We are working to gather raw data for your own analysis and to pinpoint trustworthy outside sources of data, analysis and summaries that you can use in your reporting. Below are data sources that can assist you in covering infectious diseases.
Any time there is an outbreak of an infectious disease, the public generally wants to know how common it is and what their risk of getting it is. Journalists will want to stay on top of new and continuing cases as well, but to provide context to those stories, or to others about infectious diseases or vaccines, they may want information on historical incidence or trends as well. Below are resources for infectious diseases exclusively within the United States.
Domestically, the Centers for Disease Control and Prevention maintain a National Notifiable Diseases Surveillance System (NNDSS) that tracks all National Notifiable Conditions, diseases which health departments are required to report when they have a local case with the condition. (Clicking on each disease tells you the case definition and how long it has been a notifiable condition.) This spreadsheet tells you whether a disease was reported during each of the years included. These diseases are reported for the week, month and year-to-date in each Morbidity and Mortality Weekly Report. To see how many cases have been reported during a particular month or up through the year-to-date, look for the Notifiable Diseases and Mortality Tables link for the month and year you need from 2015, 2016 or 2017. The CDC also provides MMWR summaries of cases for nationally notifiable conditions during each past year back to 1993. Be sure to read what data users should know about the National Notifiable Diseases Surveillance System before you dig into the data, and definitions of key terms are available here. Other helpful information to understanding the system is here.
Developing new drugs is time-consuming and expensive. Only one out of five drugs to treat infectious diseases make it past the initial human testing phase, leading economists to estimate that it takes about $1 billion in research and time to produce each new drug. Given that antibiotics are only used for a few days and are expected to be available at little expense, most major pharmaceutical companies have stopped investing in new antibiotics. The number in the pipeline has plummeted. The Pew Charitable Trusts is one of the only entities keeping track of how many are in the pipeline and they provide continuous updates here and they have a data visualization of the significance of the lack of a pipeline.
For more localized data on antibiotic resistance in your community, check out ResistanceOpen. It is an online platform developed by U.S. And Canadian scientists to monitor antibiotic resistance at the regional and international level. The site uses publicly available resistance data, online data from community healthcare institutions, as well as regional, national and international entities. For example, it’s European data is based on the European Antimicrobial Resistance Surveillance network and Central Asian and Eastern European data is based on the Central Asian and Eastern European Surveillance of Antimicrobial Resistance Network (CAESAR). It is also an open-collaboration database, where independent sources can contribute data. The site does not use individual level data.
If you are looking for a way to visualize the spread of antibiotic resistance globally, go to the Center for Disease Dynamics, Economics & Policy, a Washington, D.C.-based nonprofit that focuses on health policy. The organization has created an excellent interactive map, called “ResistanceMap,” which is a web-based collection of data visualization tools. There is all kinds of information about the spread of 12 of the most dangerous antibiotic resistant bacteria, like carbapenem-resistant microbes. It also provides information about antibiotic consumption across the globe, which is a useful tool for understanding where antibiotic policies need to be focused. The map is funded with the support of the Bill & Melinda Gates Foundation.
Reporters can find potential stories by looking at the Centers for Disease Control and Prevention’s antibiotic resistance investment map which provides details on superbug cases in the U.S. and worldwide. The CDC says its ResistanceMap is a collection of tools summarizing national and subnational data on antimicrobial use and resistance around the world. In 2015, ResistanceMap re-launched with a new design interface, expanded tools and the addition of antibiotic use and resistance data from several low- and middle-income countries in Africa, Asia and South America. The map was most recently updated in January 2018.
For antibiotic resistance threats in the U.S., the CDC has a page, with lots of details on its program here. There are data and surveillance reports on active bacterial threats here.
One of the only national estimate of antibiotic use in the U.S. is connected to food animal production. Beginning in 2016, the Food and Drug Administration began collecting data on sales of antibiotics considered medically important to humans that are used in animal agriculture. To see the FDA data from 2016 [the most recent data], click here.
The American Public Health Association, a Washington, D.C.,-based nonprofit that aims to improve the health of the public and achieve equity in health status, has created a series of infographics, with data, to demonstrate the impact of climate change on public health, including the expectation for the increase in vector-borne and water-borne infectious diseases.
SARS-CoV-2 Variant Classifications and Definitions. The CDC has updated its list of coronavirus variants that the agency is watching, including variants of concern, variants of interest and variants being monitored. Currently the only variant of concern, meaning that it poses as significant threat to the U.S., is the delta variant.
The website features a section on COVID-19 vaccines specifically, including frequently asked questions, as well as a general vaccination page containing information on other vaccines recommended for adults and teens. The website will be updated to provide the latest information on COVID-19 vaccines and will also soon be available in Spanish.
Community data: The National Association of County and City Health Officials (NACCHO), which represents the country’s nearly 3,000 local health departments, launched its COVID-19 Data Lab, a data tool for people to see the impact of the COVID-19 outbreak on local communities. NACCHO plans to keep evolving the site over time, as more information is gathered about the outbreak. In the first iteration, users can access the interactive COVID-19 Dashboard to explore the extent of COVID-19 tests, cases, and deaths in communities and counties. Going forward, additional data points will be included, as available, to provide clearer, more nuanced information critical to supporting the COVID-19 response at the community level. On July 2, 2020, NACCHO released an update to its COVID-19 Data Lab that will allow users to see at a glance if there is a significant difference in case and death trends due to race in their state to help inform their pandemic response at the local level.
Testing and medical system capacity: American Public Media data reporters Geoff Hing and Will Craft created this tipsheet on where you can find data about COVID-19 testing and medical system capacity compiled from sources like NICAR-L list, NewsNerdery Slack, the Data is Plural newsletter, other reporting and browsing public health agency websites.
Testing tracker by volunteer journalists: Two journalists, Robinson Meyer and Alexis Madrigal, built this tracker for a story in The Atlantic. The two efforts came together March 7, and made a call for volunteers to help keep the data updated, tune processes, work on scrapers, and make a website.Alexis Madrigal continues to lead the overall project.
The COVID Tracking Project collects information from 50 US states, the District of Columbia, and 5 other U.S. territories to provide the most comprehensive testing data we can collect for the novel coronavirus, SARS-CoV-2. Volunteers managing this tracker attempt to include positive and negative results, pending tests, and total people tested for each state or district currently reporting that data.
Scientists, Richard Neher and Emma Hodcroft, at the University of Basel in Switzerland, created a website called “Nextstrain” which is tracking the strains of COVID-19 as they mutate and spread around the world. Click on the site and watch the virus as it spreads around the world. Watch as it moves from Wuhan and eventually to the United States. Labs around the world are sequencing the genomes of the virus taken from sick people with COVID-19 and then uploading it into a database overseen by Neher and Hodcraft, who are then inputting the data into the website for everyone to see. It is worth taking a look.
Resolve to Save Lives, a nonprofit led by Tom Frieden, former director of the Centers for Disease Control and Prevention, has created a infographic tool to spotlight gaps in global preparedness for outbreaks. The site, called PreventEpidemics.org, provides an individual score to countries using a color code to rank countries by preparedness. Looking at the map provides a good way for journalists to see which country might be the next hot spot for an outbreak.
The scoring is calculated by using data from the Joint External Evaluation, an international effort developed by the World Health Organization, to help countries bolster their health systems to prepare for emergencies. Gaps in preparedness include lack of monitoring system that can spot unusual health reports or lack of trained epidemiologists who can be deployed if there is a health threat.
In December 2019, the Centers for Disease Control and Prevention, announced that it had updated its food surveillance data page, with a “FoodNet Fast,” a feature that provides information from to the Foodborne Diseases Act Surveillance Network (FoodNet), an online tool for visualizing the CDC’s national food borne illness tracking efforts. Through FoodNet Fast, Americans can visualize rates of food borne illness since 1996 for nine common pathogens, including listeria, salmonella and Shiga toxin-producing Escherichia coli (STEC). Users can also learn how diagnostic testing practices have changed over time, as well as track instances of Hemolytic Uremic Syndrome, a life threatening condition that can be triggered by STEC. FoodNet Fast data represent about 15% of the U.S. population.
To get a sense of food borne illness outbreaks across the country, the Centers for Disease Control and Prevention compiles a web-based food-borne outbreak online database tool - Food Tool. The outbreak data reported to the CDC begins in 1998 and was last updated in October 2017, with information from outbreaks in 2016.
The CDC also compiles an annual summary of food-borne outbreaks here. The data provide a picture of which foods are associated with the most illnesses.
The Food and Drug Administration created a Coordinated Outbreak Response and Evaluation Network to manage the federal government’s response to a food-related illness outbreak. See information here.
If you want the most up-to-date information about foods that have been recalled, take a look at the FDA’s recalls, market withdrawals and safety alerts related to food products here. Reporters can sign up for email alerts. More resources on FDA food alerts can be found here.
The government also maintains a federal food safety website, with contributions from the FDA, CDC and U.S. Department of Agriculture, on food illness alerts and consumer food safety information here.
Are you looking for more information about the latest foodborne illness outbreak? Check out Outbreakdatabase.com. It was created by the law firm partnered by Bill Marler, a plaintiffs’ attorney who has been suing food producers on behalf of consumers sickened by a food poisoning for decades. He is best known for representing Brianne Kiner, a 9-year-old girl most seriously injured by the Jack in the Box E. coli O157:H7 outbreak in 1983. This database provides summaries of significant food and water outbreaks that have occurred since 1984. A basic search of the data can be found by putting in a pathogen, food or beverage and year.
First modern infectious disease map: A father of epidemiology is John Snow – a London-based physician who figured out how cholera was spreading in London in 1854. He created a map of deaths, working in the way that data journalists do, to try to pinpoint the source of a cholera outbreak. At the time, most scientists believed cholera was caused by unhealthy gases. Germs, at that point, weren’t understood. By creating a map, Snow figured out that the source of a cholera outbreak was a public water pump. [Cholera is caused by a bacteria that can thrive in water.] He had the pump turned off and the cholera outbreak ended. Click here to see his map and a story about how Snow became known as one of the world’s first disease detectives.
HIV, AIDS, viral hepatitus, STDs, TB
The National Council for Home Safety and Security, a trade association representing home alarm companies, has created a research division to highlight ways for Americans to keep themselves safe, including being aware of the prevalence of sexually transmitted diseases. The organization recently published “Sexually Transmitted Diseases by State - 2019.” Utilizing CDC surveillance data from 2019, the report highlights, with eye-friendly graphics, which states have the highest rates of chlamydia, gonorrhea and syphilis and notes "There's no equivalent of a security system to help you identify carriers before having intercourse. Always make sure to use appropriate protection and choose your partners wisely."
The U.S. Centers for Disease Control and Prevention’s Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention in July 2018 added 11 new indicators on HIV and for the first time, social determinants of health to its AtlasPlus, an online tool that gives users the ability to create customized tables, maps and charts using 15 years of CDC surveillance data on HIV, viral hepatitis, sexually transmitted diseases (STD’s) and tuberculosis (TB). The social determinants of health, includes five indicators: poverty, uninsured, less than a high school education and vacant housing nationally and by state and county; percentage of population living in rural areas nationally and by state; and county urbanization level. The link to the tool is here.
Where is the flu and where might it hit next? Reporters interested in a visualization of flu outbreaks and forecast for their particular region can check out the Columbia University Mailman School of Public Health’s newly launched Influenza Observations and Forecast Map. Data for the map comes from the U.S. Centers for Disease Control & Prevention, the World Health Organization’s collaborating laboratory network, and Google searches. The site is funded by the National Institutes of Health and the Department of Health and Human Service’s Biological Advanced Research & Development Authority. More on the researchers involved in developing this model can be found here.
For journalists interested in a story about how how a hospital system might help the Centers for Disease Control with flu tracking, check out Houston Methodist hospitals’ flu-tracking website, launched in December 2018. Anyone who is interested can log in to the site to see flu epidemiology data collected from its eight hospitals. In the journal, Open Forum Infectious Disease, Houston Methodist researchers explain how they developed the flu tracking model to manage big jumps in flu cases. The site tracks influenza A and B - the most common flu viruses to infect humans - and viruses that can cause other types of severe respiratory diseases as well. The researchers noted that other hospital systems can use a similar model to prepare for flu outbreaks.
DoctorsReport.com relies on data drawn from the private health care claims database company, IQVIA.com. This sites allows reporters to look at illness data based on ZIP codes.
To find global health data and statistics on malaria, one of the world’s oldest and most prevalent disease, look at the World Health Organization’s site here. Most the most recent U.S. data, check out the Centers for Disease Control Prevention site here and here. For travel information and data, look here. To find maps that track malaria, look at the Malaria Atlas Project, a non-profit funded by the Bill and Melinda Gates Foundation, the Medical Research Council and the Wellcome Trust.
Mapping global disease
A good way to visualize global disease hot zones is to look at them, as they are unfolding on a map. In 2006, a team of computer research scientists at Boston Children’s Hospital and Harvard Medical School created HealthMap – an automated, real-time program to collect and integrate infectious disease outbreak data. The researchers then took the information and built a digital map of the planet, utilizing colors and dots to help people locate outbreaks. The map is free. Visitors can click on the dots to get specific information about each disease alert.
The program uses a custom-build algorithm to comb through Internet search engines, news reports, social media, international health organization websites, government websites, infectious disease expert alerts, and even personal blogs of health care workers. A team of people at Boston Children’s Hospital continue to keep the algorithm up-to-date.
In 2014, the site reported on a “mystery hemorrhagic fever” in West Africa, nine days before the World Health Organization announced there was an Ebola outbreak, demonstrating the site’s usefulness as a public disease surveillance network. HealthMap’s team collaborates closely with the Program for Monitoring Emerging Diseases (ProMED-mail), a curated Internet-based reporting tool administered by the International Society for Infectious Diseases. The Brookline, Mass.-based ISID represent infectious disease practitioners. HealthMap is funded and supported by companies, like Google and Merck, foundations and the Centers for Disease Control and Prevention.
Reported illnesses from mosquito, tick, and flea bites have more than tripled in the U.S., with more than 640,000 cases reported during the 13 years from 2004 through 2016, according to the Centers for Disease Control and Prevention.
Among mosquito-borne diseases, the most common illness is caused by West Nile virus, a pathogen carried by birds. Culex mosquitos feed on birds and then infect hundreds of thousands of Americans each year with their bite. Most people don’t get sick, but a small number get very sick, with symptoms include brain inflammation that can lead to death. To see the latest West Nile data (as of January 2019), look at this CDC map. For more historical data and see how West Nile has expanded, look at this CDC page. For a CDC Morbidity and Mortality Weekly Report with additional West Nile and vector-borne disease data, see here. For data on diseases caused by other mosquitos and ticks, see this CDC map. While Zika (a virus carried by mosquitos that can cause fetal anomalies and death) has diminished as a threat in the continental U.S., it remains a risk in U.S. territories and other countries. For a map of Zika cases, see this CDC map. For Zika travel information, see this CDC map.
Nearly half of the world’s population remains at risk for malaria with 216 million reported cases in 2016 and over 400,000 deaths. The life cycle of the Plasmodium parasite that causes malaria is complicated because it exists in several forms and shapes, and attacks the body in different ways. Understanding the life cycle of the parasite, which is passed to humans through the bite of a mosquito, is a key to helping researchers develop therapeutics to treat those infected with malaria.
Scientists at the Wellcome Sanger Institute developed a data analysis tool for the Plasmodium parasite that maps the gene expression of cells across its full life cycle, as it evolves from living in its mosquito host to human host. The tool is called the Malaria Cell Atlas and is being made available to all malaria researchers.
“This is the first detailed map of individual malaria parasite behavior across each stage of its complicated life cycle,” said the Sanger Institute in a statement. “The Atlas will help us to truly understand the parasite in order to effectively control malaria.”
Vaccines and immunizations
The most complete record of national and states rates of immunization coverage for each vaccine are in the National Immunization Surveys. Anyone can download the data sets in various forms for each of the most recent five years for which data is available. Adverse events occurring after vaccination are reported to the Vaccine Adverse Event Reporting System (VAERS), a passive surveillance system available for anyone (doctors, patients, parents, other health care providers, etc.) to report any adverse event that occurred after receiving a vaccine. However, because VAERS is a passive system – it only collects information, which anyone can submit as many times as they like – it does not accurately represent “side effects” that are linked to vaccines. (It is similar to MAUDE at the FDA.) Reports may be duplicates and may be coincidental or actual side effects from vaccines. (Some reports include car accidents, for example.) A YouTube training video explains how to search the VAERS database. Reports are available as CSV or ZIP files by year dating to 1990. An active surveillance system for vaccines is the Vaccine Safety Datalink. Research findings from the VSD are frequently published in medical studies (complete list here), and two datasets are available by public request.
Diseases spread by mosquitos, ticks and other insect vectors are on the rise in the U.S. as the planet continues to warm. If you are looking for ways to put vector-borne disease data into context with graphics, check out these resources:
The Centers for Disease Control and Prevention has this excellent infographic that helps people to visualize the expansion of vector-borne diseases in the U.S. The agency also has this state-by-state data set for reportable vector-borne diseases, as of 2016.
The Hamburg, Germany-based online market research company Statista offers a few infographs for free, including one on the latest data on the number of vector-borne disease reports in the U.S., here.