Last data update: Jun 03, 2024. (Total: 46935 publications since 2009)
Records 1-14 (of 14 Records) |
Query Trace: Pierson K [original query] |
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Adapterama II: Universal amplicon sequencing on Illumina platforms (TaggiMatrix) (preprint)
Glenn TC , Pierson TW , Bayona-Vásquez NJ , Kieran TJ , Hoffberg SL , Thomas IV JC , Lefever DE , Finger JW , Gao B , Bian X , Louha S , Kolli RT , Bentley KE , Rushmore J , Wong K , Shaw TI , Rothrock MJ Jr , McKee AM , Guo TL , Mauricio R , Molina M , Cummings BS , Lash LH , Lu K , Gilbert GS , Hubbell SP , Faircloth BC . bioRxiv 2019 619544 Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. Most NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5’ end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (eight forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy. |
Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).
Glenn TC , Pierson TW , Bayona-Vásquez NJ , Kieran TJ , Hoffberg SL , Thomas Iv JC , Lefever DE , Finger JW , Gao B , Bian X , Louha S , Kolli RT , Bentley KE , Rushmore J , Wong K , Shaw TI , Rothrock MJ Jr , McKee AM , Guo TL , Mauricio R , Molina M , Cummings BS , Lash LH , Lu K , Gilbert GS , Hubbell SP , Faircloth BC . PeerJ 2019 7 e7786 Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy. |
A multilingual tool for standardized laboratory biosafety and biosecurity assessment and monitoring
Orelle A , Nikiema A , Zakaryan A , Albetkova AA , Keita MS , Rayfield MA , Peruski LF , Pierson A . Health Secur 2022 20 (6) 488-496 Control of infectious diseases requires the handling of infectious materials by both clinical and public health laboratories with exposure risks for laboratory personnel and environment. A comprehensive tool for assessing the capacity to manage these risks could enable the development of action plans for mitigation. Under the framework of the Global Health Security Agenda action package for biosafety and biosecurity, the authors developed a tool dedicated to assessing laboratory biosafety and biosecurity. The Biosafety and Biosecurity Laboratory Assessment Tool (BSS LAT) assesses the status of all laboratory biosafety core requirements across 10 different modules. It consists of a standardized spreadsheet-based tool that provides automatic scoring. It is designed to support national, regional, and global efforts to strengthen biosafety in clinical, public health, and veterinary laboratories. The BSS LAT was first used in Burkina Faso in collaboration with the African Society for Laboratory Medicine and the US Centers for Disease Control and Prevention to support the country in strengthening their biorisk management system. Since then, it has been successfully used in other countries (ie, Armenia, Burundi, Cameroon, Ghana, Guinea, Kazakhstan, Liberia), various settings (medical and veterinary laboratories), and translated into several languages (eg, English, French, Russian). The BSS LAT is a multipurpose tool that assists with standardization of biosafety and biosecurity requirements for all laboratories working with infectious materials, serves as a self-assessment guide for laboratories to develop improvement plans and reinforce capacities, and serves as a training guide for individual laboratories and networks or at the national level. The BSS LAT can also be used as a monitoring tool for the assessment of biosafety and biosecurity across all laboratories working with infectious materials at the national, regional, and global levels. |
Strengthening laboratory biosafety in Liberia during the COVID-19 pandemic: Experience from the Global Laboratory Leadership Programme.
Malik S , Taweh FM , Freeman M , Dogba JB , Gwesa GO , Tokpah M , Gbondin PP , Kohar TH , Hena JY , MaCauley JA , Pierson A , Rayfield MA , Peruski LF , Albetkova A , Balish A . One Health 2022 15 100442 BACKGROUND: The Global Laboratory Leadership Programme (GLLP) has biosafety and biosecurity as one of its core competencies and advocates for a One Health approach involving all relevant sectors across the human-animal-environment interface to empower national laboratory systems and strengthen health security. Decentralization of SARS-CoV-2 testing in Liberia coupled with an increase in the number of COVID-19 infections among laboratory professionals raised biosafety concerns. In response, a set of trainings on laboratory biosafety was launched for lab personnel across the country under the framework of the GLLP. The goal was to deliver a comprehensive package for laboratory biosafety in the context of SARS-CoV-2 through active learning. METHODS: Three one-day workshops were conducted between September and October 2020, training personnel from human, animal and environmental laboratories through a One Health approach. Concepts critical to laboratory biosafety were delivered in an interactive engagement format to ensure effective learning and retention of concepts. Pre- and post-training assessments were performed, and a paired t-test was used to assess knowledge gain. RESULTS: Of the 67 participants, 64 were from the human health sector, one from veterinary sector and two from environmental health sector. The average pre-test score was 41%. The main gaps identified were failure to acknowledge surgical antisepsis as a form of hand hygiene and recognition of PPE as the best risk control measure. The average post-test score was 75.5%. The mean difference of pre-test and post-test scores was statistically significant (p-value <0.001). Participants indicated satisfaction with the workshop content, mode of delivery and trainers' proficiency. CONCLUSIONS: The workshops were impactful as evidenced by significant improvement (34.5%) in the post-test scores and positive participant feedback. Repeated refresher trainings are vital to addressing the gaps, ensuring compliance, and promoting biosafety culture. GLLP's approach to cultivating multisectoral national laboratory leaders ready to take responsibility and ownership for capacity building provides a sustainable solution for attaining strong national laboratory systems better prepared for health emergencies and pandemics like COVID-19. |
National biosafety management system: A combined framework approach based on 15 key elements
Orelle A , Nikiema A , Zakaryan A , Albetkova AA , Rayfield MA , Peruski LF , Pierson A , Kachuwaire O . Front Public Health 2021 9 609107 The pervasive nature of infections causing major outbreaks have elevated biosafety and biosecurity as a fundamental component for resilient national laboratory systems. In response to international health security demands, the Global Health Security Agenda emphasizes biosafety as one of the prerequisites to respond effectively to infectious disease threats. However, biosafety management systems (BMS) in low-medium income countries (LMIC) remain weak due to fragmented implementation strategies. In addition, inefficiencies in implementation have been due to limited resources, inadequate technical expertise, high equipment costs, and insufficient political will. Here we propose an approach to developing a strong, self-sustaining BMS based on extensive experience in LMICs. A conceptual framework incorporating 15 key components to guide implementers, national laboratory leaders, global health security experts in building a BMS is presented. This conceptual framework provides a holistic and logical approach to the development of a BMS with all critical elements. It includes a flexible planning matrix with timelines easily adaptable to different country contexts as examples, as well as resources that are critical for developing sustainable technical expertise. |
COVID-19 Outbreaks in Correctional Facilities with Work-Release Programs - Idaho, July-November 2020.
Dunne EM , Morgan E , Wells-Moore B , Pierson S , Zakroff S , Haskell L , Link K , Powell J , Holland I , Elgethun K , Ball C , Haugen R , Hahn CG , Carter KK , Starr C . MMWR Morb Mortal Wkly Rep 2021 70 (16) 589-594 As of April 16, 2021, U.S. correctional and detention facilities reported 399,631 cases of COVID-19 in incarcerated persons, resulting in 2,574 deaths (1). During July 14-November 30, 2020, COVID-19 was diagnosed in 382 persons incarcerated in Idaho correctional facilities with work-release programs. Work-release programs (which place incarcerated persons in community businesses) have social and economic benefits, but might put participants at increased risk for bidirectional transmission of SARS-CoV-2, the virus that causes COVID-19. The Idaho Department of Correction (IDOC) operates 13 state-run correctional facilities, including six low-security facilities dedicated to work-release programs. This report describes COVID-19 outbreaks in five IDOC facilities with work-release programs,* provides the mitigation strategies that IDOC implemented, and describes the collaborative public health response. As of November 30, 2020, 382 outbreak-related COVID-19 cases were identified among incarcerated persons in five Idaho correctional facilities with work-release programs; two outbreaks were linked to food processing plants. Mitigation strategies that helped to control outbreaks in IDOC facilities with work-release programs included isolation of persons with COVID-19, identification and quarantine of close contacts, mass testing of incarcerated persons and staff members, and temporary suspension of work-release programs. Implementation of public health recommendations for correctional and detention facilities with work-release programs, including mass testing and identification of high-risk work sites, can help mitigate SARS-CoV-2 outbreaks. Incarcerated persons participating in work-release should be included in COVID-19 vaccination plans. |
Acanthamoeba granulomatous amoebic encephalitis after pediatric hematopoietic stem cell transplant
Coven SL , Song E , Steward S , Pierson CR , Cope JR , Ali IK , Ardura MI , Hall MW , Chung MG , Bajwa RPS . Pediatr Transplant 2017 21 (8) Acanthamoeba encephalitis is a rare, often fatal condition, particularly after HSCT, with 9 reported cases to date in the world literature. Our case was originally diagnosed with ALL at age 3 years, and after several relapses underwent HSCT at age 9 years. At 17 years of age, he was diagnosed with secondary AML for which he underwent a second allogeneic HSCT. He presented with acute-onset worsening neurological deficits on day +226 after the second transplant and a post-mortem diagnosis of Acanthamoeba encephalitis was established, with the aid of the CDC. |
Dengue viruses cluster antigenically but not as discrete serotypes
Katzelnick LC , Fonville JM , Gromowski GD , Arriaga JB , Green A , James SL , Lau L , Montoya M , Wang C , VanBlargan LA , Russell CA , Thu HM , Pierson TC , Buchy P , Aaskov JG , Munoz-Jordan JL , Vasilakis N , Gibbons RV , Tesh RB , Osterhaus AD , Fouchier RA , Durbin A , Simmons CP , Holmes EC , Harris E , Whitehead SS , Smith DJ . Science 2015 349 (6254) 1338-43 The four genetically divergent dengue virus (DENV) types are traditionally classified as serotypes. Antigenic and genetic differences among the DENV types influence disease outcome, vaccine-induced protection, epidemic magnitude, and viral evolution. We characterized antigenic diversity in the DENV types by antigenic maps constructed from neutralizing antibody titers obtained from African green monkeys and after human vaccination and natural infections. Genetically, geographically, and temporally, diverse DENV isolates clustered loosely by type, but we found that many are as similar antigenically to a virus of a different type as to some viruses of the same type. Primary infection antisera did not neutralize all viruses of the same DENV type any better than other types did up to 2 years after infection and did not show improved neutralization to homologous type isolates. That the canonical DENV types are not antigenically homogeneous has implications for vaccination and research on the dynamics of immunity, disease, and the evolution of DENV. |
SLIPTA e-tool improves laboratory audit process in Vietnam and Cambodia
Nguyen TT , McKinney B , Pierson A , Luong KN , Hoang QT , Meharwal S , Carvalho HM , Nguyen CQ , Nguyen KT , Bond KB . Afr J Lab Med 2014 3 (2) 219 BACKGROUND: The Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) checklist is used worldwide to drive quality improvement in laboratories in developing countries and to assess the effectiveness of interventions such as the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme. However, the paperbased format of the checklist makes administration cumbersome and limits timely analysis and communication of results. Development of e-Tool: In early 2012, the SLMTA team in Vietnam developed an electronic SLIPTA checklist tool. The e-Tool was pilot tested in Vietnam in mid-2012 and revised. It was used during SLMTA implementation in Vietnam and Cambodia in 2012 and 2013 and further revised based on auditors' feedback about usability. OUTCOMES: The SLIPTA e-Tool enabled rapid turn-around of audit results, reduced workload and language barriers and facilitated analysis of national results. Benefits of the e-Tool will be magnified with in-country scale-up of laboratory quality improvement efforts and potential expansion to other countries. |
Strengthening public health laboratory capacity in Thailand for International Health Regulations (IHR) (2005)
Peruski AH , Birmingham M , Tantinimitkul C , Chungsamanukool L , Chungsamanukool P , Guntapong R , Pulsrikarn C , Saengklai L , Supawat K , Thattiyaphong A , Wongsommart D , Wootta W , Nikiema A , Pierson A , Peruski LF , Liu X , Rayfield MA . WHO South East Asia J Public Health 2014 3 266-272 INTRODUCTION: Thailand conducted a national laboratory assessment of core capacities related to the International Health Regulations (IHR) (2005), and thereby established a baseline to measure future progress. The assessment was limited to public laboratories found within the Thai Bureau of Quality and Safety of Food, National Institute of Health and regional medical science centres. METHODS: The World Health Organization (WHO) laboratory assessment tool was adapted to Thailand through a participatory approach. This adapted version employed a specific scoring matrix and comprised 16 modules with a quantitative output. Two teams jointly performed the on-site assessments in December 2010 over a two-week period, in 17 public health laboratories in Thailand. The assessment focused on the capacity to identify and accurately detect pathogens mentioned in Annex 2 of the IHR (2005) in a timely manner, as well as other public health priority pathogens for Thailand. RESULTS: Performance of quality management, budget and finance, data management and communications was considered strong (>90%); premises quality, specimen collection, biosafety, public health functions, supplies management and equipment availability were judged as very good (>70% but ≤90%); while microbiological capacity, staffing, training and supervision, and information technology needed improvement (>60% but ≤70%). CONCLUSIONS: This assessment is a major step in Thailand towards development of an optimized and standardized national laboratory network for the detection and reporting of infectious disease that would be compliant with IHR (2005). The participatory strategy employed to adapt an international tool to the Thai context can also serve as a model for use by other countries in the Region. The participatory approach probably ensured better quality and ownership of the results, while providing critical information to help decision-makers determine where best to invest finite resources. |
The body adiposity index (hip circumference / height(1.5)) is not a more accurate measure of adiposity than is BMI, waist circumference, or hip circumference
Freedman DS , Thornton J , Pi-Sunyer FX , Heymsfield SB , Wang J , Pierson Jr RN , Blanck HM , Gallagher D . Obesity (Silver Spring) 2012 20 (12) 2438-44 Based on cross-sectional analyses, it was suggested that hip circumference divided by height (1.5) minus 18 (the body adiposity index, BAI), could directly estimate percent body fat without the need for further correction for sex or age. We compared the prediction of percent body fat, as assessed by dual-energy x-ray absorptiometry (PBF(DXA)), by BAI, BMI, and circumference (waist and hip) measurements among 1151 adults who had a total body scan by DXA and circumference measurements from 1993 through 2006. After accounting for sex, we found that PBF(DXA) was related similarly to BAI, BMI, waist circumference, and hip circumference. In general, BAI underestimated PBF(DXA) among men (2.5%) and overestimated PBF(DXA) among women (4%), but the magnitudes of these biases varied with the level of body fatness. The addition of covariates and quadratic terms for the body size measures in regression models substantially improved the prediction of PBF(DXA), but none of the models based on BAI could more accurately predict PBF(DXA) than could those based on BMI or circumferences. We conclude that the use of BAI as an indicator of adiposity is likely to produce biased estimates of percent body fat, with the errors varying by sex and level of body fatness. Although regression models that account for the non-linear association, as well as the influence of sex, age and race, can yield more accurate estimates of PBF(DXA), estimates based on BAI are not more accurate than those based on BMI, waist circumference, or hip circumference. |
Varicella zoster virus DNA at inoculation sites and in saliva after Zostavax immunization.
Pierson DL , Mehta SK , Gilden D , Cohrs RJ , Nagel MA , Schmid DS , Tyring SK . J Infect Dis 2011 203 (11) 1542-5 Analysis of 36 individuals over age 60 years who were immunized with Zostavax revealed varicella zoster virus (VZV) DNA in swabs of skin inoculation sites obtained immediately after immunization in 18 (50%) of 36 subjects (copy number per nanogram of total DNA, 28 to 2.1 x 10(6)) and in saliva collected over 28 days in 21 (58%) of 36 subjects (copy number, 20 to 248). Genotypic analysis of DNA extracted from 9 random saliva samples identified vaccine virus in all instances. In some immunized individuals over age 60, vaccine virus DNA is shed in saliva up to 4 weeks. |
Risk factors associated with patient assaults of home healthcare workers
Galinsky T , Feng HA , Streit J , Brightwell W , Pierson K , Parsons K , Proctor C . Rehabil Nurs 2010 35 (5) 206-215 This study used surveys from 677 home healthcare aides and nurses to explore factors associated with assaults by patients. Among respondents, 4.6% reported one or more patient assaults (being hit, kicked, pinched, shoved, or bitten) during the past year Logistic regression analysis examined associations between several potential risk factors and assaults. Three factors were significant, including having one or more patients with dementia (OR = 4.31, 95% CI 1.47-12.67), routinely handling patients (OR = 8.48, 95% CI 1.89-37.94), and perceiving threats of violence by others in and around patients' homes (OR = 4.45, 95% CI 7.75-11.32). Assaults were not significantly associated with worker age, gender, race, job title, hours of work, or use of needles during patient care. Assaulted workers and workers who perceived threats of violence by others were significantly more likely to have shortened home care visits. More detailed research is needed to confirm these results and evaluate methods to reduce assault risk. |
Classification of body fatness by body mass index-for-age categories among children
Freedman DS , Wang J , Thornton JC , Mei Z , Sopher AB , Pierson RN Jr , Dietz WH , Horlick M . Arch Pediatr Adolesc Med 2009 163 (9) 805-11 OBJECTIVE: To examine the ability of various body mass index (BMI)-for-age categories, including the Centers for Disease Control and Prevention's 85th to 94th percentiles, to correctly classify the body fatness of children and adolescents. DESIGN: Cross-sectional. SETTING: The New York Obesity Research Center at St Luke's-Roosevelt Hospital from 1995 to 2000. PARTICIPANTS: Healthy 5- to 18-year-old children and adolescents (N = 1196) were recruited in the New York City area through newspaper notices, announcements at schools and activity centers, and word of mouth. MAIN OUTCOME MEASURES: Percent body fat as determined by dual-energy x-ray absorptiometry. Body fatness cutoffs were chosen so that the number of children in each category (normal, moderate, and elevated fatness) would equal the number of children in the corresponding BMI-for-age category (<85th percentile, 85th-94th percentile, and > or =95th percentile, respectively). RESULTS: About 77% of the children who had a BMI for age at or above the 95th percentile had an elevated body fatness, but levels of body fatness among children who had a BMI for age between the 85th and 94th percentiles (n = 200) were more variable; about one-half of these children had a moderate level of body fatness, but 30% had a normal body fatness and 20% had an elevated body fatness. The prevalence of normal levels of body fatness among these 200 children was highest among black children (50%) and among those within the 85th to 89th percentiles of BMI for age (40%). CONCLUSION: Body mass index is an appropriate screening test to identify children who should have further evaluation and follow-up, but it is not diagnostic of level of adiposity. |
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