Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-30 (of 251 Records) |
Query Trace: Carter J [original query] |
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Surveillance system integration: reporting the results of a global multicountry survey
Carter ED , Stewart DE , Rees EE , Bezuidenhoudt JE , Ng V , Lynes S , Desenclos JC , Pyone T , Lee ACK . Public Health 2024 231 31-38 OBJECTIVES: Currently, there is no comprehensive picture of the global surveillance landscape. This survey examines the current state of surveillance systems, levels of integration, barriers and opportunities for the integration of surveillance systems at the country level, and the role of national public health institutes (NPHIs). STUDY DESIGN: This was a cross-sectional survey of NPHIs. METHODS: A web-based survey questionnaire was disseminated to 110 NPHIs in 95 countries between July and August 2022. Data were descriptively analysed, stratified by World Health Organization region, World Bank Income Group, and self-reported Integrated Disease Surveillance (IDS) maturity status. RESULTS: Sixty-five NPHIs responded. Systems exist to monitor notifiable diseases and vaccination coverage, but less so for private, pharmaceutical, and food safety sectors. While Ministries of Health usually lead surveillance, in many countries, NPHIs are also involved. Most countries report having partially developed IDS. Surveillance data are frequently inaccessible to the lead public health agency and seldomly integrated into a national public health surveillance system. Common challenges to establishing IDS include information technology system issues, financial constraints, data sharing and ownership limitations, workforce capacity gaps, and data availability. CONCLUSIONS: Public health surveillance systems across the globe, although built on similar principles, are at different levels of maturity but face similar developmental challenges. Leadership, ownership and governance, supporting legal mandates and regulations, as well as adherence to mandates, and enforcement of regulations are critical components of effective surveillance. In many countries, NPHIs play a significant role in integrated disease surveillance. |
Surveillance for Coccidioidomycosis, Histoplasmosis, and Blastomycosis During the COVID-19 Pandemic - United States, 2019-2021
Williams SL , Smith DJ , Benedict K , Ahlers JR , Austin C , Birn R , Carter AM , Christophe NN , Cibulskas K , Cieslak PR , Gibbons-Burgener SN , Gosciminski M , Ireland MJ , Lazenby KV , Loftus T , Lunquest K , Mathewson AA , Nguyen AD , Oltean HN , Osborn B , Petro EM , Power DJ , Reik RR , Schlosser L , Sedivy J , Smelser CB , Chiller T , Toda M . MMWR Morb Mortal Wkly Rep 2024 73 (11) 239-244 Coccidioidomycosis, histoplasmosis, and blastomycosis are lower respiratory tract fungal infections whose signs and symptoms can resemble those of other respiratory illnesses, including pneumonia caused by bacterial or viral etiologies; this overlap in clinical presentation might lead to missed or delayed diagnoses. The causative fungi live in the environment, often in soil or plant matter. To describe the epidemiologic characteristics of cases of coccidioidomycosis, histoplasmosis, and blastomycosis during the COVID-19 pandemic, CDC analyzed case surveillance data for 2019-2021. During this period, a total of 59,655 coccidioidomycosis cases, 3,595 histoplasmosis cases, and 719 blastomycosis cases were reported to CDC. In 2020, fewer cases of each disease occurred in spring compared with other seasons, and most cases occurred in fall; national seasonality is not typically observed, and cases were seasonally distributed more evenly in 2019 and 2021. Fewer cases coinciding with the start of the COVID-19 pandemic, along with an unusually high blastomycosis case fatality rate in 2021 (17% compared with more typical rates of 8%-10%), suggest that the pandemic might have affected patients' health care-seeking behavior, public health reporting practices, or clinical management of these diseases. Increased awareness and education are needed to encourage health care providers to consider fungal diseases and to identify pneumonia of fungal etiology. Standardized diagnostic guidance and informational resources for fungal testing could be incorporated into broader respiratory disease awareness and preparedness efforts to improve early diagnosis of coccidioidomycosis, histoplasmosis, and blastomycosis. |
Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches
Carter JJ , Walker TM , Walker AS , Whitfield MG , Morlock GP , Lynch CI , Adlard D , Peto TEA , Posey JE , Crook DW , Fowler PW . JAC Antimicrob Resist 2024 6 (2) dlae037 BACKGROUND: Pyrazinamide is one of four first-line antibiotics used to treat tuberculosis; however, antibiotic susceptibility testing for pyrazinamide is challenging. Resistance to pyrazinamide is primarily driven by genetic variation in pncA, encoding an enzyme that converts pyrazinamide into its active form. METHODS: We curated a dataset of 664 non-redundant, missense amino acid mutations in PncA with associated high-confidence phenotypes from published studies and then trained three different machine-learning models to predict pyrazinamide resistance. All models had access to a range of protein structural-, chemical- and sequence-based features. RESULTS: The best model, a gradient-boosted decision tree, achieved a sensitivity of 80.2% and a specificity of 76.9% on the hold-out test dataset. The clinical performance of the models was then estimated by predicting the binary pyrazinamide resistance phenotype of 4027 samples harbouring 367 unique missense mutations in pncA derived from 24 231 clinical isolates. CONCLUSIONS: This work demonstrates how machine learning can enhance the sensitivity/specificity of pyrazinamide resistance prediction in genetics-based clinical microbiology workflows, highlights novel mutations for future biochemical investigation, and is a proof of concept for using this approach in other drugs. |
HIV-1 incidence, adherence, and drug resistance in individuals taking daily emtricitabine/tenofovir disoproxil fumarate for HIV-1 pre-exposure prophylaxis: Pooled analysis from 72 global studies
Landovitz RJ , Tao L , Yang J , de Boer M , Carter C , Das M , Baeten JM , Liu A , Hoover KW , Celum C , Grinsztejn B , Morris S , Wheeler DP , Mayer KH , Golub SA , Bekker LG , Diabaté S , Hoornenborg E , Myers J , Leech AA , McCormack S , Chan PA , Sweat M , Matthews LT , Grant R . Clin Infect Dis 2024 BACKGROUND: Oral pre-exposure prophylaxis (PrEP) with emtricitabine/tenofovir disoproxil fumarate (F/TDF) has high efficacy against HIV-1 acquisition. Seventy-two prospective studies of daily oral F/TDF PrEP were conducted to evaluate HIV-1 incidence, drug resistance, adherence, and bone and renal safety in diverse settings. METHODS: HIV-1 incidence was calculated from incident HIV-1 diagnoses after PrEP initiation and within 60 days of discontinuation. Tenofovir concentration in dried blood spots (DBS), drug resistance, and bone/renal safety indicators were evaluated in a subset of studies. RESULTS: Among 17,274 participants, there were 101 cases with new HIV-1 diagnosis (0.77 per 100 person-years; 95% CI 0.63-0.94). In 78 cases with resistance data, 18 (23%) had M184I or V, one (1.3%) had K65R, and three (3.8%) had both mutations. In 54 cases with tenofovir concentration data from DBS, 45 (83.3%), 2 (3.7%), 6 (11.1%), and 1 (1.9%) had average adherence of <2, 2-3, 4-6, and ≥7 doses/week, respectively, and the corresponding incidence was 3.9 (95% CI 2.9-5.3), 0.24 (0.060-0.95), 0.27 (0.12-0.60), and 0.054 (0.008-0.38) per 100 person-years. Adherence was low in younger participants, Hispanic/Latinx and Black participants, cisgender women, and transgender women. Bone and renal adverse event incidence rates were 0.69 and 11.8 per 100 person-years, respectively, consistent with previous reports. CONCLUSIONS: Leveraging the largest pooled analysis of global PrEP studies to date, we demonstrate that F/TDF is safe and highly effective, even with less than daily dosing, in diverse clinical settings, geographies, populations, and routes of HIV-1 exposure. |
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Xie O , Morris JM , Hayes AJ , Towers RJ , Jespersen MG , Lees JA , Ben Zakour NL , Berking O , Baines SL , Carter GP , Tonkin-Hill G , Schrieber L , McIntyre L , Lacey JA , James TB , Sriprakash KS , Beatson SA , Hasegawa T , Giffard P , Steer AC , Batzloff MR , Beall BW , Pinho MD , Ramirez M , Bessen DE , Dougan G , Bentley SD , Walker MJ , Currie BJ , Tong SYC , McMillan DJ , Davies MR . Nat Commun 2024 15 (1) 2286 Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention. |
HIV preexposure prophylaxis with emtricitabine and tenofovir disoproxil fumarate among cisgender women
Marrazzo J , Tao L , Becker M , Leech AA , Taylor AW , Ussery F , Kiragu M , Reza-Paul S , Myers J , Bekker LG , Yang J , Carter C , de Boer M , Das M , Baeten JM , Celum C . Jama 2024 IMPORTANCE: Emtricitabine and tenofovir disoproxil fumarate (F/TDF) for HIV preexposure prophylaxis (PrEP) is highly effective in cisgender men who have sex with men (MSM) when adherence is high (>4 doses/week). Real-world effectiveness and adherence with F/TDF for PrEP in cisgender women is less well characterized. OBJECTIVE: To characterize the effectiveness of F/TDF for PrEP and its relationship with adherence in cisgender women. DESIGN, SETTING, AND PARTICIPANTS: Data were pooled from 11 F/TDF PrEP postapproval studies conducted in 6 countries that included 6296 cisgender women aged 15 to 69 years conducted from 2012 to 2020. HIV incidence was evaluated according to adherence level measured objectively (tenofovir diphosphate concentration in dried blood spots or tenofovir concentration in plasma; n = 288) and subjectively (electronic pill cap monitoring, pill counts, self-report, and study-reported adherence scale; n = 2954) using group-based trajectory modeling. EXPOSURES: F/TDF prescribed orally once a day. HIV incidence was analyzed in subgroups based on adherence trajectory. MAIN OUTCOMES AND MEASURES: HIV incidence. RESULTS: Of the 6296 participants, 46% were from Kenya, 28% were from South Africa, 21% were from India, 2.9% were from Uganda, 1.6% were from Botswana, and 0.8% were from the US. The mean (SD) age at PrEP initiation across all studies was 25 (7) years, with 61% of participants being younger than 25 years. The overall HIV incidence was 0.72 per 100 person-years (95% CI, 0.51-1.01; 32 incident HIV diagnoses among 6296 participants). Four distinct groups of adherence trajectories were identified: consistently daily (7 doses/week), consistently high (4-6 doses/week), high but declining (from a mean of 4-6 doses/week and then declining), and consistently low (less than 2 doses/week). None of the 498 women with consistently daily adherence acquired HIV. Only 1 of the 658 women with consistently high adherence acquired HIV (incidence rate, 0.13/100 person-years [95% CI, 0.02-0.92]). The incidence rate was 0.49 per 100 person-years (95% CI, 0.22-1.08) in the high but declining adherence group (n = 1166) and 1.27 per 100 person-years (95% CI, 0.53-3.04) in the consistently low adherence group (n = 632). CONCLUSIONS AND RELEVANCE: In a pooled analysis of 11 postapproval studies of F/TDF for PrEP among cisgender women, overall HIV incidence was 0.72 per 100 person-years; individuals with consistently daily or consistently high adherence (4-6 doses/week) to PrEP experienced very low HIV incidence. |
An overview of the COVID-19 pediatric vaccine program - The U.S. experience vaccinating children ages 6 months through 17 years
Chatham-Stephens K , Carter RJ , Duggar C , Woodworth KR , Carnes CA , Bhatt A , Ottis C , Voegeli C , Stokley S , Vogt T . Vaccine 2024 COVID-19 vaccination decreases risk for COVID-19 illness and severe disease in children, including multisystem inflammatory syndrome (MIS-C) and death. On December 13, 2020, CDC recommended COVID-19 vaccination for persons ages ≥16 years, with expansion on May 12, 2021, to adolescents ages 12-15 years; to children ages 5-11 years on November 2, 2021; and to children ages 6 months-4 years on June 18, 2022. Following each age-specific recommendation, the U.S. government collaborated with state and local governments, vaccine manufacturers, and numerous other public and private entities, to ensure rapid, broad, and equitable COVID-19 vaccine distribution to strategic locations across the country to maximize access. However, vaccination coverage among children has been lower than among adults and lower among younger children than adolescents. As of May 10, 2023, COVID-19 primary series vaccination coverage was 61.8% among U.S. children ages 12-17 years, 32.9% among those ages 5-11 years, and 5.5% among those ages 6 months-4 years. This manuscript describes the planning and implementation of the U.S. COVID-19 pediatric vaccine program, including successes (e.g., the availability of pharmacy vaccination to extend access beyond more traditional pediatric vaccine providers) and challenges (e.g., multi-dose vaccine vials instead of single-dose vials, leading to concerns about wastage) to provide a historical record of the program and to help inform planning and implementation of future routine or pandemic-related pediatric vaccination campaigns. |
Non-derivatized Assay for the Simultaneous Detection of Amino Acids, Acylcarnitines, Succinylacetone, Creatine, and Guanidinoacetic Acid in Dried Blood Spots by Tandem Mass Spectrometry.
Asef CK , Khaksarfard KM , De Jesús VR . Int J Neonatal Screen 2016 2 (4) Guanidinoacetate methyltransferase (GAMT) deficiency is an autosomal recessive genetic disorder which results in global developmental delay and intellectual disability. There is evidence that early treatment prevents intellectual disability and seizures. GAMT deficiency is now being discussed as a potential addition to the U.S. Recommended Uniform Screening Panel (RUSP); the availability of suitable screening methods must be considered. A neonatal screening derivatized method to quantify creatine (CRE) and guanidinoacetic acid (GAA) in dried blood spots by tandem mass spectrometry (MS/MS) has been described. Its key feature is the ability to detect CRE and GAA in the same extract generated from neonatal DBS during amino acids (AA) and acylcarnitines (AC) analysis. More laboratories are adopting non-derivatized MS/MS screening methods. We describe an improved, non-derivatized DBS extraction and MS/MS analytical method (AAAC-GAMT) which incorporates quantitation of CRE and GAA into routine analysis of amino acids, acylcarnitines, and succinylacetone. The non-derivatized AAAC-GAMT method performs comparably to the stand-alone GAMT and non-derivatized AAAC screening methods, evidencing its potential suitability for high-throughput GAMT neonatal screening. |
Public perceptions of Ebola vaccines and confidence in health services to treat Ebola, malaria, and tuberculosis: Findings from a cross-sectional household survey in Uganda, 2020
Koyuncu A , Carter RJ , Musaazi J , Namageyo-Funa A , Carter VM , Lamorde M , Prybylski D , Apondi R , Bakyaita T , Boore AL , Homsy J , Brown VR , Kigozi J , Nabaggala MS , Nakate V , Nkurunziza E , Stowell DF , Walwema R , Olowo A , Jalloh MF . PLOS Glob Public Health 2023 3 (12) e0001884 Uganda used Ebola vaccines as part of its preparedness and response during the 2018-2020 10th Ebola virus disease (EVD) outbreak in neighboring Democratic Republic of the Congo (DRC). We evaluated the public's perceptions of Ebola vaccines and compared their confidence in health services to treat Ebola versus malaria and tuberculosis as part of a survey on Ebola knowledge, attitudes, and practices (KAP) conducted in March 2020. A cross-sectional household survey was implemented in six districts in Uganda using multi-stage cluster sampling to randomly select participants. The districts were purposively selected from districts classified by the government as at high- or low-risk for an EVD outbreak. We describe perceptions of Ebola vaccines and confidence in health services to treat Ebola, tuberculosis, and malaria. Modified Poisson regression modeling was used to identify the demographic correlates of these outcomes. Among 3,485 respondents, 18% were aware of Ebola vaccines. Of those, 92% agreed that the vaccines were needed to prevent Ebola. Participants aged 15-24 years were 4% more likely to perceive such need compared to those 60 years and older (adjusted prevalence ratio [aPR] 1.04, 95% confidence interval [CI] 1.0-1.08). The perceived need was 5% lower among participants with at least some secondary education compared to uneducated participants (aPR 0.95; 0.92-0.99). Overall, 81% of those aware of the vaccines believed that everyone or most people in their community would get vaccinated if offered, and 94% said they would likely get vaccinated if offered. Confidence in health services to treat Ebola was lower compared to treating malaria or tuberculosis (55% versus 93% and 77%, respectively). However, participants from the EVD high-risk districts were 22% more likely to be confident in health services to treat Ebola compared to those in low-risk districts (aPR: 1.22; 95% CI: 1.08, 1.38). Our findings suggest that intent to take an Ebola vaccine during an outbreak was strong, but more work needs to be done to increase public awareness of these vaccines. The public's high confidence in health services to treat other health threats, such as malaria and tuberculosis, offer building blocks for strengthening their confidence in health services to treat EVD in the event of an outbreak. |
Building the vector in: construction practices and the invasion and persistence of Anopheles stephensi in Jigjiga, Ethiopia
Yared S , Gebresilassie A , Aklilu E , Abdulahi E , Kirstein OD , Gonzalez-Olvera G , Che-Mendoza A , Bibiano-Marin W , Waymire E , Lines J , Lenhart A , Kitron U , Carter T , Manrique-Saide P , Vazquez-Prokopec GM . Lancet Planet Health 2023 7 (12) e999-e1005 Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a major threat to malaria control and elimination efforts on the continent. The mosquito is well adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga in Ethiopia, and report An stephensi immature stages infesting predominantly in water reservoirs made to support construction operations (ie, in construction sites or associated with brick-manufacturing businesses). Political and economic changes in Ethiopia (particularly the Somali Region) have fuelled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence, and propagation of An stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season might provide a unique opportunity for focused control of An stephensi in Jigjiga and similar areas. |
Genomic and phenotypic characterization of shiga toxin-producing Escherichia albertii strains isolated from wild birds in a major agricultural region in California
Carter MQ , Quiñones B , He X , Pham A , Carychao D , Cooley MB , Lo CC , Chain PSG , Lindsey RL , Bono JL . Microorganisms 2023 11 (11) Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx(2f) were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx(2f)-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx(2f)-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans. |
Effects of rurality on distance and time traveled to receive vaccination against Mpox - New Mexico and Idaho 2022-2023
Stadelman-Behar AM , Cahill ME , Newell K , Sievers M , Gehre M , Carter KK , Sosin DM , Torrone EA . Sex Transm Dis 2023 We compared mpox vaccination access between urban and rural residents who received ≥1 JYNNEOS dose using immunization data in Idaho and New Mexico. Rural residents traveled five times farther and three times longer than urban residents to receive mpox vaccination. Increasing mpox vaccine availability to healthcare facilities might increase uptake. |
Progress toward eradication of dracunculiasis - Worldwide, January 2022-June 2023
Hopkins DR , Weiss AJ , Yerian S , Sapp SGH , Cama VA . MMWR Morb Mortal Wkly Rep 2023 72 (45) 1230-1236 The effort to eradicate Dracunculus medinensis, the etiologic agent of dracunculiasis, or Guinea worm disease, commenced at CDC in 1980. In 1986, with an estimated 3.5 million cases worldwide in 20 African and Asian countries, the World Health Assembly called for dracunculiasis elimination. The Guinea Worm Eradication Program (GWEP) was established to help countries with endemic dracunculiasis reach this goal. GWEP is led by The Carter Center and supported by partners that include the World Health Organization, UNICEF, and CDC. In 2012, D. medinensis infections were unexpectedly confirmed in Chadian dogs, and since then, infections in dogs, cats, and baboons have posed a new challenge for GWEP, as have ongoing civil unrest and insecurity in some areas. By 2022, dracunculiasis was endemic in five countries (Angola, Chad, Ethiopia, Mali, and South Sudan), with only 13 human cases identified, the lowest yearly total ever reported. Animal infections, however, were not declining at the same rate: 686 animal infections were reported in 2022, including 606 (88%) in dogs in Chad. Despite these unanticipated challenges as well as the COVID-19 pandemic, countries appear close to reaching the eradication goal. GWEP will continue working with country programs to address animal infections, civil unrest, and insecurity, that challenge the eradication of Guinea worm. |
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets
Haas KM , McGregor MJ , Bouhaddou M , Polacco BJ , Kim EY , Nguyen TT , Newton BW , Urbanowski M , Kim H , Williams MAP , Rezelj VV , Hardy A , Fossati A , Stevenson EJ , Sukerman E , Kim T , Penugonda S , Moreno E , Braberg H , Zhou Y , Metreveli G , Harjai B , Tummino TA , Melnyk JE , Soucheray M , Batra J , Pache L , Martin-Sancho L , Carlson-Stevermer J , Jureka AS , Basler CF , Shokat KM , Shoichet BK , Shriver LP , Johnson JR , Shaw ML , Chanda SK , Roden DM , Carter TC , Kottyan LC , Chisholm RL , Pacheco JA , Smith ME , Schrodi SJ , Albrecht RA , Vignuzzi M , Zuliani-Alvarez L , Swaney DL , Eckhardt M , Wolinsky SM , White KM , Hultquist JF , Kaake RM , García-Sastre A , Krogan NJ . Nat Commun 2023 14 (1) 6030 Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT. |
U. S. federal perspective on critical research issues in nanoEHS
Carter J , Bjorkland R , Boyes WK , Geraci C , Hackley VA , Howard J , Kennedy A , Linkov I , Matheson J , Mortensen H , Muianga C , Petersen EJ , Savage N , Schulte P , Standridge S , Thomas T , Trump B , Nadadur S . Environ Sci Nano 2023 This article discusses critical issues and opportunities going forward in nanotechnology environmental, health, and safety (nanoEHS) research from the perspective of Federal Government Agency participants in the United States (U.S.) National Nanotechnology Initiative (NNI) interagency Nanotechnology Environmental and Health Implications Working Group (NEHI). NEHI is responsible for coordination of Federal Science Agency nanoEHS research. As participants in NEHI, we examine these critical issues from an integrated, transdisciplinary perspective, noting examples of impactful research efforts that are advancing knowledge in these areas. Major themes identified include detection, measurement, and characterization of real-world nanomaterial exposures, understanding the biological transformation of nanomaterials and their potential (eco) toxicological implications, understanding the landscape of nanotechnology-enabled products in commerce, and advancing the EHS knowledge infrastructure related to nanomaterials and nanotechnology. Significant investments in nanoEHS research over two decades have led to establishment of a unique and diverse multidisciplinary, multisector community of practice. These investments must be leveraged and adapted not only to future nanotechnology, but also to use as a model for accelerating acquisition of safe and reliable risk information for tomorrow's emerging technologies for a more sustainable and competitive world. © 2023 The Royal Society of Chemistry. |
Reducing vaccination disparities during a national emergency response: The US mpox vaccine equity pilot program
Bautista GJ , Madera-Garcia V , Carter RJ , Schwitters A , Byrkit R , Carnes N , Prejean J . J Public Health Manag Pract 2023 30 (1) 122-129 CONTEXT: In response to the first reported mpox cases in May 2022, the US government implemented plans to bring testing, treatment, and vaccines to communities disproportionately affected by mpox-including the population of men who have sex with men (MSM) and Black/African American and Hispanic/Latino men, 2 subpopulations experiencing vaccination disparities. We describe the development and implementation of the US Mpox Vaccine Equity Pilot Program (MVEPP), characteristics of completed vaccination projects, and challenges that occurred. We also discuss opportunities for reducing vaccination disparities in future outbreaks. PROGRAM: To address reported vaccination disparities, the US government launched MVEPP in 2 phases. Phase 1 centered around public events attended by large numbers of gay, bisexual, and other MSM, such as Pride festivals. Phase 2 asked health departments to propose mpox vaccination projects specifically aimed at reducing or eliminating racial/ethnic and other demographic disparities in mpox vaccination. IMPLEMENTATION: MVEPP received 35 vaccination project proposals. We analyzed data from 22 completed projects that resulted in 25 675 doses of JYNNEOS administered. We note 3 innovative strategies that were implemented in several projects: direct collaboration with organizations providing services to MSM and transgender women; implementation of MVEPP projects in unique nonclinical community settings and at venues frequented by MSM and transgender women; and offering an array of services as part of mpox vaccination projects, rather than offering only mpox vaccination. EVALUATION: MVEPP highlighted the importance of recognizing and working to eliminate racial/ethnic and other disparities in access to medical countermeasures during a public health emergency. Jurisdictions developed and implemented innovative strategies to bring mpox vaccination and related services to communities disproportionately affected by mpox-including MSM and the subpopulations of Black/African American and Hispanic/Latino MSM. Lessons learned from MVEPP may inform efforts to reduce disparities during future public health responses. |
Cluster of carbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa among patients in an adult intensive care unit - Idaho, 2021-2022
Cahill ME , Jaworski M , Harcy V , Young E , Ham DC , Gable P , Carter KK . MMWR Morb Mortal Wkly Rep 2023 72 (31) 844-846 Treatment of carbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa (CP-CRPA) infections is challenging because of antibiotic resistance. CP-CRPA infections are highly transmissible in health care settings because they can spread from person to person and from environmental sources such as sink drains and toilets. During September 2021-January 2022, an Idaho hospital (hospital A) isolated CP-CRPA from sputum of two patients who stayed in the same intensive care unit (ICU) room (room X), 4 months apart. Both isolates had active-on-imipenem metallo-beta-lactamase (IMP) carbapenemase gene type 84 (bla(IMP-84)) and were characterized as multilocus sequence type 235 (ST235). A health care-associated infections team from the Idaho Division of Public Health visited hospital A during March 21-22, 2022, to discuss the cluster investigation with hospital A staff members and to collect environmental samples. CP-CRPA ST235 with bla(IMP-84) was isolated from swab samples of one sink in room X, suggesting it was the likely environmental source of transmission. Recommended prevention and control measures included application of drain biofilm disinfectant, screening of future patients who stay in room X (e.g., the next 10 occupants) upon reopening, and continuing submission of carbapenem-resistant P. aeruginosa (CRPA) isolates to public health laboratories. Repeat environmental sampling did not detect any CRPA. As of December 2022, no additional CP-CRPA isolates had been reported by hospital A. Collaboration between health care facilities and public health agencies, including testing of CRPA isolates for carbapenemase genes and implementation of sink hygiene interventions, was critical in the identification of and response to this CP-CRPA cluster in a health care setting. |
Estimating typhoid incidence from community-based serosurveys: A multicohort study in Bangladesh, Nepal, Pakistan and Ghana (preprint)
Aiemjoy K , Seidman JC , Saha S , Munira SJ , Islam Sajib MS , Sium SMA , Sarkar A , Alam N , Zahan FN , Kabir MS , Tamrakar D , Vaidya K , Shrestha R , Shakya J , Katuwal N , Shrestha S , Yousafzai MT , Iqbal J , Dehraj IF , Ladak Y , Maria N , Adnan M , Pervaiz S , Carter AS , Longley AT , Fraser C , Ryan ET , Nodoushani A , Fasano A , Leonard MM , Kenyon V , Bogoch II , Jeon HJ , Haselbeck A , Park SE , Zellweger RM , Marks F , Owusu-Dabo E , Adu-Sarkodie Y , Owusu M , Teunis P , Luby SP , Garrett DO , Qamar FN , Saha SK , Charles RC , Andrews JR . medRxiv 2022 2021.10.20.21265277 Background The incidence of enteric fever, an invasive bacterial infection caused by typhoidal Salmonellae, is largely unknown in regions lacking blood culture surveillance. New serologic markers have proven accurate in diagnosing enteric fever, but whether they could be used to reliably estimate population-level incidence is unknown.Methods We collected longitudinal blood samples from blood culture-confirmed enteric fever cases enrolled from surveillance studies in Bangladesh, Nepal, Pakistan, and Ghana and conducted cross-sectional serosurveys in the catchment areas of each surveillance site. We used ELISAs to measure quantitative IgA and IgG antibody responses to Hemolysin E (HlyE) and S. Typhi lipopolysaccharide (LPS). We used Bayesian hierarchical models to fit two-phase power-function decay models to the longitudinal antibody responses among enteric fever cases and used the joint distributions of the peak antibody titers and decay rate to estimate population-level incidence rates from cross-sectional serosurveys.Findings The longitudinal antibody kinetics for all antigen-isotypes were similar across countries and did not vary by clinical severity. The seroincidence of typhoidal Salmonella infection among children <5 years ranged between 58.5 per 100 person-years (95% CI: 42.1 - 81.4) in Dhaka, Bangladesh to 6.6 (95% CI: 4.3-9.9) in Kavrepalanchok, Nepal, and followed the same rank order as clinical incidence estimates.Interpretation The approach described here has the potential to expand the geographic scope of typhoidal Salmonella surveillance and generate incidence estimates that are comparable across geographic regions and time.Funding This work was supported by the Bill and Melinda Gates Foundation (INV-000572).Evidence before this study Previous studies have identified serologic responses to two antigens (Hemolysin E [HlyE] and Salmonella lipopolysaccharide [LPS]) as promising diagnostic markers of acute typhoidal Salmonella infection. We reviewed the evidence for seroepidemiology tools for enteric fever available as of November 01, 2021, by searching the National Library of Medicine article database and medRxiv for preprint publications, published in English, using the terms “enteric fever”, “typhoid fever”, “Salmonella Typhi”, “Salmonella Paratyphi”, “typhoidal Salmonella”, “Hemolysin E”, “Salmonella lipopolysaccharide”, “seroconversion”, “serosurveillance”, “seroepidemiology”, “seroprevalence” and “seropositivity.” We found no studies using HlyE or LPS as markers to measure the incidence or prevalence of enteric fever in a population. Anti-Vi IgG responses were used as a marker of population seroprevalence in cross-sectional studies conducted in South Africa, Fiji, and Nepal, but were not used to calculate population-based incidence estimates.Added value of this study We developed and validated a method to estimate typhoidal Salmonella incidence in cross-sectional population samples using antibody responses measured from dried blood spots. First, using longitudinal dried blood spots collected from over 1400 blood culture-confirmed cases in four countries, we modeled the longitudinal dynamics of antibody responses for up to two years following infection, accounting for heterogeneity in antibody responses and age-dependence. We found that longitudinal antibody responses were highly consistent across four countries on two continents and did not differ by clinical severity. We then used these antibody kinetic parameters to estimate incidence in population-based samples in six communities across the four countries, where concomitant population-based incidence was measured using blood cultures. Seroincidence estimates were much higher than blood-culture-based case estimates across all six sites, suggestive of a high incidence of asymptomatic or unrecognized infections. Still, the rank order of seroincidence and culture-based incidence rates were the same, with the highest rates in Bangladesh and lowest in Ghana.Implications of all the available evidence Many a -risk low- and middle-income countries lack data on typhoid incidence needed to inform and evaluate vaccine introduction. Even in countries where incidence estimates are available, data are typically geographically and temporally sparse due to the resources necessary to initiate and sustain blood culture surveillance. We found that typhoidal Salmonella infection incidence can be estimated from community-based serosurveys using dried blood spots, representing an efficient and scalable approach for generating the typhoid burden data needed to inform typhoid control programs in resource-constrained settings.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis study was funded by th eBill and Melinda Gates Foundation (grant INV-000572)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:Institutional Review Boards in the United States (Centers for Disease Control and Prevention; Stanford University Institutional Review Board), Bangladesh (Bangladesh Institute of Child Health Ethical Review Committee), Nepal (Nepal Health Research Council Ethical Review Board), Pakistan (AKU Ethic Review Committee and Pakistan National Bioethics Committee), Korea (International Vaccine Institute IRB), Belgium (Institute of Tropical Medicine Antwerp Institutional Review Board) and Ghana (Komfo Anokye Teaching Hospital, Committee on Human Research, Publication and Ethics) approved the study forms and protocols.I 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 in the present study are available upon reasonable request to the authors |
Utilization of Whole Genome Sequencing to Understand SARS-CoV-2 Transmission Dynamics in Long-Term Care Facilities, Correctional Facilities and Meat Processing Plants in Minnesota, March – June 2020 (preprint)
Lehnertz NB , Wang X , Garfin J , Taylor J , Zipprich J , VonBank B , Martin K , Eikmeier D , Medus C , Wiedinmyer B , Bernu C , Plumb M , Pung K , Honein MA , Carter R , MacCannell D , Smith KE , Como-Sabetti K , Ehresmann K , Danila R , Lynfield R . medRxiv 2021 2020.12.30.20248277 Congregate settings and high-density workplaces have endured a disproportionate impact from COVID-19. In order to provide further understanding of the transmission patterns of SARS-CoV-2 in these settings, whole genome sequencing (WGS) was performed on samples obtained from 8 selected outbreaks in Minnesota from March – June, 2020. WGS and phylogenetic analysis was conducted on 319 samples, constituting 14.4% of the 2,222 total SARS-CoV-2-positive individuals associated with these outbreaks. Among the sequenced specimens, three LTCFs and both correctional facilities had spread associated with a single genetic sequence. A fourth LTCF had outbreak cases associated with two distinct sequences. In contrast, cases associated with outbreaks in the two meat processing plants represented multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak, and early identification and cohorting of cases, along with continued vigilance with infection prevention and control measures is imperative.Competing Interest StatementThe authors have declared no competing interest.Funding StatementStudy was supported by the ELC Cares grant from CDC.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:The manuscript was reviewed in accordance with standard CDC protocol, in which the approved CDC chain of command in the COVID 19 response division reviewed the manuscript and determined that it was non-research, public health response. As such, it was determined by CDC review to be exempt from further institutional review board evaluation. In summary, this manuscript and activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy (see e.g., 45 C.F.R. part 46, 21 C.F.R. part 56; 42 U.S.C. 241(d); 5 U.S.C 552a; 44 U.S.C. 351 et seq.).All 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.YesThere is no referred data. |
Impact of Diabetes Status on Immunogenicity of Trivalent Inactivated Influenza Vaccine in Older Adults (preprint)
Spencer S , Chung JR , Belongia EA , Sundaram M , Meece J , Coleman LA , Zimmerman RK , Nowalk MP , Moehling Geffel K , Ross T , Carter CE , Shay D , Levine M , Liepkalns J , Kim JH , Sambhara S , Thompson MG , Flannery B . medRxiv 2021 2021.10.04.21264429 Individuals with type 2 diabetes mellitus experience high rates of influenza virus infection and complications. We compared the magnitude and duration of serologic response to trivalent influenza vaccine in adults aged 50-80 with and without type 2 diabetes mellitus. Serologic response to influenza vaccination was similar in both groups: greater fold-increases in antibody titer occurred among individuals with lower pre-vaccination antibody titers. Waning of antibody titers was not influenced by diabetes status.Competing Interest StatementKKM, MPN and RZ have received research funds from Merck & Co., Inc and Pfizer, Inc. KKM and RZ have received research funds from Sanofi Pasteur, Inc. LC is currently employed by Novartis. The remaining authors report no conflicts of interest.Funding StatementThis study was supported by cooperative agreements U01 IP000471 and U01 IP000467 from the Centers for Disease Control and Prevention. The findings and conclusions in this report are those of those authors and do not necessarily represent the views of the Centers for Disease Control and Prevention.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:Institutional Review Boards at the University of Pittsburgh and Marshfield Clinic approved this study.All 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.YesData are not publicly available at this time. |
Investigation and public health response to a COVID-19 outbreak in a rural resort community — Blaine County, Idaho, 2020 (preprint)
Dunne EM , Maxwell T , Dawson-Skuza C , Burns M , Ball C , Turner K , Hahn CG , Bowyer M , Carter KK , Hudson L . medRxiv 2021 2021.02.09.21251216 Blaine County, Idaho, a rural area with a renowned resort, experienced an outbreak of novel coronavirus disease (COVID-19). We undertook an epidemiologic investigation to describe the outbreak and guide public health action. Confirmed cases of COVID-19 were identified from reports of SARS-CoV-2-positive laboratory test results to South Central Public Health District.Information on symptoms, hospitalization, recent travel, healthcare worker status, and close contacts was obtained by medical record review and patient interviews. Viral sequence analysis was conducted on a subset of available specimens. During March 13–April 10, 2020, a total of 451 COVID-19 cases occurred among Blaine County residents (1,959 cases per 100,000 population). An additional 37 cases occurred in out-of-state residents. Among the 451 COVID-19 patients, the median age was 51 years (Interquartile range [IQR]: 37–63), 52 (11.5%) were hospitalized, and 5 (1.1%) died. The median duration between specimen collection and a positive laboratory result was 9 days (IQR: 4–10). Forty-four (9.8%) patients reported recent travel. Healthcare workers comprised 56 (12.4%) cases; 33 of whom worked at the only hospital in the county, leading to a 15-day disruption of hospital services. Of 562 close contacts monitored by public health authorities, 22 (3.9%) had laboratory-confirmed COVID-19 and an additional 29 (5.2%) experienced compatible symptoms. Sequencing results from 34 Idaho specimens supported epidemiologic findings indicating travel as a source of SARS-CoV-2, and identified multiple lineages among hospital workers. Community mitigation strategies included school and resort closure, stay-at-home orders, and restrictions on incoming travelers. COVID-19 outbreaks in rural communities can disrupt health services. Lack of local laboratory capacity led to long turnaround times for COVID-19 test results. Rural communities frequented by tourists should consider implementing restrictions on incoming travelers among other mitigation strategies to reduce COVID-19 transmission.Competing Interest StatementThe authors have declared no competing interest.Funding StatementNo external funding was received.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:COVID-19 is a reportable disease under Idaho Department of Health and Welfare Rules, IDAPA 16.02.10. Case investigation, data collection, and analysis were conducted for public health purposes. This project was reviewed by the Center for Surveillance, Epidemiology, and Laboratory Services Human Subjects Contact at the Centers for Disease Control and Prevention (CDC). The project was determined to meet the requirements of public health surveillance covered by the U.S. Department of Health and Human Services Policy for the Protection of Human Research Subjects as defined in 45 CFR 46.102, and the decision was made that this project was nonresearch and did not require ethical review by the CDC Human Research Protection Office. Ethical approval was waived and informed consent was not required.All 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.YesSARS-CoV-2 sequence data have be n uploaded to the GISAID database, with accession numbers provided in S1 Table. Data on the estimated proportion of Blaine County residents staying at home are available at https://docs.safegraph.com/docs/social-distancing-metrics. Census block group data are available at https://data.census.gov/cedsci/. De-identified patient data are not publicly available for legal and ethical reasons. These data were collected as part of reportable disease surveillance under Idaho law, and not for research purposes. Due to the rural setting and relatively small population, there is a risk of reidentification of some patients included in the data set. De-identified data can be requested from the Idaho Division of Public Health by contacting the Bureau of Communicable Diseases Epidemiology Section at Epimail{at}dhw.Idaho.gov. https://www.gisaid.org/ |
Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad (preprint)
Ribado JV , Li N , Thiele E , Lyons H , Cotton JA , Weiss A , Tchindebet Ouakou P , Moundai T , Zirimwabagabo H , Guagliardo SAJ , Chabot-Couture G , Proctor JL . medRxiv 2020 2020.10.05.20207324 Background Guinea worm (Dracunculus medinensis) was detected in Chad in 2010 after a supposed ten year absence, posing a challenge to the global eradication effort. Initiation of a village-based surveillance system in 2012 revealed a substantial number of dogs infected with Guinea worm, raising questions about paratenic hosts and cross-species transmission.Methodology/Principal Findings We coupled genomic and surveillance data from 2012-2018 cases to investigate the modes of transmission between hosts and the geographic connectivity for genetically similar worm populations. Eighty-six variants across three loci on the mitochondrial genome identified 41 genetically distinct worm genotypes. Spatiotemporal modeling reveals genetically identical worms are within a median range of 18.6 kilometers of each other, but largely within approximately 50 kilometers. Genetically identical worms vary in their degree of spatial clustering, suggesting there may be different factors that favor or constrain transmission. Each worm is surrounded by five to ten genetically distinct worms within a 50 kilometer radius. In an independent population, we show that more variants revealed in whole mitochondrial genome data improved the discrimination between worm pairs.Conclusions/Significance In the largest study linking genetic and surveillance data to date of Guinea worm cases in Chad, we show genetic similarity and modeling can contribute to understanding local transmission. The overlap of genetically distinct worms in quantitatively identified transmission ranges highlights the necessity for genomic tools to link cases. The improved discrimination between worm pairs from variants identified across the complete mitochondrial genome indicates expanding genomic markers could link cases at a finer scale. These results suggest that scaling up genomic surveillance for Guinea worm may provide additional value for programmatic decision-making critical for monitoring cases and intervention efficacy to achieve elimination.Competing Interest StatementThe authors have declared no competing interest.Funding StatementJR, GCC, HL, and JLP would like to thank Bill and Melinda Gates for their active support of the Institute for Disease Modeling and their sponsorship through the Global Good Fund. JAC was supported by funding from The Carter Center and Wellcome, via their core support for the Wellcome Sanger Institute (grant WT206194).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:N/A; Worm collection and associated metadata are routine in country surveillance efforts.All 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.YesGenomic data and source code will be made available upon publication. Requests for epidemiological data that includes case coordinates must be submitted to and approved by the Chad Guinea Worm Eradication Program. |
Geographical distribution of Anopheles stephensi in eastern Ethiopia (preprint)
Balkew M , Mumba P , Dengela D , Yohannes G , Getachew D , Yared S , Chibsa S , Murphy M , George K , Lopez K , Janies D , Choi SH , Spear J , Irish SR , Carter TE . bioRxiv 2019 802587 Background The recent detection of the South Asian malaria vector An. stephensi in Ethiopia and other regions in the Horn of Africa has raised concerns about its potential impact on malaria transmission. We report here findings of survey for this species in eastern Ethiopia using both morphological and molecular methods for species identification.Methods Adult and larval/pupal collections were conducted at ten sites in eastern Ethiopia and Anopheles specimens’ species were determined using standard morphological keys and genetic analysis.Results In total, 2,231 morphologically identified An. stephensi were collected. A molecular approach incorporating both PCR endpoint assay and sequencing of portions of the internal transcribed spacer 2 (ITS2) and cytochrome oxidase I (COI) loci confirmed the identity of the An. stephensi in most cases (119/124 of the morphologically identified An. stephensi confirmed molecularly). Additionally, we observed Aedes aegypti larvae and pupae at many of the An. stephensi larval habitats.Conclusions Our findings show that An. stephensi is widely distributed in eastern Ethiopia and highlight the need for further surveillance in the southern, western and northern parts of the country and throughout the Horn of Africa. |
Building the vector in? Construction practices contribute to the invasion and persistence of Anopheles stephensi in Jigjiga, Ethiopia (preprint)
Yared S , Gebresilassie A , Aklilu E , Abdulahi E , Kirstein OD , Gonzalez-Olvera G , Che-Mendoza A , Bibiano-Marin W , Waymire E , Lines J , Lenhart A , Kitron U , Carter T , Manrique-Saide P , Vazquez-Prokopec GM . bioRxiv 2023 24 Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a significant threat to malaria control and elimination efforts on the continent. The mosquito is well-adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An. stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga, Ethiopia, and report the finding of An. stephensi immature stages infesting predominantly water reservoirs made to support construction operations (in construction sites or associated with brick manufacturing businesses). Political and economic changes in Ethiopia (and particularly the Somali Region) have fueled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence and propagation of An. stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season may provide a unique opportunity for focused control of An. stephensi in Jigjiga and similar areas. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Effectiveness of 2 and 3 mRNA COVID-19 Vaccines Doses against Omicron and Delta-Related Outpatient Illness among Adults, October 2021 - February 2022 (preprint)
Kim SS , Chung JR , Talbot HK , Grijalva CG , Wernli KJ , Martin ET , Monto AS , Belongia EA , McLean HQ , Gaglani M , Mamawala M , Nowalk MP , Geffel KM , Tartof SY , Florea A , Lee JS , Tenforde MW , Patel MM , Flannery B , Bentz ML , Burgin A , Burroughs M , Davis ML , Howard D , Lacek K , Madden JC , Nobles S , Padilla J , Sheth M , Arroliga A , Beeram M , Dunnigan K , Ettlinger J , Graves A , Hoffman E , Jatla M , McKillop A , Murthy K , Mutnal M , Priest E , Raiyani C , Rao A , Requenez L , Settele N , Smith M , Stone K , Thomas J , Volz M , Walker K , Zayed M , Annan E , Daley P , Kniss K , Merced-Morales A , Ayala E , Amundsen B , Aragones M , Calderon R , Hong V , Jimenez G , Kim J , Ku J , Lewin B , McDaniel A , Reyes A , Shaw S , Takhar H , Torres A , Burganowski R , Kiniry E , Moser KA , Nguyen M , Park S , Wellwood S , Wickersham B , Alvarado-Batres J , Benz S , Berger H , Bissonnette A , Blake J , Boese K , Botten E , Boyer J , Braun M , Breu B , Burbey G , Cravillion C , Delgadillo C , Donnerbauer A , Dziedzic T , Eddy J , Edgren H , Ermeling A , Ewert K , Fehrenbach C , Fernandez R , Frome W , Guzinski S , Heeren L , Herda D , Hertel M , Heuer G , Higdon E , Ivacic L , Jepsen L , Kaiser S , Karl J , Keffer B , King J , Koepel TK , Kohl S , Kohn S , Kohnhorst D , Kronholm E , Le T , Lemieux A , Marcis C , Maronde M , McCready I , McGreevey K , Meece J , Mehta N , Miesbauer D , Moon V , Moran J , Nikolai C , Olson B , Olstadt J , Ott L , Pan N , Pike C , Polacek D , Presson M , Price N , Rayburn C , Reardon C , Rotar M , Rottscheit C , Salzwedel J , Saucedo J , Scheffen K , Schug C , Seyfert K , Shrestha R , Slenczka A , Stefanski E , Strupp M , Tichenor M , Watkins L , Zachow A , Zimmerman B , Bauer S , Beney K , Cheng CK , Faraj N , Getz A , Grissom M , Groesbeck M , Harrison S , Henson K , Jermanus K , Johnson E , Kaniclides A , Kimberly A , Lamerato LE , Lauring A , Lehmann-Wandell R , McSpadden EJ , Nabors L , Truscon R , Balasubramani GK , Bear T , Bobeck J , Bowser E , Clarke K , Clarke LG , Dauer K , Deluca C , Dierks B , Haynes L , Hickey R , Johnson M , Jonsson A , Luosang N , McKown L , Peterson A , Phaturos D , Rectenwald A , Sax TM , Stiegler M , Susick M , Suyama J , Taylor L , Walters S , Weissman A , Williams JV , Blair M , Carter J , Chappell J , Copen E , Denney M , Graes K , Halasa N , Lindsell C , Liu Z , Longmire S , McHenry R , Short L , Tan HN , Vargas D , Wrenn J , Wyatt D , Zhu Y . medRxiv 2022 10 Background: We estimated SARS-CoV-2 Delta and Omicron-specific effectiveness of 2 and 3 mRNA COVID-19 vaccine doses in adults against symptomatic illness in US outpatient settings. Method(s): Between October 1, 2021, and February 12, 2022, research staff consented and enrolled eligible participants who had fever, cough, or loss of taste or smell and sought outpatient medical care or clinical SARS-CoV-2 testing within 10 days of illness onset. Using the test-negative design, we compared the odds of receiving 2 or 3 mRNA COVID-19 vaccine doses among SARS-CoV-2 cases versus controls using logistic regression. Regression models were adjusted for study site, age, onset week, and prior SARS-CoV-2 infection. Vaccine effectiveness (VE) was calculated as (1 - adjusted odds ratio) x 100%. Result(s): Among 3847 participants included for analysis, 574 (32%) of 1775 tested positive for SARS-CoV-2 during the Delta predominant period and 1006 (56%) of 1794 participants tested positive during the Omicron predominant period. When Delta predominated, VE against symptomatic illness in outpatient settings was 63% (95% CI: 51% to 72%) among mRNA 2-dose recipients and 96% (95% CI: 93% to 98%) for 3-dose recipients. When Omicron predominated, VE was 21% (95% CI: -6% to 41%) among 2-dose recipients and 62% (95% CI: 48% to 72%) among 3-dose recipients. Conclusion(s): In this adult population, 3 mRNA COVID-19 vaccine doses provided substantial protection against symptomatic illness in outpatient settings when the Omicron variant became the predominant cause of COVID-19 in the U.S. These findings support the recommendation for a 3rd mRNA COVID-19 vaccine dose. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Employer Requirements and COVID-19 Vaccination and Attitudes among Healthcare Personnel in the U.S.: Findings from National Immunization Survey Adult COVID Module, August - September 2021 (preprint)
Lee JT , Hu SS , Zhou T , Bonner K , Kriss JL , Wilhelm E , Carter RJ , Holmes C , de Perio MA , Lu PJ , Nguyen KH , Brewer NT , Singleton JA . medRxiv 2022 15 Introduction Employer vaccination requirements have been used to increase vaccination uptake among healthcare personnel (HCP). In summer 2021, HCP were the group most likely to have employer requirements for COVID-19 vaccinations as healthcare facilities led the implementation of such requirements. This study examined the association between employer requirements and HCP's COVID-19 vaccination status and attitudes about the vaccine. Methods Participants were a national representative sample of United States (US) adults who completed the National Immunization Survey Adult COVID Module (NIS-ACM) during August-September 2021. Respondents were asked about COVID-19 vaccination and intent, requirements for vaccination, place of work, attitudes surrounding vaccinations, and sociodemographic variables. This analysis focused on HCP respondents. We first calculated the weighted proportion reporting COVID-19 vaccination for HCP by sociodemographic variables. Then we computed unadjusted and adjusted prevalence ratios for vaccination coverage and key indicators on vaccine attitudes, comparing HCP based on individual self-report of vaccination requirements. Results Of 12,875 HCP respondents, 41.5% reported COVID-19 vaccination employer requirements. Among HCP with vaccination requirements, 90.5% had been vaccinated against COVID-19, as compared to 73.3% of HCP without vaccination requirements-a pattern consistent across sociodemographic groups. Notably, the greatest differences in uptake between HCP with and without employee requirements were seen in sociodemographic subgroups with the lowest vaccination uptake, e.g., HCP aged 18-29 years, HCP with high school or less education, HCP living below poverty, and uninsured HCP. In every sociodemographic subgroup examined, vaccine uptake was more equitable among HCP with vaccination requirements than in HCP without. Finally, HCP with vaccination requirements were also more likely to express confidence in the vaccine's safety (68.3% vs. 60.1%) and importance (89.6% vs 79.6%). Conclusion In a large national US sample, employer requirements were associated with higher and more equitable HCP vaccination uptake across all sociodemographic groups examined. Our findings suggest that employer requirements can contribute to improving COVID-19 vaccination coverage, similar to patterns seen for other vaccines. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Meeting report: 36th international conference on antiviral research in Lyon, France, March 13-17, 2023
Spengler JR , Carter K , Delang L , Durantel D , Gowen BB , Herrero LJ , Hurst B , Janeba Z , Jordan R , Luo D , Meier C , Moffat J , Rocha-Pereira J , Seley-Radtke KL , Welch SR , Schang LM . Antiviral Res 2023 217 105678 The 36th International Conference on Antiviral Research (ICAR), sponsored by the International Society for Antiviral Research (ISAR), was held March 13-17, 2023, in Lyon, France, and concurrently through an interactive remote meeting platform. Here we provide a report summarizing the presentations at the 36th ICAR, including the ISAR speaker awards. We also detail special events, sessions, and additional awards conferred at the meeting. ICAR returned to in-person meetings in 2022, convening in Seattle, WA, USA. The 36th ICAR is the first in-person meeting of the society in Europe since the beginning of the COVID-19 pandemic, which restricted most events to virtual attendance to help mitigate the spread and subsequent public health impact of SARS-CoV-2. An exceptionally high number of registrants and record attendance at this year's ICAR, along with a vast array of demonstrable expertise in a variety of antiviral research-related fields, reflected a strong and growing antiviral research community committed to improving health outcomes from viral diseases, including SARS-CoV-2, and to future pandemic preparedness. This report highlights the breadth of expertise, quality of research, and notable advancements that were contributed by members of ISAR and other participants at the meeting. ICAR aims to continue to provide a platform for sharing information, fostering collaborations, and supporting trainees in the field of antiviral research. The 37th ICAR will be held in Gold Coast, Australia, May 20-24, 2024. |
Public health impact of the spread of Anopheles stephensi in the WHO Eastern Mediterranean Region countries in Horn of Africa and Yemen: need for integrated vector surveillance and control
Al-Eryani SM , Irish SR , Carter TE , Lenhart A , Aljasari A , Montoya LF , Awash AA , Mohammed E , Ali S , Esmail MA , Hussain A , Amran JG , Kayad S , Nouredayem M , Adam MA , Azkoul L , Assada M , Baheshm YA , Eltahir W , Hutin YJ . Malar J 2023 22 (1) 187 BACKGROUND: Anopheles stephensi is an efficient vector of both Plasmodium falciparum and Plasmodium vivax in South Asia and the Middle East. The spread of An. stephensi to countries within the Horn of Africa threatens progress in malaria control in this region as well as the rest of sub-Saharan Africa. METHODS: The available malaria data and the timeline for the detection of An. stephensi was reviewed to analyse the role of An. stephensi in malaria transmission in Horn of Africa of the Eastern Mediterranean Region (EMR) in Djibouti, Somalia, Sudan and Yemen. RESULTS: Malaria incidence in Horn of Africa of EMR and Yemen, increased from 41.6 in 2015 to 61.5 cases per 1000 in 2020. The four countries from this region, Djibouti, Somalia, Sudan and Yemen had reported the detection of An. stephensi as of 2021. In Djibouti City, following its detection in 2012, the estimated incidence increased from 2.5 cases per 1000 in 2013 to 97.6 cases per 1000 in 2020. However, its contribution to malaria transmission in other major cities and in other countries, is unclear because of other factors, quality of the urban malaria data, human mobility, uncertainty about the actual arrival time of An. stephensi and poor entomological surveillance. CONCLUSIONS: While An. stephensi may explain a resurgence of malaria in Djibouti, further investigations are needed to understand its interpretation trends in urban malaria across the greater region. More investment for multisectoral approach and integrated surveillance and control should target all vectors particularly malaria and dengue vectors to guide interventions in urban areas. |
Voices of Black talent in chemistry: Retention strategies and personal success stories
Scott T , Adderley D , Ali Y , Amanuel M , Blake A , Callender M , Carter C , Fokwa HD , Gooden RO , Granger A , Gunn K , Henderson A , Kitimet M , Modeste E , Stewart Z , Teah J , Wairegi S , Ward LW , Parish CA . J Am Chem Soc 2023 145 (23) 12426-12428 Juneteenth, a federal holiday officially recognized in 2021, is celebrated annually in the United States to honor the emancipation of enslaved Black Americans. As a symbol of racial justice, equality, and equity, Juneteenth represents an opportunity to pay tribute to the achievements of a wide range of Black chemistry students and the initiatives taken to promote the success of every student within an environment that has historically not been inclusive. | | While the U.S. STEM workforce has become more diverse in the past 10 years, Black people continue to be underrepresented in science, and in chemistry, in particular. The recent National Science Foundation report Diversity and STEM: Women, Minorities and Persons with Disabilities 2023 shows that only 9% of the STEM workforce identifies as Black, 3 percentage points (roughly 7.7M people (1)) lower than their overall representation in the adult U.S. population. (2) The U.S. Bureau of Labor Statistics paints a similar picture─in 2022 only 10% of the chemical manufacturing workforce was Black. (3) Chemical & Engineering News culled the chemistry data from the 2023 NSF report revealing even bleaker figures─in 2021, Black people comprised only 4.4% of employed chemists, (4) and were more likely to occupy lower paying STEM jobs that do not require a college degree. (2) | | Recent publications have emphasized the importance of scientists and scientific institutions welcoming and supporting the development of individuals from groups historically marginalized in fields such as chemistry, biology, mathematics, computer science, and physics. (5) Not only is such intentional support a moral imperative, but numerous reports have demonstrated that increasing diversity and inclusion in these fields leads to a more innovative and productive scientific community. (6) | | Marginalized groups often face systemic barriers to accessing education and career opportunities, resulting in a chemical workforce that lacks diversity. To address this, chemists and chemistry organizations have taken steps to actively support and mentor individuals from historically excluded groups, providing access to resources and opportunities, and promoting a culture of inclusivity in academia and the workplace. For instance, since 1965, the American Chemical Society (ACS) Project Seed program has provided summer research experiences for more than 11,000 high school students, while the ACS Scholars program has provided renewable scholarships for more than 3,500 undergraduates interested in chemistry-related careers. |
Observed face mask use outside retail chain stores during the COVID-19 pandemic in two cities in the state of Idaho, USA
Cahill ME , Lozoya SB , Griffin MA , Blackstock A , Stockdale K , Cowman S , Graff R , Spear C , Carter K . J Community Health 2023 During the COVID-19 pandemic, public health authorities have encouraged the use of face masks to minimize transmission within the community. To assess mask wear during a COVID-19 surge and guide public health response efforts, including public messaging on mask recommendations, we compared observed mask use in the largest city in each of Idaho's 2 most populous counties, both without a current mask mandate. We recorded mask usage by every third person exiting stores of 5 retail chains in Boise and Nampa during November 8-December 5, 2021. Observations were conducted during three time periods (morning, afternoon, and evening) on weekday and weekend days. A multivariable model with city, retail chain, and city-chain interaction was used to assess mask wear differences by city for each chain. Of 3021 observed persons, 22.0% wore masks. In Boise, 31.3% (430/1376) of observed persons wore masks; in Nampa, 14.3% (236/1645) wore masks. Among all persons wearing masks, > 94% wore masks correctly; cloth and surgical masks were most common. By retail chain, observed individuals at Boise locations were 2.3-5.7 times as likely to wear masks than persons at respective Nampa locations. This study provided a rapid, nonconfrontational assessment of public use of mitigation measures in 2 Idaho cities during a COVID-19 surge. |
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