Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 191 Records) |
Query Trace: Bi D[original query] |
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Marburgvirus resurgence in Kitaka Mine bat population after extermination attempts, Uganda.
Amman BR , Nyakarahuka L , McElroy AK , Dodd KA , Sealy TK , Schuh AJ , Shoemaker TR , Balinandi S , Atimnedi P , Kaboyo W , Nichol ST , Towner JS . Emerg Infect Dis 2014 20 (10) 1761-4 Marburg virus (MARV) and Ravn virus (RAVV), collectively called marburgviruses, cause Marburg hemorrhagic fever (MHF) in humans. In July 2007, 4 cases of MHF (1 fatal) occurred in miners at Kitaka Mine in southern Uganda. Later, MHF occurred in 2 tourists who visited Python Cave, ≈50 km from Kitaka Mine. One of the tourists was from the United States (December 2007) and 1 was from the Netherlands (July 2008); 1 case was fatal (1,2,3). The cave and the mine each contained 40,000–100,000 Rousettus aegyptiacus bats (Egyptian fruit bats). | | Longitudinal investigations of the outbreaks at both locations were initiated by the Viral Special Pathogens Branch of the Centers for Disease Control and Prevention (CDC, Atlanta, GA, USA, and Entebbe, Uganda) in collaboration with the Uganda Wildlife Authority (UWA) and the Uganda Virus Research Institute (UVRI). During these studies, genetically diverse MARVs and RAVVs were isolated directly from bat tissues, and infection levels of the 2 viruses were found to increase in juvenile bats on a predictable bi-annual basis (4,5). However, investigations at Kitaka Mine were stopped when the miners exterminated the bat colony by restricting egress from the cave with papyrus reed barriers and then entangling the bats in fishing nets draped over the exits. The trapping continued for weeks, and the entrances were then sealed with sticks and plastic. These depopulation efforts were documented by researchers from UVRI, the CDC, the National Institute of Communicable Diseases (Sandringham, South Africa), and UWA during site visits to Kitaka Mine (Technical Appendix Figure). In August 2008, thousands of dead bats were found piled in the forest, and by November 2008, there was no evidence of bats living in the mine; whether 100% extermination was achieved is unknown. CDC, UVRI, and UWA recommended against extermination, believing that any results would be temporary and that such efforts could exacerbate the problem if bat exclusion methods were not complete and permanent (6,7). |
A diverse group of small circular ssDNA viral genomes in human and non-human primate stools.
Ng TF , Zhang W , Sachsenröder J , Kondov NO , da Costa AC , Vega E , Holtz LR , Wu G , Wang D , Stine CO , Antonio M , Mulvaney US , Muench MO , Deng X , Ambert-Balay K , Pothier P , Vinjé J , Delwart E . Virus Evol 2015 1 (1) vev017 Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated. |
Disparities in rates of death from HIV or tuberculosis before age 65 years, by race, ethnicity, and sex, United States, 2011-2020
Adekoya N , Chang MH , Wortham J , Truman BI . Public Health Rep 2023 333549231213328 OBJECTIVE: Death from tuberculosis or HIV among people from racial and ethnic minority groups who are aged <65 years is a public health concern. We describe age-adjusted, absolute, and relative death rates from HIV or tuberculosis from 2011 through 2020 by sex, race, and ethnicity among US residents. METHODS: We used mortality data from the Centers for Disease Control and Prevention online data system on deaths from multiple causes from 2011 through 2020 to calculate age-adjusted death rates and absolute and relative disparities in rates of death by sex, race, and ethnicity. We calculated corresponding 95% CIs for all rates and determined significance at P < .05 by using z tests. RESULTS: For tuberculosis, when compared with non-Hispanic White residents, non-Hispanic American Indian or Alaska Native residents had the highest level of disparity in rate of death (666.7%). Similarly, as compared with non-Hispanic White female residents, American Indian or Alaska Native female residents had a high relative disparity in death from tuberculosis (620.0%). For HIV, the age-adjusted death rate was more than 8 times higher among non-Hispanic Black residents than among non-Hispanic White residents, and the relative disparity was 735.1%. When compared with non-Hispanic White female residents, Black female residents had a high relative disparity in death from HIV (1529.2%). CONCLUSION: Large disparities in rates of death from tuberculosis or HIV among US residents aged <65 years based on sex, race, and ethnicity indicate an ongoing unmet need for effective interventions. Intervention strategies are needed to address disparities in rates of death and infection among racial and ethnic minority populations. |
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
Howerton E , Contamin L , Mullany LC , Qin M , Reich NG , Bents S , Borchering RK , Jung SM , Loo SL , Smith CP , Levander J , Kerr J , Espino J , van Panhuis WG , Hochheiser H , Galanti M , Yamana T , Pei S , Shaman J , Rainwater-Lovett K , Kinsey M , Tallaksen K , Wilson S , Shin L , Lemaitre JC , Kaminsky J , Hulse JD , Lee EC , McKee CD , Hill A , Karlen D , Chinazzi M , Davis JT , Mu K , Xiong X , Pastore YPiontti A , Vespignani A , Rosenstrom ET , Ivy JS , Mayorga ME , Swann JL , España G , Cavany S , Moore S , Perkins A , Hladish T , Pillai A , Ben Toh K , Longini I Jr , Chen S , Paul R , Janies D , Thill JC , Bouchnita A , Bi K , Lachmann M , Fox SJ , Meyers LA , Srivastava A , Porebski P , Venkatramanan S , Adiga A , Lewis B , Klahn B , Outten J , Hurt B , Chen J , Mortveit H , Wilson A , Marathe M , Hoops S , Bhattacharya P , Machi D , Cadwell BL , Healy JM , Slayton RB , Johansson MA , Biggerstaff M , Truelove S , Runge MC , Shea K , Viboud C , Lessler J . Nat Commun 2023 14 (1) 7260 Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections. |
How real-time case-based malaria surveillance helps Zanzibar get a step closer to malaria elimination: Description of operational platform and resources
Mkali HR , Lalji SM , Al-Mafazy AW , Joseph JJ , Mwaipape OS , Ali AS , Abbas FB , Ali MH , Hassan WS , Reaves EJ , Kitojo C , Serbantez N , Kabula BI , Nyinondi SS , McKay M , Cressman G , Ngondi JM , Reithinger R . Glob Health Sci Pract 2023 11 (5) Testing and treating asymptomatic populations have the potential to reduce the population's parasite reservoir and reduce malaria transmission. Zanzibar's malaria case notification (MCN) platform collects detailed sociodemographic and epidemiological data from all confirmed malaria cases to inform programmatic decision-making. We describe the design and operationalization process of the platform and other malaria surveillance resources that are enabling Zanzibar's progress toward malaria elimination.The MCN platform consists of an interactive short message service (SMS) system for case notification, a software application for Android mobile devices, a visual question set and workflow manager, a back-end database server, and a web browser-based application for data analytics, configuration, and management. Malaria case data were collected from August 2012 to December 2021 and reported via SMS from all public and private health facilities to a central database and then to district malaria surveillance officers' mobile devices. Data included patient names, shehia (administrative area), and date of diagnosis, enabling officers to track patients, ideally within 24 hours of reporting. Patients' household members were tested for malaria using conventional rapid diagnostic tests (RDTs). Treatment using artemisinin-based combination therapy was provided for persons testing positive.Between 2012 and 2021, a total of 48,899 index malaria cases were confirmed at health facilities, 22,152 (45.3%) within 24 hours of reporting; 41,886 (85.7%) cases were fully investigated and followed up to the household level. A total of 111,811 additional household members were tested with RDTs, of whom 10,602 (9.5%) were malaria positive.The MCN platform reports malaria case data in near real time, enabling prompt follow-up of index cases and prompt testing and treatment of members in index case households. Along with routine testing and treatment and other preventive interventions, the MCN platform is foundational to the programmatic efforts in further reducing malaria and ultimately eliminating autochthonous malaria transmission in Zanzibar. |
Persistence of mumps antibodies after 2 doses of measles-mumps-rubella vaccine
LeBaron CW , Forghani B , Beck C , Brown C , Bi D , Cossen C , Sullivan BJ . J Infect Dis 2009 199 (4) 552-60 BACKGROUND: Since 1990, most US schoolchildren have received a second dose of measles-mumps-rubella vaccine (MMR2) at kindergarten entry. The objective of the present study was to evaluate the short- and long-term mumps immunogenicity of MMR2. METHODS: At enrollment in 1994-1995, children (n=308) in a rural Wisconsin health maintenance organization received MMR2 at age 4-6 years. A comparison group of older children (n=308) was vaccinated at age 9-11 years. Serum samples were collected over 12 years. Mumps antibody levels were evaluated by plaque-reduction neutralization (lowest detectable titer, 10). RESULTS: Before MMR2, the geometric mean titer (GMT) for the younger group was 33; no subject was seronegative, but 16% had the lowest detectable titer. In response to MMR2, the GMT tripled to 97, and the proportion with low titers diminished to 3%. Four-fold boosts occurred among 54%, but only 3% were positive for immunoglobulin M. Twelve years after MMR2, the GMT declined to 46, the proportion with titers<or=10 was not significantly different from the pre-MMR2 proportion, and 5% were seronegative. The older group showed similar patterns, and at age 17 years both groups had comparable antibody levels. CONCLUSIONS: The mumps antibody response to MMR2 was vigorous, but over a 12-year period titers declined to levels similar to pre-MMR2 titers. No advantage was apparent in delaying MMR2 from kindergarten to middle school. |
HIV risk behavior profiles among men who have sex with men interested in donating blood: Findings from the Assessing Donor Variability and New Concepts in Eligibility study
Custer B , Whitaker BI , Pollack LM , Buccheri R , Bruhn RL , Crowder LA , Stramer SL , Reik RA , Pandey S , Stone M , Di Germanio C , Buchacz K , Eder AF , Lu Y , Forshee RA , Anderson SA , Marks PW . Transfusion 2023 63 (10) 1872-1884 BACKGROUND: Individual risk assessment allows donors to be evaluated based on their own behaviors. Study objectives were to assess human immunodeficiency virus (HIV) risk behaviors in men who have sex with men (MSM) and estimate the proportion of the study population who would not be deferred for higher risk HIV sexual behaviors. STUDY DESIGN AND METHODS: Cross-sectional survey and biomarker assessment were conducted in eight U.S. cities. Participants were sexually active MSM interested in blood donation aged 18-39 years, assigned male sex at birth. Participants completed surveys during two study visits to define eligibility, and self-reported sexual and HIV prevention behaviors. Blood was drawn at study visit 1 and tested for HIV and the presence of tenofovir, one of the drugs in oral HIV pre-exposure prophylaxis (PrEP). Associations were assessed between HIV infection status or HIV PrEP use and behaviors, including sex partners, new partners, and anal sex. RESULTS: A total of 1566 MSM completed the visit 1 questionnaire and blood draw and 1197 completed the visit 2 questionnaire. Among 1562 persons without HIV, 789 (50.4%) were not taking PrEP. Of those not taking PrEP, 66.2% reported one sexual partner or no anal sex and 69% reported no new sexual partners or no anal sex with a new partner in the past 3 months. CONCLUSION: The study found that questions were able to identify sexually active, HIV-negative MSM who report lower risk sexual behaviors. About a quarter of enrolled study participants would be potentially eligible blood donors using individual risk assessment questions. |
Potential pharmacokinetic interactions with concurrent use of herbal medicines and a ritonavir-boosted COVID-19 protease inhibitor in low and middle-income countries
Smith DJ , Bi H , Hamman J , Ma X , Mitchell C , Nyirenda K , Monera-Penduka T , Oketch-Rabah H , Paine MF , Pettit S , Pheiffer W , Van Breemen RB , Embry M . Front Pharmacol 2023 14 1210579 The COVID-19 pandemic sparked the development of novel anti-viral drugs that have shown to be effective in reducing both fatality and hospitalization rates in patients with elevated risk for COVID-19 related morbidity or mortality. Currently, nirmatrelvir/ritonavir (Paxlovid™) fixed-dose combination is recommended by the World Health Organization for treatment of COVID-19. The ritonavir component is an inhibitor of cytochrome P450 (CYP) 3A, which is used in this combination to achieve needed therapeutic concentrations of nirmatrelvir. Because of the critical pharmacokinetic effect of this mechanism of action for Paxlovid™, co-administration with needed medications that inhibit or induce CYP3A is contraindicated, reflecting concern for interactions with the potential to alter the efficacy or safety of co-administered drugs that are also metabolized by CYP3A. Some herbal medicines are known to interact with drug metabolizing enzymes and transporters, including but not limited to inhibition or induction of CYP3A and P-glycoprotein. As access to these COVID-19 medications has increased in low- and middle-income countries (LMICs), understanding the potential for herb-drug interactions within these regions is important. Many studies have evaluated the utility of herbal medicines for COVID-19 treatments, yet information on potential herb-drug interactions involving Paxlovid™, specifically with herbal medicines commonly used in LMICs, is lacking. This review presents data on regionally-relevant herbal medicine use (particularly those promoted as treatments for COVID-19) and mechanism of action data on herbal medicines to highlight the potential for herbal medicine interaction Herb-drug interaction mediated by ritonavir-boosted antiviral protease inhibitors This work highlights potential areas for future experimental studies and data collection, identifies herbal medicines for inclusion in future listings of regionally diverse potential HDIs and underscores areas for LMIC-focused provider-patient communication. This overview is presented to support governments and health protection entities as they prepare for an increase of availability and use of Paxlovid™. |
Better data for decision-making through Bayesian imputation of suppressed provisional COVID-19 death counts
Kao SZ , Tutwiler MS , Ekwueme DU , Truman BI . PLoS One 2023 18 (8) e0288961 PURPOSE: To facilitate use of timely, granular, and publicly available data on COVID-19 mortality, we provide a method for imputing suppressed COVID-19 death counts in the National Center for Health Statistic's 2020 provisional mortality data by quarter, county, and age. METHODS: We used a Bayesian approach to impute suppressed COVID-19 death counts by quarter, county, and age in provisional data for 3,138 US counties. Our model accounts for multilevel data structures; numerous zero death counts among persons aged <50 years, rural counties, early quarters in 2020; highly right-skewed distributions; and different levels of data granularity (county, state or locality, and national levels). We compared three models with different prior assumptions of suppressed COVID-19 deaths, including noninformative priors (M1), the same weakly informative priors for all age groups (M2), and weakly informative priors that differ by age (M3) to impute the suppressed death counts. After the imputed suppressed counts were available, we assessed three prior assumptions at the national, state/locality, and county level, respectively. Finally, we compared US counties by two types of COVID-19 death rates, crude (CDR) and age-standardized death rates (ASDR), which can be estimated only through imputing suppressed death counts. RESULTS: Without imputation, the total COVID-19 death counts estimated from the raw data underestimated the reported national COVID-19 deaths by 18.60%. Using imputed data, we overestimated the national COVID-19 deaths by 3.57% (95% CI: 3.37%-3.80%) in model M1, 2.23% (95% CI: 2.04%-2.43%) in model M2, and 2.96% (95% CI: 2.76%-3.16%) in model M3 compared with the national report. The top 20 counties that were most affected by COVID-19 mortality were different between CDR and ASDR. CONCLUSIONS: Bayesian imputation of suppressed county-level, age-specific COVID-19 deaths in US provisional data can improve county ASDR estimates and aid public health officials in identifying disparities in deaths from COVID-19. |
Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season (preprint)
Potter BI , Garten R , Hadfield J , Huddleston J , Barnes J , Rowe T , Guo L , Xu X , Neher RA , Bedford T , Wentworth DE . bioRxiv 2019 543322 The 2017-2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic. The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus’s North American diversity falling into the A2 clade. Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70% of A(H3N2) viruses circulating in North America by early 2018. Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment. Moreover, HI assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016-2017 season. Rather, we observe that the A2/re clade was the result of a reassortment event that occurred in late 2016 or early 2017 and involved the combination of the HA and PB1 segments of an A2 virus with neuraminidase (NA) and other segments a virus from the clade A1b. The success of this clade shows the need for antigenic analysis that targets NA in addition to HA. Our results illustrate the potential for non-HA drivers of viral success and necessitate the need for more thorough tracking of full viral genomes to better understand the dynamics of influenza epidemics. |
Predicting substantive biomedical citations without full text
Hoppe TA , Arabi S , Hutchins BI . Proc Natl Acad Sci U S A 2023 120 (30) e2213697120 Insights from biomedical citation networks can be used to identify promising avenues for accelerating research and its downstream bench-to-bedside translation. Citation analysis generally assumes that each citation documents substantive knowledge transfer that informed the conception, design, or execution of the main experiments. Citations may exist for other reasons. In this paper, we take advantage of late-stage citations added during peer review because these are less likely to represent substantive knowledge flow. Using a large, comprehensive feature set of open access data, we train a predictive model to identify late-stage citations. The model relies only on the title, abstract, and citations to previous articles but not the full-text or future citations patterns, making it suitable for publications as soon as they are released, or those behind a paywall (the vast majority). We find that high prediction scores identify late-stage citations that were likely added during the peer review process as well as those more likely to be rhetorical, such as journal self-citations added during review. Our model conversely gives low prediction scores to early-stage citations and citation classes that are known to represent substantive knowledge transfer. Using this model, we find that US federally funded biomedical research publications represent 30% of the predicted early-stage (and more likely to be substantive) knowledge transfer from basic studies to clinical research, even though these comprise only 10% of the literature. This is a threefold overrepresentation in this important type of knowledge flow. |
Evaluating reduced effectiveness after repeat influenza vaccination while accounting for confounding by recent infection and within-season waning (preprint)
Bi Q , Dickerman BA , McLean HQ , Martin ET , Gaglani M , Wernli KJ , Goundappa B , Flannery B , Lipsitch M , Cobey S , Murthy K , Raiyani C , Dunnigan K , Mamawala M , Chung JR , Patel M , Lamerato L , Jackson ML , Phillips CH , Kiniry E , Belongia EA , King JP , Monto AS , Zimmerman RK , Nowalk MP , Geffel KM . medRxiv 2023 17 Background. Studies have reported that prior-season influenza vaccination is associated with higher risk of clinical influenza infection among vaccinees in a given season. Understanding the underlying causes requires consideration of within-season waning and recent infection. Methods. Using the US Flu Vaccine Effectiveness (VE) Network data over 8 influenza seasons (2011-2012 to 2018-2019), we estimated the effect of prior-season vaccination on the odds of clinical infection in a given season, after accounting for waning vaccine protection using regression methods. We adjusted for potential confounding by recent clinical infection using inverse-probability weighting. We investigated theoretically whether unmeasured subclinical infection in the prior season, which is more likely in the non-repeat vaccinees, could explain the repeat vaccination effect. Results. Repeat vaccinees vaccinated earlier in a season by one week. After accounting for waning VE, repeat vaccinees were still more likely to test positive for influenza A(H3N2) (OR=1.11, 95% CI:1.02-1.21) but not for influenza B (OR=1.03, 95% CI:0.89-1.18) or A(H1N1) (OR=1.03, 95% CI:0.90-1.19) compared to those vaccinated in the given season only. Recent clinical infection with the homologous (sub)type protected against clinical infection with A(H3N2) or B. Individuals with clinical infection in one season had 1.11 (95% CI:1.03-1.19) times the odds of switching vaccination status in the following season. Adjusting for recent clinical infections did not strongly influence the estimated effect of prior-season vaccination. Adjusting for subclinical infection could theoretically attenuate this effect. Conclusion. Waning protection and recent clinical infection were insufficient to explain observed reduced VE in repeat vaccinees with a test-negative design. 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. |
How enhanced surveillance is helping Zanzibar get one step closer to malaria elimination: description of the operational platforms and resources for real-time case-based malaria surveillance (preprint)
Mkali HR , Lalji SM , Al-Mafazy AW , Joseph JJ , Mwaipape OS , Ali AS , Abbas FB , Ali MH , Hassan WS , Reaves EJ , Kitojo C , Serbantez N , Kabula BI , Nyinondi SS , McKay M , Cressman G , Ngondi JM , Reithinger R . medRxiv 2023 24 Testing and treating asymptomatic populations has the potential to reduce the population's parasite reservoir and reduce malaria transmission. Zanzibar's electronic malaria case notification (MCN) platform collects detailed socio-demographic and epidemiological data from all confirmed malaria cases to inform programmatic decision-making. This Field Action Report describes the design and operationalization process of the platform, as well as other malaria surveillance resources that are enabling Zanzibar to progress toward malaria elimination. The MCN platform consists of an interactive short message service (SMS) system for case notification, a software application for Android mobile devices, a visual question set and workflow manager, a back-end database server, and a web browser-based application for data analytics, configuration, and management. Malaria case data were collected from August 2012 to December 2021 and reported via SMS from all public and private health facilities to a central database, and then to District Malaria Surveillance Officers' mobile devices. Data included patient names, shehia and date of diagnosis, which enabled the officers to track patients, ideally within 24 hours of reporting. Patients' household members were tested for malaria using conventional rapid diagnostic tests (RDTs). Treatment using artemisinin-based combination therapy was provided for persons testing positive. Between 2012 and 2021, a total of 48,899 index malaria cases were confirmed at health facilities, 22,152 (45.3%) of whom within 24 hours of reporting; 41,886 (85.7%) cases were fully investigated and followed up to household level. A total of 111,811 additional household members were tested with RDTs, of whom 10,602 (9.5%) were malaria positive. The MCN platform reports malaria case data in near real-time, enabling prompt testing and treatment of members in index case households. Along with routine testing and treatment and other preventive interventions, combined with comprehensive reactive-case detection efforts, the continued use of the MCN platform is likely to reduce malaria transmission and malaria morbidity even further, thereby enhancing malaria elimination in Zanzibar. 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 4.0 International license. |
Predicting causal citations without full text (preprint)
Hoppe TA , Arabi S , Hutchins BI . bioRxiv 2022 07 Citation analysis generally assumes that each citation documents causal knowledge transfer that informed the conception, design, or execution of the main experiments. Citations may exist for other reasons. In this paper we identify a subset of citations that are unlikely to represent causal knowledge flow. Using a large, comprehensive feature set of open access data, we train a predictive model to identify such citations. The model relies only on the title, abstract, and reference set and not the full-text or future citations patterns, making it suitable for publications as soon as they are released, or those behind a paywall. We find that the model identifies, with high prediction scores, citations that were likely added during the peer review process, and conversely identifies with low prediction scores citations that are known to represent causal knowledge transfer. Using the model, we find that federally funded biomedical research publications represent 30% of the estimated causal knowledge transfer from basic studies to clinical research, even though these comprise only 10% of the literature, a three-fold overrepresentation in this important type of knowledge transfer. This finding underscores the importance of federal funding as a policy lever to improve human health. 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 4.0 International license. |
Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States
Feng A , Bevins S , Chandler J , DeLiberto TJ , Ghai R , Lantz K , Lenoch J , Retchless A , Shriner S , Tang CY , Tong SS , Torchetti M , Uehara A , Wan XF . Nat Commun 2023 14 (1) 4078 SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer. |
Respiratory syncytial virus infection among hospitalized infants in four middle-income countries
Biggs HM , DeGroote NP , Porter RM , Bino S , Marar BI , Gresh L , de Jesus-Cornejo J , Langley G , Thornburg NJ , Peret TCT , Whitaker B , Zhang Y , Wang L , Patel MC , McMorrow M , Campbell W , Hasibra I , Duka E , Al-Gazo M , Kubale J , Sanchez F , Lucero MG , Tallo VL , Azziz-Baumgartner E , Simaku A , Gerber SI . J Pediatric Infect Dis Soc 2023 12 (7) 394-405 BACKGROUND: Understanding respiratory syncytial virus (RSV) global epidemiology is important to inform future prevention strategies. METHODS: Hospitalized infants <1-year-old with acute illness were enrolled prospectively in Albania, Jordan, Nicaragua, and Philippines during respiratory seasons in 2015-2017. Medical chart review, parental interview, and post-discharge follow up were conducted. Respiratory specimens were tested using real-time RT-PCR for RSV. Infant characteristics associated with very severe illness (intensive care unit [ICU] admission or receipt of supplemental oxygen) were assessed using logistic regression to adjust for potential confounders (age, sex, study site, preterm birth). RESULTS: Of 3,634 enrolled hospitalized infants, 1,129 (31%) tested positive for RSV. The median age of RSV-positive infants was 2.7 (IQR: 1.4 to 6.1) months and 665 (59%) were male. Very severe illness in 583 (52%) RSV-positive infants was associated with younger age (aOR 4.1, 95% CI: 2.6-6.5 for 0-2 compared to 9-11-months; p<0.01), , low weight-for-age z-score (aOR 1.9, 95%CI: 1.2-2.8; p<0.01), ICU care after birth (aOR 1.6, 95%CI: 1.0-2.5; p=0.48), and cesarean delivery (aOR 1.4, 95% CI: 1.0-1.8; p=.03). RSV subgroups A and B co-circulated at all sites with alternating predominance by year; subgroup was not associated with severity (aOR 1.0, 95% CI: 0.8-1.4). Nine (0.8%) RSV-positive infants died during admission or within ≤30 days of discharge, of which 7 (78%) were <6-months-old. CONCLUSIONS: RSV was associated with nearly a third of infant acute illness hospitalizations in four middle-income countries during the respiratory season, where, in addition to young age, factors including low weight-for-age might be important predictors of severity. RSV prevention strategies targeting young infants could substantially reduce RSV-associated hospitalizations in middle-income countries. |
Referrals of Infection Control Breaches to Public Health Authorities: Ambulatory Care Settings Experience, 2017
Braun BI , Chitavi SO , Perkins KM , Perz JF , Link-Gelles R , Hoppe J , Donofrio KM , Shen Y , Garcia-Houchins S . Jt Comm J Qual Patient Saf 2020 46 (9) 531-541 BACKGROUND: Beginning in October 2016, the Centers for Medicare & Medicaid Services (CMS) issued expanded guidance requiring accrediting organizations and state survey agencies to report serious infection control breaches to relevant state health departments. This project sought to characterize and summarize The Joint Commission's early experiences and findings in applying this guidance to facilities accredited under the ambulatory and office-based surgery programs in 2017. METHODS: Surveyor notes were retrospectively reviewed to identify individual breaches, and then the Centers for Disease Control and Prevention's Infection Prevention Checklist for Outpatient Settings was used to categorize and code documented breaches. RESULTS: Of 845 ambulatory organizations, 39 (4.6%) had breaches observed during the survey process and reported to health departments. Within these organizations, surveyors documented 356 breaches, representing 52 different breach codes. Common breach domains were sterilization of reusable devices, device reprocessing observation, device reprocessing, disinfection of reusable devices, and infection control program and infrastructure. Eight of the 39 facilities (20.5%) were cited for not performing the minimum level of reprocessing based on the items' intended use, reusing single-use devices, and/or not using aseptic technique to prepare injections. CONCLUSION: The CMS infection control breach reporting requirement has helped highlight some of the challenges faced by ambulatory facilities in providing a safe care environment for their patients. This analysis identified numerous opportunities for improved staff training and competencies as well as leadership oversight and investment in necessary resources. More systematic assessments of infection control practices, extending to both accredited and nonaccredited ambulatory facilities, are needed to inform oversight and prevention efforts. |
Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
Allix-Béguec C , Arandjelovic I , Bi L , Beckert P , Bonnet M , Bradley P , Cabibbe AM , Cancino-Muñoz I , Caulfield MJ , Chaiprasert A , Cirillo DM , Clifton DA , Comas I , Crook DW , De Filippo MR , de Neeling H , Diel R , Drobniewski FA , Faksri K , Farhat MR , Fleming J , Fowler P , Fowler TA , Gao Q , Gardy J , Gascoyne-Binzi D , Gibertoni-Cruz AL , Gil-Brusola A , Golubchik T , Gonzalo X , Grandjean L , He G , Guthrie JL , Hoosdally S , Hunt M , Iqbal Z , Ismail N , Johnston J , Khanzada FM , Khor CC , Kohl TA , Kong C , Lipworth S , Liu Q , Maphalala G , Martinez E , Mathys V , Merker M , Miotto P , Mistry N , Moore DAJ , Murray M , Niemann S , Omar SV , Ong RT , Peto TEA , Posey JE , Prammananan T , Pym A , Rodrigues C , Rodrigues M , Rodwell T , Rossolini GM , Sánchez Padilla E , Schito M , Shen X , Shendure J , Sintchenko V , Sloutsky A , Smith EG , Snyder M , Soetaert K , Starks AM , Supply P , Suriyapol P , Tahseen S , Tang P , Teo YY , Thuong TNT , Thwaites G , Tortoli E , van Soolingen D , Walker AS , Walker TM , Wilcox M , Wilson DJ , Wyllie D , Yang Y , Zhang H , Zhao Y , Zhu B . N Engl J Med 2018 379 (15) 1403-1415 BACKGROUND: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.). |
An early warning system for emerging SARS-CoV-2 variants.
Subissi L , von Gottberg A , Thukral L , Worp N , Oude Munnink BB , Rathore S , Abu-Raddad LJ , Aguilera X , Alm E , Archer BN , Attar Cohen H , Barakat A , Barclay WS , Bhiman JN , Caly L , Chand M , Chen M , Cullinane A , de Oliveira T , Drosten C , Druce J , Effler P , El Masry I , Faye A , Gaseitsiwe S , Ghedin E , Grant R , Haagmans BL , Herring BL , Iyer SS , Kassamali Z , Kakkar M , Kondor RJ , Leite JA , Leo YS , Leung GM , Marklewitz M , Moyo S , Mendez-Rico J , Melhem NM , Munster V , Nahapetyan K , Oh DY , Pavlin BI , Peacock TP , Peiris M , Peng Z , Poon LLM , Rambaut A , Sacks J , Shen Y , Siqueira MM , Tessema SK , Volz EM , Thiel V , van der Werf S , Briand S , Perkins MD , Van Kerkhove MD , Koopmans MPG , Agrawal A . Nat Med 2022 28 (6) 1110-1115 Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic. | | In June 2020, the World Health Organization (WHO) SARS-CoV-2 evolution working group was established to track SARS-CoV-2 variants and their specific genetic changes and to monitor viral characteristics and their impact on medical and non-medical countermeasures, including vaccines against COVID-19. In November 2021, this working group transitioned to a formal WHO Technical Advisory Group on Virus Evolution (TAG-VE), with the aim of developing and implementing a global risk-monitoring framework for SARS-CoV-2 variants, based on a multidisciplinary approach that includes in silico, virological, clinical and epidemiological data. |
Health care use among Medicare beneficiaries with HIV and depression during the COVID-19 pandemic-United States, 2020
Chang MH , Moonesinghe R , Truman BI . Healthcare (Basel) 2023 11 (8) Access and use of health care services are essential to health and well-being for people with HIV and HIV-related comorbidities. Health care use during the COVID-19 pandemic among Medicare beneficiaries (MBs) with concurrent HIV and depression has not been investigated. We used 2020 Medicare data to assess the percentage of MBs with claims for HIV and depression who also received hospitalization, outpatient diagnostic services, drug treatment, and outpatient procedures. We assessed person-level association between service receipt and HIV and depression, adjusting for known risk factors. MBs with claims for HIV and depression were more likely than those with neither claim to have claims for short-stay hospitalization, long-stay hospitalization, outpatient diagnostic services, prescription drugs, or outpatient procedures, supplies, and products. Non-White beneficiaries were more likely than White beneficiaries to be hospitalized but were less likely to receive drug treatment, outpatient diagnostic services, or outpatient procedures, supplies, and products during the pandemic. Significant disparities in health care use by race/ethnicity existed among MBs. Policymakers and practitioners can use these findings to implement public health policies and programs that reduce disparities in health care access and optimize use among vulnerable populations during a public health emergency. |
COVID-19 mortality and progress toward vaccinating older adults - World Health Organization, Worldwide, 2020-2022
Wong MK , Brooks DJ , Ikejezie J , Gacic-Dobo M , Dumolard L , Nedelec Y , Steulet C , Kassamali Z , Acma A , Ajong BN , Adele S , Allan M , Cohen HA , Awofisayo-Okuyelu A , Campbell F , Cristea V , De Barros S , Edward NV , Waeber Arec , Guinko TN , Laurenson-Schafer H , Mahran M , Carrera RM , Mesfin S , Meyer E , Miglietta A , Mirembe BB , Mitri M , Nezu IH , Ngai S , Ejoh OO , Parikh SR , Peron E , Sklenovská N , Stoitsova S , Shimizu K , Togami E , Jin YW , Pavlin BI , Novak RT , Le Polain O , Fuller JA , Mahamud AR , Lindstrand A , Hersh BS , O'Brien K , Van Kerkhove MD . MMWR Morb Mortal Wkly Rep 2023 72 (5) 113-118 After the emergence of SARS-CoV-2 in late 2019, transmission expanded globally, and on January 30, 2020, COVID-19 was declared a public health emergency of international concern.* Analysis of the early Wuhan, China outbreak (1), subsequently confirmed by multiple other studies (2,3), found that 80% of deaths occurred among persons aged ≥60 years. In anticipation of the time needed for the global vaccine supply to meet all needs, the World Health Organization (WHO) published the Strategic Advisory Group of Experts on Immunization (SAGE) Values Framework and a roadmap for prioritizing use of COVID-19 vaccines in late 2020 (4,5), followed by a strategy brief to outline urgent actions in October 2021.(†) WHO described the general principles, objectives, and priorities needed to support country planning of vaccine rollout to minimize severe disease and death. A July 2022 update to the strategy brief(§) prioritized vaccination of populations at increased risk, including older adults,(¶) with the goal of 100% coverage with a complete COVID-19 vaccination series** for at-risk populations. Using available public data on COVID-19 mortality (reported deaths and model estimates) for 2020 and 2021 and the most recent reported COVID-19 vaccination coverage data from WHO, investigators performed descriptive analyses to examine age-specific mortality and global vaccination rollout among older adults (as defined by each country), stratified by country World Bank income status. Data quality and COVID-19 death reporting frequency varied by data source; however, persons aged ≥60 years accounted for >80% of the overall COVID-19 mortality across all income groups, with upper- and lower-middle-income countries accounting for 80% of the overall estimated excess mortality. Effective COVID-19 vaccines were authorized for use in December 2020, with global supply scaled up sufficiently to meet country needs by late 2021 (6). COVID-19 vaccines are safe and highly effective in reducing severe COVID-19, hospitalizations, and mortality (7,8); nevertheless, country-reported median completed primary series coverage among adults aged ≥60 years only reached 76% by the end of 2022, substantially below the WHO goal, especially in middle- and low-income countries. Increased efforts are needed to increase primary series and booster dose coverage among all older adults as recommended by WHO and national health authorities. |
Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020.
Williams T , Jackson S , Barr I , Bi S , Bhiman J , Ellis J , von Gottberg A , Lindstrom S , Peret T , Rughooputh S , Viegas M , Hirve S , Zambon M , Zhang W , Dia N , Razanazatovo N , Al-Nabet Admh , Abubakar A , Tivane A , Barakat A , Naguib A , Aziz A , Vicari A , Moen A , Govindakarnavar A , Hall A , Darmaa B , Nathalie B , Herring B , Caetano BC , Whittaker B , Baumeister E , Nakouné E , Guthrie E , Inbanathan F , Nair H , Campbell H , Kadjo HA , Oumzil H , Heraud JM , Mott JA , Namulondo J , Leite J , Nahapetyan K , Al Ariqi L , Gazo MHI , Chadha M , Pisareva M , Venter M , Siqueira MM , Lumandas M , Niang M , Albuaini M , Salman M , Oberste S , Srikantiah P , Tang P , Couto P , Smith P , Coyle PV , Dussart P , Nguyen PN , Okada PA , Wijesinghe PR , Samuel R , Brown R , Pebody R , Fasce R , Jha R , Lindstrom S , Gerber S , Potdar V , Dong X , Deng YM . Influenza Other Respir Viruses 2023 17 (1) e13073 Background: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019–2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019–2020 WHO RSV EQA. Methods: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. Results: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. Conclusions: The WHO RSV EQA 2019–2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets. © 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd. |
Emergency department claims among Medicare beneficiaries with HIV, STDs, viral hepatitis or tuberculosis before and during the COVID-19 pandemic.
Chang MH , Moonesinghe R , Truman BI . J Public Health (Oxf) 2023 45 (3) e417-e425 BACKGROUND: Changes in emergency department (ED) usage among US Medicare beneficiaries (MB) with fee-for-service claims for HIV, viral hepatitis, sexually transmitted diseases (STDs) or tuberculosis (TB) (HHST) services have not been assessed since the COVID-19 pandemic. METHODS: During 2006-20, we assessed the annual number of MB with each HHST per 1000 persons with ED claims for all conditions, and changes in demographic and geographic distribution of ED claimants for each HHST condition. RESULTS: Of all persons who attended an ED for any condition, 10.5 million (27.5%) were MB with ≥1 ED claim in 2006; that number (percentage) increased to 11.0 million (26.7%) in 2019 and decreased to 9.2 million (22.7%) in 2020; < 5 MB per 1000 ED population had HHST ED claims in 2020. The percentage increase in ED claims was higher for MB with STDs than for those with other HHST conditions, including a 10% decrease for MB with TB in 2020. CONCLUSIONS: Trends in ED usage for HHST conditions were associated with changes in demographic and geographic distribution among MB during 2006-20. Updated ED reimbursement policies and primary care practices among MB might improve prevention, diagnosis and treatment of HHST conditions in the future. |
Association of Urban-Rural Residence and Concurrent HIV Infection and Opioid Use Disorder Among Medicare Beneficiaries-United States, 2020.
Chang MH , Moonesinghe R , Truman BI . J Health Care Poor Underserved 2022 33 (2) 918-933 Published research provides minimal insights into variation by urban or rural residence of HIV infection risk and injection drug use. We used the 2020 Medicare claims data to assess the association of urban-rural residence and concurrent HIV infection and opioid use disorder (OUD), adjusted for demographic risk factors, among Medicare beneficiaries (MBs) with fee-for-service claims paid during 2020. Medicare beneficiaries with both HIV infection and OUD were more likely than those without to be aged ≤64 years, male, Black, residing in the U.S. Northeast, residing in an urban county, and to have one or more comorbid condition. Medicare beneficiaries who lived in urban counties had higher odds (adjusted odds ratio 4.04; 95% confidence interval 3.72, 4.39) of having HIV and OUD than those who lived in rural counties. Urban-rural residence was associated with concurrent HIV infection and OUD, independent of age, sex, race/ethnicity, and comorbidity among MBs with claims paid during 2020. |
Improvements in malaria surveillance through the electronic Integrated Disease Surveillance and Response (eIDSR) system in mainland Tanzania, 2013-2021
Joseph JJ , Mkali HR , Reaves EJ , Mwaipape OS , Mohamed A , Lazaro SN , Aaron S , Chacky F , Mahendeka A , Rulagirwa HS , Mwenesi M , Mwakapeje E , Ally AY , Kitojo C , Serbantez N , Nyinondi S , Lalji SM , Wilillo R , Al-Mafazy AW , Kabula BI , John C , Bisanzio D , Eckert E , Reithinger R , Ngondi JM . Malar J 2022 21 (1) 321 BACKGROUND: Tanzania has made remarkable progress in reducing malaria burden and aims to transition from malaria control to sub-national elimination. In 2013, electronic weekly and monthly reporting platforms using the District Health Information System 2 (DHIS2) were introduced. Weekly reporting was implemented through the mobile phone-based Integrated Disease Surveillance and Response (eIDSR) platform and progressively scaled-up from 67 to 7471 (100%) public and private health facilities between 2013 and 2020. This study describes the roll-out and large-scale implementation of eIDSR and compares the consistency between weekly eIDSR and monthly DHIS2 malaria indicator data reporting, including an assessment of its usefulness for malaria outbreak detection and case-based surveillance (CBS) in low transmission areas. METHODS: The indicators included in the analysis were number of patients tested for malaria, number of confirmed malaria cases, and clinical cases (treated presumptively for malaria). The analysis described the time trends of reporting, testing, test positivity, and malaria cases between 2013 and 2021. For both weekly eIDSR and monthly DHIS2 data, comparisons of annual reporting completeness, malaria cases and annualized incidence were performed for 2020 and 2021; additionally, comparisons were stratified by malaria epidemiological strata (parasite prevalence: very low < 1%, low 1 ≤ 5%, moderate 5 ≤ 30%, and high > 30%). RESULTS: Weekly eIDSR reporting completeness steadily improved over time, with completeness being 90.2% in 2020 and 93.9% in 2021; conversely, monthly DHIS2 reporting completeness was 98.9% and 98.7% in 2020 and 2021, respectively. Weekly eIDSR reporting completeness and timeliness were highest in the very low epidemiological stratum. Annualized malaria incidence as reported by weekly eIDSR was 17.5% and 12.4% lower than reported by monthly DHIS2 in 2020 and 2021; for both 2020 and 2021, annualized incidence was similar across weekly and monthly data in the very low stratum. CONCLUSION: The concurrence of annualized weekly eIDSR and monthly DHIS2 reporting completeness, malaria cases and incidence in very low strata suggests that eIDSR could be useful tool for early outbreak detection, and the eIDSR platform could reliably be expanded by adding more indicators and modules for CBS in the very low epidemiological stratum. |
Bi-national Outbreak of Salmonella Newport Infections Linked to Onions: the United States Experience.
McCormic ZD , Patel K , Higa J , Bancroft J , Donovan D , Edwards L , Cheng J , Adcock B , Bond C , Pereira E , Doyle M , Wise ME , Gieraltowski L . Epidemiol Infect 2022 150 1-23 From 2016-2019, dry bulb onions were the suspected cause of three multistate outbreaks in the United States. We investigated a large multistate outbreak of Salmonella Newport infections that caused illnesses in both the United States and Canada in 2020. Epidemiologic, laboratory and traceback investigations were conducted to determine the source of the infections, and data were shared among U.S. and Canadian public health officials. We identified 1127 U.S. illnesses from 48 states with illness onset dates ranging from 19 June to 11 September 2020. Sixty-six per cent of ill people reported consuming red onions in the week before illness onset. Thirty-five illness sub-clusters were identified during the investigation and seventy-four per cent of sub-clusters served red onions to customers during the exposure period. Traceback for the source of onions in illness sub-clusters identified a common onion grower in Bakersfield, CA as the source of red onions, and onions were recalled at this time. Although other strains of Salmonella Newport were identified in environmental samples collected at the Bakersfield, CA grower, extensive environmental and product testing did not yield the outbreak strain. This was the third largest U.S. foodborne Salmonella outbreak in the last 30 years. It is the first U.S. multistate outbreak with a confirmed link to dry bulb onions, and it was nearly 10-fold larger than prior outbreaks with a suspected link to onions. This outbreak is notable for its size and scope, as well as the international data sharing that led to implication of red onions as the primary cause of the outbreak. Although an environmental assessment at the grower identified several factors that likely contributed to the outbreak, no main reason was identified. The expedient identification of the outbreak vehicle and response of multiple public health agencies allowed for recall and removal of product from the marketplace, and rapid messaging to both the public and industry on actions to protect consumers; these features contributed to a decrease in cases and expeditious conclusion of the outbreak. |
Use of leading practices in US hospital antimicrobial stewardship programs
Stenehjem EA , Braun BI , Chitavi SO , Hyun DY , Schmaltz SP , Fakih MG , Neuhauser MM , Davidson LE , Meyer MJ , Tamma PD , Dodds-Ashley ES , Baker DW . Infect Control Hosp Epidemiol 2022 44 (6) 1-8 OBJECTIVE: To determine the proportion of hospitals that implemented 6 leading practices in their antimicrobial stewardship programs (ASPs). Design: Cross-sectional observational survey. SETTING: Acute-care hospitals. PARTICIPANTS: ASP leaders. METHODS: Advance letters and electronic questionnaires were initiated February 2020. Primary outcomes were percentage of hospitals that (1) implemented facility-specific treatment guidelines (FSTG); (2) performed interactive prospective audit and feedback (PAF) either face-to-face or by telephone; (3) optimized diagnostic testing; (4) measured antibiotic utilization; (5) measured C. difficile infection (CDI); and (6) measured adherence to FSTGs. RESULTS: Of 948 hospitals invited, 288 (30.4%) completed the questionnaire. Among them, 82 (28.5%) had <99 beds, 162 (56.3%) had 100-399 beds, and 44 (15.2%) had ≥400+ beds. Also, 230 (79.9%) were healthcare system members. Moreover, 161 hospitals (54.8%) reported implementing FSTGs; 214 (72.4%) performed interactive PAF; 105 (34.9%) implemented procedures to optimize diagnostic testing; 235 (79.8%) measured antibiotic utilization; 258 (88.2%) measured CDI; and 110 (37.1%) measured FSTG adherence. Small hospitals performed less interactive PAF (61.0%; P = .0018). Small and nonsystem hospitals were less likely to optimize diagnostic testing: 25.2% (P = .030) and 21.0% (P = .0077), respectively. Small hospitals were less likely to measure antibiotic utilization (67.8%; P = .0010) and CDI (80.3%; P = .0038). Nonsystem hospitals were less likely to implement FSTGs (34.3%; P < .001). CONCLUSIONS: Significant variation exists in the adoption of ASP leading practices. A minority of hospitals have taken action to optimize diagnostic testing and measure adherence to FSTGs. Additional efforts are needed to expand adoption of leading practices across all acute-care hospitals with the greatest need in smaller hospitals. |
Tenant-based housing voucher programs: A Community Guide Systematic Review
Finnie RKC , Peng Y , Hahn RA , Schwartz A , Emmons K , Montgomery AE , Muntaner C , Garrison VH , Truman BI , Johnson RL , Fullilove MT , Cobb J , Williams SP , Jones C , Bravo P , Buchanan S . J Public Health Manag Pract 2022 28 (6) E795-e803 CONTEXT: Unaffordable or insecure housing is associated with poor health in children and adults. Tenant-based housing voucher programs (voucher programs) limit rent to 30% or less of household income to help households with low income obtain safe and affordable housing. OBJECTIVE: To determine the effectiveness of voucher programs in improving housing, health, and other health-related outcomes for households with low income. DESIGN: Community Guide systematic review methods were used to assess intervention effectiveness and threats to validity. An updated systematic search based on a previous Community Guide review was conducted for literature published from 1999 to July 2019 using electronic databases. Reference lists of included studies were also searched. ELIGIBILITY CRITERIA: Studies were included if they assessed voucher programs in the United States, had concurrent comparison populations, assessed outcomes of interest, were written in English, and published in peer-reviewed journals or government reports. MAIN OUTCOME MEASURES: Housing quality and stability, neighborhood opportunity (safety and poverty), education, income, employment, physical and mental health, health care use, and risky health behavior. RESULTS: Seven studies met inclusion criteria. Compared with low-income households not offered vouchers, voucher-using households reported increased housing quality (7.9 percentage points [pct pts]), decreased housing insecurity or homelessness (-22.4 pct pts), and decreased neighborhood poverty (-5.2 pct pts).Adults in voucher-using households had improved health care access and physical and mental health. Female youth experienced better physical and mental health but not male youth. Children who entered the voucher programs under 13 years of age had improved educational attainment, employment, and income in their adulthood; children's gains in these outcomes were inversely related to their age at program entry. CONCLUSION: Voucher programs improved health and several health-related outcomes for voucher-using households, particularly young children. Research is still needed to better understand household's experiences and contextual factors that influence achievement of desired outcomes. |
Psychiatric treatment and repeat suicide attempts among adults with substance use, by HIV status, United States, 2014-2020
Iqbal SA , Truman BI , Crosby AE . Public Health Rep 2022 138 (5) 333549221120452 OBJECTIVES: The association among psychiatric treatment history, HIV, and suicide reattempts among people starting treatment for substance use is not well understood. The objective of this study was to describe, by HIV status, the risk and protective factors associated with suicide reattempts among adults seeking treatment for substance use. METHODS: The study included 340 390 US adult residents aged ≥18 years in the Addiction Severity Index-Multimedia Version network from January 1, 2014, through December 31, 2020. We used adjusted logistic regression models to estimate strength of association between prior psychiatric treatment, HIV status, and sociodemographic factors and suicide reattempts within 30 days of treatment evaluation. RESULTS: Adults who had been prescribed psychiatric medication were less likely to have a recent suicide reattempt (adjusted odds ratio [aOR] = 0.8; 95% CI, 0.7-0.8) than adults with no prescription history. Adjusted models found similar protective effects between psychiatric treatment and suicide reattempts among adults reporting abuse, mental illness, injection drug use, and limited activity because of a medical condition. Conversely, the following were associated with recent suicide reattempts: being male (aOR = 1.4; 95% CI, 1.3-1.5), having a high school education/GED (General Educational Development) or less (aOR = 1.2; 95% CI, 1.1-1.2), being single (aOR = 1.2; 95% CI, 1.1-1.3), experiencing a pain problem (aOR = 1.2; 95% CI, 1.2-1.3), and not being referred to substance use treatment by court (aOR = 3.4; 95% CI, 3.2-3.7). CONCLUSIONS: A history of prescribed psychiatric medication is significantly associated with a reduced risk for suicide reattempts among adults seeking substance use treatment. Clinicians should consider incorporating mental health and suicide assessments into substance use treatment plans. |
Lessons learned for surveillance system strengthening through capacity building and partnership engagement in post-Ebola Guinea, 2015-2019
Hemingway-Foday JJ , Diallo BI , Compaore S , Bah S , Keita S , Diallo IT , Martel LD , Standley CJ , Bah MB , Bah M , Camara D , Kaba AK , Keita L , Kone M , Reynolds E , Souare O , Stolka KB , Tchwenko S , Wone A , Worrell MC , MacDonald PDM . Front Public Health 2022 10 715356 The 2014-2016 Ebola outbreak in Guinea revealed systematic weaknesses in the existing disease surveillance system, which contributed to delayed detection, underreporting of cases, widespread transmission in Guinea and cross-border transmission to neighboring Sierra Leone and Liberia, leading to the largest Ebola epidemic ever recorded. Efforts to understand the epidemic's scale and distribution were hindered by problems with data completeness, accuracy, and reliability. In 2017, recognizing the importance and usefulness of surveillance data in making evidence-based decisions for the control of epidemic-prone diseases, the Guinean Ministry of Health (MoH) included surveillance strengthening as a priority activity in their post-Ebola transition plan and requested the support of partners to attain its objectives. The U.S. Centers for Disease Control and Prevention (US CDC) and four of its implementing partners-International Medical Corps, the International Organization for Migration, RTI International, and the World Health Organization-worked in collaboration with the Government of Guinea to strengthen the country's surveillance capacity, in alignment with the Global Health Security Agenda and International Health Regulations 2005 objectives for surveillance and reporting. This paper describes the main surveillance activities supported by US CDC and its partners between 2015 and 2019 and provides information on the strategies used and the impact of activities. It also discusses lessons learned for building sustainable capacity and infrastructure for disease surveillance and reporting in similar resource-limited settings. |
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