Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-10 (of 10 Records) |
Query Trace: McGarry S [original query] |
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Disparities in COVID-19 vaccine uptake, attitudes, and experiences between food system and non–food system essential workers
Smarsh BL , Yankey D , Hung MC , Blanck HM , Kriss JL , Flynn MA , Lu PJ , McGarry S , Eastlake AC , Lainz AR , Singleton JA , Lincoln JM . J Agric Food Syst Community Dev 2024 13 (2) The COVID-19 pandemic has disproportionately affected the health of food system (FS) essential workers compared with other essential and non-essential workers. Even greater disparity exists for workers in certain FS work settings and for certain FS worker subpopulations. We analyzed essential worker respondents (n = 151,789) in May–Novem-ber 2021 data from the National Immunization Survey Adult COVID Module (NIS-ACM) to assess and characterize COVID-19 vaccination uptake (≥1 dose) and intent (reachable, reluctant), attitudes about COVID-19 and the vaccine, and experiences and difficulties getting the vaccine. We compared rates, overall and by certain characteristics, between workers of the same group, and between FS (n = 17,414) and non–food system (NFS) worker groups (n = 134,375), to determine if differences exist. FS worker groups were classified as “agriculture, forestry, fishing, or hunting” (AFFH; n = 2,730); “food manufacturing facility” (FMF; n = 3,495); and “food and beverage store” (FBS; n = 11,189). Compared with NFS workers, significantly lower percentages of FS workers reported >1 dose of COVID-19 vaccine or vaccine requirements at work or school, but overall vaccine experiences and difficulties among vaccinated FS workers were statistically similar to NFS workers. When we examined intent regarding COVID-19 vaccination among unvaccinated FS workers compared with NFS counterparts, we found a higher percentage of FMF and FBS workers were reachable whereas a higher percentage of AFFH workers were reluctant about vaccination, with differences by sociodemographic characteristics. Overall, results showed differences in uptake, intent, and attitudes between worker groups and by some sociodemographic characteristics. The findings reflect the diversity of FS workers and underscore the importance of collecting occupational data to assess health inequalities and of tailoring efforts to worker groups to improve confidence and uptake of vaccinations for infectious diseases such as COVID-19. The findings can inform future research, adult infectious disease interventions, and emergency management planning. © 2024 by the Authors. |
Mashtree: a rapid comparison of whole genome sequence files
Katz LS , Griswold T , Morrison SS , Caravas JA , Zhang S , den Bakker HC , Deng X , Carleton HA . J Open Source Softw 2019 4 (44) In the past decade, the number of publicly available bacterial genomes has increased dramatically. These genomes have been generated for impactful initiatives, especially in the field of genomic epidemiology (Brown, Dessai, McGarry, & Gerner-Smidt, 2019; Timme et al., 2017). Genomes are sequenced, shared publicly, and subsequently analyzed for phylogenetic relatedness. If two genomes of epidemiological interest are found to be related, further investigation might be prompted. However, comparing the multitudes of genomes for phylogenetic relatedness is computationally expensive and, with large numbers, laborious. Consequently, there are many strategies to reduce the complexity of the data for downstream analysis, especially using nucleotide stretches of length k (kmers). |
The Use of Whole-Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.
Stevens EL , Carleton HA , Beal J , Tillman GE , Lindsey RL , Lauer AC , Pightling A , Jarvis KG , Ottesen A , Ramachandran P , Hintz L , Katz LS , Folster JP , Whichard JM , Trees E , Timme RE , McDermott P , Wolpert B , Bazaco M , Zhao S , Lindley S , Bruce BB , Griffin PM , Brown E , Allard M , Tallent S , Irvin K , Hoffmann M , Wise M , Tauxe R , Gerner-Smidt P , Simmons M , Kissler B , Defibaugh-Chavez S , Klimke W , Agarwala R , Lindsay J , Cook K , Austerman SR , Goldman D , McGarry S , Hale KR , Dessai U , Musser SM , Braden C . J Food Prot 2022 85 (5) 755-772 This multi-agency report developed under the Interagency Collaboration for Genomics for Food and Feed Safety (Gen-FS) provides an overview of the use of and transition to Whole-Genome Sequencing (WGS) technology to detect and characterize pathogens transmitted commonly by food and identify their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among federal agencies, including the National Institutes of Health (NIH); the Department of Health and Human Services' Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA); and the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS), Agricultural Research Service (ARS), and Animal and Plant Health Inspection Service (APHIS). We describe single nucleotide polymorphism (SNP), core-genome (cg) and whole-genome multi-locus sequence typing (wgMLST) data analysis methods as used in CDC's PulseNet and FDA's GenomeTrakr networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Gen-FS agency partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles), source attribution efforts, and increasing transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information (NCBI). Finally, we highlight the impact of current trends in the use of culture-independent diagnostics tests (CIDT) for human diagnostic testing on analytical approaches related to food safety. Lastly, we highlight what is next for WGS in food safety. |
Inpatient admissions and costs for adolescents and young adults with congenital heart defects in New York, 2009-2013
Hsu WH , Sommerhalter KM , McGarry CE , Farr SL , Downing KF , Lui GK , Zaidi AN , Hsu DT , Van Zutphen AR . Birth Defects Res 2020 113 (2) 173-188 OBJECTIVES: Most individuals born with congenital heart defects (CHDs) survive to adulthood, but healthcare utilization patterns for adolescents and adults with CHDs have not been well described. We sought to characterize the healthcare utilization patterns and associated costs for adolescents and young adults with CHDs. METHODS: We examined 2009-2013 New York State inpatient admissions of individuals ages 11-30 years with ≥1 CHD diagnosis codes recorded during any admission. We conducted multivariate linear regression using generalized estimating equations to examine associations between inpatient costs and sociodemographic and clinical variables. RESULTS: We identified 5,100 unique individuals with 9,593 corresponding hospitalizations over the study period. Median inpatient cost and length of stay (LOS) were $10,720 and 3.0 days per admission, respectively; 55.1% were emergency admissions. Admission volume increased 48.7% from 2009 (1,538 admissions) to 2013 (2,287 admissions), while total inpatient costs increased 91.8% from 2009 ($27.2 million) to 2013 ($52.2 million). Inpatient admissions and costs rose more sharply over the study period for those with nonsevere CHDs compared to severe CHDs. Characteristics associated with higher costs were longer LOS, severe CHD, cardiac/vascular hospitalization classification, surgical procedures, greater severity of illness, and admission in New York City. CONCLUSION: This study provides an informative baseline of health care utilization patterns and associated costs among adolescents and young adults with CHDs in New York State. Structured transition programs may aid in keeping this population in appropriate cardiac care as they move to adulthood. |
Characteristics of adults with congenital heart defects in the United States
Gurvitz M , Dunn JE , Bhatt A , Book WM , Glidewell J , Hogue C , Lin AE , Lui G , McGarry C , Raskind-Hood C , Van Zutphen A , Zaidi A , Jenkins K , Riehle-Colarusso T . J Am Coll Cardiol 2020 76 (2) 175-182 BACKGROUND: In the United States, >1 million adults are living with congenital heart defects (CHDs), but gaps exist in understanding the health care needs of this growing population. OBJECTIVES: This study assessed the demographics, comorbidities, and health care use of adults ages 20 to 64 years with CHDs. METHODS: Adults with International Classification of Disease-9th Revision-Clinical Modification CHD-coded health care encounters between January 1, 2008 (January 1, 2009 for Massachusetts) and December 31, 2010 were identified from multiple data sources at 3 U.S. sites: Emory University (EU) in Atlanta, Georgia (5 counties), Massachusetts Department of Public Health (statewide), and New York State Department of Health (11 counties). Demographics, insurance type, comorbidities, and encounter data were collected. CHDs were categorized as severe or not severe, excluding cases with isolated atrial septal defect and/or patent foramen ovale. RESULTS: CHD severity and comorbidities varied across sites, with up to 20% of adults having severe CHD and >50% having ≥1 additional cardiovascular comorbidity. Most adults had ≥1 outpatient encounters (80% EU, 90% Massachusetts, and 53% New York). Insurance type differed across sites, with Massachusetts having a large proportion of Medicaid (75%) and EU and New York having large proportions of private insurance (44% EU, 67% New York). Estimated proportions of adults with CHD-coded health care encounters varied greatly by location, with 1.2 (EU), 10 (Massachusetts), and 0.6 (New York) per 1,000 adults based on 2010 census data. CONCLUSIONS: This was the first surveillance effort of adults with CHD-coded inpatient and outpatient health care encounters in 3 U.S. geographic locations using both administrative and clinical data sources. This information will provide a clearer understanding of health care use in this growing population. |
Assessing pregnancy, gestational complications, and co-morbidities in women with congenital heart defects (Data from ICD-9-CM Codes in 3 US Surveillance Sites)
Raskind-Hood C , Saraf A , Riehle-Colarusso T , Glidewell J , Gurvitz M , Dunn JE , Lui GK , Van Zutphen A , McGarry C , Hogue CJ , Hoffman T , Rodriguez Iii FH , Book WM . Am J Cardiol 2019 125 (5) 812-819 Improved treatment of congenital heart defects (CHDs) has resulted in women with CHDs living to childbearing age. However, no US population-based systems exist to estimate pregnancy frequency or complications among women with CHDs. Cases were identified in multiple data sources from 3 surveillance sites: Emory University (EU) whose catchment area included 5 metropolitan Atlanta counties; Massachusetts Department of Public Health (MA) whose catchment area was statewide; and New York State Department of Health (NY) whose catchment area included 11 counties. Cases were categorized into one of 5 mutually exclusive CHD severity groups collapsed to severe versus not severe; specific ICD-9-CM codes were used to capture pregnancy, gestational complications, and nongestational co-morbidities in women, age 11 to 50 years, with a CHD-related ICD-9-CM code. Pregnancy, CHD severity, demographics, gestational complications, co-morbidities, and insurance status were evaluated. ICD-9-CM codes identified 26,655 women with CHDs, of whom 5,672 (21.3%, range: 12.8% in NY to 22.5% in MA) had codes indicating a pregnancy. Over 3 years, age-adjusted proportion pregnancy rates among women with severe CHDs ranged from 10.0% to 24.6%, and 14.2% to 21.7% for women with nonsevere CHDs. Pregnant women with CHDs of any severity, compared with nonpregnant women with CHDs, reported more noncardiovascular co-morbidities. Insurance type varied by site and pregnancy status. These US population-based, multisite estimates of pregnancy among women with CHD indicate a substantial number of women with CHDs may be experiencing pregnancy and complications. In conclusion, given the growing adult population with CHDs, reproductive health of women with CHD is an important public health issue. |
Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States.
Brown E , Dessai U , McGarry S , Gerner-Smidt P . Foodborne Pathog Dis 2019 16 (7) 441-450 Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health agencies in the United States to facilitate the detection, investigation, and control of foodborne bacterial outbreaks, and food regulatory and other activities in support of food safety. WGS has added a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections. In this review, we report the history of WGS technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety. The basic principle of the method, the analysis, and interpretation of the data are explained as is its major strengths and limitations. We also describe the benefits and possibilities of the WGS technology to the food industry throughout the farm-to-fork continuum and the prospects of metagenomic sequencing applied directly to the sample specimen with or without pre-enrichment culture. |
Surveillance of congenital heart defects among adolescents at three U.S. sites
Lui GK , McGarry C , Bhatt A , Book W , Riehle-Colarusso TJ , Dunn JE , Glidewell J , Gurvitz M , Hoffman T , Hogue CJ , Hsu D , Obenhaus S , Raskind-Hood C , Rodriguez FH 3rd , Zaidi A , Van Zutphen AR . Am J Cardiol 2019 124 (1) 137-143 The prevalence, co-morbidities, and healthcare utilization in adolescents with congenital heart defects (CHDs) is not well understood. Adolescents (11 to 19 years old) with a healthcare encounter between January 1, 2008 (January 1, 2009 for MA) and December 31, 2010 with a CHD diagnosis code were identified from multiple administrative data sources compiled at 3 US sites: Emory University, Atlanta, Georgia (EU); Massachusetts Department of Public Health (MA); and New York State Department of Health (NY). The estimated prevalence for any CHD was 4.77 (EU), 17.29 (MA), and 4.22 (NY) and for severe CHDs was 1.34 (EU), 3.04 (MA), and 0.88 (NY) per 1,000 adolescents. Private or commercial insurance was the most common insurance type for EU and NY, and Medicaid for MA. Inpatient encounters were more frequent in severe CHDs. Cardiac co-morbidities included rhythm and conduction disorders at 20% (EU), 46% (MA), and 9% (NY) as well as heart failure at 3% (EU), 15% (MA), and 2% (NY). Leading noncardiac co-morbidities were respiratory/pulmonary (22% EU, 34% MA, 16% NY), infectious disease (17% EU, 22% MA, 20% NY), non-CHD birth defects (12% EU, 23% MA, 14% NY), gastrointestinal (10% EU, 28% MA, 13% NY), musculoskeletal (10% EU, 32% MA, 11% NY), and mental health (9% EU, 30% MA, 11% NY). In conclusion, this study used a novel approach of uniform CHD definition and variable selection across administrative data sources in 3 sites for the first population-based CHD surveillance of adolescents in the United States. High resource utilization and co-morbidities illustrate ongoing significant burden of disease in this vulnerable population. |
Population-based surveillance of congenital heart defects among adolescents and adults: surveillance methodology
Glidewell J , Book W , Raskind-Hood C , Hogue C , Dunn JE , Gurvitz M , Ozonoff A , McGarry C , Van Zutphen A , Lui G , Downing K , Riehle-Colarusso T . Birth Defects Res 2018 110 (19) 1395-1403 BACKGROUND: Improved treatment of congenital heart defects (CHDs) has increased survival of persons with CHDs; however, no U.S. population-based systems exist to assess prevalence, healthcare utilization, or longer-term outcomes among adolescents and adults with CHDs. METHODS: Novel approaches identified individuals aged 11-64 years who received healthcare with ICD-9-CM codes for CHDs at three sites: Emory University in Atlanta, Georgia (EU), Massachusetts Department of Public Health (MA), New York State Department of Health (NY) between January 1, 2008 (2009 for MA) and December 31, 2010. Case-finding sources included outpatient clinics; Medicaid and other claims data; and hospital inpatient, outpatient, and emergency visit data. Supplemental information came from state vital records (EU, MA), and birth defects registries (EU, NY). Demographics and diagnostic and procedural codes were linked, de-duplicated, and shared in a de-identified dataset. Cases were categorized into one of five mutually exclusive CHD severity groups; non-cardiac comorbidity codes were grouped into broad categories. RESULTS: 73,112 individuals with CHD codes in healthcare encounters were identified. Primary data source type varied: clinics (EU, NY for adolescents), claims (MA), hospital (NY for adults). There was a high rate of missing data for some variables and data varied in format and quality. Some diagnostic codes had poor specificity for CHD ascertainment. CONCLUSIONS: To our knowledge, this is the first population-based, multi-site CHD surveillance among adolescents and adults in the U.S. Identification of people living with CHDs through healthcare encounters using multiple data sources was feasible, though data quality varied and linkage/de-duplication was labor-intensive. |
Proximity to pediatric cardiac surgical care among adolescents with congenital heart defects in 11 New York counties
Sommerhalter KM , Insaf TZ , Akkaya-Hocagil T , McGarry CE , Farr SL , Downing KF , Lui GK , Zaidi AN , Van Zutphen AR . Birth Defects Res 2017 109 (18) 1494-1503 BACKGROUND: Many individuals with congenital heart defects (CHDs) discontinue cardiac care in adolescence, putting them at risk of adverse health outcomes. Because geographic barriers may contribute to cessation of care, we sought to characterize geographic access to comprehensive cardiac care among adolescents with CHDs. METHODS: Using a population-based, 11-county surveillance system of CHDs in New York, we characterized proximity to the nearest pediatric cardiac surgical care center among adolescents aged 11 to 19 years with CHDs. Residential addresses were extracted from surveillance records documenting 2008 to 2010 healthcare encounters. Addresses were geocoded using ArcGIS and the New York State Street and Address Maintenance Program, a statewide address point database. One-way drive and public transit time from residence to nearest center were calculated using R packages gmapsdistance and rgeos with the Google Maps Distance Matrix application programming interface. A marginal model was constructed to identify predictors associated with one-way travel time. RESULTS: We identified 2522 adolescents with 3058 corresponding residential addresses and 12 pediatric cardiac surgical care centers. The median drive time from residence to nearest center was 18.3 min, and drive time was 30 min or less for 2475 (80.9%) addresses. Predicted drive time was longest for rural western addresses in high poverty census tracts (68.7 min). Public transit was available for most residences in urban areas but for few in rural areas. CONCLUSION: We identified areas with geographic barriers to surgical care. Future research is needed to determine how these barriers influence continuity of care among adolescents with CHDs. Birth Defects Research 109:1494-1503, 2017.(c) 2017 Wiley Periodicals, Inc. |
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