Electronic Disease Surveillance System Research Articles

Using Quality Improvement to Expand and Align State Public Health Long-Term Follow-up Data Collection Across Newborn Screening Conditions

Context: Despite the undeniable success of newborn screening (NBS), numerous barriers exist regarding long-term follow-up (LTFU) of children with conditions included in NBS. Furthermore, there is a focus on condition-specific follow-up with no national guidelines for standard quality measures collected by state public health LTFU programs. Program: Minnesota Department of Health (MDH) Longitudinal Follow-up for NBS. Implementation: A state public health LTFU for NBS quality improvement (QI) project was carried out with collaboration between MDH project team members and a QI Steering Team who provided clinical, public health, education, caregiver, and community perspectives and expertise to MDH. Relevant measures were selected from existing data elements, and additional measures were developed based on exchange between MDH project team and the QI Steering Team. Potential data sources were explored and prioritized. Processes for querying existing data sources such as death records were refined, new sources such as electronic health records and paper/PDF health records were established, and data collection was piloted. The Minnesota Electronic Disease Surveillance System was modified, and an electronic data form was created to promote consistent data abstraction from sources. Throughout the project, progress was evaluated and shared. At project conclusion, MDH project team and the QI Steering Team reviewed project outcomes and approaches to evolve the project into ongoing surveillance. Evaluation: Five common public health LTFU measures were determined. Overall, 77% of attempted measures were successfully collected. Primary and secondary data sources were adopted. In addition, collected data resulted in 7% of cases that were closed to further public health LTFU, often related to a move out of state. Discussion: This project established the feasibility of state public health LTFU surveillance of outcomes and health care use by collecting a common data set applicable across NBS conditions.

Endemic La Crosse Virus Neuroinvasive Disease in North Carolina Residents: 2000-2020.

La Crosse virus neuroinvasive disease (LACVND) is the most common cause of arboviral encephalitis in children within the United States; in North Carolina, it is the most prevalent endemic mosquito-borne disease in humans. Here we report a surveillance summary of confirmed and probable LACVND during 2000-2020 using North Carolina Electronic Disease Surveillance System data, and we describe associated demographic characteristics, spatiotemporal distribution, clinical features, and mortality rates. A total of 355 cases (74.9% confirmed) were reported from 41 North Carolina counties; most cases (92%) occurred in 19 Western North Carolina counties. An average of 17 cases were reported annually with the majority (94%) of cases occurring between mid-June and early October (epiweeks 25-41). The median case age was nine years (range: 1-95 years), 79% were aged ≤ 18 years, and 56.6% were male. Cases commonly presented with headache (95.4%), fever (95.1%), and altered mental status (80.8%); encephalitis (82.0%) and meningitis (45.9%) were frequently diagnosed. Encephalitis was more common in children (87%) than adults (62%) (P < .001). Similarly, seizures were more common in children (54%) than adults (27%) (P < .01). The case fatality rate was 1.4%; however, differences in age-specific rates were observed. Changes in case definitions and reporting requirements, missing data, different reporting sources, and the retrospective nature of this study are all important limitations of our study. Given the persistent endemicity of La Crosse virus in Western North Carolina, clinicians and public health providers should consider La Crosse virus disease in all individuals, especially children, with compatible symptoms and a travel history to endemic counties. Prevention measures and educational outreach/public health messaging should focus on caregivers and children in Western North Carolina counties and during times when transmission risk is higher (i.e., summer and early fall).

Digitalizing disease surveillance: experience from Sierra Leone.

The Integrated Disease Surveillance and Response (IDSR) system was adopted by the Sierra Leone Ministry of Health (MOH) in 2008, which was based on paper-based tools for health data recording and reporting from health facilities to the national level. The Sierra Leone MoH introduced the implementation of electronic case-based disease surveillance reporting of immediately notifiable diseases. This study aimed to document and describe the experience of Sierra Leone in transforming her paper-based disease surveillance system into an electronic disease surveillance system. Retrospective mixed methods of qualitative and quantitative data were reviewed. Qualitative data was collected by reviewing surveillance technical reports, epidemiological bulletins, COVID-19, IDSR technical guidelines, Digital Health strategy, and DHIS2 documentation. Content and thematic data analysis were performed for the qualitative data, while Microsoft Excel and DHIS2 platform were used for the quantitative data analysis to document the experience of Sierra Leone in digitalizing its disease surveillance system. In early 2017, a web-based electronic Case-Based Disease Surveillance (eCBDS) for real-time reporting of immediately notifiable diseases and health threats was piloted using the District Health Information System 2 (DHIS2) software. The eCBDS, integrates case profile, laboratory, and final outcome data. All captured data and information are immediately accessible to users with the required credentials. The system can be accessed via a browser or an Android DHIS2 application. By 2021, there was a significant increase in the proportion of immediately notifiable cases reported through the facility-level electronic platform, and more than 80% of the cases reported through the weekly surveillance platform had case-based data in eCBDS. Case-based data from the platform is analyzed and disseminated to stakeholders for public health decision-making. Several outbreaks of Lassa fever, Measles, vaccine-derived Polio, and Anthrax have been tracked in real-time through the eCBDS.

The impact of COVID-19 vaccination on the risk of hospitalization in Fayoum healthcare workers

Background: Healthcare workers (HCWs) face several challenges including treating COVID-19 patients. The immunization of the population through vaccination is recognized as a public health priority. The aim of the study is to assess the impact of vaccination on the risk of hospitalization and mortality in HCWs due to COVID-19 infection. Methods: This study was conducted in Egypt in El Fayoum governorate on the HCWs from April 2021 to the end of the year 2021. A cohort retrospective approach was carried out using (the national electronic disease surveillance system) NEDSS and COVID-19 vaccine registration system. Hospitalization is determined by assessment of the cases according to the protocol of COVID-19 management of MOHP November 2020. Results: There was no association between hospitalization and both sex and residence (p=0.1, and 0.06 respectively). There was no statistical significant association between hospitalization and vaccination (time, status, or type). The p=0.2, 0.6, and 0.07 respectively. Age and the presence of comorbidities were statistically significant predictors with p=0.004 and 0.04, respectively, as increasing age and the presence of comorbidities will increase the likelihood of hospitalization by 1.04 and 1.9 folds, respectively. Conclusions: This study shows no significant association between vaccination and hospitalization of HCWs.

Development and Evaluation of Surveillance System for Identifying Jail-Associated COVID-19 Cases in Minnesota, USA, 2022.

Confinement facilities are high-risk settings for the spread of infectious disease, necessitating timely surveillance to inform public health action. To identify jail-associated COVID-19 cases from electronic laboratory reports maintained in the Minnesota Electronic Disease Surveillance System (MEDSS), Minnesota, USA, the Minnesota Department of Health developed a surveillance system that used keyword and address matching (KAM). The KAM system used a SAS program (SAS Institute Inc., https://www.sas.com) and an automated program within MEDSS to identify confinement keywords and addresses. To evaluate KAM, we matched jail booking data from the Minnesota Statewide Supervision System by full name and birthdate to the MEDSS records of adults with COVID-19 for 2022. The KAM system identified 2,212 cases in persons detained in jail; sensitivity was 92.40% and specificity was 99.95%. The success of KAM demonstrates its potential to be applied to other diseases and congregate-living settings for real-time surveillance without added reporting burden.

Effectiveness of XBB.1.5 Vaccines Against Omicron Subvariants

Background: The updated Moderna, Pfizer-BioNTech, and Novavax COVID-19 vaccines containing the SARS-CoV-2 omicron XBB.1.5 strain have replaced their predecessors in the United States and in other countries since the fall of 2023. The clinical impact of these vaccines on currently circulating variants was unknown. Aims: We aimed to assess the effectiveness of the updated XBB.1.5 vaccines against currently circulating omicron subvariants. Methods: We examined data on the administration of XBB.1.5 vaccines and the incidence of COVID-19 between September 11 and November 27, 2023 for approximately 2 million persons by linking records from the Nebraska Electronic Disease Surveillance System and the Nebraska State Immunization Information System. We used Cox regression to estimate the effects of XBB.1.5 vaccines on the risk of COVID-19, as a function of time elapsed since vaccination, while adjusting for demographic factors, previous infection history, and previous vaccination history. Results: The effectiveness (i.e., proportionate reduction of risk) for XBB.1.5 vaccines against SARS-CoV-2 infection was 63.0% (95% confidence interval [CI], 48.6 to 73.4) 4 weeks after vaccination and 67.1% (95% CI, 49.9 to 78.4) 6 weeks after vaccination; vaccine effectiveness started to decline after 6 weeks. Vaccine effectiveness was broadly similar across subgroups defined by age, sex, race and ethnicity, socioeconomic status, and previous immunity status. Conclusion: XBB.1.5 vaccines were effective against currently circulating variants, regardless of age, sex, race and ethnicity, socioeconomic status, or previous immunity status. These findings can be used to develop effective prevention strategies against COVID-19.

Occupational Carbon Monoxide Poisoning in Wisconsin: Results From a Statewide Electronic Disease Surveillance System and From the Wisconsin Poison Center, 2018-2021.

Prevention methods for carbon monoxide (CO) poisoning in Wisconsin address occupational and nonoccupational exposures together, but differences between the settings could inform new approaches to preventing occupational CO poisonings. We described occupational CO poisonings in Wisconsin from July 1, 2018, through July 1, 2021, using surveillance data from the Wisconsin Electronic Disease Surveillance System and Wisconsin Poison Center. We identified cases of CO poisoning from the Wisconsin Electronic Disease Surveillance System and Wisconsin Poison Center. Occupational CO poisonings were records where "workplace" was recorded as the location of exposure. We excluded records classified as suspect/not a case, those missing laboratory results or information on exposure source/location, and intentional poisonings. We compared characteristics between occupational and nonoccupational settings using odds ratios (ORs), and we estimated crude incidence rates of occupational exposures by occupation. We identified 614 cases of CO poisoning, of which 168 (27.4%) were occupational exposures. When compared with patients with nonoccupational exposures, patients with occupational exposures were more likely to be male (OR = 3.8; 95% CI, 2.4-6.1), Hispanic (OR = 2.4; 95% CI, 1.4-4.2), and younger (mean difference [SD] = 6.6 [20.9]). Several CO sources were significantly associated with occupational poisonings: forklifts (OR = 58.4; 95% CI, 13.9-246.1; P < .001), pressure sprayers (OR = 2.4; 95% CI, 1.3-4.4; P = .003), and other gasoline-powered tools (OR = 3.8; 95% CI, 2.3-6.3; P < .001). The natural resources, construction, and maintenance occupation group had the highest crude incidence rate-45.0 poisonings per 100 000 full-time equivalent employees. Incorporating data from the Wisconsin Poison Center improved data quality, but surveillance is limited by underreporting. Creating strategies to increase reporting would allow for a more comprehensive understanding of occupational CO poisoning.

Implementing a Surveillance-Based Approach to Create a Statewide Viral Clearance Cascade for Hepatitis C Among People With HIV and HCV Coinfection in Connecticut.

Highly effective direct-acting antiviral medications have made it feasible to achieve elimination of hepatis C virus (HCV), including for people with HIV and HCV coinfection. The Centers for Disease Control and Prevention offers guidance for a laboratory surveillance-based HCV viral clearance cascade, which allows public health departments to track the outcomes of people with HCV based on the following steps: ever infected, virally tested, initial infection, and cured or cleared. We examined the feasibility of this approach among people with HIV and HCV coinfection in Connecticut. We matched an HIV surveillance database, which included cases from the enhanced HIV/AIDS Reporting System as of December 31, 2019, and the HCV surveillance database, the Connecticut Electronic Disease Surveillance System, to define a cohort of coinfected people. We used HCV laboratory results obtained from January 1, 2016, through August 3, 2020, to determine HCV status. Of 1361 people who were ever infected with HCV as of December 31, 2019, 1256 (92.3%) received HCV viral testing, 865 of 1256 people tested (68.9%) were HCV infected, and 336 of 865 infected people (38.8%) were cleared or cured. People who had undetectable HIV viral loads at most recent HIV test (<200 copies/mL) were more likely than those with detectable HIV viral loads to achieve HCV cure (P = .02). A surveillance-based approach that includes data based on the Centers for Disease Control and Prevention HCV viral clearance cascade is feasible to implement, can help track population-level outcomes longitudinally, and can help identify gaps to inform HCV elimination strategies.

Adolescent COVID-19 Cases During the SARS-CoV-2 Delta and Omicron Variant Surges in Kentucky: Association With Vaccination and Prior Infection

PurposeEffectiveness of COVID-19 mRNA vaccines is influenced by SARS-CoV-2 variant and history of prior infection. Data regarding protection against SARS-CoV-2 infection among adolescents, accounting for prior infection and time since vaccination, are limited. MethodsSARS-CoV-2 testing and immunization data from the Kentucky Electronic Disease Surveillance System and the Kentucky Immunization Registry, August–September 2021 (Delta predominance) and January 2022 (Omicron Predominance) among adolescents aged 12–17 years, were used to assess association of SARS-CoV-2 infection with mRNA vaccination and prior SARS-CoV-2 infection. Estimated protection was derived from prevalence ratios ([1-PR] × 100%). ResultsDuring Delta predominance, 89,736 tested adolescents were evaluated. Completion of primary series (second dose of mRNA vaccine ≥ 14 days prior to testing) and history of prior infection (> 90 days prior to testing) were both protective against SARS-CoV-2 infection (primary series: 81%, 95% confidence interval [CI] 79.7–82.3; prior infection: 66%, 95% CI 62.0–69.6). Prior infection plus primary series provided the greatest protection (92.3%, 95% CI 88.0–95.1). During Omicron predominance, 67,331 tested adolescents were evaluated. Primary series alone provided no benefit against SARS-CoV-2 infection after 90 days; prior infection was protective for up to one year (24.2%, 95% CI 17.2–30.7). Prior infection plus booster vaccination provided the greatest protection against infection (82.4%, 95% CI 62.1–91.8). DiscussionStrength and duration of protection against infection provided by COVID-19 vaccination and prior SARS-CoV-2 infection differed by variant. Vaccination provided additional benefit to the protection offered by prior infection alone. Remaining up to date with vaccination is recommended for all adolescents regardless of infection history.

Nontuberculous Mycobacterial Infection in Wisconsin Adults and Its Relationship to Race and Social Disadvantage.

Rationale: Population-based data on the epidemiology of nontuberculosis mycobacterial (NTM) infections are limited, particularly with respect to variation in NTM infection among racial groups and socioeconomic strata. Wisconsin is one of a handful of states where mycobacterial disease is notifiable, allowing large, population-based analyses of the epidemiology of NTM infection in this state. Objectives: To estimate the incidence of NTM infection in Wisconsin adults, describe the geographic distribution of NTM infection across the state, identify the frequency and type of infection caused by different NTM species, and investigate associations between NTM infection and demographics and socioeconomic status. Methods: We conducted a retrospective cohort study using laboratory reports of all NTM isolates from Wisconsin residents submitted to the Wisconsin Electronic Disease Surveillance System from 2011 to 2018. For the analyses of NTM frequency, multiple reports from the same individual were enumerated as separate isolates when nonidentical, collected from different sites or collected more than one year apart. Results: A total of 8,135 NTM isolates from 6,811 adults were analyzed. Mycobacterium avium complex accounted for 76.4% of respiratory isolates. The M. chelonae-abscessus group was the most common species isolated from skin and soft tissue. The annual incidence of NTM infection was stable over the study period (from 22.1 per 100,000 to 22.4 per 100,000). The cumulative incidence of NTM infection among Black (224 per 100,000) and Asian (244 per 100,000) individuals was significantly higher compared with that among their White counterparts (97 per 100,000). Total NTM infections were significantly more frequent (P < 0.001) in individuals from disadvantaged neighborhoods, and racial disparities in the incidence of NTM infection generally remained consistent when stratified by measures of neighborhood disadvantage. Conclusions: More than 90% of NTM infections were from respiratory sites, with the vast majority caused by M. avium complex. Rapidly growing mycobacteria predominated as skin and soft tissue pathogens and were important minor respiratory pathogens. We found a stable annual incidence of NTM infection in Wisconsin between 2011 and 2018. NTM infection occurred more frequently in non-White racial groups and in individuals experiencing social disadvantage, suggesting that NTM disease may be more frequent in these groups as well.

Renin-angiotensin system inhibition and in-hospital mortality in acute coronary syndrome patients with advanced renal dysfunction: findings from CCC-ACS project and a nationwide electronic health record-based cohort in China.

In acute coronary syndrome (ACS) patients without advanced renal dysfunction [estimated glomerular filtration rate (eGFR) < 30mL/min/1.73 m2], early (within 24 h of admission) angiotensin-converting enzyme inhibitor/angiotensin receptor blocker (ACEI/ARB) is the guideline-directed medical therapy. The clinical efficacy of early ACEI/ARB therapy among ACS patients with advanced renal dysfunction remains unclear. Among 184 850 ACS patients hospitalized from July 2014 to December 2018 in the Chinese National Electronic Disease Surveillance System Platform (CNEDSSP) cohort and 113 650 ACS patients enrolled from November 2014 to December 2019 in the Improving Care for Cardiovascular Disease in China-ACS Project (CCC-ACS) cohort, we identified 3288 and 3916 ACS patients with admission eGFR < 30mL/min/1.73 m2 [2647 patients treated with ACEI/ARB (36.7%)], respectively. After 1:1 propensity score matching (PSM) in each cohort, Kaplan-Meier analysis showed that early ACEI/ARB use was associated with a 39% [hazard ratio (HR): 0.61, 95% confidence interval (95% CI): 0.45-0.82] and a 34% (HR: 0.66, 95% CI: 0.46-0.95) reduction in in-hospital mortality in CNEDSSP and CCC-ACS cohorts, respectively, which was consistent in multiple sensitivity analyses. A random effect meta-analysis of the two cohorts after PSM revealed a 32% reduction (risk ratio: 0.68, 95% CI: 0.55-0.84) in in-hospital mortality among ACEI/ARB users. Based on two nationwide cohorts in China in contemporary practice, we demonstrated that ACEI/ARB therapy initiated within 24 h of admission is associated with a reduction in in-hospital mortality in ACS patients with advanced renal dysfunction. CCC-ACS project was registered at URL: https://www.clinicaltrials.gov. (Unique identifier: NCT02306616).

Rapid Increase in Suspected SARS-CoV-2 Reinfections, Clark County, Nevada, USA, December 2021.

Genetic differences between SARS-CoV-2 variants raise concerns about reinfection. Public health authorities monitored the incidence of suspected reinfection in Clark County, Nevada, USA, during March 2020–March 2022. Suspected reinfections, defined as a second positive PCR test collected >90 days after an initial positive test, were monitored through an electronic disease surveillance system. We calculated the proportion of all new cases per week that were suspected reinfections and rates per 1,000 previously infected persons by demographic groups. The rate of suspected reinfection remained <2.7% until December 2021, then increased to ≈11%, corresponding with local Omicron variant detection. Reinfection rates were higher among adults 18–50 years of age, women, and minority groups, especially persons identifying as American Indian/Alaska Native. Suspected reinfection became more common in Clark County after introduction of the Omicron variant, and some demographic groups are disproportionately affected. Public health surveillance could clarify the SARS-CoV-2 reinfection burden in communities.

Blood Lead Level Testing and Retesting Among Newly Arriving Refugee Children, Pennsylvania, 2015-2019.

Objectives. To (1) determine the prevalence of elevated blood lead levels (EBLLs; ≥ 5 µg/dL) among newly arrived refugee children, (2) understand the demographic characteristics of refugee children with EBLLs, and (3) assess health care providers' compliance with Centers for Disease Control and Prevention (CDC) recommendations for retesting. Methods. We matched refugee demographic data (2015-2019) from the CDC's Electronic Disease Notification (EDN) system with lead-testing laboratory report data from the Pennsylvania National Electronic Disease Surveillance System using Match*Pro software. Results. Of 3833 refugee children 16 years or younger in the EDN system, matching identified 3142 children with blood lead level data. Among children with blood lead level data, 578 (18.4%) had EBLLs. Among children with EBLLs, 341 (59.0%) were male. Of the 1370 children aged 6 years or younger with blood level test results, 335 (24.5%) had initial EBLLs, and only 78 (5.7%) were retested within 3 to 6 months. Of the 335 children 6 years or younger with an initial EBLL, only 44 (13.1%) were retested within 3 to 6 months. Conclusions. Following up on refugee children with EBLLs is necessary to ensure that they do not have continued lead exposure. (Am J Public Health. 2022;112(S7):S706-S714. https://doi.org/10.2105/AJPH.2022.306856).

Digital Tools Adopted by Public Health Agencies to Support COVID-19 Case Investigation and Contact Tracing, United States, 2020-2021.

During the COVID-19 pandemic, public health agencies implemented an array of technologies and digital tools to support case investigation and contact tracing. Beginning in May 2020, the Association of State and Territorial Health Officials compiled information on digital tools used by its membership, which comprises 59 chief health officials from each of the 50 states, 5 US territories, 3 freely associated states, and the District of Columbia. This information was presented online through a publicly available technology and digital tools inventory. We describe the national landscape of digital tools implemented by public health agencies to support functions of the COVID-19 response from May 2020 through May 2021. We also discuss how public health officials and their informatics leadership referenced the information about the digital tools implemented by their peers to guide and refine their own implementation plans. We used a consensus-based approach through monthly discussions with partners to group digital tools into 5 categories: surveillance systems, case investigation, proximity technology/exposure notification, contact tracing, and symptom tracking/monitoring. The most commonly used tools included the National Electronic Disease Surveillance System Base System (NBS), Sara Alert, REDCap, and Maven. Some tools such as NBS, Sara Alert, REDCap, Salesforce, and Microsoft Dynamics were repurposed or adapted for >1 category. Having access to the publicly available technology and digital tools inventory provided public health officials and their informatics leadership with information on what tools other public health agencies were using and aided in decision making as they considered repurposing existing tools or adopting new ones.

Characteristics of patients positive for COVID-19 and multidrug-resistant organisms in Tennessee, 2020–2021

Background: Multidrug-resistant organisms (MDROs) are a global threat. To track and contain the spread, the Tennessee Department of Health (TDH) performs targeted surveillance of carbapenemase-producing and pan-nonsusceptible organisms. When these MDROs are identified, TDH conducts a containment response and collects epidemiological data, which includes risk factors such as indwelling devices and previous hospitalizations. The impact of the COVID-19 pandemic on these MDROs is not well understood. Therefore, we have described the characteristics of cases positive for both COVID-19 and select MDROs. Methods: MDRO investigation data from January 1, 2020–September 30, 2021 were matched with all COVID-19 case data from the TDH statewide surveillance system, National Electronic Disease Surveillance System Base System. MDRO-positive date was defined as the specimen collection date; COVID-19 case date was first defined as the date of symptom onset and if missing, then diagnosis date, and investigation creation date, respectively. Descriptive statistics and Fisher exact tests were calculated using SAS version 9.4 software. Results: Among 336 MDRO cases, 50 had a reported SARS-CoV-2–positive result. MDRO types were Enterobacterales (CRE) (n = 31), Acinetobacter spp (CRA) (n = 18), and Pseudomonas aeruginosa (n = 1). Of these 50 cases, 20 were MDRO-positive before and 30 days after the COVID-19 case date, respectively. Of the 18 CRA cases, 16 (89%), were positive after the COVID-19 case date, compared to 13 (42%) among 31 CRE cases (P &lt; .01). Also, 35 patients (70%) had a record of hospitalization, and 22 (63%) had their MDRO specimen collected after the COVID-19 case date (P = .37). Of these 22 patients, 4 had their MDRO specimen collected during their COVID-19 hospitalization, with an average duration from admission to MDRO collection date of 17 days (range, 4–36). Among the 50 coinfected cases, 8 died, 7 (88%) of whom were MDRO-positive after their COVID-19 case date. Data on indwelling devices at time of MDRO positivity were completed for 17 cases; 14 had an indwelling device and, among these, 13 (93%) were MDRO-positive after their COVID-19 case date. Conclusions: MDRO cases with specimen collections after COVID-19 comprised the majority of hospitalized patients, patients who died, and patients with indwelling devices compared to those with MDROs collected before their COVID-19 case date. These results show a stark difference with CRA as the most common MDRO among post–COVID-19 cases. Our data were limited by reporting gaps. We recognize that patients can remain colonized with MDROs for lengthy durations, which could have result in undetected MDRO cases prior to the COVID-19 case date. More data and analyses are needed to make targeted public health recommendations. However, these findings highlight the burden of MDROs among COVID-19 cases. including adverse health outcomes.Funding: NoneDisclosures: None

Identifying COVID-19 Outbreaks From Contact-Tracing Interview Forms for Public Health Departments: Development of a Natural Language Processing Pipeline.

BackgroundIn Wisconsin, COVID-19 case interview forms contain free-text fields that need to be mined to identify potential outbreaks for targeted policy making. We developed an automated pipeline to ingest the free text into a pretrained neural language model to identify businesses and facilities as outbreaks.ObjectiveWe aimed to examine the precision and recall of our natural language processing pipeline against existing outbreaks and potentially new clusters.MethodsData on cases of COVID-19 were extracted from the Wisconsin Electronic Disease Surveillance System (WEDSS) for Dane County between July 1, 2020, and June 30, 2021. Features from the case interview forms were fed into a Bidirectional Encoder Representations from Transformers (BERT) model that was fine-tuned for named entity recognition (NER). We also developed a novel location-mapping tool to provide addresses for relevant NER. Precision and recall were measured against manually verified outbreaks and valid addresses in WEDSS.ResultsThere were 46,798 cases of COVID-19, with 4,183,273 total BERT tokens and 15,051 unique tokens. The recall and precision of the NER tool were 0.67 (95% CI 0.66-0.68) and 0.55 (95% CI 0.54-0.57), respectively. For the location-mapping tool, the recall and precision were 0.93 (95% CI 0.92-0.95) and 0.93 (95% CI 0.92-0.95), respectively. Across monthly intervals, the NER tool identified more potential clusters than were verified in WEDSS.ConclusionsWe developed a novel pipeline of tools that identified existing outbreaks and novel clusters with associated addresses. Our pipeline ingests data from a statewide database and may be deployed to assist local health departments for targeted interventions.

Structural racism and COVID-19 response: higher risk of exposure drives disparate COVID-19 deaths among Black and Hispanic/Latinx residents of Illinois, USA

BackgroundStructural racism has driven and continues to drive policies that create the social, economic, and community factors resulting in residential segregation, lack of access to adequate healthcare, and lack of employment opportunities that would allow economic mobility. This results in overall poorer population health for minoritized people. In 2020, Black and Hispanic/Latinx communities throughout the United States, including the state of Illinois, experienced disproportionately high rates of COVID-19 cases and deaths. Public health officials in Illinois implemented targeted programs at state and local levels to increase intervention access and reduce disparities.MethodsTo quantify how disparities in COVID outcomes evolved through the epidemic, data on SARS-CoV-2 diagnostic tests, COVID-19 cases, and COVID-19 deaths were obtained from the Illinois National Electronic Disease Surveillance System for the period from March 1 to December 31, 2020. Relative risks of COVID-19 cases and deaths were calculated for Black and Hispanic/Latinx vs. White residents, stratified by age group and epidemic interval. Deaths attributable to racial/ethnic disparities in incidence and case fatality were estimated with counterfactual simulations.ResultsDisparities in case and death rates became less drastic after May 2020, but did not disappear, and were more pronounced at younger ages. From March to May of 2020, the risk of a COVID-19 case for Black and Hispanic/Latinx populations was more than twice that of Whites across all age groups. The relative risk of COVID-19 death reached above 10 for Black and Hispanic/Latinx individuals under 50 years of age compared to age-matched Whites in the early epidemic. In all Illinois counties, relative risk of a COVID-19 case was the same or significantly increased for minoritized populations compared to the White population. 79.3 and 86.7% of disparities in deaths among Black and Hispanic/Latinx populations, respectively, were attributable to differences in age-adjusted incidence compared to White populations rather than differences in case fatality ratios.ConclusionsRacial and ethnic disparities in the COVID-19 pandemic are products of society, not biology. Considering age and geography in addition to race/ethnicity can help to identify the structural factors driving poorer outcomes for certain groups. Studies and policies aimed at reducing inequalities in disease exposure may reduce disparities in mortality more than those focused on drivers of case fatality.

Evaluation of the National Electronic Disease Surveillance System Amid the COVID-19 Pandemic in Elsahel District, Cairo Governorate, Egypt, 2020

Background The Egypt National Disease Surveillance is a routine system established in 2002. The system electronically reports on 41 infectious diseases including COVID-19. Reporting sites include all Egyptian governorates, districts, governmental infectious disease hospitals, and primary health units. Surveillance is essential during the pandemic to detect cases early, describe the epidemiology of health problems, guide priority setting, and plan and evaluate public health policy and strategies. Objective This study aims to evaluate the surveillance system during the pandemic to assess its effectiveness in achieving its objectives and to find and fill the gaps. Methods The evaluation was performed using the Centers for Disease Control and Prevention guidelines. A structured questionnaire was used to evaluate the qualitative attributes including simplicity, flexibility, and acceptability through interviewing surveillance teams at the central level, health directorate, and Sahel district. Quantitative attributes, including completeness, timeliness, and predictive positive value, were performed using COVID-19 surveillance data of Sahel district in March-December 2020. Data were assessed for completeness and accuracy. The usefulness of surveillance was assessed in terms of achieving its objectives and use of data. Results Of 33 respondents, 90% thought that the system was simple, and 77% thought it was acceptable; work overload reduced the acceptability rate. The system is funded by the Ministry of Health and Population and was operational 53% of the time due to connectivity problems. The system was flexible when adapting to include COVID-19 in a short time with minimal cost. It is quite representative, as it covers 60% of the population. Completeness was 82%, positive value predictive was 58%, and data validity was 86%. The median duration between patient admissions and reporting was 2.7 days. Conclusions The evaluation of the Egypt COVID-19 surveillance system indicated that the system partly achieved its objectives in the area of simplicity and flexibility with adequate data quality. There is a need to improve acceptability and timeliness through increasing manpower and to enhance stability through effective connectivity. Expansion of the system to cover all of the Egyptian population is recommended to improve representativeness.

1392. Nontuberculous Mycobacteria Isolated from Wisconsin Residents, 2010-2018

BackgroundWisconsin is one of a handful of states in which laboratory identification of nontuberculous mycobacteria (NTM) from clinical samples is reportable to public health. The aims of this study were to characterize the demographic features of Wisconsin adults with NTM, assess the relative abundance of NTM species recovered, and describe trends in NTM isolation over the study period.MethodsWe conducted a retrospective cohort study of Wisconsin residents 18 years of age and older from whom NTM isolates were recovered and reported to the Wisconsin Electronic Disease Surveillance System (WEDSS) between 2010 and 2018. Isolates of M. gordonae were excluded. For the analysis of NTM frequency, multiple reports from the same individual were enumerated as separate isolates when non-identical or collected from different sites. Because NTM were usually reported into WEDSS without clinical data, this study couldn’t discern the clinical significance of the isolates.ResultsA total of 9,032 NTM isolates from 7,722 adults were analyzed. The average annual number of reported NTM cases was 950 (21.7/100,000 adults) during 2011-2018. Table 1 shows the demographic characteristics of individuals with NTM isolates, stratified by specimen collection site and NTM species. M. avium complex (MAC) accounted for 75.7% of respiratory isolates. An important pathogenic NTM, M. xenopi, accounted for 8.9% of non-MAC respiratory isolates. As shown in Table 2, M. chelonae, a rapidly growing mycobacteria (RGM), was the most common species isolated from skin and soft tissue, head, ears, nose and throat, and eye specimens. MAC was the most common isolate from other tissue sites. Table 1. Demographic characteristics of individuals with NTM isolates. Categorization was based upon the initially recovered sample when multiple samples were obtained from a given individual. “Respiratory” samples included sputum, bronchoalveolar lavage, and tracheal aspirate specimens. IQR, interquartile range. RGM, rapidly growing mycobacteria (M. chelonae and the M. abscessus, M. chelonae-abscessus, and M. fortuitum groups). SST, skin and soft tissue.Table 2. Most common NTM species isolated from non-respiratory sites. *’Respiratory specimens’ was inclusive of sputum, bronchoalveolar lavage, and tracheal aspirate specimens. CNS, central nervous system. HENT, head, ears, nose, or throat. SST, skin and soft tissue.ConclusionConsistent with prior studies, MAC is the predominant NTM isolated from respiratory specimens in Wisconsin. RGM are important minority respiratory pathogens, and predominate as skin and soft tissue NTMs. We highlight M. xenopi as an important pathogen in Wisconsin compared to other parts of the United States. In contrast to recent reports of increasing incidence of NTM disease, we found a stable annual incidence of NTM isolation between 2010 and 2018. Disclosures All Authors: No reported disclosures

Protective Immunity after Natural Infection with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) – Kentucky, USA, 2020

BackgroundAs vaccine supply and access remain limited in many parts of the world, understanding the duration of protection from reinfection after natural infection is important. MethodsDistinct individuals testing positive and negative for SARS-CoV-2 between March 6, 2020, and August 31, 2020, in Kentucky, USA, were identified using the Kentucky National Electronic Disease Surveillance System. Individuals were followed for occurrence of a positive test for SARS-CoV-2 from 91 days after their initial test result through December 31, 2020. Protection from reinfection provided by a prior infection was calculated and additional analyses evaluated impact of age, sex, symptom status, long-term care facility connection, testing occurrence and frequency, and time from initial infection. ResultsThe protective effect from prior infection was 80.3% (95% CI, 78.2%–82.2%) for those aged 20–59 years and 67.4% (95% CI, 62.8%–71.4%) for those aged ≥60 years. At 30-day time periods through 270 days (with limited exceptions), protection was estimated to be >75% for those aged 20–59 years and >65% for those aged ≥60 years. Factors associated with repeat positive testing included a connection to a long-term care facility, duration of potential exposure, and absence of symptoms during initial infection. ConclusionsNatural infection provides substantial and persistent immunologic protection for a period of several months for most individuals, although subpopulations may be at greater risk of repeat positive testing and potential poor outcomes associated with reinfection. These subgroups include individuals aged ≥60 years, residents and staff of long-term care facilities, and those who have mild or asymptomatic illness with initial infection. Continued emphasis on vaccination and infection prevention and control strategies remains critically important in reducing the risk of reinfection and associated severe outcomes for these groups.