The R programming language has become a critical data science tool for the scientific community but has also helped launch a new era of “citizen data scientists” due to the wealth of packages that make it easy to access rich data sources, perform a wide array of computations and produce striking and informative visualizations. This talk will review the history of the ‘cdcfluview’ package, show how it has been used by researchers and citizens, and provide insight into the rationale that created it.
Disease Surveillance
Description
Cryptosporidiosis is a diarrheal disease caused by microscopic parasite Cryptosporidium. Modes of transmission include eating undercooked food contaminated with the parasite, swallowing something that has come into contact with human or animal feces, or swallowing pool water contaminated with the parasite. The disease is clinically manifested usually with chronic diarrhea and abdominal cramps. It is found to be more prevalent in immunocompromised patients like HIV and AIDS. Cryptosporidiosis usually causes potentially life-threatening disease in people with AIDS.
Objective:
To demonstrate the demographic and clinical distribution of reported Cryptosporidiosis cases in Houston, Texas, from 2013-2016
A report jointly released by the de Beaumont Foundation and Johns Hopkins University, Using Electronic Health Data for Community Health: Example Cases and Legal Analysis provides public health departments with a framework that will allow them to request data from hospitals and health systems in order to move the needle on critical public health challenges.
Description
The SAGES (Suite for Automated Global Electronic bioSurveillance) team at the John Hopkins University Applied Physics Laboratory was approached by the Public Health Division of the Research, Evidence and Information Programme of the Secretariat of the Pacific Community (SPC) to explore the feasibility of using the SAGES disease surveillance toolkit for two mass gathering events, the 8th Micronesian Games held from 19-31 July in Pohnpei Federated States of Micronesia and the 3rd International Conference on Small Island Developing States (SIDS) held from 1-4 September 2014 in Apia Samoa.
Mass gatherings are congregations of large numbers of people in a specific location(s) for a defined period of time such as major sporting events, concerts and festivals. A downside of these gatherings is the potential for communicable/infectious diseases to spread efficiently and rapidly. Infected individuals may subsequently return home and disseminate these infections in their local populations.
The Pacific syndromic surveillance system commenced in 2010. Enhanced syndromic surveillance is increasingly being used in mass gatherings. This involves inclusion of more syndromes and more regular reporting than routine syndromic surveillance. While enhanced syndromic surveillance is an important mechanism at mass gatherings, also, and somewhat opportunistically, mass gatherings can provide a unique chance to initiate or strengthen existing surveillance systems.
Objective
Present how a surveillance tool such as SAGES was used for disease surveillance for mass gathering activities.
Description
Previous studies have demonstrated the benefit of laboratory surveillance and its capability to accurately detect influenza outbreaks earlier than syndromic surveillance. Current laboratory surveillance has an approximate 2-week lag due to laboratory test turn–around time and data collection. In order to provide real-time access to aggregated test results, we utilized direct cloud connectivity with a rapid PCR-based influenza test, Xpert Flu, to centrally consolidate test results along with GIS data. On-site, type-specific results were available to physicians and uploaded for public health awareness within 100 minutes of patient nasopharyngeal swab.
Objective
To demonstrate the feasibility and validity of a novel electronic surveillance system utilizing a cloud-based interface that consolidates laboratory test results and geographical information in real-time.
Description
Zanzibar is comprised primarily of two large islands with a population of 1.3 million. Indoor Residual Spraying (IRS) campaigns, distribution of long-lasting insecticide treated bed nets (LLINs), ensuring treatment medication is available, and use of Rapid Diagnostic Tests (RDTs) have reduced Malaria prevalence from 39% in 2005[1] to less than 1% in 2011-2012. This is the third time Zanzibar has been close to eliminating malaria, but there are serious challenges. These include vector resistance to pyrethroids, the shortlived efficacy of LLINs, and resistance to behavior change. Constant traffic with mainland Tanzania and foreign countries also poses the risk of outbreaks. An effective and sustained surveillance and rapid response system is essential to control outbreaks and optimize interventions.
Objective
This presentation aims to share the results of a six-year effort to use mobile health (mHealth) technology to help eliminate malaria from a well-defined geographic area. This presentation will review the history, technology, results, lessons-learned, and applicability to other contexts.
Description
Chikungunya virus disease (CHIK) is a mosquito-borne viral infection currently widespread in the Caribbean with the potential for emergence and endemicity in the U.S. via infected travelers and local mosquito vectors. CHIK disease can be severe and disabling with symptoms similar to dengue. CHIK is not a U.S. nationally notifiable disease and tracking travel-associated and locally acquired cases is currently dependent on voluntary reporting via ArboNET. While ArboNET cases are laboratory confirmed and highly specific, ArboNET is a passive surveillance system where representativeness and timeliness may be lacking. In contrast, submitting an electronic bill following HC services is the most mature and widely used form of eHealth. Providers are highly motivated to submit claims for reimbursement and the eHRC process is ubiquitous in the U.S. HC system. HIPAA-compliant eHRCs from provider offices can be captured in e-commerce and consolidated into electronic data warehouses and used for many purposes including public health surveillance. eHRCs are standardized and each claim contains pertinent person, place, and time information as well as ICD-9 diagnostic codes. IMS Health (IMS) is a global HC information company and maintains one of world’s largest eHealth data warehouses that processes ~1 billion provider office eHRCs annually. IMS consolidates eHRCs from >60% of all U.S. office-based providers from all parts of the U.S. The size and predictability of the eHRC flow into the IMS data warehouse supports projections of national estimates and time trends of conditions of interest.
Objective
This paper describes how high-volume electronic healthcare (HC) reimbursement claims (eHRCs) from providers’ offices can be used to supplement Chikungunya surveillance in the U.S.
Description
Regional disease surveillance as well as data transparency and sharing are the global trend for mitigating the threat of infectious diseases. The WHO has already played a leading role in FluNet (http:// www.who.int/influenza/gisrs_laboratory/flunet/en/ ) and DenguNet (http://www.who.int/csr/disease/dengue/denguenet/en/). However, the enterovirus-related infections which caused a high disease burden for pre-school children in South-East Asian regions over the last two decades still lack a comprehensive surveillance system in the region [1]. If the spreading pattern and a possible alert mechanism can be identified and set up, it will be beneficial for controlling hand, foot and mouth disease (HFMD) epidemics in East Asia. In some research findings, the transmission of HFMD was correlated with temperature, relative humidity, wind speed, precipitation, population density and the periods in which schools were open [2]. A delayed temporal trend was also found with the increase in latitude [3,4] . In this study, we tried to apply publicly available weekly surveillance data in Japan, Taiwan and Singapore to evaluate the spatio-temporal evolution of HFMD epidemics and how the weather conditions affect the HFMD epidemics.
Objective
Enterovirus epidemics, especially affecting young children, have occurred in South-East Asia every year. If the epidemic periods are inter-correlated among different areas, early warning signals could be issued to prevent or reduce the severity of the later epidemics in other areas. In this study, we integrated the available surveillance and weather data in East Asia to elucidate possible spatio-temporal correlations and weather conditions among different areas from low to high latitude.
Description
According to world health organization report 2011, coronary artery diseases are the number one cause of death globally: more people die annually from coronary artery diseases than from any other cause. An estimated 17.3 million people died from coronary artery diseases in 2008, representing 30% of all global deaths. Of these deaths, an estimated 7.3 million were due to coronary heart disease and 6.2 million were due to stroke. Low- and middle-income countries are disproportionally affected: over 80% of coronary artery diseases deaths take place in low- and middle-income countries and occur almost equally in men and women. Populations living in low and middle income countries are exposed to more risk factors associated with coronary artery disease as well as other non-communicable diseases and are less exposed to prevention efforts than people in high income countries.
Objective
To investigate the prevalence of cardiovascular risk factors among patients undergoing elective Coronary Artery Bypass Graft surgery (CABG) in Karachi, Pakistan.
Description
Utilization of local surveillance data has been shown to help risk stratify patients presenting to the emergency department presenting with GAS pharyngitis or meningitis. (1, 2) Adolescents frequently present to the emergency department (ED) with symptoms that may be associated with a sexually transmitted infection (STI). (3) When ED providers perceive high local rates of STI and low rates of follow-up, empiric treatment is considered. This strategy may result in unnecessary treatment. Knowledge of the local spatial distribution of adolescents with STIs diagnosed in local pediatric emergency departments EDs may enhance risk stratification and allow targeted testing and/or treatment among future ED patients in whom STI is considered.
Objective
(1) To describe the spatial distribution of adolescents with EDdiagnosed STIs in a large urban area with a high prevalence of STI
(2) To compare census block groups and identify “hot spots” of STI.