Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-5 (of 5 Records) |
Query Trace: Boyles T[original query] |
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MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response (preprint)
Campbell EM , Boyles A , Shankar A , Kim J , Knyazev S , Switzer WM . bioRxiv 2020 2020.07.22.216275 Motivation Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions.Results We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Using publicly available HIV sequences and other data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020.Availability and Implementation MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully-operational without an internet connection. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. The source code is available at https://github.com/cdcgov/microbetrace.Contact ells{at}cdc.govCompeting Interest StatementThe authors have declared no competing interest. |
Factors Associated With Severe Illness in Patients Aged <21 Years Hospitalized for COVID-19.
Choudhary R , Webber BJ , Womack LS , Dupont HK , Chiu SK , Wanga V , Gerdes ME , Hsu S , Shi DS , Dulski TM , Idubor OI , Wendel AM , Agathis NT , Anderson K , Boyles T , Click ES , Silva JD , Evans ME , Gold JAW , Haston JC , Logan P , Maloney SA , Martinez M , Natarajan P , Spicer KB , Swancutt M , Stevens VA , Rogers-Brown J , Chandra G , Light M , Barr FE , Snowden J , Kociolek LK , McHugh M , Wessel DL , Simpson JN , Gorman KC , Breslin KA , DeBiasi RL , Thompson A , Kline MW , Boom JA , Singh IR , Dowlin M , Wietecha M , Schweitzer B , Morris SB , Koumans EH , Ko JY , Siegel DA , Kimball AA . Hosp Pediatr 2022 12 (9) 760-783 OBJECTIVES: To describe COVID-19-related pediatric hospitalizations during a period of B.1.617.2 (Delta) variant predominance and to determine age-specific factors associated with severe illness. PATIENTS AND METHODS: We abstracted data from medical charts to conduct a cross-sectional study of patients aged <21 years hospitalized at 6 US children's hospitals during July-August 2021 for COVID-19 or with an incidental positive SARS-CoV-2 test. Among patients with COVID-19, we assessed factors associated with severe illness by calculating age-stratified prevalence ratios (PR). We defined severe illness as receiving high-flow nasal cannula, positive airway pressure, or invasive mechanical ventilation. RESULTS: Of 947 hospitalized patients, 759 (80.1%) had COVID-19, of whom 287 (37.8%) had severe illness. Factors associated with severe illness included coinfection with RSV (PR 3.64) and bacteria (PR 1.88) in infants; RSV coinfection in patients aged 1-4 years (PR 1.96); and obesity in patients aged 5-11 (PR 2.20) and 12-17 years (PR 2.48). Having ≥2 underlying medical conditions was associated with severe illness in patients aged <1 (PR 1.82), 5-11 (PR 3.72), and 12-17 years (PR 3.19). CONCLUSIONS: Among patients hospitalized for COVID-19, factors associated with severe illness included RSV coinfection in those aged <5 years, obesity in those aged 5-17 years, and other underlying conditions for all age groups <18 years. These findings can inform pediatric practice, risk communication, and prevention strategies, including vaccination against COVID-19. |
Characteristics and Clinical Outcomes of Children and Adolescents Aged <18 Years Hospitalized with COVID-19 - Six Hospitals, United States, July-August 2021.
Wanga V , Gerdes ME , Shi DS , Choudhary R , Dulski TM , Hsu S , Idubor OI , Webber BJ , Wendel AM , Agathis NT , Anderson K , Boyles T , Chiu SK , Click ES , Da Silva J , Dupont H , Evans M , Gold JAW , Haston J , Logan P , Maloney SA , Martinez M , Natarajan P , Spicer KB , Swancutt M , Stevens VA , Brown J , Chandra G , Light M , Barr FE , Snowden J , Kociolek LK , McHugh M , Wessel D , Simpson JN , Gorman KC , Breslin KA , DeBiasi RL , Thompson A , Kline MW , Bloom JA , Singh IR , Dowlin M , Wietecha M , Schweitzer B , Morris SB , Koumans EH , Ko JY , Kimball AA , Siegel DA . MMWR Morb Mortal Wkly Rep 2021 70 (5152) 1766-1772 During June 2021, the highly transmissible(†) B.1.617.2 (Delta) variant of SARS-CoV-2, the virus that causes COVID-19, became the predominant circulating strain in the United States. U.S. pediatric COVID-19-related hospitalizations increased during July-August 2021 following emergence of the Delta variant and peaked in September 2021.(§) As of May 12, 2021, CDC recommended COVID-19 vaccinations for persons aged ≥12 years,(¶) and on November 2, 2021, COVID-19 vaccinations were recommended for persons aged 5-11 years.** To date, clinical signs and symptoms, illness course, and factors contributing to hospitalizations during the period of Delta predominance have not been well described in pediatric patients. CDC partnered with six children's hospitals to review medical record data for patients aged <18 years with COVID-19-related hospitalizations during July-August 2021.(††) Among 915 patients identified, 713 (77.9%) were hospitalized for COVID-19 (acute COVID-19 as the primary or contributing reason for hospitalization), 177 (19.3%) had incidental positive SARS-CoV-2 test results (asymptomatic or mild infection unrelated to the reason for hospitalization), and 25 (2.7%) had multisystem inflammatory syndrome in children (MIS-C), a rare but serious inflammatory condition associated with COVID-19.(§§) Among the 713 patients hospitalized for COVID-19, 24.7% were aged <1 year, 17.1% were aged 1-4 years, 20.1% were aged 5-11 years, and 38.1% were aged 12-17 years. Approximately two thirds of patients (67.5%) had one or more underlying medical conditions, with obesity being the most common (32.4%); among patients aged 12-17 years, 61.4% had obesity. Among patients hospitalized for COVID-19, 15.8% had a viral coinfection(¶¶) (66.4% of whom had respiratory syncytial virus [RSV] infection). Approximately one third (33.9%) of patients aged <5 years hospitalized for COVID-19 had a viral coinfection. Among 272 vaccine-eligible (aged 12-17 years) patients hospitalized for COVID-19, one (0.4%) was fully vaccinated.*** Approximately one half (54.0%) of patients hospitalized for COVID-19 received oxygen support, 29.5% were admitted to the intensive care unit (ICU), and 1.5% died; of those requiring respiratory support, 14.5% required invasive mechanical ventilation (IMV). Among pediatric patients with COVID-19-related hospitalizations, many had severe illness and viral coinfections, and few vaccine-eligible patients hospitalized for COVID-19 were vaccinated, highlighting the importance of vaccination for those aged ≥5 years and other prevention strategies to protect children and adolescents from COVID-19, particularly those with underlying medical conditions. |
MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
Campbell EM , Boyles A , Shankar A , Kim J , Knyazev S , Cintron R , Switzer WM . PLoS Comput Biol 2021 17 (9) e1009300 Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email microbetrace@cdc.gov for support. The source code is available at https://github.com/cdcgov/microbetrace. |
Essential in vitro diagnostics for advanced HIV and serious fungal diseases: international experts' consensus recommendations
Bongomin F , Govender NP , Chakrabarti A , Robert-Gangneux F , Boulware DR , Zafar A , Oladele RO , Richardson MD , Gangneux JP , Alastruey-Izquierdo A , Bazira J , Boyles TH , Sarcarlal J , Nacher M , Obayashi T , Worodria W , Pasqualotto AC , Meya DB , Cheng B , Sriruttan C , Muzoora C , Kambugu A , Rodriguez Tudela JL , Jordan A , Chiller TM , Denning DW . Eur J Clin Microbiol Infect Dis 2019 38 (9) 1581-1584 An accurate, timely diagnosis is the cornerstone of good medical practice. For opportunistic fungal infections in AIDS and other invasive mycoses, this is dependent on the availability of and accessibility to the relevant diagnostic tests. A call for a model List of Essential In Vitro Diagnostics (EDL)—“listed tests that should be reasonably available for people who need them, whether in the form of point-of-care tests in physicians’ offices and pharmacies or as high-complexity tests in reference laboratories”—has been published [1]. In addition to better medical practice, other potential benefits of an EDL include clarification of priorities for policy makers, setting common goals for laboratory testing, improved healthcare delivery and overall better patient outcomes [1]. In the context of extensive antimicrobial resistance (AMR), a reduction in empiricism with more accurate diagnosis will play a key role in AMR control [2]. |
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