Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 331 Records) |
Query Trace: Baker B [original query] |
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Interlaboratory comparison of a multiplex immunoassay that measures human serum IgG antibodies against six-group B streptococcus polysaccharides
Le Doare K , Gaylord MA , Anderson AS , Andrews N , Baker CJ , Bolcen S , Felek A , Giardina PC , Grube CD , Hall T , Hallis B , Izu A , Madhi SA , Maniatis P , Matheson M , Mawas F , McKeen A , Rhodes J , Alston B , Patel P , Schrag S , Simon R , Tan CY , Taylor S , Kwatra G , Gorringe A . Hum Vaccin Immunother 2024 20 (1) 2330138 Measurement of IgG antibodies against group B streptococcus (GBS) capsular polysaccharide (CPS) by use of a standardized and internationally accepted multiplex immunoassay is important for the evaluation of candidate maternal GBS vaccines in order to compare results across studies. A standardized assay is also required if serocorrelates of protection against invasive GBS disease are to be established in infant sera for the six predominant GBS serotypes since it would permit the comparison of results across the six serotypes. We undertook an interlaboratory study across five laboratories that used standardized assay reagents and protocols with a panel of 44 human sera to measure IgG antibodies against GBS CPS serotypes Ia, Ib, II, III, IV, and V. The within-laboratory intermediate precision, which included factors like the lot of coated beads, laboratory analyst, and day, was generally below 20% relative standard deviation (RSD) for all six serotypes, across all five laboratories. The cross-laboratory reproducibility was < 25% RSD for all six serotypes, which demonstrated the consistency of results across the different laboratories. Additionally, anti-CPS IgG concentrations for the 44-member human serum panel were established. The results of this study showed assay robustness and that the resultant anti-CPS IgG concentrations were reproducible across laboratories for the six GBS CPS serotypes when the standardized assay was used. |
Deaths associated with pediatric hepatitis of unknown etiology, United States, October 2021-June 2023
Almendares O , Baker JM , Sugerman DE , Parashar UD , Reagan-Steiner S , Kirking HL , Gastañaduy PA , Tate JE . Emerg Infect Dis 2024 30 (4) 644-53 During October 2021-June 2023, a total of 392 cases of acute hepatitis of unknown etiology in children in the United States were reported to Centers for Disease Control and Prevention as part of national surveillance. We describe demographic and clinical characteristics, including potential involvement of adenovirus in development of acute hepatitis, of 8 fatally ill children who met reporting criteria. The children had diverse courses of illness. Two children were immunocompromised when initially brought for care. Four children tested positive for adenovirus in multiple specimen types, including 2 for whom typing was completed. One adenovirus-positive child had no known underlying conditions, supporting a potential relationship between adenovirus and acute hepatitis in previously healthy children. Our findings emphasize the importance of continued investigation to determine the mechanism of liver injury and appropriate treatment. Testing for adenovirus in similar cases could elucidate the role of the virus. |
Carceral health is public health
Hagan LM , Mosites E , Hughes-Baker L , Butler J . Emerg Infect Dis 2024 30 (13) S1-s4 The articles in this supplement of Emerging Infectious Diseases, Infectious Diseases and Carceral Health, explore ways that persons with infectious disease risks are concentrated within carceral systems, how the physical environment and culture within facilities can contribute to disease spread, the wide variations in access to healthcare during confinement, and implications that those compounding factors have on re-entry and broader community health. Many articles identify actionable ways to address those challenges and to promote a mainstream understanding of carceral health as a critical component of public health. |
Plasma per- and polyfluoroalkyl substance mixtures during pregnancy and duration of breastfeeding in the New Hampshire birth cohort study
Romano ME , Gallagher LG , Price G , Crawford KA , Criswell R , Baker E , Botelho JC , Calafat AM , Karagas MR . Int J Hyg Environ Health 2024 258 114359 BACKGROUND: Prior studies suggest that prenatal per- and polyfluoroalkyl substances (PFAS) exposures are associated with shorter breastfeeding duration. Studies assessing PFAS mixtures and populations in North America are sparse. METHODS: We quantified PFAS concentrations in maternal plasma collected during pregnancy in the New Hampshire Birth Cohort Study (2010-2017). Participants completed standardized breastfeeding surveys at regular intervals until weaning (n = 813). We estimated associations between mixtures of 5 PFAS and risk of stopping exclusive breastfeeding before 6 months or any breastfeeding before 12 months using probit Bayesian kernel machine regression. For individual PFAS, we calculated the relative risk and hazard ratio (HR) of stopping breastfeeding using modified Poisson regression and accelerated failure time models respectively. RESULTS: PFAS mixtures were associated with stopping exclusive breastfeeding before 6 months, primarily driven by perfluorooctanoate (PFOA). We observed statistically significant trends in the association of perfluorohexane sulfonate (PFHxS), PFOA, and perfluorononanoate (PFNA) (p-trends≤0.02) with stopping exclusive breastfeeding. Participants in the highest PFOA quartile had a 28% higher risk of stopping exclusive breastfeeding before 6 months compared to those in the lowest quartile (95% Confidence Interval: 1.04, 1.56). Similar trends were observed for PFHxS and PFNA with exclusive breastfeeding (p-trends≤0.05). PFAS were not associated with stopping any breastfeeding before 12 months. CONCLUSIONS: In this cohort, we observed that participants with greater overall plasma PFAS concentrations had greater risk of stopping exclusive breastfeeding before 6 months and associations were driven largely by PFOA. These findings further support the growing literature indicating that PFAS may be associated with shorter duration of breastfeeding. |
Neuroinvasive bacillus cereus infection in immunocompromised hosts: Epidemiologic investigation of 5 patients with acute myeloid leukemia
Little JS , Coughlin C , Hsieh C , Lanza M , Huang WY , Kumar A , Dandawate T , Tucker R , Gable P , Vazquez Deida AA , Moulton-Meissner H , Stevens V , McAllister G , Ewing T , Diaz M , Glowicz J , Winkler ML , Pecora N , Kubiak DW , Pearson JC , Luskin MR , Sherman AC , Woolley AE , Brandeburg C , Bolstorff B , McHale E , Fortes E , Doucette M , Smole S , Bunnell C , Gross A , Platt D , Desai S , Fiumara K , Issa NC , Baden LR , Rhee C , Klompas M , Baker MA . Open Forum Infect Dis 2024 11 (3) ofae048 BACKGROUND: Bacillus cereus is a ubiquitous gram-positive rod-shaped bacterium that can cause sepsis and neuroinvasive disease in patients with acute leukemia or neutropenia. METHODS: A single-center retrospective review was conducted to evaluate patients with acute leukemia, positive blood or cerebrospinal fluid test results for B cereus, and abnormal neuroradiographic findings between January 2018 and October 2022. Infection control practices were observed, environmental samples obtained, a dietary case-control study completed, and whole genome sequencing performed on environmental and clinical Bacillus isolates. RESULTS: Five patients with B cereus neuroinvasive disease were identified. All patients had acute myeloid leukemia (AML), were receiving induction chemotherapy, and were neutropenic. Neurologic involvement included subarachnoid or intraparenchymal hemorrhage or brain abscess. All patients were treated with ciprofloxacin and survived with limited or no neurologic sequelae. B cereus was identified in 7 of 61 environmental samples and 1 of 19 dietary protein samples-these were unrelated to clinical isolates via sequencing. No point source was identified. Ciprofloxacin was added to the empiric antimicrobial regimen for patients with AML and prolonged or recurrent neutropenic fevers; no new cases were identified in the ensuing year. CONCLUSIONS: B cereus is ubiquitous in the hospital environment, at times leading to clusters with unrelated isolates. Fastidious infection control practices addressing a range of possible exposures are warranted, but their efficacy is unknown and they may not be sufficient to prevent all infections. Thus, including B cereus coverage in empiric regimens for patients with AML and persistent neutropenic fever may limit the morbidity of this pathogen. |
Evaluation of changes in knowledge and attitude among youth after a one-hour introduction to workplace safety and health: Safety Matters
Okun A , Guerin R , Smith R , Baker D , DiMeo-Ediger M . J Safety Res 2024 [Epub ahead of print] Introduction: Young workers in the United States are injured at higher rates than adults, a trend that has persisted for more than two decades. Despite known risks, young people enter the workforce with little-or-no preparation for the hazards they may face. In 2016, the National Institute for Occupational Safety and Health and American Industrial Hygiene Association developed Safety Matters, a one-hour educational module to raise awareness of workplace safety and health among young people. Method: A pilot project was conducted to evaluate the effectiveness of Safety Matters to positively change workplace safety and health knowledge and attitude scores among a sample of 283 youth in Colorado. Train-the-trainer sessions prepared volunteer safety and health professionals to deliver Safety Matters with fidelity and to conduct the assessment immediately prior to and following the program. Results: After receiving Safety Matters, participants had statistically significant (p < 0.001) increased scores for both workplace safety and health knowledge (Cohen's d = 1.12; large effect size) and importance (attitude) (Cohen's d = 0.51; medium effect size). Although univariate analyses showed knowledge and attitude scores significantly increased for all demographic groups examined, there were statistically significant differences in knowledge scores by participant age (p < 0.01), ethnicity (p < 0.05), and race (p < 0.001) and statistically significant differences in attitude scores by participant race (p < 0.001). However, when race and ethnicity were both used as predictors in a regression model, only race continued to predict statistically significant (p < 0.01) changes in knowledge and attitude. Conclusions: This project introduces a promising, community-based model for a one-hour introduction to workplace safety and health on which future, job-specific safety training can be built. Practical Applications: Safety and health professionals can play a critical role in promoting the health and safety of young workers. Adapting health and safety programs to diverse youth populations may enhance program relevance and receptivity. |
Vaccine-associated varicella and rubella infections in severe combined immunodeficiency with isolated CD4 lymphocytopenia and mutations in IL7R detected by tandem whole exome sequencing and chromosomal microarray.
Bayer DK , Martinez CA , Sorte HS , Forbes LR , Demmler-Harrison GJ , Hanson IC , Pearson NM , Noroski LM , Zaki SR , Bellini WJ , Leduc MS , Yang Y , Eng CM , Patel A , Rodningen OK , Muzny DM , Gibbs RA , Campbell IM , Shaw CA , Baker MW , Zhang V , Lupski JR , Orange JS , Seeborg FO , Stray-Pedersen A . Clin Exp Immunol 2014 178 (3) 459-69 In areas without newborn screening for severe combined immunodeficiency (SCID), disease-defining infections may lead to diagnosis, and in some cases, may not be identified prior to the first year of life. We describe a female infant who presented with disseminated vaccine-acquired varicella (VZV) and vaccine-acquired rubella infections at 13 months of age. Immunological evaluations demonstrated neutropenia, isolated CD4 lymphocytopenia, the presence of CD8(+) T cells, poor lymphocyte proliferation, hypergammaglobulinaemia and poor specific antibody production to VZV infection and routine immunizations. A combination of whole exome sequencing and custom-designed chromosomal microarray with exon coverage of primary immunodeficiency genes detected compound heterozygous mutations (one single nucleotide variant and one intragenic copy number variant involving one exon) within the IL7R gene. Mosaicism for wild-type allele (20-30%) was detected in pretransplant blood and buccal DNA and maternal engraftment (5-10%) demonstrated in pretransplant blood DNA. This may be responsible for the patient's unusual immunological phenotype compared to classical interleukin (IL)-7Rα deficiency. Disseminated VZV was controlled with anti-viral and immune-based therapy, and umbilical cord blood stem cell transplantation was successful. Retrospectively performed T cell receptor excision circle (TREC) analyses completed on neonatal Guthrie cards identified absent TREC. This case emphasizes the danger of live viral vaccination in severe combined immunodeficiency (SCID) patients and the importance of newborn screening to identify patients prior to high-risk exposures. It also illustrates the value of aggressive pathogen identification and treatment, the influence newborn screening can have on morbidity and mortality and the significant impact of newer genomic diagnostic tools in identifying the underlying genetic aetiology for SCID patients. |
Francisella tularensis bone and joint infections: United States, 2004-2023
Beeson AM , Baker M , Dell B , Schnitzler H , Oltean HN , Woodall T , Riedo F , Schwartz A , Petersen J , Hinckley AF , Marx GE . Clin Infect Dis 2024 78 S67-s70 Tularemia is caused by the highly infectious bacterium Francisella tularensis, which is recognized as a Tier 1 bioterrorism agent. Tularemia has a range of recognized clinical manifestations, but fewer than 20 bone or joint infections from 6 countries have been reported in the literature to date. This series includes 13 cases of F. tularensis septic arthritis or osteomyelitis in the United States during 2004-2023 and describes exposures, clinical presentation, diagnosis, and outcomes for this rare but severe form of tularemia. Clinicians should consider F. tularensis in patients with compatible exposures or a history of joint replacement or immunosuppression. |
Rabies experts on demand: A cross-sectional study describing the use of a rabies telehealth service
Baker SE , Ross YB , Ellison JA , Monroe BP , Orciari LA , Petersen BW , Rao AK , Wallace RM . Public Health Chall 2023 2 (3) BACKGROUND: Rabies expert on demand (REOD) telehealth service is provided by the U.S. Centers for Disease Control and Prevention (CDC) to assist public health practitioners, health providers, and the public to interpret national and international rabies prevention guidelines. REOD is staffed by subject matter experts of the CDC Poxvirus and Rabies Branch to assess each unique situation and provide evidence-based guidance to stakeholders. This study aims to describe the utilization of a rabies telehealth system and provide insight into common consultations. METHODS: A cross-sectional study of the nature of inquiries to REOD was done using the data collected from September 1, 2017 to September 30, 2021. An inquiry tracking form and Microsoft Access database were developed to document all inquiries received. Inquired ones were summarized to determine the frequency of inquiries by month, category, and location. RESULTS: Over a 49-month period, REOD received 5228 inquiries. Peak inquiries (n = 108) occurred during August 2019. The most frequent inquiries received pertained to risk assessment and management of rabies exposures (n = 1109), requests for testing assistance (n = 912), consultation for suspected human rabies (n = 746), rabies exposures and post-bite treatment occurring internationally (n = 310), and consultation for deviations in the recommended pre- and postexposure prophylaxis regimen (n = 300). CONCLUSION: REOD is a global resource for consultation related to managing rabies exposures, diagnostic issues, and rabies control strategies. REOD is a regularly utilized CDC service, as the demand for up-to-date rabies guidance remains high. REOD fulfills a critical role for the interpretation and consultation on rabies prevention guidelines to stakeholder. |
Prevention and control of meningococcal disease: recommendations of the Advisory Committee on Immunization Practices (ACIP)
Cohn AC , MacNeil JR , Clark TA , Ortega-Sanchez IR , Briere EZ , Meissner HC , Baker CJ , Messonnier NE . MMWR Recomm Rep 2013 62 1-28 Meningococcal disease describes the spectrum of infections caused by Neisseria meningiditis, including meningitdis, bacteremia, and bacteremic pneumonia. Two quadrivalent meningococcal polysaccharide-protein conjugate vaccines that provide protection against meningococcal serogroups A, C, W, and Y (MenACWY-D [Menactra, manufactured by Sanofi Pasteur, Inc., Swiftwater, Pennsylvania] and MenACWY-CRM [Menveo, manufactured by Novartis Vaccines, Cambridge, Massachusetts]) are licensed in the United States for use among persons aged 2 through 55 years. MenACWY-D also is licensed for use among infants and toddlers aged 9 through 23 months. Quadrivalent meningococcal polysaccharide vaccine (MPSV4 [Menommune, manufactured by sanofi pasteur, Inc., Swiftwater, Pennsylvania]) is the only vaccine licensed for use among persons aged ≥56 years. A bivalent meningococcal polysaccharide protein conjugate vaccine that provides protection against meningococcal serogroups C and Y along with Haemophilus influenzae type b (Hib) (Hib-MenCY-TT [MenHibrix, manufactured by GlaxoSmithKline Biologicals, Rixensart, Belgium]) is licensed for use in children aged 6 weeks through 18 months. This report compiles and summarizes all recommendations from CDC's Advisory Committee on Immunization Practices (ACIP) regarding prevention and control of meningococcal disease in the United States, specifically the changes in the recommendations published since 2005 (CDC. Prevention and control of meningococcal disease: recommendations of the Advisory Committee on Immunization Practices [ACIP]. MMWR 2005;54 [No. RR-7]). As a comprehensive summary of previously published recommendations, this report does not contain any new recommendations; it is intended for use by clinicians as a resource. ACIP recommends routine vaccination with a quadrivalent meningococcal conjugate vaccine (MenACWY) for adolescents aged 11 or 12 years, with a booster dose at age 16 years. ACIP also recommends routine vaccination for persons at increased risk for meningococcal disease (i.e., persons who have persistent complement component deficiencies, persons who have anatomic or functional asplenia, microbiologists who routinely are exposed to isolates of N. meningitidis, military recruits, and persons who travel to or reside in areas in which meningococcal disease is hyperendemic or epidemic). Guidelines for antimicrobial chemoprophylaxis and for evaluation and management of suspected outbreaks of meningococcal disease also are provided. |
The distribution of triatomine (Hemiptera: Reduviidae) vectors of Trypanosoma cruzi (Kinetoplastida: Trypanosomatidae) in Illinois and Missouri: historical records and specimen submissions from community science programs
Santos EM , Santanello CD , Curtis-Robles R , Killets K , Lawrence G , Sevenshadows J , Mahoney MJ , Baker M , Hamer SA . J Med Entomol 2023 Triatomine species (kissing bugs) infected with Trypanosoma cruzi are found across the southern United States. The northern limits of Trypanosoma cruzi infected kissing bugs are less understood. The objective of this work was to describe the locations of kissing bugs from Illinois and Missouri based on historical records, submissions to Texas A&M University's (TAMU) Kissing Bug Community Science Program and the Centers for Disease Control and Prevention (CDC), and records from online platforms (iNaturalist, BugGuide, and GBIF) up to and including 2022. A total of 228 records were discovered, including 186 from historical or observation platforms and 42 specimens submitted to TAMU or CDC. Species included Triatoma sanguisuga (221 total records, 9 nymphs) and Triatoma lecticularia (7 records). Notably, nearly all (24/26) records submitted to TAMU were collected indoors. Twelve of the 30 (40%) specimens tested were positive for the presence of T. cruzi, including parasite discrete taxonomic units TcI and TcIV. One triatomine sample had been found in a bed feeding on the submitter; this bug was positive for T. cruzi and had evidence of human blood in its gut. Records suggest a ubiquitous distribution in Missouri and potentially to the northernmost border in Illinois. Further investigations into triatomine distribution and infection status are needed within states assumed to be northern limits in order to create public health and veterinary health messaging and baseline distributional maps from which to measure future range shifts in relation to a changing climate. |
2022 American College of Rheumatology Guideline for Exercise, Rehabilitation, Diet, and Additional Integrative Interventions for Rheumatoid Arthritis
England BR , Smith BJ , Baker NA , Barton JL , Oatis CA , Guyatt G , Anandarajah A , Carandang K , Chan KK , Constien D , Davidson E , Dodge CV , Bemis-Dougherty A , Everett S , Fisher N , Fraenkel L , Goodman SM , Lewis J , Menzies V , Moreland LW , Navarro-Millan I , Patterson S , Phillips LR , Shah N , Singh N , White D , AlHeresh R , Barbour KE , Bye T , Guglielmo D , Haberman R , Johnson T , Kleiner A , Lane CY , Li LC , Master H , Pinto D , Poole JL , Steinbarger K , Sztubinski D , Thoma L , Tsaltskan V , Turgunbaev M , Wells C , Turner AS , Treadwell JR . Arthritis Rheumatol 2023 75 (8) 1299-1311 OBJECTIVE: To develop initial American College of Rheumatology (ACR) guidelines on the use of exercise, rehabilitation, diet, and additional interventions in conjunction with disease-modifying antirheumatic drugs (DMARDs) as part of an integrative management approach for people with rheumatoid arthritis (RA). METHODS: An interprofessional guideline development group constructed clinically relevant Population, Intervention, Comparator, and Outcome (PICO) questions. A literature review team then completed a systematic literature review and applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate the certainty of evidence. An interprofessional Voting Panel (n = 20 participants) that included 3 individuals with RA achieved consensus on the direction (for or against) and strength (strong or conditional) of recommendations. RESULTS: The Voting Panel achieved consensus on 28 recommendations for the use of integrative interventions in conjunction with DMARDs for the management of RA. Consistent engagement in exercise received a strong recommendation. Of 27 conditional recommendations, 4 pertained to exercise, 13 to rehabilitation, 3 to diet, and 7 to additional integrative interventions. These recommendations are specific to RA management, recognizing that other medical indications and general health benefits may exist for many of these interventions. CONCLUSION: This guideline provides initial ACR recommendations on integrative interventions for the management of RA to accompany DMARD treatments. The broad range of interventions included in these recommendations illustrates the importance of an interprofessional, team-based approach to RA management. The conditional nature of most recommendations requires clinicians to engage persons with RA in shared decision-making when applying these recommendations. |
The impact of injury control research centers: Advancing the field of injury and violence prevention
Baker W , Skillman M , Rocha L , Bayne A , Whitehouse S , Murphy E , Papanikolaou M , Caples M , Choudhary E . J Saf Res 2023 Introduction: The Centers for Disease Control and Prevention's (CDC) National Center for Injury Prevention and Control (NCIPC) funds Injury Control Research Centers (ICRCs). These centers study injury and violence prevention through three core areas: (1) Research conducts cutting-edge, multidisciplinary research in the injury and violence prevention field; (2) Outreach translates injury and violence prevention research into action; and (3) Training educates and trains the next generation of injury and violence prevention professionals. We examined ICRC work from 2012 to 2019 to determine whether they fulfilled their goal of furthering injury and violence prevention research and practice. Methods: We created a database of core area accomplishments reported through annual and interim progress reports. These reports track core area accomplishments by injury and violence prevention topic area, publications, partnerships, and trainings. Results: From 2012 to 2019, ten ICRCs from two funding cycles received approximately $49 million. ICRCs reported 703 research, 1,432 outreach, and 660 training accomplishments. There were also 342 accomplishments contributing to a special tool or resource. These accomplishments focused on preventing traumatic brain injury, suicide, adverse childhood experiences, and transportation safety. ICRCs produced over 3,500 peer-reviewed publications. ICRCs reported over 3,600 accomplishments partnered with academic institutions, public health agencies, healthcare, and non-profit organizations. ICRCs created resources for audiences such as students, law enforcement, and policy makers. ICRCs trained 3,131 students and faculty. Practical Applications: ICRCs are the hubs of modern research and practice in the injury and violence prevention field. They successfully bring together stakeholders from disparate disciplines, perspectives, and agencies to join forces and tackle critical public health problems. Conclusion: ICRCs are an integral component of NCIPC's, CDC's and the Department of Health and Human Service's missions to protect and enhance the health of Americans. Research covered NCIPC research priorities over the funding period, furthering injury and violence prevention research and working as a foundation to practice and policy. Outreach and partnerships with an array of organizations put research into action. Trainings educated the new generation of injury and violence prevention professionals. © 2023 National Safety Council and Elsevier Ltd |
Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group
Baker KS , Jauneikaite E , Nunn JG , Midega JT , Atun R , Holt KE , Walia K , Howden BP , Tate H , Okeke IN , Carattoli A , Hsu LY , Hopkins KL , Muloi DM , Wheeler NE , Aanensen DM , Mason LCE , Rodgus J , Hendriksen RS , Essack SY , Egyir B , Halpin AL , MacCannell DR , Campos J , Srikantiah P , Feasey NA , Peacock SJ . Lancet Microbe 2023 4 (12) e1035-e1039 Nearly a century after the beginning of the antibiotic era, which has been associated with unparalleled improvements in human health and reductions in mortality associated with infection, the dwindling pipeline for new antibiotic classes coupled with the inevitable spread of antimicrobial resistance (AMR) poses a major global challenge. Historically, surveillance of bacteria with AMR typically relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionise AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and providing real-time actionable information for treating and preventing infection. However, many barriers remain to be overcome before genomic technologies can be adopted as a standard part of routine AMR surveillance around the world. Accordingly, the Surveillance and Epidemiology of Drug-resistant Infections Consortium convened an expert working group to assess the benefits and challenges of using genomics for AMR surveillance. In this Series, we detail these discussions and provide recommendations from the working group that can help to realise the massive potential benefits for genomics in surveillance of AMR. |
Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities
Jauneikaite E , Baker KS , Nunn JG , Midega JT , Hsu LY , Singh SR , Halpin AL , Hopkins KL , Price JR , Srikantiah P , Egyir B , Okeke IN , Holt KE , Peacock SJ , Feasey NA . Lancet Microbe 2023 4 (12) e1040-e1046 Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the identified challenges and potential benefits of genomic AMR surveillance in health-care settings, and outline the recommendations of the working group to realise this potential. These recommendations include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics), and building capacity at local, national, and regional levels using hub and spoke models. |
Persons 'never treated' in mass drug administration for lymphatic filariasis: identifying programmatic and research needs from a series of research review meetings 2020-2021
Brady MA , Toubali E , Baker M , Long E , Worrell C , Ramaiah K , Graves P , Hollingsworth TD , Kelly-Hope L , Stukel D , Tripathi B , Means AR , Matendechero SH , Krentel A . Int Health 2023 As neglected tropical disease programs rely on participation in rounds of mass drug administration (MDA), there is concern that individuals who have never been treated could contribute to ongoing transmission, posing a barrier to elimination. Previous research has suggested that the size and characteristics of the never-treated population may be important but have not been sufficiently explored. To address this critical knowledge gap, four meetings were held from December 2020 to May 2021 to compile expert knowledge on never treatment in lymphatic filariasis (LF) MDA programs. The meetings explored four questions: the number and proportion of people never treated, their sociodemographic characteristics, their infection status and the reasons why they were not treated. Meeting discussions noted key issues requiring further exploration, including how to standardize measurement of the never treated, adapt and use existing tools to capture never-treated data and ensure representation of never-treated people in data collection. Recognizing that patterns of never treatment are situation specific, participants noted measurement should be quick, inexpensive and focused on local solutions. Furthermore, programs should use existing data to generate mathematical models to understand what levels of never treatment may compromise LF elimination goals or trigger programmatic action. |
Paediatric acute hepatitis of unknown aetiology: a national surveillance investigation in the USA during 2021 and 2022
Cates J , Baker JM , Almendares O , Balachandran N , McKeever ER , Kambhampati AK , Cubenas C , Vinjé J , Cannon JL , Chhabra P , Freeman B , Reagan-Steiner S , Bhatnagar J , Gastañaduy PA , Kirking HL , Sugerman D , Parashar UD , Tate JE . Lancet Child Adolesc Health 2023 7 (11) 773-785 BACKGROUND: Adenovirus is a known cause of hepatitis in immunocompromised children, but not in immunocompetent children. In April, 2022, following multiple reports of hepatitis of unknown aetiology and adenovirus viraemia in immunocompetent children in the USA and UK, the US Centers for Disease Control and Prevention (CDC) and jurisdictional health departments initiated national surveillance of paediatric acute hepatitis of unknown aetiology. We aimed to describe the clinical and epidemiological characteristics of children identified with hepatitis of unknown aetiology between Oct 1, 2021, and Sept 30, 2022, in the USA and to compare characteristics of those who tested positive for adenovirus with those who tested negative. METHODS: In this national surveillance investigation in the USA, children were identified for investigation if they were younger than 10 years with elevated liver transaminases (>500 U/L) who had an unknown cause for their hepatitis and onset on or after Oct 1, 2021. We reviewed medical chart abstractions, which included data on demographics, underlying health conditions, signs and symptoms of illness, laboratory results, vaccination history, radiological and liver pathology findings, diagnoses and treatment received, and outcomes. Caregiver interviews were done to obtain information on symptoms and health-care utilisation for the hepatitis illness, medical history, illness in close contacts or at school or daycare, diet, travel, and other potential exposures. Blood, stool, respiratory, and tissue specimens were evaluated according to clinician discretion and available specimens were submitted to CDC for additional laboratory testing or pathology evaluation. FINDINGS: Surveillance identified 377 patients from 45 US jurisdictions with hepatitis of unknown aetiology with onset from Oct 1, 2021, to Sept 30, 2022. The median age of patients was 2·8 years (IQR 1·2-5·0) and 192 (51%) were male, 184 (49%) were female, and one patient had sex unknown. Only 22 (6%) patients had a notable predisposing underlying condition. 347 patients (92%) were admitted to hospital, 21 (6%) subsequently received a liver transplant, and nine (2%) died. Among the 318 patients without notable underlying conditions, 275 were tested for adenovirus. Of these 116 (42%) had at least one positive specimen, and species F type 41 was the most frequent type identified (19 [73%] of 26 typed specimens were HAdV-41). Proportions of patients who had acute liver failure, received a liver transplant, and died were similar between those who tested positive for adenovirus compared with those who tested negative. Adenovirus species F was detected by polymerase chain reaction in nine pathology liver evaluations, but not by immunohistochemistry in seven of the nine with adequate liver tissue available. Interviews with caregivers yielded no common exposures. INTERPRETATION: Adenovirus, alone or in combination with other factors, might play a potential role in acute hepatitis among immunocompetent children identified in this investigation, but the pathophysiologic mechanism of liver injury is unclear. To inform both prevention and intervention measures, more research is warranted to determine if and how adenovirus might contribute to hepatitis risk and the potential roles of other pathogens and host factors. FUNDING: None. |
Redescription of the larval stage of Dermacentor parumapertus Neumann (Acari: Ixodidae), with notes on hosts
Goddard J , Baker GT , Paddock CD , Smith TC , Robbins RG . Syst Appl Acarol 2023 28 (8) 1297-1304 The larva of the ixodid tick Dermacentor parumapertus Neumann, chiefly a parasite of hares and rabbits, is redescribed using scanning electron micrographs of seven specimens derived from two engorged females collected from two black-tailed jackrabbits, Lepus californicus, at the Black Gap Wildlife Management Area, Brewster County, southwestern Texas. The use of chaetotaxy for separating the genera of Ixodidae is discussed, and a morphological key is provided for separating the larvae of D. parumapertus from those of five other Dermacentor species with partly sympatric geographic ranges. © 2023 Systematic and Applied Acarology Society. All rights reserved. |
Application of a life table approach to assess duration of BNT162b2 vaccine-derived immunity by age using COVID-19 case surveillance data during the Omicron variant period
Sternberg MR , Johnson A , King J , Ali AR , Linde L , Awofeso AO , Baker JS , Bayoumi NS , Broadway S , Busen K , Chang C , Cheng I , Cima M , Collingwood A , Dorabawila V , Drenzek C , Fleischauer A , Gent A , Hartley A , Hicks L , Hoskins M , Jara A , Jones A , Khan SI , Kamal-Ahmed I , Kangas S , Kanishka F , Kleppinger A , Kocharian A , León TM , Link-Gelles R , Lyons BC , Masarik J , May A , McCormick D , Meyer S , Milroy L , Morris KJ , Nelson L , Omoike E , Patel K , Pietrowski M , Pike MA , Pilishvili T , Peterson Pompa X , Powell C , Praetorius K , Rosenberg E , Schiller A , Smith-Coronado ML , Stanislawski E , Strand K , Tilakaratne BP , Vest H , Wiedeman C , Zaldivar A , Silk B , Scobie HM . PLoS One 2023 18 (9) e0291678 BACKGROUND: SARS-CoV-2 Omicron variants have the potential to impact vaccine effectiveness and duration of vaccine-derived immunity. We analyzed U.S. multi-jurisdictional COVID-19 vaccine breakthrough surveillance data to examine potential waning of protection against SARS-CoV-2 infection for the Pfizer-BioNTech (BNT162b) primary vaccination series by age. METHODS: Weekly numbers of SARS-CoV-2 infections during January 16, 2022-May 28, 2022 were analyzed by age group from 22 U.S. jurisdictions that routinely linked COVID-19 case surveillance and immunization data. A life table approach incorporating line-listed and aggregated COVID-19 case datasets with vaccine administration and U.S. Census data was used to estimate hazard rates of SARS-CoV-2 infections, hazard rate ratios (HRR) and percent reductions in hazard rate comparing unvaccinated people to people vaccinated with a Pfizer-BioNTech primary series only, by age group and time since vaccination. RESULTS: The percent reduction in hazard rates for persons 2 weeks after vaccination with a Pfizer-BioNTech primary series compared with unvaccinated persons was lowest among children aged 5-11 years at 35.5% (95% CI: 33.3%, 37.6%) compared to the older age groups, which ranged from 68.7%-89.6%. By 19 weeks after vaccination, all age groups showed decreases in the percent reduction in the hazard rates compared with unvaccinated people; with the largest declines observed among those aged 5-11 and 12-17 years and more modest declines observed among those 18 years and older. CONCLUSIONS: The decline in vaccine protection against SARS-CoV-2 infection observed in this study is consistent with other studies and demonstrates that national case surveillance data were useful for assessing early signals in age-specific waning of vaccine protection during the initial period of SARS-CoV-2 Omicron variant predominance. The potential for waning immunity during the Omicron period emphasizes the importance of continued monitoring and consideration of optimal timing and provision of booster doses in the future. |
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Carey ME , Dyson ZA , Ingle DJ , Amir A , Aworh MK , Chattaway MA , Chew KL , Crump JA , Feasey NA , Howden BP , Keddy KH , Maes M , Parry CM , Van Puyvelde S , Webb HE , Afolayan AO , Alexander AP , Anandan S , Andrews JR , Ashton PM , Basnyat B , Bavdekar A , Bogoch II , Clemens JD , da Silva KE , De A , de Ligt J , Diaz Guevara PL , Dolecek C , Dutta S , Ehlers MM , Francois Watkins L , Garrett DO , Godbole G , Gordon MA , Greenhill AR , Griffin C , Gupta M , Hendriksen RS , Heyderman RS , Hooda Y , Hormazabal JC , Ikhimiukor OO , Iqbal J , Jacob JJ , Jenkins C , Jinka DR , John J , Kang G , Kanteh A , Kapil A , Karkey A , Kariuki S , Kingsley RA , Koshy RM , Lauer AC , Levine MM , Lingegowda RK , Luby SP , Mackenzie GA , Mashe T , Msefula C , Mutreja A , Nagaraj G , Nagaraj S , Nair S , Naseri TK , Nimarota-Brown S , Njamkepo E , Okeke IN , Perumal SPB , Pollard AJ , Pragasam AK , Qadri F , Qamar FN , Rahman SIA , Rambocus SD , Rasko DA , Ray P , Robins-Browne R , Rongsen-Chandola T , Rutanga JP , Saha SK , Saha S , Saigal K , Sajib MSI , Seidman JC , Shakya J , Shamanna V , Shastri J , Shrestha R , Sia S , Sikorski MJ , Singh A , Smith AM , Tagg KA , Tamrakar D , Tanmoy AM , Thomas M , Thomas MS , Thomsen R , Thomson NR , Tupua S , Vaidya K , Valcanis M , Veeraraghavan B , Weill FX , Wright J , Dougan G , Argimón S , Keane JA , Aanensen DM , Baker S , Holt KE . Elife 2023 12 BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]). | Salmonella Typhi (Typhi) is a type of bacteria that causes typhoid fever. More than 110,000 people die from this disease each year, predominantly in areas of sub-Saharan Africa and South Asia with limited access to safe water and sanitation. Clinicians use antibiotics to treat typhoid fever, but scientists worry that the spread of antimicrobial-resistant Typhi could render the drugs ineffective, leading to increased typhoid fever mortality. The World Health Organization has prequalified two vaccines that are highly effective in preventing typhoid fever and may also help limit the emergence and spread of resistant Typhi. In low resource settings, public health officials must make difficult trade-off decisions about which new vaccines to introduce into already crowded immunization schedules. Understanding the local burden of antimicrobial-resistant Typhi and how it is spreading could help inform their actions. The Global Typhoid Genomics Consortium analyzed 13,000 Typhi genomes from 110 countries to provide a global overview of genetic diversity and antimicrobial-resistant patterns. The analysis showed great genetic diversity of the different strains between countries and regions. For example, the H58 Typhi variant, which is often drug-resistant, has spread rapidly through Asia and Eastern and Southern Africa, but is less common in other regions. However, distinct strains of other drug-resistant Typhi have emerged in other parts of the world. Resistance to the antibiotic ciprofloxacin was widespread and accounted for over 85% of cases in South Africa. Around 70% of Typhi from Pakistan were extensively drug-resistant in 2020, but these hard-to-treat variants have not yet become established elsewhere. Variants that are resistant to both ciprofloxacin and ceftriaxone have been identified, and azithromycin resistance has also appeared in several different variants across South Asia. The Consortium’s analyses provide valuable insights into the global distribution and transmission patterns of drug-resistant Typhi. Limited genetic data were available fromseveral regions, but data from travel-associated cases helped fill some regional gaps. These findings may help serve as a starting point for collective sharing and analyses of genetic data to inform local public health action. Funders need to provide ongoing supportto help fill global surveillance data gaps. | eng |
The United States COVID-19 Forecast Hub dataset (preprint)
Cramer EY , Huang Y , Wang Y , Ray EL , Cornell M , Bracher J , Brennen A , Rivadeneira AJC , Gerding A , House K , Jayawardena D , Kanji AH , Khandelwal A , Le K , Mody V , Mody V , Niemi J , Stark A , Shah A , Wattanchit N , Zorn MW , Reich NG , US COVID-19 Forecast Hub Consortium , Lopez VK , Walker JW , Slayton RB , Johansson MA , Biggerstaff M . medRxiv 2021 2021.11.04.21265886 Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident hospitalizations, incident cases, incident deaths, and cumulative deaths due to COVID-19 at national, state, and county levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages.Competing Interest StatementAV, MC, and APP report grants from Metabiota Inc outside the submitted work. Funding StatementFor teams that reported receiving funding for their work, we report the sources and disclosures below: AIpert-pwllnod: Natural Sciences and Engineering Research Council of Canada; Caltech-CS156: Gary Clinard Innovation Fund; CEID-Walk: University of Georgia; CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook; COVIDhub: This work has been supported by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of CDC, NIGMS or the National Institutes of Health; Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information & Data Science Pilot Project; Tilmann Gneiting gratefully acknowledges support by the Klaus Tschira Foundation; CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation; DDS-NBDS: NSF III-1812699; epiforecasts-ensemble1: Wellcome Trust (210758/Z/18/Z) FDANIHASU: supported by the Intramural Research Program of the NIH/NIDDK; GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowment, NSF DGE-1650044, NSF MRI 1828187, research cyberinfrastructure resources and services provided by the Partnership for an Advanced Computing Environment (PACE) at Georgia Tech, and the following benefactors at Georgia Tech: Andrea Laliberte, Joseph C. Mello, Richard Rick E. & Charlene Zalesky, and Claudia & Paul Raines, CDC MInD-Healthcare U01CK000531-Supplement; IHME: This work was supported by the Bill & Melinda Gates Foundation, as well as funding from the state of Washington and the National Science Foundation (award no. FAIN: 2031096); Imperial-ensemble1: SB acknowledges funding from the Wellcome Trust (219415); Institute of Business Forecasting: IBF; IowaStateLW-STEM: NSF DMS-1916204, Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics; IUPUI CIS: NSF; JHU_CSSE-DECOM: JHU CSSE: National Science Foundation (NSF) RAPID Real-time Forecasting of COVID-19 risk in the USA. 2021-2022. Award ID: 2108526. National Science Foundation (NSF) RAPID Development of an interactive web-based dashboard to track COVID-19 in real-time. 2020. Award ID: 2028604; JHU_IDD-CovidSP: State of California, US Dept of Health and Human Services, US Dept of Homeland Security, Johns Hopkins Health System, Office of the Dean at Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Modeling and Policy Hub, Centers for Disease Control and Prevention (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant); JHU_UNC_GAS-StatMechP ol: NIH NIGMS: R01GM140564; JHUAPL-Bucky: US Dept of Health and Human Services; KITmetricslab-select_ensemble: Daniel Wolffram gratefully acknowledges support by the Klaus Tschira Foundation; LANL-GrowthRate: LANL LDRD 20200700ER; MIT-Cassandra: MIT Quest for Intelligence; MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01; CA NU38OT000297 from the Council of State and Territorial Epidemiologists (CSTE); NotreDame-FRED: NSF RAPID DEB 2027718; NotreDame-mobility: NSF RAPID DEB 2027718; PSI-DRAFT: NSF RAPID Grant # 2031536; QJHong-Encounter: NSF DMR-2001411 and DMR-1835939; SDSC_ISG-TrendModel: The development of the dashboard was partly funded by the Fondation Privee des Hopitaux Universitaires de Geneve; UA-EpiCovDA: NSF RAPID Grant # 2028401; UChicagoCHATTOPADHYAY-UnIT: Defense Advanced Research Projects Agency (DARPA) #HR00111890043/P00004 (I. Chattopadhyay, University of Chicago); UCSB-ACTS: NSF RAPID IIS 2029626; UCSD_NEU-DeepGLEAM: Google Faculty Award, W31P4Q-21-C-0014; UMass-MechBayes: NIGMS #R35GM119582, NSF #1749854, NIGMS #R35GM119582; UMich-RidgeTfReg: This project is funded by the University of Michigan Physics Department and the University of Michigan Office of Research; UVA-Ensemble: National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and Virginia Dept of Health Grant VDH-21-501-0141; Wadnwani_AI-BayesOpt: This study is made possible by the generous support of the American People through the United States Agency for International Development (USAID). The work described in this article was implemented under the TRACETB Project, managed by WIAI under the terms of Cooperative Agreement Number 72038620CA00006. The contents of this manuscript are the sole responsibility of the authors and do not necessarily reflect the views of USAID or the United States Government; WalmartLabsML-LogForecasting: Team acknowledges Walmart to support this study Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesI confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data produced are available online at https://github.com/reichlab/covid19-forecast-hub https://github.com/reichlab/covid19-forecast-hub |
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US (preprint)
Cramer EY , Ray EL , Lopez VK , Bracher J , Brennen A , Castro Rivadeneira AJ , Gerding A , Gneiting T , House KH , Huang Y , Jayawardena D , Kanji AH , Khandelwal A , Le K , Mühlemann A , Niemi J , Shah A , Stark A , Wang Y , Wattanachit N , Zorn MW , Gu Y , Jain S , Bannur N , Deva A , Kulkarni M , Merugu S , Raval A , Shingi S , Tiwari A , White J , Abernethy NF , Woody S , Dahan M , Fox S , Gaither K , Lachmann M , Meyers LA , Scott JG , Tec M , Srivastava A , George GE , Cegan JC , Dettwiller ID , England WP , Farthing MW , Hunter RH , Lafferty B , Linkov I , Mayo ML , Parno MD , Rowland MA , Trump BD , Zhang-James Y , Chen S , Faraone SV , Hess J , Morley CP , Salekin A , Wang D , Corsetti SM , Baer TM , Eisenberg MC , Falb K , Huang Y , Martin ET , McCauley E , Myers RL , Schwarz T , Sheldon D , Gibson GC , Yu R , Gao L , Ma Y , Wu D , Yan X , Jin X , Wang YX , Chen Y , Guo L , Zhao Y , Gu Q , Chen J , Wang L , Xu P , Zhang W , Zou D , Biegel H , Lega J , McConnell S , Nagraj VP , Guertin SL , Hulme-Lowe C , Turner SD , Shi Y , Ban X , Walraven R , Hong QJ , Kong S , van de Walle A , Turtle JA , Ben-Nun M , Riley S , Riley P , Koyluoglu U , DesRoches D , Forli P , Hamory B , Kyriakides C , Leis H , Milliken J , Moloney M , Morgan J , Nirgudkar N , Ozcan G , Piwonka N , Ravi M , Schrader C , Shakhnovich E , Siegel D , Spatz R , Stiefeling C , Wilkinson B , Wong A , Cavany S , España G , Moore S , Oidtman R , Perkins A , Kraus D , Kraus A , Gao Z , Bian J , Cao W , Lavista Ferres J , Li C , Liu TY , Xie X , Zhang S , Zheng S , Vespignani A , Chinazzi M , Davis JT , Mu K , Pastore YPiontti A , Xiong X , Zheng A , Baek J , Farias V , Georgescu A , Levi R , Sinha D , Wilde J , Perakis G , Bennouna MA , Nze-Ndong D , Singhvi D , Spantidakis I , Thayaparan L , Tsiourvas A , Sarker A , Jadbabaie A , Shah D , Della Penna N , Celi LA , Sundar S , Wolfinger R , Osthus D , Castro L , Fairchild G , Michaud I , Karlen D , Kinsey M , Mullany LC , Rainwater-Lovett K , Shin L , Tallaksen K , Wilson S , Lee EC , Dent J , Grantz KH , Hill AL , Kaminsky J , Kaminsky K , Keegan LT , Lauer SA , Lemaitre JC , Lessler J , Meredith HR , Perez-Saez J , Shah S , Smith CP , Truelove SA , Wills J , Marshall M , Gardner L , Nixon K , Burant JC , Wang L , Gao L , Gu Z , Kim M , Li X , Wang G , Wang Y , Yu S , Reiner RC , Barber R , Gakidou E , Hay SI , Lim S , Murray C , Pigott D , Gurung HL , Baccam P , Stage SA , Suchoski BT , Prakash BA , Adhikari B , Cui J , Rodríguez A , Tabassum A , Xie J , Keskinocak P , Asplund J , Baxter A , Oruc BE , Serban N , Arik SO , Dusenberry M , Epshteyn A , Kanal E , Le LT , Li CL , Pfister T , Sava D , Sinha R , Tsai T , Yoder N , Yoon J , Zhang L , Abbott S , Bosse NI , Funk S , Hellewell J , Meakin SR , Sherratt K , Zhou M , Kalantari R , Yamana TK , Pei S , Shaman J , Li ML , Bertsimas D , Skali Lami O , Soni S , Tazi Bouardi H , Ayer T , Adee M , Chhatwal J , Dalgic OO , Ladd MA , Linas BP , Mueller P , Xiao J , Wang Y , Wang Q , Xie S , Zeng D , Green A , Bien J , Brooks L , Hu AJ , Jahja M , McDonald D , Narasimhan B , Politsch C , Rajanala S , Rumack A , Simon N , Tibshirani RJ , Tibshirani R , Ventura V , Wasserman L , O'Dea EB , Drake JM , Pagano R , Tran QT , Ho LST , Huynh H , Walker JW , Slayton RB , Johansson MA , Biggerstaff M , Reich NG . medRxiv 2021 2021.02.03.21250974 Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. In 2020, the COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized hundreds of thousands of specific predictions from more than 50 different academic, industry, and independent research groups. This manuscript systematically evaluates 23 models that regularly submitted forecasts of reported weekly incident COVID-19 mortality counts in the US at the state and national level. One of these models was a multi-model ensemble that combined all available forecasts each week. The performance of individual models showed high variability across time, geospatial units, and forecast horizons. Half of the models evaluated showed better accuracy than a naïve baseline model. In combining the forecasts from all teams, the ensemble showed the best overall probabilistic accuracy of any model. Forecast accuracy degraded as models made predictions farther into the future, with probabilistic accuracy at a 20-week horizon more than 5 times worse than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.Competing Interest StatementAV, MC, and APP report grants from Metabiota Inc outside the submitted work.Funding StatementFor teams that reported receiving funding for their work, we report the sources and disclosures below. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook. CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation. COVIDhub: This work has been supported by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of CDC, NIGMS or the National Institutes of Health. Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information& Data Science Pilot Project. Tilmann Gneiting gratefully acknowledges support by the Klaus Tschira Foundation. DDS-NBDS: NSF III-1812699. EPIFORECASTS-ENSEMBLE1: Wellcome Trust (210758/Z/18/Z) GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowments, NSF DGE-1650044, NSF MRI 1828187, research cyberinfrastructure resources and services provided by the Partnership for an Advanced Computing Environment (PACE) at Georgia Tech, and the following benefactors at Georgia Tech: Andrea Laliberte, Joseph C. Mello, Richard Rick E. & Charlene Zalesky, and Claudia & Paul Raines GT-DeepCOVID: CDC MInD-Healthcare U01CK000531-Supplement. NSF (Expeditions CCF-1918770, CAREER IIS-2028586, RAPID IIS-2027862, Medium IIS-1955883, NRT DGE-1545362), CDC MInD program, ORNL and funds/computing resources from Georgia Tech and GTRI. IHME: This work was supported by the Bill & Melinda Gates Foundation, as well as funding from the state of Washington and the National Science Foundation (award no. FAIN: 2031096). IowaStateLW-STEM: Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1916204, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics. JHU_IDD-CovidSP: State of California, US Dept of Health and Human Services, US Dept of Homeland Security, US Office of Foreign Disaster Assistance, Johns Hopkins Health System, Office of the Dean at Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Modeling and Policy Hub, Centers fo Disease Control and Prevention (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant). LANL-GrowthRate: LANL LDRD 20200700ER. MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01. NotreDame-mobility and NotreDame-FRED: NSF RAPID DEB 2027718 UA-EpiCovDA: NSF RAPID Grant # 2028401. UCSB-ACTS: NSF RAPID IIS 2029626. UCSD-NEU: Google Faculty Award, DARPA W31P4Q-21-C-0014, COVID Supplement CDC-HHS-6U01IP001137-01. UMass-MechBayes: NIGMS R35GM119582, NSF 1749854. UMich-RidgeTfReg: The University of Michigan Physics Department and the University of Michigan Office of Research.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:UMass-Amherst IRBAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data and code referred to in the manuscript are publicly available. https://github.com/reichlab/covid19-forecast-hub/ https://github.com/reichlab/covidEnsembles https://zoltardata.com/project/44 |
Climate and urbanization drive mosquito preference for humans (preprint)
Rose NH , Sylla M , Badolo A , Lutomiah J , Ayala D , Aribodor OB , Ibe N , Akorli J , Otoo S , Mutebi JP , Kriete AL , Ewing EG , Sang R , Gloria-Soria A , Powell JR , Baker RE , White BJ , Crawford JE , McBride CS . bioRxiv 2020 2020.02.12.939041 The majority of mosquito-borne illness is spread by a few mosquito species that have evolved to specialize in biting humans, yet the precise causes of this behavioral shift are poorly understood. We address this gap in the arboviral vector Aedes aegypti. We first characterize the behaviour of mosquitoes from 27 sites scattered across the species’ ancestral range in sub-Saharan Africa, revealing previously unrecognized diversity in female preference for human versus animal odor. We then use modelling to show that this diversity can be almost fully predicted by two ecological factors – dry season intensity and human population density. Finally we integrate this information with whole genome sequence data from 345 individual mosquitoes to identify a single underlying ancestry component linked to human preference, with genetic changes concentrated in a few key chromosomal regions. Our findings strongly suggest that human-biting in this important disease vector originally evolved as a by-product of breeding in human-stored water in areas where doing so provided the only means to survive the long, hot dry season. Our model also predicts that changes in human population density are likely to drive future mosquito evolution. Rapid urbanization may drive a shift to human-biting in many cities across Africa by 2050. |
High-resolution characterization of recent tuberculosis transmission in Botswana using geospatial and genomic data - the Kopanyo Study (preprint)
Baker CR , Barilar I , de Araujo LS , Rimoin AW , Parker DM , Boyd R , Tobias JL , Moonan PK , Click ES , Finlay A , Oeltmann JE , Minin VN , Modongo C , Zetola NM , Niemann S , Shin SS . medRxiv 2022 18 Introduction. Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis (Mtb) transmission in high tuberculosis burden settings. Methods. We performed whole genome sequencing (WGS) on Mtb DNA extracted from sputum cultures from a population-based tuberculosis study conducted in 2012-2016 in Gaborone, Botswana. We used kernel density estimation, spatial K-functions, and created spatial distributions of phylogenetic trees. WGS-based clusters of isolates <5 single nucleotide polymorphisms were considered recent transmission, and large WGS-based clusters (>10 members) were considered outbreaks. Results. We analyzed data from 1449 participants with culture-confirmed TB. Among these, 946 (65%) participants had both molecular and geospatial data. A total of 62 belonged to five large outbreaks (10-19 participants each). Geospatial clustering was detected in two of the five large outbreaks, suggesting heterogeneous spatial patterns within the community. Conclusions. Integration of genomic and geospatial data identified distinct patterns of tuberculosis transmission in a high-tuberculosis burden setting. Targeted interventions in these smaller geographies may interrupt on-going transmission. 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. |
Interspecies transmission from pigs to ferrets of antigenically distinct swine H1 influenza A viruses with loss in reactivity to human vaccine virus antisera as measures of relative zoonotic risk (preprint)
Brian Kimble J , Souza CK , Anderson TK , Arendsee ZW , Hufnagel DE , Young KM , Lewis NS , Todd Davis C , Vincent Baker AL . bioRxiv 2022 13 During the last decade, endemic swine H1 influenza A viruses (IAV) from six different genetic clades of the hemagglutinin gene caused zoonotic infections in humans. The majority of zoonotic events with swine IAV were restricted to a single case with no subsequent transmission. However, repeated introduction of human-seasonal H1N1, continual reassortment between endemic swine IAV, and subsequent drift in the swine host resulted in highly diverse swine IAV with human-origin genes that may become a risk to the human population. To prepare for the potential of a future swine-origin IAV pandemic in humans, public health laboratories selected candidate vaccine viruses (CVV) for use as vaccine seed strains. To assess the pandemic risk of contemporary US swine H1N1 or H1N2 strains, we quantified the genetic diversity of swine H1 HA genes, and identified representative strains from each circulating clade. We then characterized the representative swine IAV against human seasonal vaccine and CVV strains using ferret antisera in hemagglutination inhibition assays (HI). HI assays revealed that 1A.3.3.2 (pdm) and 1B.2.1 (delta-2) demonstrated strong cross reactivity to human seasonal vaccines or CVVs. However, swine IAV from three clades that represent more than 50% of the detected swine IAVs in the USA showed significant reduction in cross-reactivity compared to the closest CVV virus: 1A.1.1.3 (alpha-deletion), 1A.3.3.3-clade 3 (gamma), and 1B.2.2.1 (delta-1a). Representative viruses from these three clades were further characterized in a pig-to-ferret transmission model and shown to exhibit variable transmission efficiency. Our data prioritize specific genotypes of swine H1N1 and H1N2 to further investigate in the risk they pose to the human population. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv 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. |
A staffing perspective on barriers to and facilitators of temporary worker safety and health
Menger-Ogle LM , Baker D , Guerin RJ , Cunningham TR . Am J Ind Med 2023 66 (9) 736-749 BACKGROUND: Research has documented occupational health disparities, including higher rates of work-related injuries, among temporary workers compared with workers in standard employment arrangements. According to guidance from the Occupational Safety and Health Administration (OSHA) and the National Institute for Occupational Safety and Health (NIOSH), both staffing companies and host employers are responsible for protecting the occupational safety and health (OSH) of temporary workers. To date, there has been little qualitative research on temporary worker OSH in the United States and a lack of evidence-based OSH programs designed to meet the needs of temporary workers. The aim of this study was to better understand the barriers to and facilitators of temporary worker OSH from the perspective of US staffing companies. METHODS: In-depth interviews were conducted with a convenience sample of representatives from 15 US staffing companies. Interviews were audio recorded, transcribed verbatim, and analyzed through a three-step process. RESULTS: Commonly mentioned barriers to temporary worker OSH include differential treatment of temporary workers by host employers; lack of understanding among host employers and staffing companies of joint OSH responsibilities; and workers' fear of job loss or other negative repercussions if they report an injury or illness or voice OSH concerns. Commonly mentioned facilitators of temporary worker OSH include conducting client assessments and site visits and fostering strong communication and relationships with both host employers and temporary workers. CONCLUSIONS: These findings can help inform the tailoring of OSH programs to promote health equity in temporary workers. |
Rickettsial antibodies and Rickettsia bellii detection in lagomorphs and their ectoparasites in Northern Baja California, Mexico
Backus LH , López-Pérez AM , Marcek J , Shultz L , Zazueta OE , Shooter S , Foley J . J Med Entomol 2023 60 (5) 1073-1080 Lagomorphs-principally rabbits and hares-have been implicated as hosts for vectors and reservoirs for pathogens associated with multiple rickettsial diseases. Western North America is home to diverse rickettsial pathogens which circulate among multiple wild and domestic hosts and tick and flea vectors. The purpose of this study was to assess lagomorphs and their ectoparasites in 2 locations in northern Baja California, Mexico, for exposure to and infection with rickettsial organisms. In total, 55 desert cottontail rabbits (Sylvilagus audubonii) (Baird) and 2 black-tailed jackrabbits (Lepus californicus) (Gray) were captured. In Mexicali, ticks were collected from 44% (14/32) of individuals, and were exclusively Haemaphysalis leporispalustris Neumann (Acari: Ixodidae); in Ensenada, ticks were collected from 70% (16/23) individuals, and 95% were Dermacentor parumapertus. Euhoplopsyllus glacialis affinis Baker (Siphonaptera: Pulicidae) fleas were collected from 72% of rabbits and 1 jackrabbit from Mexicali, while the few fleas found on hosts in Ensenada were Echidnophaga gallinacea Westwood (Siphonaptera: Pulicidae) and Cediopsylla inaequalis (Siphonaptera: Pulicidae). Rickettsia bellii was the only rickettsial organism detected and was identified in 88% of D. parumapertus and 67% of H. leporispalustris ticks from Ensenada. A single tissue sample from a jackrabbit was positive for R. belli (Rickettsiales: Rickettsiaceae). Hosts in Ensenada had a significantly higher prevalence of rickettsial antibodies than hosts in Mexicali (52.3% vs. 21.4%). Although R. bellii is not regarded as pathogenic in humans or other mammals, it may contribute to immunity to other rickettsiae. The marked difference in distribution of ticks, fleas, and rickettsial exposure between the 2 locations suggests that disease transmission risk may vary markedly between communities within the same region. |
2022 American College of Rheumatology Guideline for exercise, rehabilitation, diet, and additional integrative interventions for rheumatoid arthritis
England BR , Smith BJ , Baker NA , Barton JL , Oatis CA , Guyatt G , Anandarajah A , Carandang K , Chan KK , Constien D , Davidson E , Dodge CV , Bemis-Dougherty A , Everett S , Fisher N , Fraenkel L , Goodman SM , Lewis J , Menzies V , Moreland LW , Navarro-Millan I , Patterson S , Phillips LR , Shah N , Singh N , White D , AlHeresh R , Barbour KE , Bye T , Guglielmo D , Haberman R , Johnson T , Kleiner A , Lane CY , Li LC , Master H , Pinto D , Poole JL , Steinbarger K , Sztubinski D , Thoma L , Tsaltskan V , Turgunbaev M , Wells C , Turner AS , Treadwell JR . Arthritis Care Res (Hoboken) 2023 75 (8) 1603-1615 OBJECTIVE: To develop initial American College of Rheumatology (ACR) guidelines on the use of exercise, rehabilitation, diet, and additional interventions in conjunction with disease-modifying antirheumatic drugs (DMARDs) as part of an integrative management approach for people with rheumatoid arthritis (RA). METHODS: An interprofessional guideline development group constructed clinically relevant Population, Intervention, Comparator, and Outcome (PICO) questions. A literature review team then completed a systematic literature review and applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate the certainty of evidence. An interprofessional Voting Panel (n = 20 participants) that included 3 individuals with RA achieved consensus on the direction (for or against) and strength (strong or conditional) of recommendations. RESULTS: The Voting Panel achieved consensus on 28 recommendations for the use of integrative interventions in conjunction with DMARDs for the management of RA. Consistent engagement in exercise received a strong recommendation. Of 27 conditional recommendations, 4 pertained to exercise, 13 to rehabilitation, 3 to diet, and 7 to additional integrative interventions. These recommendations are specific to RA management, recognizing that other medical indications and general health benefits may exist for many of these interventions. CONCLUSION: This guideline provides initial ACR recommendations on integrative interventions for the management of RA to accompany DMARD treatments. The broad range of interventions included in these recommendations illustrates the importance of an interprofessional, team-based approach to RA management. The conditional nature of most recommendations requires clinicians to engage persons with RA in shared decision-making when applying these recommendations. |
Fluoroquinolone-resistant latent tuberculosis infection: A literature review and case series of 5 patients treated with linezolid monotherapy
Baker JJ , Nahar R , Petroelje BK , Goswami ND , Lardizabal AA . J Clin Tuberc Other Mycobact Dis 2023 32 100376 Latent tuberculosis infection (LTBI) constitutes an important public health problem because of risk of progression to TB disease. Effective treatment of multi-drug resistant (MDR) LTBI would prevent progression to MDR TB disease, which would improve patient and public health outcomes. The majority of MDR LTBI treatment studies have focused on the use of fluoroquinolone-based antibiotic regimens. Options for and experience in the treatment of fluoroquinolone-resistant MDR LTBI are limited in the published literature and not comprehensively addressed in current guidelines. In this review, we share our experience with the treatment of fluoroquinolone-resistant MDR LTBI with linezolid. We discuss treatment options for MDR TB that provide context for predicting effective MDR LTBI treatment, with a focus on the microbiologic and pharmacokinetic properties of linezolid that support its use. We then summarize the evidence for treatment of MDR LTBI. Finally, we present our experiences treating fluoroquinolone-resistant MDR LTBI with linezolid with an emphasis on dosing considerations to optimize efficacy and minimize potential toxicities. |
Comparison of the "tall and fall" versus "drop and drive" pitching styles: Analysis of Major League Baseball pitchers during a single season
Beaudry MF , Beaudry AG , Bradley JP , Haynes DE , Holland G , Edwards A , Baker BA , Jacobson BR , Chetlin RD . Orthop J Sports Med 2023 11 (5) 23259671231173691 BACKGROUND: Previous research has documented the proportion of "tall and fall" (TF) and "drop and drive" (DD) pitching styles among Major League Baseball (MLB) pitchers who underwent ulnar collateral ligament reconstruction (UCLR). The proportion of these 2 styles among all MLB pitchers remains unknown. PURPOSE: To determine the proportion of the TF and DD pitching styles in all rostered MLB pitchers during a single season as well as the proportion of TF and DD pitchers who sustained an upper extremity (UE) injury and those who underwent UCLR. STUDY DESIGN: Cross-sectional study; Level of evidence, 3. METHODS: Pitcher demographic characteristics from the 2019 MLB season and pitching information were obtained via open-access sources. Two-dimensional video analysis was used to categorize the included pitchers into TF and DD groups. Statistical comparisons and contrasts were made using 2-tailed t tests, chi-square tests, and Pearson correlation analyses as appropriate. RESULTS: Of the 660 MLB rostered pitchers in 2019 (age, 27.39 ± 3.51 years; body mass index, 26.34 ± 2.47 kg/m(2); fastball velocity, 150.49 ± 3.99 kph [93.51 ± 2.48 mph]), 412 (62.4%) pitchers used the TF style and 248 (37.6%) pitchers used the DD style. Significantly more UE injuries were seen in the TF group compared with the DD group (112 vs 38 injuries, respectively; P < .001). Twelve pitchers underwent UCLR (TF, 10; DD, 2), representing a 1.8% UCLR rate among all pitchers. This was a second surgery for 2 pitchers, both of whom used the TF pitching style. Significantly more pitchers in the TF group than the DD group had undergone UCLR before 2019 (135 vs 56 pitchers, respectively; P = .005). CONCLUSION: The results of the present study demonstrated a higher prevalence of both UE injury and prior UCLR in TF pitchers. Further research is needed to explore the potential association between pitching style and UE injury. |
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