Aggregate Surveillance Data Research Articles

Monitoring Trends and Differences in COVID-19 Case Fatality Rates in a Union Territory of India: Inferential Data Analysis

Objective: To understand the challenges posed by the second wave of COVID-19 cases in the Union Territory of Jammu and Kashmir, India. Materials and Methods: The study utilised weekly aggregated surveillance data from November 2020 to May 2021. Ethical clearance was obtained, and an exploratory trend analysis was performed using Excel 2019. Results: Distinct trends in active cases, symptomatic patients tested, case fatality rate (CFR) and rapid antigen test (RAT) positivity rates were observed across the 10 districts in the Kashmir division. Srinagar exhibited notable variations, and CFR showed district-specific differences. Conclusion: This study underscores the significance of tailored strategies, government interventions and community resilience.

Foodborne botulism in Poland in 2018-2021.

The aim of this study is to assess the epidemiological situation of foodborne botulism in Poland in 2018-2021, compared to previous years. The assessment is based on an analysis of aggregated surveillance data from the annual bulletin "Infectious Diseases and Poisons in Poland" from 2013-2021, as well as botulism case reports collected by sanitary-epidemiological stations and sent to the Department of Epidemiology of Infectious Diseases and Surveillance of the NIPH NIH - NRI or provided by EpiBase. A total of 54 foodborne botulism cases were registered between 2018 and 2021, including 31 (57.4%) cases of laboratory-confirmed botulism intoxication. Most cases (46 cases, 85.2%) were sporadic. The declining trend in the number of notifications continued throughout the time period, and the incidence recorded in 2021 (0.02 per 100,000 population) was the lowest since the introduction of mandatory reporting and registration of botulism in Poland. The highest median annual incidence was recorded in the Warmisko-Mazurskie (0.18), but many voivodeships reported only single notifications or none. The decreasing trend in rural areas relative to the level of incidence in urban areas continued. Men (incidence in men more than twice that of women) and people aged 50-59 predominated. All patients were hospitalized. According to the State Sanitary Inspection, there were 3 deaths (mortality of 5.6%). In 2018-2021, the downward trend in the number of foodborne botulism notifications in Poland continued. At the same time, the considerable proportion of cases reported by physicians without laboratory confirmation and not meeting the definition of botulism adopted in other EU countries is noteworthy. The incidence in rural areas decreases to the level of incidence in urban areas, and the previously observed geographical distribution of cases diminishes.

Analysis of reservoir sources of Campylobacter isolates to free-range broilers in Denmark

Campylobacter is a common cause of food poisoning in many countries, with broilers being the main source. Organic and free-range broilers are more frequently Campylobacter-positive than conventionally raised broilers and may constitute a higher risk for human infections. Organic and free-range broilers may get exposed to Campylobacter from environmental reservoirs and livestock farms, but the relative importance of these sources is unknown. The aim of the study was to describe similarities and differences between the genetic diversity of the Campylobacter isolates collected from free-range/organic broilers with those isolated from conventional broilers and other animal hosts (cattle, pigs, and dogs) in Denmark to make inferences about the reservoir sources of Campylobacter to free-range broilers. The applied aggregated surveillance data consisted of sequenced Campylobacter isolates sampled in 2015 to 2017 and 2018 to 2021. The data included 1,102 isolates from free-range (n=209), conventional broilers (n=577), cattle (n=261), pigs (n=30), and dogs (n=25). The isolates were cultivated from either fecal material (n=434), food matrices (n=569), or of nondisclosed origin (n=99). Campylobacter jejuni (94.5%) dominated and subtyping analysis found 170 different sequence types (STs) grouped into 75 clonal complexes (CCs). The results suggest that CC-21 and CC-45 are the most frequent CCs found in broilers. The relationship between the CCs in the investigated sources showed that the different CCs were shared by most of the animals, but not pigs. The ST-profiles of free-range broilers were most similar to that of conventional broilers, dogs and cattle, in that order. The similarity was stronger between conventional broilers and cattle than between conventional and free-range broilers. The results suggest that cattle may be a plausible reservoir of C. jejuni for conventional and free-range broilers, and that conventional broilers are a possible source for free-range broilers or reflect a dominance of isolates adapted to the same host environment. Aggregated data provided valuable insight into the epidemiology of Campylobacter sources for free-range broilers, but time-limited sampling of isolates from different sources within a targeted area would hold a higher predictive value.

Socio-political and organizational influences on national infectious disease surveillance for refugees: A qualitative case study in Lebanon.

Infectious disease surveillance provides actionable information on displaced populations and helps identify outbreaks. Though not a signatory to the 1951 Refugee Convention, Lebanon has experienced large refugee influxes (e.g. Palestinians in 1948, Syrians in 2011), yet information on socio-political and organizational influences shaping surveillance targeting refugees is limited. We thus aimed to examine how Lebanese socio-politics affected infectious disease surveillance for refugees in Lebanon. We conducted a qualitative multimethod single case study of government engagement with refugee infectious disease surveillance (2011-2018) drawing from document analysis, semi-structured observations, and semi-structured key informant interviews at four surveillance sites in Lebanon. We analysed data thematically, using deductive and inductive coding. National politics delayed government and thus its epidemiological surveillance program's (ESU) engagement with refugee disease surveillance, largely due to Lebanon not being a 1951 Refugee Convention signatory and internal policy disagreements. Thus, it was initially difficult for the ESU to lead surveillance activities, though it later became more active. The ESU was limited by unclear reporting mechanisms and resources and its reliance on aggregated surveillance data prevented provision of data-informed responses. Though the ESU led surveillance nationally, and we identified positive provincial level collaborations due to individual efforts, some partners still conducted parallel surveillance. We found no systematic approach to infectious disease surveillance for refugees. The ESU could improve surveillance for refugees by collaborative strategic planning with partners for preparedness, surveillance, reporting, and sustainable resource allocation during refugee crises. Further suggestions include collecting disaggregated data, and piloting potentially more efficient syndromic surveillance, based on symptom clusters, for refugee populations.

Is aggregated surveillance data a reliable method for constructing tuberculosis care cascades? A secondary data analysis from Uganda.

To accelerate tuberculosis (TB) control and elimination, reliable data is needed to improve the quality of TB care. We assessed agreement between a surveillance dataset routinely collected for Uganda's national TB program and a high-fidelity dataset collected from the same source documents for a research study from 32 health facilities in 2017 and 2019 for six measurements: 1) Smear-positive and 2) GeneXpert-positive diagnoses, 3) bacteriologically confirmed and 4) clinically diagnosed treatment initiations, and the number of people initiating TB treatment who were also 5) living with HIV or 6) taking antiretroviral therapy. We measured agreement as the average difference between the two methods, expressed as the average ratio of the surveillance counts to the research data counts, its 95% limits of agreement (LOA), and the concordance correlation coefficient. We used linear mixed models to investigate whether agreement changed over time or was associated with facility characteristics. We found good overall agreement with some variation in the expected facility-level agreement for the number of smear positive diagnoses (average ratio [95% LOA]: 1.04 [0.38-2.82]; CCC: 0.78), bacteriologically confirmed treatment initiations (1.07 [0.67-1.70]; 0.82), and people living with HIV (1.11 [0.51-2.41]; 0.82). Agreement was poor for Xpert positives, with surveillance data undercounting relative to research data (0.45 [0.099-2.07]; 0.36). Although surveillance data overcounted relative to research data for clinically diagnosed treatment initiations (1.52 [0.71-3.26]) and number of people taking antiretroviral therapy (1.71 [0.71-4.12]), their agreement as assessed by CCC was not poor (0.82 and 0.62, respectively). Average agreement was similar across study years for all six measurements, but facility-level agreement varied from year to year and was not explained by facility characteristics. In conclusion, the agreement of TB surveillance data with high-fidelity research data was highly variable across measurements and facilities. To advance the use of routine TB data as a quality improvement tool, future research should elucidate and address reasons for variability in its quality.

Estimation of reproduction numbers in real time: Conceptual and statistical challenges.

The reproduction number has been a central metric of the COVID-19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations of , the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g.the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulating becomes increasingly complicated and inevitably model-dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency.

The changing spectrum of microbial aetiology of respiratory tract infections in hospitalized patients before and during the COVID-19 pandemic

BackgroundThe COVID-19 pandemic was met with strict containment measures. We hypothesized that societal infection control measures would impact the number of hospital admissions for respiratory tract infections, as well as, the spectrum of pathogens detected in patients with suspected community acquired pneumonia (CAP).MethodsThis study is based on aggregated surveillance data from electronic health records of patients admitted to the hospitals in Bergen Hospital Trust from January 2017 through June 2021, as well as, two prospective studies of patients with suspected CAP conducted prior to and during the COVID-19 pandemic (pre-COVID cohort versus COVID cohort, respectively). In the prospective cohorts, microbiological detections were ascertained by comprehensive PCR-testing in lower respiratory tract specimens. Mann–Whitney’s U test was used to analyse continuous variables. Fisher’s exact test was used for analysing categorical data. The number of admissions before and during the outbreak of SARS-CoV-2 was compared using two-sample t-tests on logarithmic transformed values.ResultsAdmissions for respiratory tract infections declined after the outbreak of SARS-CoV-2 (p < 0.001). The pre-COVID and the COVID cohorts comprised 96 and 80 patients, respectively. The proportion of viruses detected in the COVID cohort was significantly lower compared with the pre-COVID cohort [21% vs 36%, difference of 14%, 95% CI 4% to 26%; p = 0.012], and the proportion of bacterial- and viral co-detections was less than half in the COVID cohort compared with the pre-COVID cohort (19% vs 45%, difference of 26%, 95% CI 13% to 41%; p < 0.001). The proportion of bacteria detected was similar (p = 0.162), however, a difference in the bacterial spectrum was observed in the two cohorts. Haemophilus influenzae was the most frequent bacterial detection in both cohorts, followed by Streptococcus pneumoniae in the pre-COVID and Staphylococcus aureus in the COVID cohort.ConclusionDuring the first year of the COVID-19 pandemic, the number of admissions with pneumonia and the microbiological detections in patients with suspected CAP, differed from the preceding year. This suggests that infection control measures related to COVID-19 restrictions have an overall and specific impact on respiratory tract infections, beyond reducing the spread of SARS-CoV-2.

91756 A participatory approach to develop regional health priorities for clinical and translational research

ABSTRACT IMPACT: Regional health issues can be best addressed at the population-level and input from the communities is vital for prioritization of health issues. OBJECTIVES/GOALS: The Great Plains IDeA-CTR (GP IDeA-CTR) was developed to increase clinical and translational research (CTR) that can address regional health priorities. Here we describe a collaborative process used to identify regional health priorities using existing surveillance data and community input. METHODS/STUDY POPULATION: We used a participatory approach that included a partnership between the GP IDeA CTR Community-Engagement and Biostatistics, Epidemiology, and Research Design Cores to ensure priorities were data driven and also aligned with community-based perceptions of need. First, aggregated surveillance data across Nebraska, North Dakota, and South Dakota was presented to the GP IDeA CTR Community Advisory Board (CAB). Second, CAB members formed small groups and considered the information and generated priority health area lists. Third, small group lists were considered and discussed by the full CAB to finalize priority areas. Finally, the CAB reviewed the priorities annually thereafter. RESULTS/ANTICIPATED RESULTS: We identified priority areas for CTR that included (1) behavioral health, (2) injury prevention, (3) obesity, (4) technology to improve health care access, (5) connecting clinical/community services, and (5) addressing health disparities. These priorities align with population-based surveillance data that show lack of mental health care access, high prevalence of obesity, higher incidence of accidents, and existing racial, ethnic, and geographic health disparities. The CAB highlighted that research was also needed to improve how people can access the health innovations developed through CTR to address the other priority health issues with a goal to have an impact on population health. DISCUSSION/SIGNIFICANCE OF FINDINGS: By integrating data- and community-driven approaches we identified regional health priority areas that if addressed, can have significant impact in the GP IDeA CTR region. The priorities are listed on all GP IDeA-CTR funding announcements to encourage CTR in these areas.

Accrued – An R Package for Visualizing Data Quality for Aggregate Surveillance Data

We will describe an R package developed for visualizing and analyzing the quality of aggregate surveillance data.

Toward Rubella Elimination in Poland: Need for Supplemental Immunization Activities, Enhanced Surveillance, and Further Integration with Measles Elimination Efforts

All Member States of the World Health Organization (WHO) European Region have endorsed rubella elimination and congenital rubella syndrome (CRS) prevention. However, Poland has continued high levels of reported rubella. We reviewed rubella incidence in Poland since 1966 and analyzed national aggregated surveillance data from the period 2003-2008 and case-based data from 4 provinces from the period 2006-2008. We described CRS cases since 1997 and assessed maternal receipt of vaccine. We reviewed national vaccination coverage from 1992 through 2008. Since 1966, rubella outbreaks have occurred every 4-6 years in Poland. Aggregate and case-based data from the period 2003-2008 indicate that rubella virus transmission has occurred across wide age ranges (from <1 year to 60 years), with disproportionately higher percentage of cases among adolescent boys. Of 18 children with reported CRS cases from 1997 through 2008, 15 (83%) of their mothers had not been vaccinated. Measles-mumps-rubella dose 1 vaccination coverage ranged from 97% to 99%. Poland had the highest incidence of rubella in the WHO European Region in 2007 and 2008. Rubella occurs predominantly in age and sex cohorts historically not included in vaccination recommendations. The risk for CRS continues. To achieve rubella elimination, supplemental immunization activities among adolescent boys are needed, as is integration with measles elimination efforts.

Validation of surgical site infection surveillance in orthopedic procedures

Valid data are essential for a national surveillance system of nosocomial infections. In 8 hospitals conducting surgical site infection (SSI) surveillance for orthopedic procedures, a validation team performed a blinded retrospective chart review (10 operations with reported infections, 40 without) and interviewed infection control nurses. In total, 397 patient charts were reviewed. Positive and negative predictive values for routine surveillance were 94% (95% CI: 89%-99%) and 99% (95% CI: 99%-100%), respectively. When these results were applied to the aggregated surveillance data (403 infections, 10,068 noninfections), sensitivity was 75% (95% CI: 56%-93%) and specificity 100% (95% CI: 97%-100%). The following case finding methods were used: ward visits (in 7/8 hospitals), microbiology reports (5/8), ward notifications by link nurses (8/8), and other nursing (7/8) and medical (5/8) staff. The wound culture rate ranged from 9 to 67 per 1000 patient-days. All hospitals carried out postdischarge surveillance on readmission and all but 1 at follow-up visits and by an additional questionnaire. Most SSIs reported by the hospitals were true infections, showing that, when an SSI was reported, the definitions were correctly implemented. Some SSIs were missed, which might be due to weaknesses in case finding. Variation in diagnostic practices may also affect SSI rates.

Tuberculosis in health care workers during declining tuberculosis incidence in New York State

Nosocomial tuberculosis (TB) transmission has decreased dramatically in New York State since 1992; however, health care workers (HCWs) still compose >3% of TB cases. Aggregate surveillance data on incident TB cases from 1994 to 2002 were examined for trends among HCWs. Additional information was available for HCW cases from 1998 to 2002, including facility type, tuberculin skin test (TST) result at hire, and treatment of latent TB infection (TLTBI). In New York State, 2.5% of TB cases in 1994 and 4.0% in 2002 were in HCWs (P value for trend <.001). Fifty percent of HCWs TB cases in 1994 and 77.6% in 2002 were in non-US born (P = .002) HCWs. Multidrug-resistant TB in HCWs decreased from 15.6% in 1994 to 6.9% in 2002 (P = .001). Of 297 HCWs TB cases in 1998-2002, 54.9% were TST positive at hire, and 21.2% had unknown TST result; 50.2% of 221 HCWs who were TST positive at or after hire met guidelines for TLTBI, and 23.4% received treatment. The highest proportion with unknown TST at hire and the lowest proportion receiving TLTBI were in ambulatory facilities. Many HCWs who developed TB were either TST positive at hire and did not receive TLTBI or did not receive TST at hire. Facilities should encourage treatment for HCWs who meet criteria for TLTBI. Provider education should focus on ambulatory facilities.