracts. It is challenging to plot sparse data in ‘small’ local administrative areas, characteristically which may have a single-count datum for each geographic area. Bayesian methods overcome this problem by assimilating prior information to the underlying RR, making the predicted RR estimates robust.

Results

The RR of NL is higher in 59 (33%) out of 179 census tracts in DC. The RR of NRC was high in 46 (26%) of the census tracts while 52 census tracts (29%) show a high risk of having NVSP among its residents. This study also identifies clear correlated heterogeneity or clustering is evident in the northern tracts of the district.

Conclusion

The study finds census tracts with higher RR of poor linkage to care outcomes in the District. These results will inform the Plan which aims to increase targeted testing leading to early initiation of antiretroviral therapy. The uniqueness of this study lies in its translational scope where surveillance data can be used to inform local public health programs and enhance the quality of health for the people with HIV.

Electronic supplementary material

The online version of this article (10.1186/s12981-018-0189-8) contains supplementary material, which is available to authorized users.

Exploring spatial and temporal patterns of visceral leishmaniasis in endemic areas of Bangladesh

Background

Visceral leishmaniasis is a considerable public health burden on the Indian subcontinent. The disease is highly endemic in the north-central part of Bangladesh, affecting the poorest and most marginalized communities. Despite the fact that visceral leishmaniasis (VL) results in mortality, severe morbidity, and socioeconomic stress in the region, the spatiotemporal dynamics of the disease have largely remained unexplored, especially in Bangladesh.

Methods

Monthly VL cases between 2010 and 2014, obtained from subdistrict hospitals, were studied in this work. Both global and local spatial autocorrelation techniques were used to identify spatial heterogeneity of the disease. In addition, a spatial scan test was used to identify statistically significant space-time clusters in endemic locations of Bangladesh.

Results

Global and local spatial autocorrelation indicated that the distribution of VL was spatially autocorrelated, exhibiting both contiguous and relocation-type of diffusion; however, the former was the main type of VL spread in the study area. The spatial scan test revealed that the disease had ten times higher incidence rate within the clusters than in non-cluster zones. Both tests identified clusters in the same geographic areas, despite the differences in their algorithm and cluster detection approach.

Conclusion

The cluster maps, generated in this work, can be used by public health officials to prioritize areas for intervention. Additionally, initiatives to control VL can be handled more efficiently when areas of high risk of the disease are known. Because global environmental change is expected to shift the current distribution of vectors to new locations, the results of this work can help to identify potentially exposed populations so that adaptation strategies can be formulated.

Evidence in Practice - A Pilot Study Leveraging Companion Animal and Equine Health Data from Primary Care Veterinary Clinics in New Zealand

Veterinary practitioners have extensive knowledge of animal health from their day-to-day observations of clinical patients. There have been several recent initiatives to capture these data from electronic medical records for use in national surveillance systems and clinical research. In response, an approach to surveillance has been evolving that leverages existing computerized veterinary practice management systems to capture animal health data recorded by veterinarians. Work in the United Kingdom within the VetCompass program utilizes routinely recorded clinical data with the addition of further standardized fields. The current study describes a prototype system that was developed based on this approach. In a 4-week pilot study in New Zealand, clinical data on presentation reasons and diagnoses from a total of 344 patient consults were extracted from two veterinary clinics into a dedicated database and analyzed at the population level. New Zealand companion animal and equine veterinary practitioners were engaged to test the feasibility of this national practice-based health information and data system. Strategies to ensure continued engagement and submission of quality data by participating veterinarians were identified, as were important considerations for transitioning the pilot program to a sustainable large-scale and multi-species surveillance system that has the capacity to securely manage big data. The results further emphasized the need for a high degree of usability and smart interface design to make such a system work effectively in practice. The geospatial integration of data from multiple clinical practices into a common operating picture can be used to establish the baseline incidence of disease in New Zealand companion animal and equine populations, detect unusual trends that may indicate an emerging disease threat or welfare issue, improve the management of endemic and exotic infectious diseases, and support research activities. This pilot project is an important step toward developing a national surveillance system for companion animals and equines that moves beyond emerging infectious disease detection to provide important animal health information that can be used by a wide range of stakeholder groups, including participating veterinary practices.

Methodological challenges to multivariate syndromic surveillance: a case study using Swiss animal health data

BACKGROUND

In an era of ubiquitous electronic collection of animal health data, multivariate surveillance systems (which concurrently monitor several data streams) should have a greater probability of detecting disease events than univariate systems. However, despite their limitations, univariate aberration detection algorithms are used in most active syndromic surveillance (SyS) systems because of their ease of application and interpretation. On the other hand, a stochastic modelling-based approach to multivariate surveillance offers more flexibility, allowing for the retention of historical outbreaks, for overdispersion and for non-stationarity. While such methods are not new, they are yet to be applied to animal health surveillance data. We applied an example of such stochastic model, Held and colleagues' two-component model, to two multivariate animal health datasets from Switzerland.

RESULTS

In our first application, multivariate time series of the number of laboratories test requests were derived from Swiss animal diagnostic laboratories. We compare the performance of the two-component model to parallel monitoring using an improved Farrington algorithm and found both methods yield a satisfactorily low false alarm rate. However, the calibration test of the two-component model on the one-step ahead predictions proved satisfactory, making such an approach suitable for outbreak prediction. In our second application, the two-component model was applied to the multivariate time series of the number of cattle abortions and the number of test requests for bovine viral diarrhea (a disease that often results in abortions). We found that there is a two days lagged effect from the number of abortions to the number of test requests. We further compared the joint modelling and univariate modelling of the number of laboratory test requests time series. The joint modelling approach showed evidence of superiority in terms of forecasting abilities.

CONCLUSIONS

Stochastic modelling approaches offer the potential to address more realistic surveillance scenarios through, for example, the inclusion of times series specific parameters, or of covariates known to have an impact on syndrome counts. Nevertheless, many methodological challenges to multivariate surveillance of animal SyS data still remain. Deciding on the amount of corroboration among data streams that is required to escalate into an alert is not a trivial task given the sparse data on the events under consideration (e.g. disease outbreaks).

Advances in spatial epidemiology and geographic information systems

The field of spatial epidemiology has evolved rapidly in the past 2 decades. This study serves as a brief introduction to spatial epidemiology and the use of geographic information systems in applied research in epidemiology. We highlight technical developments and highlight opportunities to apply spatial analytic methods in epidemiologic research, focusing on methodologies involving geocoding, distance estimation, residential mobility, record linkage and data integration, spatial and spatio-temporal clustering, small area estimation, and Bayesian applications to disease mapping. The articles included in this issue incorporate many of these methods into their study designs and analytical frameworks. It is our hope that these studies will spur further development and utilization of spatial analysis and geographic information systems in epidemiologic research.

Avian Influenza Risk Surveillance in North America with Online Media

The use of Internet-based sources of information for health surveillance applications has increased in recent years, as a greater share of social and media activity happens through online channels. The potential surveillance value in online sources of information about emergent health events include early warning, situational awareness, risk perception and evaluation of health messaging among others. The challenge in harnessing these sources of data is the vast number of potential sources to monitor and developing the tools to translate dynamic unstructured content into actionable information. In this paper we investigated the use of one social media outlet, Twitter, for surveillance of avian influenza risk in North America. We collected AI-related messages over a five-month period and compared these to official surveillance records of AI outbreaks. A fully automated data extraction and analysis pipeline was developed to acquire, structure, and analyze social media messages in an online context. Two methods of outbreak detection; a static threshold and a cumulative-sum dynamic threshold; based on a time series model of normal activity were evaluated for their ability to discern important time periods of AI-related messaging and media activity. Our findings show that peaks in activity were related to real-world events, with outbreaks in Nigeria, France and the USA receiving the most attention while those in China were less evident in the social media data. Topic models found themes related to specific AI events for the dynamic threshold method, while many for the static method were ambiguous. Further analyses of these data might focus on quantifying the bias in coverage and relation between outbreak characteristics and detectability in social media data. Finally, while the analyses here focused on broad themes and trends, there is likely additional value in developing methods for identifying low-frequency messages, operationalizing this methodology into a comprehensive system for visualizing patterns extracted from the Internet, and integrating these data with other sources of information such as wildlife, environment, and agricultural data.

Spatio-temporal variation of mood and anxiety symptom treatments in Christchurch in the context of the 2010/11 Canterbury earthquake sequence

This article explores the spatio-temporal variation of mood and anxiety treatments in the context of a severe earthquake sequence. The aim was to examine a possible earthquake exposure effect, identify populations at risk and areas with particularly large mood and anxiety treatment rate increases or decreases in the affected Christchurch urban area. A significantly stronger increase of mood and anxiety treatments among residents in Christchurch compared to others in New Zealand have been found, as well as children and elderly identified as especially vulnerable. Spatio-temporal cluster analysis and Bayesian spatio-temporal modelling revealed little changes in mood and anxiety treatment patterns for most parts of the city, whereas areas in the less affected north and northwest showed the strongest increases in risk. This effect may be linked to inner-city mobility activity as a consequence of the earthquakes, but also different levels of community cohesion after the disaster, which merit further research.

Spatio-temporal filtering techniques for the detection of disaster-related communication

Individuals predominantly exchange information with one another through informal, interpersonal channels. During disasters and other disrupted settings, information spread through informal channels regularly outpaces official information provided by public officials and the press. Social scientists have long examined this kind of informal communication in the rumoring literature, but studying rumoring in disrupted settings has posed numerous methodological challenges. Measuring features of informal communication-timing, content, location-with any degree of precision has historically been extremely challenging in small studies and infeasible at large scales. We address this challenge by using online, informal communication from a popular microblogging website and for which we have precise spatial and temporal metadata. While the online environment provides a new means for observing rumoring, the abundance of data poses challenges for parsing hazard-related rumoring from countless other topics in numerous streams of communication. Rumoring about disaster events is typically temporally and spatially constrained to places where that event is salient. Accordingly, we use spatio and temporal subsampling to increase the resolution of our detection techniques. By filtering out data from known sources of error (per rumor theories), we greatly enhance the signal of disaster-related rumoring activity. We use these spatio-temporal filtering techniques to detect rumoring during a variety of disaster events, from high-casualty events in major population centers to minimally destructive events in remote areas. We consistently find three phases of response: anticipatory excitation where warnings and alerts are issued ahead of an event, primary excitation in and around the impacted area, and secondary excitation which frequently brings a convergence of attention from distant locales onto locations impacted by the event. Our results demonstrate the promise of spatio-temporal filtering techniques for "tuning" measurement of hazard-related rumoring to enable observation of rumoring at scales that have long been infeasible.

An improved cumulative sum-based procedure for prospective disease surveillance for count data in multiple regions

We present an improved procedure for detecting outbreaks in multiple spatial regions using count data. We combine well-known methods for disease surveillance with recent developments from other areas to provide a more powerful procedure that is still relatively simple and fast to implement. Disease counts from neighboring regions are aggregated to compute a Poisson cumulative sum statistic for each region of interest. Instead of controlling the average run length criterion in the monitoring process, we instead utilize the FDR, which is more appropriate in a public health context. Additionally, p-values are used to make decisions instead of traditional critical values. The use of the FDR and p-values in testing allows us to utilize recently developed multiple testing methodologies, greatly increasing the power of this procedure. This is verified using a simulation experiment. The simplicity and rapid detection ability of this procedure make it useful in disease surveillance settings. The procedure is successfully applied in detecting the 2011 Salmonella Newport outbreak in 16 German federal states. Copyright © 2016 John Wiley & Sons, Ltd.

Accelerating the discovery of space-time patterns of infectious diseases using parallel computing

Infectious diseases have complex transmission cycles, and effective public health responses require the ability to monitor outbreaks in a timely manner. Space-time statistics facilitate the discovery of disease dynamics including rate of spread and seasonal cyclic patterns, but are computationally demanding, especially for datasets of increasing size, diversity and availability. High-performance computing reduces the effort required to identify these patterns, however heterogeneity in the data must be accounted for. We develop an adaptive space-time domain decomposition approach for parallel computation of the space-time kernel density. We apply our methodology to individual reported dengue cases from 2010 to 2011 in the city of Cali, Colombia. The parallel implementation reaches significant speedup compared to sequential counterparts. Density values are visualized in an interactive 3D environment, which facilitates the identification and communication of uneven space-time distribution of disease events. Our framework has the potential to enhance the timely monitoring of infectious diseases.

Utility of algorithms for the analysis of integratedSalmonellasurveillance data

The objective of this study was to assess the use of statistical algorithms in identifying significant clusters ofSalmonellaspp. across different sectors of the food chain within an integrated surveillance programme. Three years of weeklySalmonellaserotype data from farm animals, meat, and humans were used to create baseline models (first two years) and identify weeks with counts higher than expected using surveillance algorithms in the third (test) year. During the test year, an expert working group identified events of interest reviewing descriptive analyses of same data. The algorithms did not identifySalmonellaevents presenting as gradual increases or seasonal patterns as identified by the working group. However, the algorithms did identify clusters for further investigation, suggesting they could be a valuable complementary tool within an integrated surveillance system.

Syndromic surveillance of abortions in beef cattle based on the prospective analysis of spatio-temporal variations of calvings

Our objective was to study the ability of a syndromic surveillance system to identify spatio-temporal clusters of drops in the number of calvings among beef cows during the Bluetongue epizootic of 2007 and 2008, based on calving seasons. France was partitioned into 300 iso-populated units, i.e. units with quite the same number of beef cattle. Only 1% of clusters were unlikely to be related to Bluetongue. Clusters were detected during the calving season of primary infection by Bluetongue in 28% (n = 23) of the units first infected in 2007, and in 87% (n = 184) of the units first infected in 2008. In units in which a first cluster was detected over their calving season of primary infection, Bluetongue was detected more rapidly after the start of the calving season and its prevalence was higher than in other units. We believe that this type of syndromic surveillance system could improve the surveillance of abortive events in French cattle. Besides, our approach should be used to develop syndromic surveillance systems for other diseases and purposes, and in other settings, to avoid "false" alarms due to isolated events and homogenize the ability to detect abnormal variations of indicator amongst iso-populated units.

Towards a geocomputational landscape epidemiology: surveillance, modelling, and interventions

The ability to explicitly represent infectious disease distributions and their risk factors over massive geographical and temporal scales has transformed how we investigate how environment impacts health. While landscape epidemiology studies have shed light on many aspects of disease distribution and risk differentials across geographies, new computational methods combined with new data sources such as citizen sensors, global spatial datasets, sensor networks, and growing availability and variety of satellite imagery offer opportunities for a more integrated approach to understanding these relationships. Additionally, a large number of new modelling and mapping methods have been developed in recent years to support the adoption of these new tools. The complexity of this research context results in study-dependent solutions and prevents landscape approaches from deeper integration into operational models and tools. In this paper we consider three common research contexts for spatial epidemiology; surveillance, modelling to estimate a spatial risk distribution and the need for intervention, and evaluating interventions and improving healthcare. A framework is proposed and a categorization of existing methods is presented. A case study into leptospirosis in Sri Lanka provides a working example of how the different phases of the framework relate to real research problems. The new framework for geocomputational landscape epidemiology encompasses four key phases: characterizing assemblages, characterizing functions, mapping interdependencies, and examining outcomes. Results from Sri Lanka provide evidence that the framework provides a useful way to structure and interpret analyses. The framework reported here is a new way to structure existing methods and tools of geocomputation that are increasingly relevant to researchers working on spatially explicit disease-landscape studies.

Simulation-Based Evaluation of the Performances of an Algorithm for Detecting Abnormal Disease-Related Features in Cattle Mortality Records

We performed a simulation study to evaluate the performances of an anomaly detection algorithm considered in the frame of an automated surveillance system of cattle mortality. The method consisted in a combination of temporal regression and spatial cluster detection which allows identifying, for a given week, clusters of spatial units showing an excess of deaths in comparison with their own historical fluctuations. First, we simulated 1,000 outbreaks of a disease causing extra deaths in the French cattle population (about 200,000 herds and 20 million cattle) according to a model mimicking the spreading patterns of an infectious disease and injected these disease-related extra deaths in an authentic mortality dataset, spanning from January 2005 to January 2010. Second, we applied our algorithm on each of the 1,000 semi-synthetic datasets to identify clusters of spatial units showing an excess of deaths considering their own historical fluctuations. Third, we verified if the clusters identified by the algorithm did contain simulated extra deaths in order to evaluate the ability of the algorithm to identify unusual mortality clusters caused by an outbreak. Among the 1,000 simulations, the median duration of simulated outbreaks was 8 weeks, with a median number of 5,627 simulated deaths and 441 infected herds. Within the 12-week trial period, 73% of the simulated outbreaks were detected, with a median timeliness of 1 week, and a mean of 1.4 weeks. The proportion of outbreak weeks flagged by an alarm was 61% (i.e. sensitivity) whereas one in three alarms was a true alarm (i.e. positive predictive value). The performances of the detection algorithm were evaluated for alternative combination of epidemiologic parameters. The results of our study confirmed that in certain conditions automated algorithms could help identifying abnormal cattle mortality increases possibly related to unidentified health events.

A Review of the Statistical and Quantitative Methods Used to Study Alcohol-Attributable Crime

Modelling the relationship between alcohol consumption and crime generates new knowledge for crime prevention strategies. Advances in data, particularly data with spatial and temporal attributes, have led to a growing suite of applied methods for modelling. In support of alcohol and crime researchers we synthesized and critiqued existing methods of spatially and quantitatively modelling the effects of alcohol exposure on crime to aid method selection, and identify new opportunities for analysis strategies. We searched the alcohol-crime literature from 1950 to January 2014. Analyses that statistically evaluated or mapped the association between alcohol and crime were included. For modelling purposes, crime data were most often derived from generalized police reports, aggregated to large spatial units such as census tracts or postal codes, and standardized by residential population data. Sixty-eight of the 90 selected studies included geospatial data of which 48 used cross-sectional datasets. Regression was the prominent modelling choice (n = 78) though dependent on data many variations existed. There are opportunities to improve information for alcohol-attributable crime prevention by using alternative population data to standardize crime rates, sourcing crime information from non-traditional platforms (social media), increasing the number of panel studies, and conducting analysis at the local level (neighbourhood, block, or point). Due to the spatio-temporal advances in crime data, we expect a continued uptake of flexible Bayesian hierarchical modelling, a greater inclusion of spatial-temporal point pattern analysis, and shift toward prospective (forecast) modelling over small areas (e.g., blocks).

Spatial-temporal clustering of companion animal enteric syndrome: detection and investigation through the use of electronic medical records from participating private practices

There is interest in the potential of companion animal surveillance to provide data to improve pet health and to provide early warning of environmental hazards to people. We implemented a companion animal surveillance system in Calgary, Alberta and the surrounding communities. Informatics technologies automatically extracted electronic medical records from participating veterinary practices and identified cases of enteric syndrome in the warehoused records. The data were analysed using time-series analyses and a retrospective space-time permutation scan statistic. We identified a seasonal pattern of reports of occurrences of enteric syndromes in companion animals and four statistically significant clusters of enteric syndrome cases. The cases within each cluster were examined and information about the animals involved (species, age, sex), their vaccination history, possible exposure or risk behaviour history, information about disease severity, and the aetiological diagnosis was collected. We then assessed whether the cases within the cluster were unusual and if they represented an animal or public health threat. There was often insufficient information recorded in the medical record to characterize the clusters by aetiology or exposures. Space-time analysis of companion animal enteric syndrome cases found evidence of clustering. Collection of more epidemiologically relevant data would enhance the utility of practice-based companion animal surveillance.

The application of a novel 'rising activity, multi-level mixed effects, indicator emphasis' (RAMMIE) method for syndromic surveillance in England

MOTIVATION

Syndromic surveillance is the real-time collection and interpretation of data to allow the early identification of public health threats and their impact, enabling public health action. The 'rising activity, multi-level mixed effects, indicator emphasis' method was developed to provide a single robust method enabling detection of unusual activity across a wide range of syndromes, nationally and locally.

RESULTS

The method is shown here to have a high sensitivity (92%) and specificity (99%) compared to previous methods, whilst halving the time taken to detect increased activity to 1.3 days.

AVAILABILITY AND IMPLEMENTATION

The method has been applied successfully to syndromic surveillance systems in England providing realistic models for baseline activity and utilizing prioritization rules to ensure a manageable number of 'alarms' each day.

CONTACT

roger.morbey@phe.gov.uk.