A search-based geographic metadata curation pipeline to refine sequencing institution information and support public health

Background

The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) has amassed a vast reservoir of genetic data since its inception in 2007. These public data hold immense potential for supporting pathogen surveillance and control. However, the lack of standardized metadata and inconsistent submission practices in SRA may impede the data's utility in public health.

Methods

To address this issue, we introduce the Search-based Geographic Metadata Curation (SGMC) pipeline. SGMC utilized Python and web scraping to extract geographic data of sequencing institutions from NCBI SRA in the Cloud and its website. It then harnessed ChatGPT to refine the sequencing institution and location assignments. To illustrate the pipeline's utility, we examined the geographic distribution of the sequencing institutions and their countries relevant to polio eradication and categorized them.

Results

SGMC successfully identified 7,649 sequencing institutions and their global locations from a random selection of 2,321,044 SRA accessions. These institutions were distributed across 97 countries, with strong representation in the United States, the United Kingdom and China. However, there was a lack of data from African, Central Asian, and Central American countries, indicating potential disparities in sequencing capabilities. Comparison with manually curated data for U.S. institutions reveals SGMC's accuracy rates of 94.8% for institutions, 93.1% for countries, and 74.5% for geographic coordinates.

Conclusion

SGMC may represent a novel approach using a generative AI model to enhance geographic data (country and institution assignments) for large numbers of samples within SRA datasets. This information can be utilized to bolster public health endeavors.

Geographic Disparities in Case Fatality and Discharge Disposition Among Patients With Primary Intracerebral Hemorrhage

Background We evaluate nationwide trends and urban-rural disparities in case fatality (in-hospital mortality) and discharge dispositions among patients with primary intracerebral hemorrhage (ICH). Methods and Results In this repeated cross-sectional study, we identified adult patients (≥18 years of age) with primary ICH from the National Inpatient Sample (2004-2018). Using a series of survey design Poisson regression models, with hospital location-time interaction, we report the adjusted risk ratio (aRR), 95% CI, and average marginal effect (AME) for factors associated with ICH case fatality and discharge dispositions. We performed a stratified analysis of each model among patients with extreme loss of function and minor to major loss of function. We identified 908 557 primary ICH hospitalizations (overall mean age [SD], 69.0 [15.0] years; 445 301 [49.0%] women; 49 884 [5.5%] rural ICH hospitalizations). The crude ICH case fatality rate was 25.3% (urban hospitals: 24.9%, rural hospitals:32.5%). Urban (versus rural) hospital patients had a lower likelihood of ICH case fatality (aRR, 0.86 [95% CI, 0.83-0.89]). ICH case fatality is declining over time; however, it is declining faster in urban hospitals (AME, -0.049 [95% CI, -0.051 to -0.047]) compared with rural hospitals (AME, -0.034 [95% CI, -0.040 to -0.027]). Conversely, home discharge is increasing significantly among urban hospitals (AME, 0.011 [95% CI, 0.008-0.014]) but not significantly changing in rural hospitals (AME, -0.001 [95% CI, -0.010 to 0.007]). Among patients with extreme loss of function, hospital location was not significantly associated with ICH case fatality or home discharge. Conclusions Improving access to neurocritical care resources, particularly in resource-limited communities, may reduce the ICH outcomes disparity gap.

Red clover root-associated microbiota is shaped by geographic location and choice of farming system

AIMS

This study evaluated the red clover (Trifolium pratense) root associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites.

METHODS AND RESULTS

16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys and Tetracladium fungal genera known for endophytic, saprotrophic and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms.

CONCLUSIONS

We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the R. leguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.

Trends in Up-To-Date Colorectal Cancer Screening Among U.S. Adults Aged 50-75 Years and Variations by Race/Ethnicity and U.S. Census Bureau Divisions

Introduction

Mortality rates from colorectal cancer have declined over the past decades owing to population-based life-saving screening interventions. However, screening inequalities continue among racial and ethnic minorities despite having a higher disease burden. In this study, we assessed the patterns of up-to-date colorectal cancer screening rates among racial/ethnic groups across the U.S. Census Bureau Divisions.

Methods

This population-based cross-sectional study used weighted data from 4 cycles of the Behavioral Risk Factors Surveillance System (2014, 2016, 2018, and 2020) of adults aged 50‒75 years without a previous diagnosis of colorectal cancer. The primary outcome was guideline-recommended up-to-date colorectal cancer screening. We used logistic regression models to examine temporal trends in up-to-date colorectal cancer screening from 2014 to 2020. In addition, we conducted detailed descriptive statistics of up-to-date screening rates, comparing trends in 2020 with those in 2014 overall by race/ethnicity and U.S. census divisions.

Results

The overall proportion of individuals with up-to-date colorectal cancer screening increased from 66.5% in 2014 to 72.5% in 2020 (p<0.001). For racial/ethnic subgroups, from 2014 to 2020, screening rates increased significantly among non-Hispanic Whites (68.5%‒74.5%, p<0.001), non-Hispanic Blacks (68.0%‒74.6%, p<0.001), and Hispanics (51.5%‒62.8%, p<0.001). However, increases were not observed in all U.S. Census Bureau Divisions.

Conclusions

Although colorectal cancer screening rates improved over time, they fall short of the 80% target. Substantial racial/ethnic and geographic disparities remain. Future studies investigating the factors influencing these disparities are needed.

The influence of species identity and geographic locations on gut microbiota of small rodents

Although the correlation between gut microbiota, species identity and geographic locations has long attracted the interest of scientists, to what extent species identity and geographic locations influence the gut microbiota assemblages in granivorous rodents needs further investigation. In this study, we performed a survey of gut microbial communities of four rodent species (Apodemus agrarius, A. peninsulae, Tamias sibiricus and Clethrionomys rufocanus) distributed in two areas with great distance (> 600 km apart), to assess if species identity dominates over geographic locations in shaping gut microbial profiles using 16S rRNA gene sequencing. We found that gut microbiota composition varied significantly across host species and was closely correlated with host genetics. We identified strong species identity effects on gut microbial composition, with a comparatively weaker signal of geographic provenance on the intestinal microbiota. Specifically, microbiota of one species was on average more similar to that of conspecifics living in separate sites than to members of a closely related species living in the same location. Our study suggests that both host genetics and geographical variations influence gut microbial diversity of four rodent species, which merits further investigation to reveal the patterns of phylogenetic correlation of gut microbial community assembly in mammals across multiple habitats.

Variation in Out-of-Hospital Cardiac Arrest Survival Across Emergency Medical Service Agencies

BACKGROUND

Although studies have reported variation in out-of-hospital cardiac arrest (OHCA) survival by geographic location, little is known about variation in OHCA survival at the level of emergency medical service (EMS) agencies-which may have modifiable practices, unlike counties and regions. We quantified the variation in OHCA survival across EMS agencies and explored whether variation in 2 specific EMS resuscitation practices were associated with survival to hospital admission.

METHODS

Within the Cardiac Arrest Registry to Enhance Survival, a prospective registry representing ≈51% of the US population, we identified 258 342 OHCAs from 764 EMS agencies with >10 OHCA cases annually during 2015 to 2019. Using hierarchical logistic regression, risk-standardized rates of survival to hospital admission were computed for each EMS agency. We quantified inter-agency variation in survival with median odds ratios and assessed the association of 2 resuscitation practices (EMS response time and the proportion of OHCAs with termination of resuscitation without meeting futility criteria) with EMS agency survival rates to hospital admission.

RESULTS

Across 764 EMS agencies comprising 258 342 OHCAs, the median risk-standardized rate of survival to hospital admission was 27.3% (interquartile range, 24.5%-30.1%; range: 16.0%-45.6%). The adjusted median odds ratio was 1.35 (95% CI, 1.32-1.39), denoting that the odds of survival of 2 patients with identical covariates varied by 35% at 2 randomly selected EMS agencies. EMS agencies in the lowest quartile of risk-standardized survival had longer EMS response times when compared with the highest quartile (12.0±3.4 versus 9.0±2.6 minutes; P<0.001), and a higher proportion of OHCAs with termination of resuscitation without meeting futility criteria (27.9±16.1% versus 18.9±11.4%; P<0.001).

CONCLUSIONS

Survival after OHCA varies widely across EMS agencies. EMS response times and termination of resuscitation practices were associated with agency-level rates of survival to hospital admission, suggesting potentially modifiable practices which can improve OHCA survival.

Country-level determinants of COVID-19 case rates and death rates: An ecological study

The Coronavirus Disease 2019 (COVID‐19) pandemic has had a variable worldwide impact, likely related to country‐level characteristics. In this ecological study, we explored the association of COVID‐19 case rates (per 100,000 people) and death rates (per 100,000 people) with country‐level population health characteristics, economic and human development indicators, and habitat‐related variables. To calculate country‐level COVID‐19 case and death rates, the number of cases and deaths were extracted from the Johns Hopkins Coronavirus Resource Center through September 30, 2021. Country‐level population health characteristics, economic, human development, and habitat‐related indicators were extracted from several publicly available online sources of international organizations. Results were tabulated according to world zones and country economies. Unadjusted and adjusted multiple imputation linear regression analyses were performed to examine the association between country‐level variables (per 1‐standard deviation [SD] increase) and COVID‐19 case and death rates. To satisfy the linear regression model assumptions of normality of residuals, we used the square root transformation of both outcomes. A total of 187 countries and territories were analyzed, with a median (25th, 75th percentiles) aggregate COVID‐19 case rate of 3,605 (463, 8,228) per 100,000, a COVID‐19 death rate of 45.9 (8.9, 137.1) per 100,000, and a case‐fatality rate of 1.6% (1.2%, 2.6%). On multivariable analyses, each country‐level 1‐SD higher percentage of adults with obesity (β coefficient 13.7; 95% confidence interval [CI] 13.7; 8.9, 18.4), percentage of smokers (5.8; 95% CI 1.2, 10.5), percentage of adults with high blood pressure (4.9; 95% CI 0.3, 9.6), and gross national income (GNI) per capita (9.5; 95% CI 4.6, 14.5) was independently associated with higher square root of COVID‐19 case rate, while average household size (−1.7; 95% CI −12.3, −3.2) was independently associated with lower square root of COVID‐19 case rate. Similarly, each 1‐SD higher percentage of adults with obesity (1.76; 95% CI 0.99, 2.52), percentage of adults with high blood pressure (1.11; 95% CI 0.48, 1.74), percentage of adults with physical inactivity (1.01; 95% CI 0.10, 1.191), and travel & tourism competitiveness index (1.05; 95% CI 0.06, 2.04) was independently associated with higher square root of COVID‐19 death rate, whereas GNI per capita (−0.92; 95% CI −1.81, −0.03), and average household size (−1.07; 95% CI −1.87, −0.27) was independently associated with lower square root of COVID‐19 death rate. This ecological study informs the need to develop country‐specific public health interventions to better target populations at high risk for COVID‐19, and test interventions to prevent transmission of SARS‐CoV‐2, taking into consideration cross‐country differences in population health characteristics, and economic, human development and habitat‐related factors.

Geographic and Regional Variability in Racial and Ethnic Disparities in Stroke Thrombolysis in the United States

BACKGROUND AND PURPOSE

Intravenous thrombolysis (IVT) after ischemic stroke is underutilized in racially/ethnically minoritized groups. We aimed to determine the regional and geographic variability in racial/ethnic IVT disparities in the United States.

METHODS

Acute ischemic stroke admissions between 2012 and 2018 were identified in the National Inpatient Sample. Multivariable logistic regression was used to test the association between IVT and race/ethnicity, stratified by geographic region and controlling for demographic, clinical, and hospital characteristics.

RESULTS

Of the 545 509 included cases, 47 031 (8.6%) received IVT. Racially/ethnically minoritized groups had significantly lower adjusted odds of IVT compared with White people in the South Atlantic region (odds ratio [OR], 0.86 [95% CI, 0.82-0.91]), the East North Central region (OR, 0.91 [95% CI, 0.85-0.97]) and the Pacific region (OR, 0.90 [95% CI, 0.85-0.96]). In the South Atlantic region, IVT use in racial/ethnic minority groups was below the national average of all racial/ethnic minority patients (P=0.002). Compared with White patients, Black patients had lower odds of IVT in the Middle Atlantic region (OR, 0.84 [95% CI, 0.78-0.91]), the South Atlantic region (OR, 0.78 [95% CI, 0.74-0.82]), and the East North Central region (OR, 0.86 [95% CI, 0.79-0.93]). In the South Atlantic region, this difference was below the national average for Black people (P<0.001). Hispanic patients had significantly lower use of IVT only in the Pacific region (OR, 0.92 [95% CI, 0.85-0.99]), while Asian/Pacific Islander patients had lower odds of IVT in the Mountain (OR, 0.76 [95% CI, 0.59-0.98]) and Pacific region (OR, 0.89 [95% CI, 0.82-0.97]).

CONCLUSIONS

Racial/ethnic disparities in IVT use in the United States vary by region. Geographic hotspots of lower IVT use in racially/ethnically minoritized groups are the South Atlantic region, driven predominantly by lower use of IVT in Black patients, and the East North Central and Pacific regions.

Geographic Variation in Knowledge of Palliative Care Among US Adults: Findings From 2018 Health Information National Trends Survey

BACKGROUND

Public knowledge and awareness of palliative care (PC) is important to its effective use. However, it remains unclear whether the geographic variation in knowledge of PC exits in the United States. This study examined the national geographic variation in knowledge of PC.

METHODS

The study sample was obtained from the 2018 National Cancer Institute's Health Information National Trends Survey. Basic knowledge of PC, goal concordant treatment, misconceptions, and primary information source of PC were compared across 4 census regions. Multivariable logistic regression was used to examine factors associated with awareness of PC among 9 census divisions.

RESULTS

A total of 3194 respondents (weighted sample size: 229 591 005) were included in this study. Overall, 29% of all respondents reported having knowledge of PC; 32.9% of those residing in Northeast had some knowledge of PC, followed by 30.8% in the South, 26.2% in Midwest, and 25.6% in West. By census divisions, respondents residing in 3 divisions were more likely to have PC knowledge (New England, odds ratio: 3.06, 95% CI: 1.48-6.32, P = .003; South Atlantic, odds ratio: 1.96, 95% CI: 1.15-3.35, P = .014; Pacific, odds ratio: 1.86, 95% CI: 1.12-3.09, P = .018) compared to those in the Mountain division.

CONCLUSIONS

The variation of PC knowledge on census division and state level in 2018 was consistent with the real-world geographic disparities in the availability of PC programs. These findings represent an opportunity for minimizing the gap of geographic disparity by initiating strategic programs and promoting PC programs nationwide.

Accuracy of Distance Recordings in Eight Positioning-Enabled Sport Watches: Instrument Validation Study

Background

Elite athletes and recreational runners rely on the accuracy of global navigation satellite system (GNSS)–enabled sport watches to monitor and regulate training activities. However, there is a lack of scientific evidence regarding the accuracy of such sport watches.

Objective

The aim was to investigate the accuracy of the recorded distances obtained by eight commercially available sport watches by Apple, Coros, Garmin, Polar, and Suunto when assessed in different areas and at different speeds. Furthermore, potential parameters that affect the measurement quality were evaluated.

Methods

Altogether, 3 × 12 measurements in urban, forest, and track and field areas were obtained while walking, running, and cycling under various outdoor conditions.

Results

The selected reference distances ranged from 404.0 m to 4296.9 m. For all the measurement areas combined, the recorded systematic errors (±limits of agreements) ranged between 3.7 (±195.6) m and –101.0 (±231.3) m, and the mean absolute percentage errors ranged from 3.2% to 6.1%. Only the GNSS receivers from Polar showed overall errors <5%. Generally, the recorded distances were significantly underestimated (all P values <.04) and less accurate in the urban and forest areas, whereas they were overestimated but with good accuracy in 75% (6/8) of the sport watches in the track and field area. Furthermore, the data assessed during running showed significantly higher error rates in most devices compared with the walking and cycling activities.

Conclusions

The recorded distances might be underestimated by up to 9%. However, the use of all investigated sport watches can be recommended, especially for distance recordings in open areas.

Geographic distribution of dental specialists permitted to advertise dental practices in Japan

OBJECTIVE

The purpose of this study was to determine the geographic distribution of dental specialists permitted to advertise dental practices in Japan.

METHOD

We identified the populations of 349 secondary medical zones nationwide from the 2015 population census, as well as the number of dentists in five specialties, namely oral surgeons, pedodontists, periodontists, dental anesthesiologists, and dental radiologists, who had been permitted to advertise dental practices, from a 2016 survey of physicians, dentists, and pharmacists. We determined the placement rate, Lorenz curve, and Gini coefficient for dentists in each specialty in order to describe their geographic distributions.

RESULTS

The placement rates of at least one of these types of dentist in each secondary medical zone were 73.9% for oral surgeons, 66.2% for pedodontists, 60.5% for periodontists, 31.8% for dental anesthesiologists, and 18.3% for dental radiologists. The Gini coefficients were 0.397, 0.400, 0.491, 0.650, and 0.761, respectively.

CONCLUSION

The dentists in each specialty were few in number and were unequally distributed among the zones, but less so for oral surgeons and pedodontists. Dental anesthesiologists and radiologists were located primarily at university hospitals in urban areas and, therefore, were more unequally distributed.

Emulation of Community Water Fluoridation Coverage Across US Counties

INTRODUCTION

Expansion of community water fluoridation has stalled in the United States, leaving 115 million Americans without fluoridated drinking water.

OBJECTIVE

This study used spatial regression methods to assess contributions of supply-side factors (neighboring counties' fluoridation coverage) and demand-side factors (health literacy, education, and population density of the local county) in predicting the extent of fluoridation in US counties.

METHODS

For this cross-sectional ecological analysis, data from the 2014 Water Fluoridation Reporting System for all 3,135 US counties were merged with sociodemographic data from the 2014 American Community Survey and county-level estimates of health literacy based on the National Association of Adult Literacy Survey. We employed multilevel geographically weighted autoregressive models to predict fluoridation coverage of each county as a function of fluoridation coverage of neighboring counties and local-county covariates: either health literacy or sociodemographic characteristics. Akaike's Information Criterion was used to distinguish the better model in terms of explanatory power and parsimony.

RESULTS

In the best-fit model, an increase from the first to third quartile of neighboring counties' fluoridation coverage was associated with an increase of 27.76 percentage points (95% confidence limits [CI] = 27.71, 27.81) in a local county's fluoridation coverage, while an increase from the first to third quartile of local county's health literacy was associated with an increase of 2.8 percentage points (95% CL = 2.68, 2.89). The results are consistent with a process of emulation, in which counties implement fluoridation based upon their population's health literacy and the extent of fluoridation practiced in neighboring counties.

CONCLUSION

These results suggest that demand for community water fluoridation will increase as health literacy increases within a county. Furthermore, when considering expansion of fluoridation, non-fluoridated communities can benefit from precedents from nearby communities that are fluoridated.

KNOWLEDGE TRANSFER STATEMENT

Expanded coverage of community water fluoridation has stalled in the United States. The economic theory of diffusion describes how, over time and space, policy enacted in one community can influence public opinion in a neighboring community. This study applies geospatial analysis of county-level data and the theory of policy diffusion to demonstrate that fluoridated counties can promote the implementation of community water fluoridation in their neighboring, non-fluoridated communities.

Completeness and Reliability of Location Data Collected on the Web: Assessing the Quality of Self-Reported Locations in an Internet Sample of Men Who Have Sex With Men

BACKGROUND

Place is critical to our understanding of human immunodeficiency virus (HIV) infections among men who have sex with men (MSM) in the United States. However, within the scientific literature, place is almost always represented by residential location, suggesting a fundamental assumption of equivalency between neighborhood of residence, place of risk, and place of prevention. However, the locations of behaviors among MSM show significant spatial variation, and theory has posited the importance of nonresidential contextual exposures. This focus on residential locations has been at least partially necessitated by the difficulties in collecting detailed geolocated data required to explore nonresidential locations.

OBJECTIVE

Using a Web-based map tool to collect locations, which may be relevant to the daily lives and health behaviors of MSM, this study examines the completeness and reliability of the collected data.

METHODS

MSM were recruited on the Web and completed a Web-based survey. Within this survey, men used a map tool embedded within a question to indicate their homes and multiple nonresidential locations, including those representing work, sex, socialization, physician, and others. We assessed data quality by examining data completeness and reliability. We used logistic regression to identify demographic, contextual, and location-specific predictors of answering all eligible map questions and answering specific map questions. We assessed data reliability by comparing selected locations with other participant-reported data.

RESULTS

Of 247 men completing the survey, 167 (67.6%) answered the entire set of eligible map questions. Most participants (>80%) answered specific map questions, with sex locations being the least reported (80.6%). Participants with no college education were less likely than those with a college education to answer all map questions (prevalence ratio, 0.4; 95% CI, 0.2-0.8). Participants who reported sex at their partner's home were less likely to indicate the location of that sex (prevalence ratio, 0.8; 95% CI, 0.7-1.0). Overall, 83% of participants placed their home's location within the boundaries of their reported residential ZIP code. Of locations having a specific text description, the median distance between the participant-selected location and the location determined using the specific text description was 0.29 miles (25th and 75th percentiles, 0.06-0.88).

CONCLUSIONS

Using this Web-based map tool, this Web-based sample of MSM was generally willing and able to provide accurate data regarding both home and nonresidential locations. This tool provides a mechanism to collect data that can be used in more nuanced studies of place and sexual risk and preventive behaviors of MSM.

Presence of Aedes (Stegomyia) aegypti (Linnaeus, 1762) and its natural infection with dengue virus at unrecorded heights in Colombia

INTRODUCTION

Aedes aegypti is the main vector of urban yellow fever, dengue, chikungunya and Zika viruses. The biogeographical distribution of this species has expanded due to global warming, and socioeconomic and cultural factors. The changes in the altitudinal distribution patterns of this vector and its natural infection are priority fields of research to develop entomological, virological and public health surveillance strategies. 

OBJECTIVE

To evaluate the presence of A. aegypti and its natural infection with dengue virus in altitudes above 1.800 meters above sea level in two peripheral municipalities of the Valle de Aburrá, Antioquia, Colombia. 

MATERIALS AND METHODS

Twenty-one ovitraps were set in the municipalities of Bello and San Pedro de los Milagros, at altitudes ranging from 1.882 to 2.659 masl. Emerged adults caught in the ovitraps were tested by RT-PCR for dengue virus detection. 

RESULTS

We collected 367 A. aegypti adults, seven of which were found as high as 2.302 masl in Tierradentro, Bello. We detected serotype 2 dengue infection in 12 A. aegypti specimens collected in the neighbourhood of París, in Bello, at 1.984 masl. 

CONCLUSION

We recorded A. aegypti at 2.302 masl, so far the highest altitudinal record in Colombia for this vector. Furthermore, mosquitoes collected at 1.984 masl were positive for dengue virus. These findings are significant as they identify regions in Colombia at risk of potential autochthonous transmission of dengue and other arboviruses by A. aegypti.