Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-30 (of 85 Records) |
Query Trace: Blake I[original query] |
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Current or recent malaria infection is associated with elevated inflammation-adjusted ferritin concentrations in pre-school children: a secondary analysis of the BRINDA database
Sandalinas F , MacDougall A , Filteau S , Hopkins H , Blake T , Luo H , Suchdev PS , Ruth L , Young MF , Joy EJM . Br J Nutr 2024 1-11 Inflammation and infections such as malaria affect micronutrient biomarker concentrations and hence estimates of nutritional status. It is unknown whether correction for C-reactive protein (CRP) and α1-acid glycoprotein (AGP) fully captures the modification in ferritin concentrations during a malaria infection, or whether environmental and sociodemographic factors modify this association. Cross-sectional data from eight surveys in children aged 6-59 months (Cameroon, Cote d'Ivoire, Kenya, Liberia, Malawi, Nigeria and Zambia; n 6653) from the Biomarkers Reflecting Inflammation and Nutritional Determinants of Anaemia (BRINDA) project were pooled. Ferritin was adjusted using the BRINDA adjustment method, with values < 12 μg/l indicating iron deficiency. The association between current or recent malaria infection, detected by microscopy or rapid test kit, and inflammation-adjusted ferritin was estimated using pooled multivariable linear regression. Age, sex, malaria endemicity profile (defined by the Plasmodium falciparum infection prevalence) and malaria diagnostic methods were examined as effect modifiers. Unweighted pooled malaria prevalence was 26·0 % (95 % CI 25·0, 27·1) and unweighted pooled iron deficiency was 41·9 % (95 % CI 40·7, 43·1). Current or recent malaria infection was associated with a 44 % (95 % CI 39·0, 52·0; P < 0·001) increase in inflammation-adjusted ferritin after adjusting for age and study identifier. In children, ferritin increased less with malaria infection as age and malaria endemicity increased. Adjustment for malaria increased the prevalence of iron deficiency, but the effect was small. Additional information would help elucidate the underlying mechanisms of the role of endemicity and age in the association between malaria and ferritin. |
Immunogenicity of quadrivalent human papillomavirus vaccine among Alaska Native children aged 9-14 years at 5 years after vaccination
Davis BM , Blake I , Panicker G , Meites E , Thompson G , Geis J , Bruden D , Fischer M , Singleton R , Unger ER , Markowitz LE , Bruce MG . Vaccine 2024 BACKGROUND: Persistent human papillomavirus (HPV) infection can cause anogenital and oropharyngeal cancers. Many HPV infections and HPV-associated cancers are vaccine-preventable. Studies suggest long-term persistence of vaccine-induced antibodies. However, data are limited among Alaska Native people. METHODS: During 2011-2014, we enrolled Alaska Native children aged 9-14 years who received a 3-dose series of quadrivalent HPV vaccine (4vHPV). We collected sera at 1 month and 1, 2, 3, and 5 years post-vaccination to evaluate trends in type-specific immunoglobulin G antibody concentrations for the 4vHPV types (HPV 6/11/16/18). RESULTS: All participants (N = 469) had detectable antibodies against all 4vHPV types at all timepoints post-vaccination. For all 4vHPV types, antibody levels peaked by 1 month post-vaccination and gradually declined in subsequent years. At 5 years post-vaccination, antibody levels were higher among children who received 4vHPV at a younger age. CONCLUSIONS: Alaska Native children maintained antibodies against all 4vHPV types at 5 years post-vaccination. |
COVID-19 infection and incident diabetes in American Indian and Alaska Native people: a retrospective cohort study
Keck JW , Lacy ME , Bressler S , Blake I , Chukwuma U , Bruce MG . Lancet Reg Health Am 2024 33 100727 BACKGROUND: Evidence suggests an increased risk of new-onset diabetes following COVID-19 infection. American Indian/Alaska Native (AI/AN) people were disparately impacted by the COVID-19 pandemic and historically have had higher diabetes incidence than other racial/ethnic groups in the US. We measured the association between COVID-19 infection and incident diabetes in AI/AN people. METHODS: We conducted a retrospective cohort study using de-identified patient data from the Indian Health Service's (IHS) National Patient Information Reporting System. We estimated age-adjusted diabetes incidence rates, incidence rate ratios, and adjusted hazard ratios among three cohorts spanning pre-pandemic (1/1/2018-2/28/2020) and pandemic (3/1/2020-12/31/2021) timeframes: 1) pre-pandemic cohort (1,503,085 individuals); 2) no-COVID-19 pandemic cohort (1,344,339 individuals); and 3) COVID-19 cohort (176,483 individuals). FINDINGS: The COVID-19 cohort had an increased hazard of diabetes compared to the no-COVID-19 group (adjusted hazard ratio (aHR) = 1.56; 95% CI: 1.50-1.62) and the pre-pandemic group (aHR = 1.27; 95% CI: 1.22-1.32). The association between COVID-19 infection and new-onset diabetes was stronger in those with severe COVID-19 illness. A sensitivity analysis comparing the COVID-19 cohort to members of other cohorts that had acute upper respiratory infections showed an attenuated but higher risk of new-onset diabetes in those with COVID-19. INTERPRETATION: AI/AN people diagnosed with COVID-19 had an elevated risk of a new diabetes diagnosis when compared to the no-COVID-19 group and the pre-pandemic group. The increased diabetes risk in the COVID-19 group remained in a sensitivity analysis that limited the comparator groups to individuals with an AURI diagnosis. FUNDING: US National Institute of Diabetes and Digestive and Kidney Diseases. |
Recapitulation of human pathophysiology and identification of forensic biomarkers in a translational model of chlorine inhalation injury
Achanta S , Gentile MA , Albert CJ , Schulte KA , Pantazides BG , Crow BS , Quinones-Gonzalez J , Perez JW , Ford DA , Patel RP , Blake TA , Gunn MD , Jordt SE . Am J Physiol Lung Cell Mol Physiol 2024 Chlorine gas (Cl(2)) has been repeatedly used as a chemical weapon, first in World War I and most recently in Syria. Life-threatening Cl(2) exposures frequently occur in domestic and occupational environments, and in transportation accidents. Modeling the human etiology of Cl(2)-induced acute lung injury (ALI), forensic biomarkers, and targeted countermeasures development have been hampered by inadequate large animal models. The objective of this study was to develop a translational model of Cl(2)-induced ALI in swine to understand toxico-pathophysiology and is suitable for screening potential medical countermeasures, and identify biomarkers useful for forensic analysis. Specific pathogen-free Yorkshire swine (30-40 kg) of either sex were exposed to Cl(2) (≤ 240 ppm for 1 h) or filtered air under anesthesia and controlled mechanical ventilation. Exposure to Cl(2) resulted in severe hypoxia and hypoxemia, increased airway resistance and peak inspiratory pressure, and decreased dynamic lung compliance. Cl(2) exposure resulted in increased total leucocyte and neutrophil counts in bronchoalveolar lavage fluid (BALF), vascular leakage, and pulmonary edema compared to the air-exposed group. The model recapitulated all three key histopathological features of human ALI, such as neutrophilic alveolitis, deposition of hyaline membranes, and formation of microthrombi. Free and lipid-bound 2‑chlorofatty acids and chlorotyrosine-modified proteins (3-chloro-L-tyrosine and 3,5-dichloro-L-tyrosine) were detected in plasma and lung tissue after Cl(2)‑exposure. In this study, we developed a translational swine model that recapitulates key features of human Cl(2) inhalation injury and is suitable for testing medical countermeasures, and validated chlorinated fatty acids and protein adducts as biomarkers of Cl(2) inhalation. |
Lessons learned: COVID-19 vaccinations and people with disabilities
Rattay K , Thierry JM , Yeargin-Allsopp M , Griffin-Blake S , Rice CE , Chatham-Stephens K , Remley K . Vaccine 2024 This manuscript is being submitted as a Commentary; Abstract not applicable. |
Establishing population values for chlorine exposure in the United States (2015-2016) Using 2 chlorine biomarkers, 3-chlorotyrosine and 3,5-dichlorotyrosine
Boles SL , Pantazides BG , Perez JW , Sternberg MR , Crow BS , Blake TA . J Appl Lab Med 2024 BACKGROUND: In the United States, 12 million short tons of chlorine are manufactured and transported each year. Due to the volume of this volatile chemical, large- and small-scale chemical exposures occur frequently. To diagnose and treat potentially exposed individuals, reference range values for confirmatory biomarkers are required to differentiate between normal and abnormal exposure levels. METHODS: Serum surplus samples (n = 1780) from the National Health and Nutrition Examination Survey (NHANES) 2015-2016 were measured for 2 chlorine biomarkers, 3-chlorotyrosine (Cl-Tyr) and 3,5-dichlorotyrosine (Cl2-Tyr), by liquid chromatography coupled to a triple quadrupole mass spectrometer. We evaluated demographic factors associated with elevated biomarker levels. RESULTS: Participant samples were analyzed for the chlorine biomarkers Cl-Tyr and Cl2-Tyr. In the unweighted analysis of these samples, 1349 (75.8%) were under the limit of detection (< LOD) of 2.50 ng/mL for Cl-Tyr and 1773 (99.6%) were < LOD for Cl2-Tyr. Samples within the method reportable range were 2.50 to 35.6 ng/mL for Cl-Tyr and 2.69 to 11.2 ng/mL for Cl2-Tyr. Since only 7 of the 1780 participants had detectable Cl2-Tyr, statistical analysis was limited to Cl-Tyr. Of the demographic characteristics examined, age, body mass index (BMI), estimated glomerular filtration rate (eGFR), and sex exhibited statistically significant differences in the weighted prevalence of detectable Cl-Tyr. CONCLUSIONS: This is the first reported set of Cl-Tyr and Cl2-Tyr population values for the United States. This population range coupled with NHANES demographic information could help healthcare professionals distinguish between normal and abnormal chlorine biomarker levels in an emergency. With this information, an inference could be made when determining acute chlorine exposure in individuals. |
Sodium and potassium consumption in Jamaica: National estimates and associated factors from the Jamaica Health and Lifestyle Survey 2016-2017
Ferguson TS , Younger-Coleman NOM , Webster-Kerr K , Tulloch-Reid MK , Bennett NR , Davidson T , Grant AS , Gordon-Johnson KM , Govia I , Soares-Wynter S , McKenzie JA , Walker E , Cunningham-Myrie CA , Anderson SG , Blake AL , Ho J , Stephenson R , Edwards SE , McFarlane SR , Spence S , Wilks RJ . Medicine (Baltimore) 2023 102 (40) e35308 This study aimed to estimate dietary sodium and potassium consumption among Jamaicans and evaluate associations with sociodemographic and clinical characteristics. A cross-sectional study was conducted using data from the Jamaica Health and Lifestyle Survey 2016-2017. Participants were noninstitutionalized Jamaicans aged ≥15 years. Trained staff collected sociodemographic and health data via interviewer-administered questionnaires and spot urine samples. The Pan American Health Organization formula was used to estimate 24-hour urine sodium and potassium excretion. High sodium level was defined as ≥2000 mg/day, and low potassium levels as <3510 mg/day (World Health Organization criteria). Associations between these outcomes and sociodemographic and clinical characteristics were explored using multivariable ANOVA models using log-transformed 24-hour urine sodium and potassium as outcome variables. Analyses included 1009 participants (368 males, 641 females; mean age 48.5 years). The mean sodium excretion was 3582 mg/day (males 3943 mg/day, females 3245 mg/day, P < .001). The mean potassium excretion was 2052 mg/day (males, 2210 mg/day; females, 1904 mg/day; P = .001). The prevalence of high sodium consumption was 66.6% (males 72.8%, females 60.7%, P < .001) and that of low potassium intake was 88.8% (85.1% males, 92.3% females, P < .001). Sodium consumption was inversely associated with older age, higher education, and low glomerular filtration rate but was directly associated with being male, current smoking, and obesity. Overall, males had higher sodium consumption than women, with the effect being larger among hypertensive men. Women with hypertension had lower sodium consumption than nonhypertensive women; however, hypertensive men had higher sodium consumption than nonhypertensive men. Potassium consumption was higher among men, persons with obesity, and those with high total cholesterol but was lower among men with "more than high school" education compared to men with "less than high school" education. We conclude that most Jamaican adults have diets high in sodium and low in potassium. In this study, sodium consumption was directly associated with male sex, obesity, and current smoking but was inversely associated with older age and higher education. High potassium consumption was associated with obesity and high cholesterol levels. These associations should be further explored in longitudinal studies and population-based strategies should be developed to address these cardiovascular risk factors. |
One-year association of drug possession law change with fatal drug overdose in Oregon and Washington
Joshi S , Rivera BD , Cerdá M , Guy GP Jr , Strahan A , Wheelock H , Davis CS . JAMA Psychiatry 2023 IMPORTANCE: Two states modified laws to remove or substantially reduce criminal penalties for any drug possession. The hypothesis was that removing criminal penalties for drug possession may reduce fatal drug overdoses due to reduced incarceration and increased calls for help at the scene of an overdose. OBJECTIVE: To evaluate whether decriminalization of drug possession in Oregon and Washington was associated with changes in either direction in fatal drug overdose rates. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used a synthetic control method approach to examine whether there were changes in drug possession laws and fatal drug overdose rates in Oregon and Washington in the postpolicy period (February 1, 2021, to March 31, 2022, in Oregon and March 1, 2021, to March 31, 2022, in Washington). A counterfactual comparison group (synthetic controls) was created for Oregon and Washington, using 48 states and the District of Columbia, that did not implement similar policies during the study period (January 1, 2018, to March 31, 2022). For 2018-2021, final multiple cause-of-death data from the National Vital Statistics System (NVSS) were used. For 2022, provisional NVSS data were used. Drug overdose deaths were identified using International Statistical Classification of Diseases and Related Health Problems, 10th Revision underlying cause-of-death codes X40-X44, X60-X64, X85, and Y10-Y14. EXPOSURES: In Oregon, Measure 110 went into effect on February 1, 2021. In Washington, the Washington Supreme Court decision in State v Blake occurred on February 25, 2021. MAIN OUTCOME: Monthly fatal drug overdose rates. RESULTS: Following the implementation of Measure 110, absolute monthly rate differences between Oregon and its synthetic control were not statistically significant (probability = 0.26). The average rate difference post Measure 110 was 0.268 fatal drug overdoses per 100 000 state population. Following the implementation of the policy change in Washington, the absolute monthly rate differences between Washington and synthetic Washington were not statistically significant (probability = 0.06). The average rate difference post Blake was 0.112 fatal drug overdoses per 100 000 state population. CONCLUSIONS AND RELEVANCE: This study found no evidence of an association between legal changes that removed or substantially reduced criminal penalties for drug possession in Oregon and Washington and fatal drug overdose rates. Additional research could examine potential other outcomes as well as longer-term associations with fatal drug overdose overall and across racial and ethnic groups. |
Sodium and Potassium Consumption in Jamaica: National Estimates and Associated Factors from the Jamaica Health and Lifestyle Survey 2016-2017 (preprint)
Ferguson TS , Younger-Coleman NOM , Webster-Kerr K , Tulloch-Reid MK , Bennett NR , Davidson T , Grant AS , Gordon-Johnson KAM , Govia I , Soares-Wynter S , McKenzie JA , Walker E , Cunningham-Myrie CA , Anderson SG , Blake AL , Ho J , Stephenson R , Edwards SE , McFarlane SR , Spence S , Wilks RJ . medRxiv 2023 19 Objective: To estimate dietary sodium and potassium consumption among Jamaicans and evaluate associations with sociodemographic and clinical characteristics. Method(s): We conducted a cross-sectional analysis of data from the Jamaica Health and Lifestyle Survey 2016-2017. Participants were non-institutionalized Jamaicans, >=15 years. Trained staff collected sociodemographic and health data via interviewer administered questionnaires and collected spot urine samples. The Pan American Health Organization Formulae were used to estimate 24-hour urine sodium and potassium excretion. High sodium was defined as >=2000 mg/day and low potassium as <3510 mg/day (World Health Organization criteria). Associations of these outcomes with sociodemographic and clinical characteristics were explored in sex specific multivariable ANOVA models. Result(s): Analyses included 1009 participants (368 males, 641 females; mean age 48.5 years). Mean sodium excretion was 3582 mg/day (males 3943 mg/day, females 3245 mg/day, p<0.001). Mean potassium excretion was 2052 mg/day (males 2210 mg/day, females 1904 mg/day, p=0.001). The prevalence of high sodium consumption was 66.6% (males 72.8%, female 60.7%, p<0.001) and low potassium intake was 88.8% (85.1% males, 92.3% females, p<0.001). Among males, sodium consumption was inversely associated with older age and prehypertension, but directly associated with current smoking and obesity. Among females, sodium consumption was inversely associated with hypertension, impaired fasting glucose, low GFR and high physical activity, but was directly associated with obesity. Conclusion(s): Most Jamaican adults have diets high in sodium and low in potassium. Sodium consumption was directly associated with obesity in both men and women. Population based strategies are therefore required to address these cardiovascular risk factors. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Evaluation of Sampling and Concentration Methods for Salmonella enterica Serovar Typhi Detection from Wastewater
Zhou N , Ong A , Fagnant-Sperati C , Harrison J , Kossik A , Beck N , Shirai J , Burnor E , Swanstrom R , Demeke B , Patel S , Scott Meschke J , Kang G , Giri S , Raghava V , Abraham D , Moe C , Kapoor R , Wang Y , Liu P , Feasey N , Rigby J , Dines Y , Elviss N , Alm E , Moniz K , Xiao A , Karmacharya D , Napit R , Poudel A , Muhammad S , Ashraf Z , Boyle D , Andrews J , Aiemjoy K , LeBoa C , Tamrakar D , Shrestha S , Shakya J , Murphy JL , Narayanan J , Brown TW , Taniuchi M , Islam Md O , Blake I . Am J Trop Med Hyg 2023 108 (3) 482-491 Salmonella enterica serovar (Salmonella Typhi) is the causative bacterial agent of typhoid fever. Environmental surveillance of wastewater and wastewater-impacted surface waters has proven effective in monitoring various pathogens and has recently been applied to Salmonella Typhi. This study evaluated eight sample collection and concentration methods with 12 variations currently being developed and used for Salmonella Typhi surveillance globally to better understand the performance of each method based on its ability to detect Salmonella Typhi and its feasibility. Salmonella Typhi strains Ty21a and Ty2 were seeded to influent wastewater at known concentrations to evaluate the following methods: grab sampling using electropositive filters, centrifugation, direct enrichment, or membrane filtration and trap sampling using Moore swabs. Concentrated samples underwent nucleic acid extraction and were detected and/or quantified via quantitative polymerase chain reaction (qPCR). Results suggest that all methods tested can be successful at concentrating Salmonella Typhi for subsequent detection by qPCR, although each method has its own strengths and weaknesses, including the Salmonella Typhi concentration it is best suited for, with a range of positive detections observed as low as 0.1-0.001 colony-forming units (CFU) Ty21a/mL and 0.01 CFU Ty2/mL. These factors should be considered when identifying a method for environmental surveillance and will greatly depend on the use case planned. |
Recapitulation of Human Pathophysiology and Identification of Forensic Biomarkers in a Translational Swine Model of Chlorine Inhalation Injury (preprint)
Achanta S , Gentile MA , Albert CJ , Schulte KA , Pantazides BG , Crow BS , Quinones-Gonzalez J , Perez JW , Ford DA , Patel RP , Blake TA , Gunn MD , Jordt SE . bioRxiv 2022 10 Rationale: Chlorine gas (Cl<inf>2</inf>) has been repeatedly used as a chemical weapon, first in World War I and most recently in Syria. Life-threatening Cl<inf>2</inf> exposures frequently occur in domestic and occupational environments, and in transportation accidents. There is a knowledge gap in large animal models of Cl<inf>2</inf>-induced acute lung injury (ALI) required to accurately model human etiology and for the development of targeted countermeasures Objective: To develop a translational model of Cl<inf>2</inf>-induced ALI in swine to study toxicopathophysiology and identify biomarkers useful for forensic analysis. Method(s): Specific pathogen-free Yorkshire swine (30-40 kg) of either sex were exposed to Cl<inf>2</inf> gas (<= 240 ppm for 1 h) or filtered air under anesthesia and controlled mechanical ventilation. Result(s): Exposure to Cl<inf>2</inf> resulted in severe hypoxia and hypoxemia, increased airway resistance and peak inspiratory pressure, and decreased dynamic lung compliance. Chlorine exposure resulted in increased total BALF and neutrophil counts, vascular leakage, and edema compared to the control group. The model recapitulated all three key histopathological features of human ALI, such as neutrophilic alveolitis, deposition of hyaline membranes, and formation of microthrombi. Free and lipid-bound 2-chlorofatty acids and chlorotyrosine-modified proteins (3-chloro-L-tyrosine and 3,5-dichloro-L-tyrosine) were detected in plasma and lung after Cl<inf>2</inf>-exposure. Conclusion(s): The translational model developed in this study replicates key features of humans exposed to Cl<inf>2</inf> and is suitable to test medical countermeasures. Specific biomarkers of Cl<inf>2</inf> exposure have been identified in plasma and lung tissue samples. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Effectiveness of 2 and 3 mRNA COVID-19 Vaccines Doses against Omicron and Delta-Related Outpatient Illness among Adults, October 2021 - February 2022 (preprint)
Kim SS , Chung JR , Talbot HK , Grijalva CG , Wernli KJ , Martin ET , Monto AS , Belongia EA , McLean HQ , Gaglani M , Mamawala M , Nowalk MP , Geffel KM , Tartof SY , Florea A , Lee JS , Tenforde MW , Patel MM , Flannery B , Bentz ML , Burgin A , Burroughs M , Davis ML , Howard D , Lacek K , Madden JC , Nobles S , Padilla J , Sheth M , Arroliga A , Beeram M , Dunnigan K , Ettlinger J , Graves A , Hoffman E , Jatla M , McKillop A , Murthy K , Mutnal M , Priest E , Raiyani C , Rao A , Requenez L , Settele N , Smith M , Stone K , Thomas J , Volz M , Walker K , Zayed M , Annan E , Daley P , Kniss K , Merced-Morales A , Ayala E , Amundsen B , Aragones M , Calderon R , Hong V , Jimenez G , Kim J , Ku J , Lewin B , McDaniel A , Reyes A , Shaw S , Takhar H , Torres A , Burganowski R , Kiniry E , Moser KA , Nguyen M , Park S , Wellwood S , Wickersham B , Alvarado-Batres J , Benz S , Berger H , Bissonnette A , Blake J , Boese K , Botten E , Boyer J , Braun M , Breu B , Burbey G , Cravillion C , Delgadillo C , Donnerbauer A , Dziedzic T , Eddy J , Edgren H , Ermeling A , Ewert K , Fehrenbach C , Fernandez R , Frome W , Guzinski S , Heeren L , Herda D , Hertel M , Heuer G , Higdon E , Ivacic L , Jepsen L , Kaiser S , Karl J , Keffer B , King J , Koepel TK , Kohl S , Kohn S , Kohnhorst D , Kronholm E , Le T , Lemieux A , Marcis C , Maronde M , McCready I , McGreevey K , Meece J , Mehta N , Miesbauer D , Moon V , Moran J , Nikolai C , Olson B , Olstadt J , Ott L , Pan N , Pike C , Polacek D , Presson M , Price N , Rayburn C , Reardon C , Rotar M , Rottscheit C , Salzwedel J , Saucedo J , Scheffen K , Schug C , Seyfert K , Shrestha R , Slenczka A , Stefanski E , Strupp M , Tichenor M , Watkins L , Zachow A , Zimmerman B , Bauer S , Beney K , Cheng CK , Faraj N , Getz A , Grissom M , Groesbeck M , Harrison S , Henson K , Jermanus K , Johnson E , Kaniclides A , Kimberly A , Lamerato LE , Lauring A , Lehmann-Wandell R , McSpadden EJ , Nabors L , Truscon R , Balasubramani GK , Bear T , Bobeck J , Bowser E , Clarke K , Clarke LG , Dauer K , Deluca C , Dierks B , Haynes L , Hickey R , Johnson M , Jonsson A , Luosang N , McKown L , Peterson A , Phaturos D , Rectenwald A , Sax TM , Stiegler M , Susick M , Suyama J , Taylor L , Walters S , Weissman A , Williams JV , Blair M , Carter J , Chappell J , Copen E , Denney M , Graes K , Halasa N , Lindsell C , Liu Z , Longmire S , McHenry R , Short L , Tan HN , Vargas D , Wrenn J , Wyatt D , Zhu Y . medRxiv 2022 10 Background: We estimated SARS-CoV-2 Delta and Omicron-specific effectiveness of 2 and 3 mRNA COVID-19 vaccine doses in adults against symptomatic illness in US outpatient settings. Method(s): Between October 1, 2021, and February 12, 2022, research staff consented and enrolled eligible participants who had fever, cough, or loss of taste or smell and sought outpatient medical care or clinical SARS-CoV-2 testing within 10 days of illness onset. Using the test-negative design, we compared the odds of receiving 2 or 3 mRNA COVID-19 vaccine doses among SARS-CoV-2 cases versus controls using logistic regression. Regression models were adjusted for study site, age, onset week, and prior SARS-CoV-2 infection. Vaccine effectiveness (VE) was calculated as (1 - adjusted odds ratio) x 100%. Result(s): Among 3847 participants included for analysis, 574 (32%) of 1775 tested positive for SARS-CoV-2 during the Delta predominant period and 1006 (56%) of 1794 participants tested positive during the Omicron predominant period. When Delta predominated, VE against symptomatic illness in outpatient settings was 63% (95% CI: 51% to 72%) among mRNA 2-dose recipients and 96% (95% CI: 93% to 98%) for 3-dose recipients. When Omicron predominated, VE was 21% (95% CI: -6% to 41%) among 2-dose recipients and 62% (95% CI: 48% to 72%) among 3-dose recipients. Conclusion(s): In this adult population, 3 mRNA COVID-19 vaccine doses provided substantial protection against symptomatic illness in outpatient settings when the Omicron variant became the predominant cause of COVID-19 in the U.S. These findings support the recommendation for a 3rd mRNA COVID-19 vaccine dose. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Evaluation of sampling and concentration methods for Salmonella enterica serovar Typhi detection from wastewater (preprint)
Zhou NA , Ong AQW , Fagnant-Sperati CS , Harrison JC , Kossik AL , Beck NK , Shirai JH , Burnor E , Swanstrom R , Demeke B , Patel S , Meschke JS , Kang G , Giri S , Raghava V , Abraham D , Moe C , Kapoor R , Wang Y , Liu P , Feasey N , Rigby J , Dines Y , Elviss N , Alm E , Moniz K , Xiao A , Karmacharya D , Napit R , Poudel A , Muhammad S , Ashraf Z , Boyle D , Andrews J , Aiemjoy K , LeBoa C , Tamrakar D , Shrestha S , Shakya J , Murphy JL , Narayanan J , Brown TW , Taniuchi M , Islam Md O , Blake I . medRxiv 2022 08 Salmonella enterica serovar (Salmonella Typhi) is the causative bacterial agent of Typhoid fever. Environmental surveillance of wastewater and wastewater-impacted surface waters has proven effective in monitoring various pathogens, and has recently been applied to Salmonella Typhi. This study evaluated eight sample collection and concentration methods with twelve variations currently being developed and used for Salmonella Typhi surveillance globally to better understand the performance of each method based on their ability to detect Salmonella Typhi and feasibility. Salmonella Typhi strains, Ty21a and Ty2, were seeded to influent wastewater at known concentrations to evaluate the following methods: grab sampling using electropositive filters, centrifugation, direct enrichment, or membrane filtration and trap sampling using Moore swabs. Concentrated samples underwent nucleic acid extraction and were detected and/or quantified via qPCR. Results suggest that all methods tested can be successful at concentrating Salmonella Typhi for subsequent detection by qPCR, although each method has its own strengths and weaknesses including the Salmonella Typhi concentrations they are best suited for with a range of positive detections observed as low as 0.1-0.001 CFU Ty21a/mL and 0.01 CFU Ty2/mL. These factors should be considered when identifying a method for environmental surveillance and will greatly depend on the use case planned. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Streamlining micronutrient biomarker statistical analysis in populations: an introduction to the SAMBA R package
Luo H , Beal T , Blake T , Zeiler M , Geng J , Werner ER , Addo OY , Suchdev PS , Young MF . J Nutr 2023 153 (9) 2753-2761 Micronutrient deficiency is a common global health problem, and accurately assessing micronutrient biomarkers is crucial for planning and managing effective intervention programs. However, analyzing micronutrient data and applying appropriate cutoffs to define deficiencies can be challenging, particularly when considering the confounding effects of inflammation on certain micronutrient biomarkers. To address this challenge, we developed the Statistical Apparatus of Micronutrient Biomarker Analysis (SAMBA) R package, a new tool that increases ease and accessibility of population-based micronutrient biomarker analysis. The SAMBA package can analyze various micronutrient biomarkers to assess status of iron, vitamin A, zinc, and B vitamins, adjust for inflammation, account for complex survey design when appropriate, and produce reports of summary statistics and prevalence estimates of micronutrient deficiencies using recommended age- and sex-specific cutoffs. We have provided a step-by-step procedure for how to use the SAMBA R package, including how to customize it for broader use, and made both the package and user manual publicly available on GitHub. SAMBA was validated by comparing results from analyzing 24 datasets on non-pregnant women of reproductive age from 23 countries and 30 datasets on preschool-age children from 26 countries with those obtained by an independent analyst. SAMBA generated identical means, percentiles, and prevalence of micronutrient deficiencies to those calculated by the independent analyst. In conclusion, SAMBA simplifies and standardizes the process for deriving survey-weighted and inflammation-adjusted (when appropriate) estimates of the prevalence of micronutrient deficiencies, reducing the time from data cleaning to result generation. SAMBA is a valuable tool that facilitates the accurate and rapid analysis of population-based micronutrient biomarker data, which can inform public health research, programs, and policy across contexts. |
Voices of Black talent in chemistry: Retention strategies and personal success stories
Scott T , Adderley D , Ali Y , Amanuel M , Blake A , Callender M , Carter C , Fokwa HD , Gooden RO , Granger A , Gunn K , Henderson A , Kitimet M , Modeste E , Stewart Z , Teah J , Wairegi S , Ward LW , Parish CA . J Am Chem Soc 2023 145 (23) 12426-12428 Juneteenth, a federal holiday officially recognized in 2021, is celebrated annually in the United States to honor the emancipation of enslaved Black Americans. As a symbol of racial justice, equality, and equity, Juneteenth represents an opportunity to pay tribute to the achievements of a wide range of Black chemistry students and the initiatives taken to promote the success of every student within an environment that has historically not been inclusive. | | While the U.S. STEM workforce has become more diverse in the past 10 years, Black people continue to be underrepresented in science, and in chemistry, in particular. The recent National Science Foundation report Diversity and STEM: Women, Minorities and Persons with Disabilities 2023 shows that only 9% of the STEM workforce identifies as Black, 3 percentage points (roughly 7.7M people (1)) lower than their overall representation in the adult U.S. population. (2) The U.S. Bureau of Labor Statistics paints a similar picture─in 2022 only 10% of the chemical manufacturing workforce was Black. (3) Chemical & Engineering News culled the chemistry data from the 2023 NSF report revealing even bleaker figures─in 2021, Black people comprised only 4.4% of employed chemists, (4) and were more likely to occupy lower paying STEM jobs that do not require a college degree. (2) | | Recent publications have emphasized the importance of scientists and scientific institutions welcoming and supporting the development of individuals from groups historically marginalized in fields such as chemistry, biology, mathematics, computer science, and physics. (5) Not only is such intentional support a moral imperative, but numerous reports have demonstrated that increasing diversity and inclusion in these fields leads to a more innovative and productive scientific community. (6) | | Marginalized groups often face systemic barriers to accessing education and career opportunities, resulting in a chemical workforce that lacks diversity. To address this, chemists and chemistry organizations have taken steps to actively support and mentor individuals from historically excluded groups, providing access to resources and opportunities, and promoting a culture of inclusivity in academia and the workplace. For instance, since 1965, the American Chemical Society (ACS) Project Seed program has provided summer research experiences for more than 11,000 high school students, while the ACS Scholars program has provided renewable scholarships for more than 3,500 undergraduates interested in chemistry-related careers. |
A pilot PT scheme for external assessment of laboratory performance in testing synthetic opioid compounds in urine, plasma, and whole blood
Hart ED , Bynum ND , Evans A , Swanson KD , Blake TA . Forensic Sci Int 2023 347 111679 A proficiency testing (PT) scheme was prepared for laboratories engaged in bioanalytical testing for synthetic opioid compounds in urine, plasma, and whole blood. Samples were prepared using compounds included in the Opioid Certified Reference Material Kit (Opioid CRM Kit) developed by the U.S. Centers for Disease Control and Prevention. Laboratories received samples during a 2-year project with each year consisting of two PT events 6 months apart. In the first year (pilot test), participants included 10 public health laboratories throughout the United States. In the second year, the group of laboratories expanded to include clinical and forensic drug testing laboratories, and 12 additional participating labs joined the program. In Year 1, overall detection percentages for the compounds present in the PT samples were 95.5% in Event 1% and 97.2% in Event 2. There were 31 apparent false positives reported in Event 1 and four apparent false positives reported in Event 2. Carryover or contamination in laboratory analytical systems were found to be the most significant causes of the false positive results, and none of the laboratories that reported false positives in Event 1 did so in Event 2. In Year 2, overall detection percentages for the compounds present in the PT samples were 89.5% in Event 3% and 94.8% in Event 4. There was one apparent false positive reported in Event 3 and three apparent false positives reported in Event 4. Improvements in drug detection between the two PT events in each year demonstrated the benefit of PT schemes in identifying and addressing potential deficiencies in laboratory systems. |
Information for Persons Who Are Immunocompromised Regarding Prevention and Treatment of SARS-CoV-2 Infection in the Context of Currently Circulating Omicron Sublineages - United States, January 2023.
Patel P , Twentyman E , Koumans E , Rosenblum H , Griffin-Blake S , Jackson B , Vagi S . MMWR Morb Mortal Wkly Rep 2023 72 (5) 128-131 As of January 20, 2023, >90% of circulating SARS-CoV-2 variants in the United States, specifically Omicron BQ.1, BQ.1.1, XBB, and XBB.1.5 sublineages, are unlikely to be susceptible to the combined monoclonal antibodies, tixagevimab and cilgavimab (Evusheld) used for preexposure prophylaxis against SARS-CoV-2 infection (1). The Food and Drug Administration announced on January 26, 2023, that Evusheld is not currently authorized for preexposure prophylaxis against SARS-CoV-2 infection in the United States (2). It is important that persons who are moderately to severely immunocompromised,* those who might have an inadequate immune response to COVID-19 vaccination, and those with contraindications to receipt of COVID-19 vaccines, exercise caution and recognize the need for additional preventive measures (Box). In addition, persons should have a care plan that includes prompt testing at the onset of COVID-19 symptoms and rapid access to antivirals if SARS-CoV-2 infection is detected. |
Epidemiologic and clinical characteristics of Monkeypox cases - United States, May 17-July 22, 2022
Philpott D , Hughes CM , Alroy KA , Kerins JL , Pavlick J , Asbel L , Crawley A , Newman AP , Spencer H , Feldpausch A , Cogswell K , Davis KR , Chen J , Henderson T , Murphy K , Barnes M , Hopkins B , Fill MA , Mangla AT , Perella D , Barnes A , Hughes S , Griffith J , Berns AL , Milroy L , Blake H , Sievers MM , Marzan-Rodriguez M , Tori M , Black SR , Kopping E , Ruberto I , Maxted A , Sharma A , Tarter K , Jones SA , White B , Chatelain R , Russo M , Gillani S , Bornstein E , White SL , Johnson SA , Ortega E , Saathoff-Huber L , Syed A , Wills A , Anderson BJ , Oster AM , Christie A , McQuiston J , McCollum AM , Rao AK , Negrón ME . MMWR Morb Mortal Wkly Rep 2022 71 (32) 1018-1022 Monkeypox, a zoonotic infection caused by an orthopoxvirus, is endemic in parts of Africa. On August 4, 2022, the U.S. Department of Health and Human Services declared the U.S. monkeypox outbreak, which began on May 17, to be a public health emergency (1,2). After detection of the first U.S. monkeypox case), CDC and health departments implemented enhanced monkeypox case detection and reporting. Among 2,891 cases reported in the United States through July 22 by 43 states, Puerto Rico, and the District of Columbia (DC), CDC received case report forms for 1,195 (41%) cases by July 27. Among these, 99% of cases were among men; among men with available information, 94% reported male-to-male sexual or close intimate contact during the 3 weeks before symptom onset. Among the 88% of cases with available data, 41% were among non-Hispanic White (White) persons, 28% among Hispanic or Latino (Hispanic) persons, and 26% among non-Hispanic Black or African American (Black) persons. Forty-two percent of persons with monkeypox with available data did not report the typical prodrome as their first symptom, and 46% reported one or more genital lesions during their illness; 41% had HIV infection. Data suggest that widespread community transmission of monkeypox has disproportionately affected gay, bisexual, and other men who have sex with men and racial and ethnic minority groups. Compared with historical reports of monkeypox in areas with endemic disease, currently reported outbreak-associated cases are less likely to have a prodrome and more likely to have genital involvement. CDC and other federal, state, and local agencies have implemented response efforts to expand testing, treatment, and vaccination. Public health efforts should prioritize gay, bisexual, and other men who have sex with men, who are currently disproportionately affected, for prevention and testing, while addressing equity, minimizing stigma, and maintaining vigilance for transmission in other populations. Clinicians should test patients with rash consistent with monkeypox,(†) regardless of whether the rash is disseminated or was preceded by prodrome. Likewise, although most cases to date have occurred among gay, bisexual, and other men who have sex with men, any patient with rash consistent with monkeypox should be considered for testing. CDC is continually evaluating new evidence and tailoring response strategies as information on changing case demographics, clinical characteristics, transmission, and vaccine effectiveness become available.(§). |
Genetic characterization of novel oral polio vaccine type 2 viruses during initial use phase under emergency use listing - worldwide, March-October 2021
Martin J , Burns CC , Jorba J , Shulman LM , Macadam A , Klapsa D , Majumdar M , Bullows J , Frolov A , Mate R , Bujaki E , Castro CJ , Bullard K , Konz J , Hawes K , Gauld J , Blake IM , Mercer LD , Kurji F , Voorman A , Diop OM , Oberste MS , Modlin J , Macklin G , Eisenhawer M , Bandyopadhyay AS , Zipursky S . MMWR Morb Mortal Wkly Rep 2022 71 (24) 786-790 The emergence and international spread of neurovirulent circulating vaccine-derived polioviruses (cVDPVs) across multiple countries in Africa and Asia in recent years pose a major challenge to the goal of eradicating all forms of polioviruses. Approximately 90% of all cVDPV outbreaks are caused by the type 2 strain of the Sabin vaccine, an oral live, attenuated vaccine; cVDPV outbreaks typically occur in areas of persistently low immunization coverage (1). A novel type 2 oral poliovirus vaccine (nOPV2), produced by genetic modification of the type 2 Sabin vaccine virus genome (2), was developed and evaluated through phase I and phase II clinical trials during 2017-2019. nOPV2 was demonstrated to be safe and well-tolerated, have noninferior immunogenicity, and have superior genetic stability compared with Sabin monovalent type 2 (as measured by preservation of the primary attenuation site [domain V in the 5' noncoding region] and significantly lower neurovirulence of fecally shed vaccine virus in transgenic mice) (3-5). These findings indicate that nOPV2 could be an important tool in reducing the risk for generating vaccine-derived polioviruses (VDPVs) and the risk for vaccine-associated paralytic poliomyelitis cases. Based on the favorable preclinical and clinical data, and the public health emergency of international concern generated by ongoing endemic wild poliovirus transmission and cVDPV type 2 outbreaks, the World Health Organization authorized nOPV2 for use under the Emergency Use Listing (EUL) pathway in November 2020, allowing for its first use for outbreak response in March 2021 (6). As required by the EUL process, among other EUL obligations, an extensive plan was developed and deployed for obtaining and monitoring nOPV2 isolates detected during acute flaccid paralysis (AFP) surveillance, environmental surveillance, adverse events after immunization surveillance, and targeted surveillance for adverse events of special interest (i.e., prespecified events that have the potential to be causally associated with the vaccine product), during outbreak response, as well as through planned field studies. Under this monitoring framework, data generated from whole-genome sequencing of nOPV2 isolates, alongside other virologic data for isolates from AFP and environmental surveillance systems, are reviewed by the genetic characterization subgroup of an nOPV working group of the Global Polio Eradication Initiative. Global nOPV2 genomic surveillance during March-October 2021 confirmed genetic stability of the primary attenuating site. Sequence data generated through this unprecedented global effort confirm the genetic stability of nOPV2 relative to Sabin 2 and suggest that nOPV2 will be an important tool in the eradication of poliomyelitis. nOPV2 surveillance should continue for the duration of the EUL. |
Antigen Test Positivity After COVID-19 Isolation - Yukon-Kuskokwim Delta Region, Alaska, January-February 2022.
Lefferts B , Blake I , Bruden D , Hagen MB , Hodges E , Kirking HL , Bates E , Hoeldt A , Lamont B , Saydah S , MacNeil A , Bruce MG , Plumb ID . MMWR Morb Mortal Wkly Rep 2022 71 (8) 293-298 Isolation is recommended during acute infection with SARS-CoV-2, the virus that causes COVID-19, but the duration of infectiousness varies among individual persons. Rapid antigen test results have been correlated with detection of viable virus (1-3) and might inform isolation guidance, but data are limited for the recently emerged SARS-CoV-2 B.1.1.529 (Omicron) variant. On January 5, 2022, the Yukon-Kuskokwim Health Corporation (YKHC) recommended that persons with SARS-CoV-2 infection isolate for 10 days after symptom onset (or, for asymptomatic persons, 10 days after a positive nucleic acid amplification or antigen test result). However, isolation could end after 5-9 days if symptoms were resolving or absent, fever was absent for 24 hours without fever-reducing medications, and an Abbott BinaxNOW COVID-19 Ag (BinaxNOW) rapid antigen test result was negative. Antigen test results and associated individual characteristics were analyzed among 3,502 infections reported to YKHC during January 1-February 9, 2022. After 5-9 days, 396 of 729 persons evaluated (54.3%) had a positive antigen test result, with a declining percentage positive over time. In a multivariable model, a positive antigen test result was more likely after 5 days compared with 9 days (adjusted odds ratio [aOR]=6.39) or after symptomatic infection (aOR=9.63), and less likely after previous infection (aOR=0.30), receipt of a primary COVID-19 vaccination series (aOR=0.60), or after both previous infection and receipt of a primary COVID-19 vaccination series (aOR=0.17). Antigen tests might be a useful tool to guide recommendations for isolation after SARS-CoV-2 infection. During the 10 days after infection, persons might be infectious to others and are recommended to wear a well-fitting mask when around others, even if ending isolation after 5 days. |
Public support for cigarette pack pictorial health warnings among U.S. adults: A cross-sectional analysis of the 2020 Health Information National Trends Survey
Kaufman AR , D'Angelo H , Gaysynsky A , Seidenberg AB , Vollinger RE , Blake K . Nicotine Tob Res 2022 24 (6) 924-928 INTRODUCTION: To examine population-level characteristics of support for - versus neutrality or opposition toward - cigarette pack warnings that use text and images to portray the negative health effects of smoking. METHODS: We used nationally representative cross-sectional data of U.S. adults age 18 and older from the 2020 Health Information National Trends Survey (n=3865). Frequencies and weighted proportions were calculated for neutrality toward, opposition to, and support for pictorial warnings across sociodemographics and other predictors. Weighted, multivariable logistic regression examined predictors of being neutral or opposed versus supportive of pictorial warnings. RESULTS: In 2020, an estimated 69.9% of U.S. adults supported pictorial warnings, 9.1% opposed, and 20.9% neither supported nor opposed them. In fully adjusted models, current smokers had almost twice the odds of being neutral or opposed to pictorial warnings as never smokers (OR=1.99, CI 1.12,3.52). Adults 75 years and older (vs. 18-34) (OR=0.55, CI 0.33,0.94) and those with children under 18 in their household (vs. no children) (OR=0.67, CI 0.46,0.98) were less likely to be neutral or opposed. CONCLUSIONS: In advance of the Food and Drug Administration's implementation of pictorial warnings on cigarette packages, nearly 70% of American adults support this policy. Disseminating information about the effectiveness of pictorial warnings may further strengthen support among current smokers who are less supportive than never smokers. Furthermore, framing messages around the benefits of pictorial warnings for protecting youth may increase public support. IMPLICATIONS: While public support for pictorial warnings on cigarette packages is high in the U.S., it may increase further after policy implementation and be strengthened by utilizing information campaigns that convey the evidence that pictorial warnings are an effective public health strategy. |
A Million Persons, A Million Dreams: A Vision For A National Center Of Radiation Epidemiology And Biology
Boice JD Jr , Quinn B , Al-Nabulsi I , Ansari A , Blake PK , Blattnig SR , Caffrey EA , Cohen SS , Golden AP , Held KD , Jokisch DW , Leggett RW , Mumma MT , Samuels C , Till JE , Tolmachev SY , Yoder RC , Zhou JY , Dauer LT . Int J Radiat Biol 2021 98 (4) 1-50 BACKGROUND: Epidemiologic studies of radiation-exposed populations form the basis for human safety standards. They also help shape public health policy and evidence-based health practices by identifying and quantifying health risks of exposure in defined populations. For more than a century, epidemiologists have studied the consequences of radiation exposures, yet the health effects of low levels delivered at a low-dose rate remain equivocal. MATERIALS AND METHODS: The Million Person Study (MPS) of U.S. Radiation Workers and Veterans was designed to examine health effects following chronic exposures in contrast with brief exposures as experienced by the Japanese atomic bomb survivors. Radiation associations for rare cancers, intakes of radionuclides, and differences between men and women are being evaluated, as well as noncancers such as cardiovascular disease and conditions such as dementia and cognitive function. The first international symposium, held November 6, 2020, provided a broad overview of the MPS. Representatives from four U.S. government agencies addressed the importance of this research for their respective missions: U.S. Department of Energy (DOE), the Centers for Disease Control and Prevention (CDC), the U.S. Department of Defense (DOD), and the National Aeronautical Space Agency (NASA). The major components of the MPS were discussed and recent findings summarized. The importance of radiation dosimetry, an essential feature of each MPS investigation, was emphasized. RESULTS: The seven components of the MPS are DOE workers, nuclear weapons test participants, nuclear power plant workers, industrial radiographers, medical radiation workers, nuclear submariners, other U.S. Navy personnel, and radium dial painters. The MPS cohorts include tens of thousands of workers with elevated intakes of alpha particle emitters for which organ-specific doses are determined. Findings to date for chronic radiation exposure suggest that leukemia risk is lower than after acute exposure; lung cancer risk is much lower and there is little difference in risks between men and women; an increase in ischemic heart disease is yet to be seen; esophageal cancer is frequently elevated but not myelodysplastic syndrome; and Parkinson's disease may be associated with radiation exposure. CONCLUSIONS: The MPS has provided provocative insights into the possible range of health effects following low-level chronic radiation exposure. When the 34 MPS cohorts are completed and combined, a powerful evaluation of radiation-effects will be possible. This final article in the MPS special issue summarizes the findings to date and the possibilities for the future. A National Center for Radiation Epidemiology and Biology is envisioned. |
Epidemiologic characteristics associated with SARS-CoV-2 antigen-based test results, rRT-PCR cycle threshold values, subgenomic RNA, and viral culture results from university testing.
Ford L , Lee C , Pray IW , Cole D , Bigouette JP , Abedi GR , Bushman D , Delahoy MJ , Currie DW , Cherney B , Kirby M , Fajardo G , Caudill M , Langolf K , Kahrs J , Zochert T , Kelly P , Pitts C , Lim A , Aulik N , Tamin A , Harcourt JL , Queen K , Zhang J , Whitaker B , Browne H , Medrzycki M , Shewmaker P , Bonenfant G , Zhou B , Folster J , Bankamp B , Bowen MD , Thornburg NJ , Goffard K , Limbago B , Bateman A , Tate JE , Gieryn D , Kirking HL , Westergaard R , Killerby M . Clin Infect Dis 2021 73 (6) e1348-e1355 BACKGROUND: Real-time reverse transcription polymerase chain reaction (rRT-PCR) and antigen tests are important diagnostics for SARS-CoV-2. Sensitivity of antigen tests has been shown to be lower than that of rRT-PCR; however, data to evaluate epidemiologic characteristics that affect test performance are limited. METHODS: Paired mid-turbinate nasal swabs were collected from university students and staff and tested for SARS-CoV-2 using both Quidel Sofia SARS Antigen Fluorescent Immunoassay (FIA) and rRT-PCR assay. Specimens positive by either rRT-PCR or antigen FIA were placed in viral culture and tested for subgenomic RNA (sgRNA). Logistic regression models were used to evaluate characteristics associated with antigen results, rRT-PCR cycle threshold (Ct) values, sgRNA, and viral culture. RESULTS: Antigen FIA sensitivity was 78.9% and 43.8% among symptomatic and asymptomatic participants respectively. Among rRT-PCR positive participants, negative antigen results were more likely among asymptomatic participants (OR 4.6, CI:1.3-15.4) and less likely among participants reporting nasal congestion (OR 0.1, CI:0.03-0.8). rRT-PCR-positive specimens with higher Ct values (OR 0.5, CI:0.4-0.8) were less likely, and specimens positive for sgRNA (OR 10.2, CI:1.6-65.0) more likely, to yield positive virus isolation. Antigen testing was >90% positive in specimens with Ct values <29. Positive predictive value of antigen test for positive viral culture (57.7%) was similar to that of rRT-PCR (59.3%). CONCLUSIONS: SARS-CoV-2 antigen test advantages include low cost, wide availability and rapid turnaround time, making them important screening tests. The performance of antigen tests may vary with patient characteristics, so performance characteristics should be accounted for when designing testing strategies and interpreting results. |
Mass SARS-CoV-2 Testing in a Dormitory-Style Correctional Facility in Arkansas.
Tompkins LK , Gunn JKL , Cherney B , Ham JE , Horth R , Rossetti R , Bower WA , Benson K , Hagan LM , Crist MB , Mettee Zarecki SL , Dixon MG , Dillaha JA , Patil N , Dusseau C , Ross T , Matthews HS , Garner K , Starks AM , Weiner Z , Bowen MD , Bankamp B , Newton AE , Logan N , Schuh AJ , Trimble S , Pfeiffer H , James AE , Tian N , Jacobs JR , Ruiz F , McDonald K , Thompson M , Cooley L , Honein MA , Rose DA . Am J Public Health 2021 111 (5) e1-e10 Objectives. To assess SARS-CoV-2 transmission within a correctional facility and recommend mitigation strategies.Methods. From April 29 to May 15, 2020, we established the point prevalence of COVID-19 among incarcerated persons and staff within a correctional facility in Arkansas. Participants provided respiratory specimens for SARS-CoV-2 testing and completed questionnaires on symptoms and factors associated with transmission.Results. Of 1647 incarcerated persons and 128 staff tested, 30.5% of incarcerated persons (range by housing unit = 0.0%-58.2%) and 2.3% of staff tested positive for SARS-CoV-2. Among those who tested positive and responded to symptom questions (431 incarcerated persons, 3 staff), 81.2% and 33.3% were asymptomatic, respectively. Most incarcerated persons (58.0%) reported wearing cloth face coverings 8 hours or less per day, and 63.3% reported close contact with someone other than their bunkmate.Conclusions. If testing remained limited to symptomatic individuals, fewer cases would have been detected or detection would have been delayed, allowing transmission to continue. Rapid implementation of mass testing and strict enforcement of infection prevention and control measures may be needed to mitigate spread of SARS-CoV-2 in this setting. (Am J Public Health. Published online ahead of print March 18, 2021: e1-e10. https://doi.org/10.2105/AJPH.2020.306117). |
Development of a clinical assay to measure chlorinated tyrosine in hair and tissue samples using a mouse chlorine inhalation exposure model
Pantazides BG , Crow BS , Quiñones-González J , Perez JW , Harvilchuck JA , Wallery JJ , Hu TC , Thomas JD , Johnson RC , Blake TA . Anal Bioanal Chem 2021 413 (6) 1765-1776 Chlorine is a toxic industrial chemical with a history of use as a chemical weapon. Chlorine is also produced, stored, and transported in bulk making it a high-priority pulmonary threat in the USA. Due to the high reactivity of chlorine, few biomarkers exist to identify exposure in clinical and environmental samples. Our laboratory evaluates acute chlorine exposure in clinical samples by measuring 3-chlorotyrosine (Cl-Tyr) and 3,5-dichlorotyrosine (Cl(2)-Tyr) using liquid chromatography tandem mass spectrometry (LC-MS/MS). Individuals can have elevated biomarker levels due to their environment and chronic health conditions, but levels are significantly lower in individuals exposed to chlorine. Historically these biomarkers have been evaluated in serum, plasma, blood, and bronchoalveolar lavage (BAL) fluid. We report the expansion into hair and lung tissue samples using our newly developed tissue homogenization protocol which fits seamlessly with our current chlorinated tyrosine quantitative assay. Furthermore, we have updated the chlorinated tyrosine assay to improve throughput and ruggedness and reduce sample volume requirements. The improved assay was used to measure chlorinated tyrosine levels in 198 mice exposed to either chlorine gas or air. From this animal study, we compared Cl-Tyr and Cl(2)-Tyr levels among three matrices (i.e., lung, hair, and blood) and found that hair had the most abundant chlorine exposure biomarkers. Furthermore, we captured the first timeline of each analyte in the lung, hair, and blood samples. In mice exposed to chlorine gas, both Cl-Tyr and Cl(2)-Tyr were present in blood and lung samples up to 24 h and up to 30 days in hair samples. |
Performance of an Antigen-Based Test for Asymptomatic and Symptomatic SARS-CoV-2 Testing at Two University Campuses - Wisconsin, September-October 2020.
Pray IW , Ford L , Cole D , Lee C , Bigouette JP , Abedi GR , Bushman D , Delahoy MJ , Currie D , Cherney B , Kirby M , Fajardo G , Caudill M , Langolf K , Kahrs J , Kelly P , Pitts C , Lim A , Aulik N , Tamin A , Harcourt JL , Queen K , Zhang J , Whitaker B , Browne H , Medrzycki M , Shewmaker P , Folster J , Bankamp B , Bowen MD , Thornburg NJ , Goffard K , Limbago B , Bateman A , Tate JE , Gieryn D , Kirking HL , Westergaard R , Killerby M . MMWR Morb Mortal Wkly Rep 2021 69 (5152) 1642-1647 Antigen-based tests for SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), are inexpensive and can return results within 15 minutes (1). Antigen tests have received Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for use in asymptomatic and symptomatic persons within the first 5-12 days after symptom onset (2). These tests have been used at U.S. colleges and universities and other congregate settings (e.g., nursing homes and correctional and detention facilities), where serial testing of asymptomatic persons might facilitate early case identification (3-5). However, test performance data from symptomatic and asymptomatic persons are limited. This investigation evaluated performance of the Sofia SARS Antigen Fluorescent Immunoassay (FIA) (Quidel Corporation) compared with real-time reverse transcription-polymerase chain reaction (RT-PCR) for SARS-CoV-2 detection among asymptomatic and symptomatic persons at two universities in Wisconsin. During September 28-October 9, a total of 1,098 paired nasal swabs were tested using the Sofia SARS Antigen FIA and real-time RT-PCR. Virus culture was attempted on all antigen-positive or real-time RT-PCR-positive specimens. Among 871 (79%) paired swabs from asymptomatic participants, the antigen test sensitivity was 41.2%, specificity was 98.4%, and in this population the estimated positive predictive value (PPV) was 33.3%, and negative predictive value (NPV) was 98.8%. Antigen test performance was improved among 227 (21%) paired swabs from participants who reported one or more symptoms at specimen collection (sensitivity = 80.0%; specificity = 98.9%; PPV = 94.1%; NPV = 95.9%). Virus was isolated from 34 (46.6%) of 73 antigen-positive or real-time RT-PCR-positive nasal swab specimens, including two of 18 that were antigen-negative and real-time RT-PCR-positive (false-negatives). The advantages of antigen tests such as low cost and rapid turnaround might allow for rapid identification of infectious persons. However, these advantages need to be balanced against lower sensitivity and lower PPV, especially among asymptomatic persons. Confirmatory testing with an FDA-authorized nucleic acid amplification test (NAAT), such as RT-PCR, should be considered after negative antigen test results in symptomatic persons, and after positive antigen test results in asymptomatic persons (1). |
SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
Zhang S , Den-Bakker HC , Li S , Chen J , Dinsmore BA , Lane C , Lauer AC , Fields PI , Deng X . Appl Environ Microbiol 2019 85 (23) SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include: 1) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes; 2) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies; and 3) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common US serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification.IMPORTANCE: Serotyping is the basis of public health surveillance of Salmonella It remains a first-line subtyping method even as surveillance continues to be transformed by whole genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole genome sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large scale surveillance of Salmonella by whole genome sequencing. |
A quantitative method to detect human exposure to sulfur and nitrogen mustards via protein adducts
Pantazides BG , Quinones-Gonzalez J , Rivera Nazario DM , Crow BS , Perez JW , Blake TA , Johnson RC . J Chromatogr B Analyt Technol Biomed Life Sci 2019 1121 9-17 Sulfur and nitrogen mustards are internationally banned vesicants listed as Schedule 1 chemical agents in the Chemical Weapons Convention. These compounds are highly reactive electrophiles that form stable adducts to a variety of available amino acid residues on proteins upon exposure. We present a quantitative exposure assay that simultaneously measures agent specific protein adducts to cysteine for sulfur mustard (HD) and three nitrogen mustards (HN1, HN2, and HN3). Proteinase K was added to a serum or plasma sample to digest protein adducts and form the target analyte, the blister agent bound to the tripeptide cysteine-proline-phenylalanine (CPF). The mustard adducted-tripeptide was purified by solid phase extraction and analyzed using isotope dilution LC-MS/MS. Product ion structures were identified using high-resolution product ion scan data for HD-CPF, HN1-CPF, HN2-CPF, and HN3-CPF. Thorough matrix comparison, analyte recovery, ruggedness, and stability studies were incorporated during method validation to produce a robust method. The method demonstrated long term-stability, precision (RSD<15%), and intra- and inter-day accuracies>85% across the reportable range of 3.00-200ng/mL for each analyte. Compared to previously published assays, this method quantitates both sulfur and nitrogen mustard exposure biomarkers, requires only 10muL of sample volume, and can use either a liquid sample or dried sample spot. |
Prevalence of disabilities and health care access by disability status and type among adults - United States, 2016
Okoro CA , Hollis ND , Cyrus AC , Griffin-Blake S . MMWR Morb Mortal Wkly Rep 2018 67 (32) 882-887 Persons with disabilities face greater barriers to health care than do those without disabilities (1). To identify characteristics of noninstitutionalized adults with six specific disability types (hearing, vision, cognition, mobility, self-care, and independent living),* and to assess disability-specific disparities in health care access, CDC analyzed 2016 Behavioral Risk Factor Surveillance System (BRFSS) data. The prevalences of disability overall and by disability type, and access to health care by disability type, were estimated. Analyses were stratified by three age groups: 18-44 years (young adults), 45-64 years (middle-aged adults), and >/=65 years (older adults). Among young adults, cognitive disability (10.6%) was the most prevalent type. Mobility disability was most prevalent among middle-aged (18.1%) and older adults (26.9%). Generally, disability prevalences were higher among women, American Indians/Alaska Natives (AI/AN), adults with income below the federal poverty level (FPL), and persons in the South U.S. Census region. Disability-specific disparities in health care access were prevalent, particularly among young and middle-aged adults. These data might inform public health programs of the sociodemographic characteristics and disparities in health care access associated with age and specific disability types and guide efforts to improve access to care for persons with disabilities. |
Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association.
Nguyen SV , Harhay DM , Bono JL , Smith TPL , Fields PI , Dinsmore BA , Santovenia M , Wang R , Bosilevac JM , Harhay GP . Microb Genom 2018 4 (8) Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses. |
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