The Emerging Infections Program (EIP) is a collaboration between the Centers for Disease Control and Prevention and 10 state health departments working with academic partners to conduct active population-based surveillance and special studies for several emerging infectious disease issues determined to need special attention. The Centers for Disease Control and Prevention funds the 10 EIP sites through cooperative agreements. Our objective was to highlight 1) what being an EIP site has meant for participating health departments and associated academic centers, including accomplishments and challenges, and 2) the synergy between the state and federal levels that has resulted from the collaborative relationship. Sharing these experiences should provide constructive insight to other public health programs and other countries contemplating a collaborative federal–local approach to collective public health challenges.

One objective of the Emerging Infections Program (EIP) of the US Centers for Disease Control and Prevention is to provide training opportunities in infectious disease epidemiology. To determine the extent of training performed since the program's inception in 1995, we reviewed training efforts at the 10 EIP sites. By 2015, all sites hosted trainees (most were graduate public health students and physicians) who worked on a variety of infectious disease surveillance and epidemiologic projects. Trainee projects at all sites were used for graduate student theses or practicums. Numerous projects resulted in conference presentations and publications in peer-reviewed journals. Local public health and health care partners have also benefitted from EIP presentations and training. Consideration should be given to standardizing and documenting EIP training and to sharing useful training initiatives with other state and local health departments and academic institutions.

Active Bacterial Core surveillance (ABCs) was established in 1995 as part of the Centers for Disease Control and Prevention Emerging Infections Program (EIP) network to assess the extent of invasive bacterial infections of public health importance. ABCs is distinctive among surveillance systems because of its large, population-based, geographically diverse catchment area; active laboratory-based identification of cases to ensure complete case capture; detailed collection of epidemiologic information paired with laboratory isolates; infrastructure that allows for more in-depth investigations; and sustained commitment of public health, academic, and clinical partners to maintain the system. ABCs has directly affected public health policies and practices through the development and evaluation of vaccines and other prevention strategies, the monitoring of antimicrobial drug resistance, and the response to public health emergencies and other emerging infections.

The Foodborne Diseases Active Surveillance Network (FoodNet) provides a foundation for food safety policy and illness prevention in the United States. FoodNet conducts active, population-based surveillance at 10 US sites for laboratory-confirmed infections of 9 bacterial and parasitic pathogens transmitted commonly through food and for hemolytic uremic syndrome. Through FoodNet, state and federal scientists collaborate to monitor trends in enteric illnesses, identify their sources, and implement special studies. FoodNet’s major contributions include establishment of reliable, active population-based surveillance of enteric diseases; development and implementation of epidemiologic studies to determine risk and protective factors for sporadic enteric infections; population and laboratory surveys that describe the features of gastrointestinal illnesses, medical care–seeking behavior, frequency of eating various foods, and laboratory practices; and development of a surveillance and research platform that can be adapted to address emerging issues. The importance of FoodNet’s ongoing contributions probably will grow as clinical, laboratory, and informatics technologies continue changing rapidly.

The Healthcare-Associated Infections Community Interface (HAIC), launched in 2009, is the newest major activity of the Emerging Infections Program. The HAIC activity addresses population- and laboratory-based surveillance for Clostridium difficile infections, candidemia, and multidrug-resistant gram-negative bacilli. Other activities include special projects: the multistate Healthcare-Associated Infections and Antimicrobial Use Prevalence Survey and projects that evaluate new approaches for improving surveillance. The HAIC activity has provided information about the epidemiology and adverse health outcomes of health care–associated infections and antimicrobial drug use in the United States and informs efforts to improve patient safety through prevention of these infections.

In 2003, surveillance for influenza in hospitalized persons was added to the Centers for Disease Control and Prevention Emerging Infections Program network. This surveillance enabled monitoring of the severity of influenza seasons and provided a platform for addressing priority questions associated with influenza. For enhanced surveillance capacity during the 2009 influenza pandemic, new sites were added to this platform. The combined surveillance platform is called the Influenza Hospitalization Surveillance Network (FluSurv-NET). FluSurv-NET has helped to determine the risk for influenza-associated illness in various segments of the US population, define the severity of influenza seasons and the 2009 pandemic, and guide recommendations for treatment and vaccination programs.

Two decades ago, the Emerging Infections Program of the US Centers for Disease Control and Prevention implemented what seemed like a simple yet novel idea: a population- and laboratory-based surveillance system designed to identify and characterize invasive bacterial infections, including those caused by Streptococcus pneumoniae. This system, known as Active Bacterial Core surveillance, has since served as a flexible platform for following trends in invasive pneumococcal disease and studying vaccination as the most effective method for prevention. We report the contributions of Active Bacterial Core surveillance to every pneumococcal vaccine policy decision in the United States during the past 20 years.

In 2007, five Emerging Infections Program (EIP) sites were funded to determine the feasibility of establishing a population-based surveillance system for monitoring the effect of human papillomavirus (HPV) vaccine on pre-invasive cervical lesions. The project involved active population-based surveillance of cervical intraepithelial neoplasia grades 2 and 3 and adenocarcinoma in situ as well as associated HPV types in women >18 years of age residing in defined catchment areas; collecting relevant clinical information and detailed HPV vaccination histories for women 18–39 years of age; and estimating the annual rate of cervical cancer screening among the catchment area population. The first few years of the project provided key information, including data on HPV type distribution, before expected effect of vaccine introduction. The project’s success exemplifies the flexibility of EIP’s network to expand core activities to include emerging surveillance needs beyond acute infectious diseases. Project results contribute key information regarding the impact of HPV vaccination in the United States.

Encephalitis is a devastating illness that commonly causes neurologic disability and has a case fatality rate >5% in the United States. An etiologic agent is identified in <50% of cases, making diagnosis challenging. The Centers for Disease Control and Prevention Emerging Infections Program (EIP) Encephalitis Project established syndromic surveillance for encephalitis in New York, California, and Tennessee, with the primary goal of increased identification of causative agents and secondary goals of improvements in treatment and outcome. The project represents the largest cohort of patients with encephalitis studied to date and has influenced case definition and diagnostic evaluation of this condition. Results of this project have provided insight into well-established causal pathogens and identified newer causes of infectious and autoimmune encephalitis. The recognition of a possible relationship between enterovirus D68 and acute flaccid paralysis with myelitis underscores the need for ongoing vigilance for emerging causes of neurologic disease.

Despite high coverage with pertussis-containing vaccines, pertussis remains endemic to the United States. There have been increases in reported cases in recent years, punctuated by striking epidemics and shifting epidemiology, both of which raise questions about current policies regarding its prevention and control. Limited data on pertussis reported through the National Notifiable Disease Surveillance System have proved insufficient to answer these questions. To address shortcomings of national pertussis data, the Emerging Infections Program at the US Centers for Disease Control and Prevention launched Enhanced Pertussis Surveillance (EPS), which is characterized by systematic case ascertainment, augmented data collection, and collection of Bordetella pertussis isolates. Data collected through EPS have been instrumental in understanding the rapidly evolving epidemiology and molecular epidemiology of pertussis and have contributed essential information regarding pertussis vaccines. EPS also serves as a platform for conducting critical and timely evaluations of pertussis prevention and control strategies, including targeting of vaccinations and antimicrobial prophylaxis.

TickNET, a public health network, was created in 2007 to foster greater collaboration between state health departments, academic centers, and the Centers for Disease Control and Prevention on surveillance and prevention of tickborne diseases. Research activities are conducted through the Emerging Infections Program and include laboratory surveys, high-quality prevention trials, and pathogen discovery.

Across the United States, antimicrobial drug–resistant infections affect a diverse population, and effective interventions require concerted efforts across various public health and clinical programs. Since its onset in 1994, the Centers for Disease Control and Prevention Emerging Infections Program has provided robust and timely data on antimicrobial drug–resistant infections that have been used to inform public health action across a spectrum of partners with regard to many highly visible antimicrobial drug–resistance threats. These data span several activities within the Program, including respiratory bacterial infections, health care–associated infections, and some aspects of foodborne diseases. These data have contributed to estimates of national burden, identified populations at risk, and determined microbiological causes of infection and their outcomes, all of which have been used to inform national policy and guidelines to prevent antimicrobial drug–resistant infections.

The Centers for Disease Control and Prevention Emerging Infections Program (EIP) network conducts population-based surveillance for pathogens of public health importance. Central to obtaining estimates of disease burden and tracking microbiological characteristics of these infections is accurate laboratory detection of pathogens. The use of culture-independent diagnostic tests (CIDTs) in clinical settings presents both opportunities and challenges to EIP surveillance. Because CIDTs offer better sensitivity than culture and are relatively easy to perform, their use could potentially improve estimates of disease burden. However, changes in clinical testing practices, use of tests with different sensitivities and specificities, and changes to case definitions make it challenging to monitor trends. Isolates are still needed for performing strain typing, antimicrobial resistance testing, and identifying other molecular characteristics of organisms. In this article, we outline current and future EIP activities to address issues associated with adoption of CIDTs, which may apply to other public health surveillance.

The Emerging Infections Program (EIP), a collaboration between (currently) 10 state health departments, their academic center partners, and the Centers for Disease Control and Prevention, was established in 1995. The EIP performs active, population-based surveillance for important infectious diseases, addresses new problems as they arise, emphasizes projects that lead to prevention, and develops and evaluates public health practices. The EIP has increasingly addressed the health equity challenges posed by Healthy People 2020. These challenges include objectives to increase the proportion of Healthy People–specified conditions for which national data are available by race/ethnicity and socioeconomic status as a step toward first recognizing and subsequently eliminating health inequities. EIP has made substantial progress in moving from an initial focus on monitoring social determinants exclusively through collecting and analyzing data by race/ethnicity to identifying and piloting ways to conduct population-based surveillance by using area-based socioeconomic status measures.

Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza–associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003–2008 to ≈70% during 2009–2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3–50.5 for children <18 years of age, 3.0–30.3 for adults 18–64 years, and 13.6–181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18–64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.

We examined population-based surveillance data from the Tennessee Emerging Infections Program to determine whether neighborhood socioeconomic status was associated with influenza hospitalization rates. Hospitalization data collected during October 2007–April 2014 were geocoded (N = 1,743) and linked to neighborhood socioeconomic data. We calculated age-standardized annual incidence rates, relative index of inequality, and concentration curves for socioeconomic variables. Influenza hospitalizations increased with increased percentages of persons who lived in poverty, had female-headed households, lived in crowded households, and lived in population-dense areas. Influenza hospitalizations decreased with increased percentages of persons who were college educated, were employed, and had health insurance. Higher incidence of influenza hospitalization was also associated with lower neighborhood socioeconomic status when data were stratified by race.

Preventing transmission of carbapenemase-producing, carbapenem-resistant Enterobacteriaceae (CP-CRE) is a public health priority. A phenotype-based definition that reliably identifies CP-CRE while minimizing misclassification of non–CP-CRE could help prevention efforts. To assess possible definitions, we evaluated enterobacterial isolates that had been tested and deemed nonsusceptible to >1 carbapenem at US Emerging Infections Program sites. We determined the number of non-CP isolates that met (false positives) and CP isolates that did not meet (false negatives) the Centers for Disease Control and Prevention CRE definition in use during our study: 30% (94/312) of CRE had carbapenemase genes, and 21% (14/67) of Klebsiella pneumoniae carbapenemase–producing Klebsiella isolates had been misclassified as non-CP. A new definition requiring resistance to 1 carbapenem rarely missed CP strains, but 55% of results were false positive; adding the modified Hodge test to the definition decreased false positives to 12%. This definition should be considered for use in carbapenemase-producing CRE surveillance and prevention.

Foodborne pathogens cause >9 million illnesses annually. Food safety efforts address the entire food chain, but an essential strategy for preventing foodborne disease is educating consumers and food preparers. To better understand the epidemiology of foodborne disease and to direct prevention efforts, we examined incidence of Salmonella infection, Shiga toxin–producing Escherichia coli infection, and hemolytic uremic syndrome by census tract–level socioeconomic status (SES) in the Connecticut Foodborne Diseases Active Surveillance Network site for 2000–2011. Addresses of case-patients were geocoded to census tracts and linked to census tract–level SES data. Higher census tract–level SES was associated with Shiga toxin–producing Escherichia coli, regardless of serotype; hemolytic uremic syndrome; salmonellosis in persons ≥5 years of age; and some Salmonella serotypes. A reverse association was found for salmonellosis in children <5 years of age and for 1 Salmonella serotype. These findings will inform education and prevention efforts as well as further research.

National surveillance provides important information about Lyme disease (LD) but is subject to underreporting and variations in practice. Information is limited about the national epidemiology of LD from other sources. Retrospective analysis of a nationwide health insurance claims database identified patients from 2005–2010 with clinician-diagnosed LD using International Classification of Diseases, Ninth Revision, Clinical Modification, codes and antimicrobial drug prescriptions. Of 103,647,966 person-years, 985 inpatient admissions and 44,445 outpatient LD diagnoses were identified. Epidemiologic patterns were similar to US surveillance data overall. Outpatient incidence was highest among boys 5–9 years of age and persons of both sexes 60–64 years of age. On the basis of extrapolation to the US population and application of correction factors for coding, we estimate that annual incidence is 106.6 cases/100,000 persons and that ≈329,000 (95% credible interval 296,000–376,000) LD cases occur annually. LD is a major US public health problem that causes substantial use of health care resources.

Lyme disease is underreported in the United States. We used insurance administrative claims data to determine the value of such data in enhancing case ascertainment in Tennessee during January 2011–June 2013. Although we identified ≈20% more cases of Lyme disease (5/year), the method was resource intensive and not sustainable in this low-incidence state.

Mycobacterium abscessus complex comprises a group of rapidly growing, multidrug-resistant, nontuberculous mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, bacteremia, and ocular and other infections. M. abscessus complex is differentiated into 3 subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. The 2 major subspecies, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, have different erm(41) gene patterns. This gene provides intrinsic resistance to macrolides, so the different patterns lead to different treatment outcomes. M. abscessus complex outbreaks associated with cosmetic procedures and nosocomial transmissions are not uncommon. Clarithromycin, amikacin, and cefoxitin are the current antimicrobial drugs of choice for treatment. However, new treatment regimens are urgently needed, as are rapid and inexpensive identification methods and measures to contain nosocomial transmission and outbreaks.

We characterized the complete genome of a putative novel Usutu virus (USUV) strain (Usutu-BONN) detected in a dead blackbird from Germany. Genomic analysis revealed several unique amino acid substitutions among the polyprotein gene. Phylogenetic analyses demonstrated that Usutu-BONN constitutes a putative novel African USUV lineage, which was probably recently introduced to central Europe.

A simple mathematical model without seasonality indicated that the apparently chaotic dengue epidemics in Singapore have characteristics similar to epidemics resulting from chance. Randomness as a sufficient condition for patterns of dengue epidemics in equatorial regions calls into question existing explanations for dengue outbreaks there.

We examined which respiratory pathogens were identified during screening for Middle East respiratory syndrome coronavirus in 177 symptomatic travelers returning to Ontario, Canada, from regions affected by the virus. Influenza A and B viruses (23.1%) and rhinovirus (19.8%) were the most common pathogens identified among these travelers.

Fourteen influenza A(H7N9) viruses were isolated from poultry or the environment in live poultry markets in Guangdong Province, China during 2014−2015. Phylogenetic analysis showed that all viruses were descended from viruses of the second wave of influenza A(H7N9) virus infections during 2013. These viruses can be divided into 2 branches.

Two cases of disseminated enteroviral infection occurred in patients who received the CD20 monoclonal antibody obinutuzumab. Clinical features included hepatitis, edema, and a dermatomyositis-like syndrome. These manifestations may be unfamiliar to clinicians and are possibly responsive to intravenous immunoglobulin. Clinicians should remain vigilant for enteroviral infections in patients receiving obinutuzumab.

Since Middle East respiratory syndrome coronavirus (MERS-CoV) first emerged, the California Department of Public Health has coordinated efforts to identify possible cases in travelers to California, USA, from affected areas. During 2013–2014, the department investigated 54 travelers for MERS-CoV; none tested positive, but 32 (62%) of 52 travelers with suspected MERS-CoV had other respiratory viruses.

Notification of 2 imported cases of infection with Middle East respiratory syndrome coronavirus in the Netherlands triggered comprehensive monitoring of contacts. Observed low rates of virus transmission and the psychological effect of contact monitoring indicate that thoughtful assessment of close contacts is prudent and must be guided by clinical and epidemiologic risk factors.

In 2014, 20 dengue cases were reported in the cities of Wenzhou (5 cases) and Wuhan (15 cases), China, where dengue has rarely been reported. Dengue virus 1 was detected in 4 patients. Although most of these cases were likely imported, epidemiologic analysis provided evidence for autochthonous transmission.