Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 255 Records) |
Query Trace: Fisher R [original query] |
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Literature review of pathogen agnostic molecular testing of clinical specimens from difficult-to-diagnose patients: Implications for public health
Downie DL , Rao P , David-Ferdon C , Courtney S , Lee JS , Kugley S , MacDonald PDM , Barnes K , Fisher S , Andreadis JL , Chaitram J , Mauldin MR , Salerno RM , Schiffer J , Gundlapalli AV . Health Secur 2024 To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals. |
Surveillance for emerging and reemerging pathogens using pathogen agnostic metagenomic sequencing in the United States: A critical role for federal government agencies
Downie DL , Rao P , David-Ferdon C , Courtney S , Lee JS , Quiner C , MacDonald PDM , Barnes K , Fisher S , Andreadis JL , Chaitram J , Mauldin MR , Salerno RM , Schiffer J , Gundlapalli AV . Health Secur 2024 The surveillance and identification of emerging, reemerging, and unknown infectious disease pathogens is essential to national public health preparedness and relies on fluidity, coordination, and interconnectivity between public and private pathogen surveillance systems and networks. Developing a national sentinel surveillance network with existing resources and infrastructure could increase efficiency, accelerate the identification of emerging public health threats, and support coordinated intervention strategies that reduce morbidity and mortality. However, implementing and sustaining programs to detect emerging and reemerging pathogens in humans using advanced molecular methods, such as metagenomic sequencing, requires making large investments in testing equipment and developing networks of clinicians, laboratory scientists, and bioinformaticians. In this study, we sought to gain an understanding of how federal government agencies currently support such pathogen agnostic testing of human specimens in the United States. We conducted a landscape analysis of federal agency websites for publicly accessible information on the availability and type of pathogen agnostic testing and details on flow of clinical specimens and data. The website analysis was supplemented by an expert review of results with representatives from the federal agencies. Operating divisions within the US Department of Health and Human Services and the US Department of Veterans Affairs have developed and sustained extensive clinical and research networks to obtain patient specimens and perform metagenomic sequencing. Metagenomic facilities supported by US agencies were not equally geographically distributed across the United States. Although many entities have work dedicated to metagenomics and/or support emerging infectious disease surveillance specimen collection, there was minimal formal collaboration across agencies. |
Birth prevalence of sickle cell disease and county-level social vulnerability - sickle cell data collection program, 11 States, 2016-2020
Kayle M , Blewer AL , Pan W , Rothman JA , Polick CS , Rivenbark J , Fisher E , Reyes C , Strouse JJ , Weeks S , Desai JR , Snyder AB , Zhou M , Sutaria A , Valle J , Horiuchi SS , Sontag MK , Miller JI , Singh A , Dasgupta M , Janson IA , Galadanci N , Reeves SL , Latta K , Hurden I , Cromartie SJ , Plaxco AP , Mukhopadhyay A , Smeltzer MP , Hulihan M . MMWR Morb Mortal Wkly Rep 2024 73 (12) 248-254 Sickle cell disease (SCD) remains a public health priority in the United States because of its association with complex health needs, reduced life expectancy, lifelong disabilities, and high cost of care. A cross-sectional analysis was conducted to calculate the crude and race-specific birth prevalence for SCD using state newborn screening program records during 2016-2020 from 11 Sickle Cell Data Collection program states. The percentage distribution of birth mother residence within Social Vulnerability Index quartiles was derived. Among 3,305 newborns with confirmed SCD (including 57% with homozygous hemoglobin S or sickle β-null thalassemia across 11 states, 90% of whom were Black or African American [Black], and 4% of whom were Hispanic or Latino), the crude SCD birth prevalence was 4.83 per 10,000 (one in every 2,070) live births and 28.54 per 10,000 (one in every 350) non-Hispanic Black newborns. Approximately two thirds (67%) of mothers of newborns with SCD lived in counties with high or very high levels of social vulnerability; most mothers lived in counties with high or very high levels of vulnerability for racial and ethnic minority status (89%) and housing type and transportation (64%) themes. These findings can guide public health, health care systems, and community program planning and implementation that address social determinants of health for infants with SCD. Implementation of tailored interventions, including increasing access to transportation, improving housing, and advancing equity in high vulnerability areas, could facilitate care and improve health outcomes for children with SCD. |
Tubal sterilization and cervical cancer underscreening in the United States
Holt HK , Martinez G , Reyes MF , Saraiya M , Qin J , Sawaya GF . J Womens Health (Larchmt) 2024 Background: Tubal sterilization is more commonly utilized by racial/ethnic minority groups and has been implicated in underscreening for cervical cancer. The objective is to determine if prior tubal sterilization is a risk factor for cervical cancer underscreening. Methods: National Survey of Family Growth dataset from 2015 to 2019 used for analysis; data were weighted to represent the 72 million women in the U.S. population aged 22-49. Chi-square tests, Fisher exact tests, and logistic regression were used for analysis. The primary predictor variable was tubal sterilization which was categorized into no previous sterilization, sterilization completed <5 years ago, and sterilization completed ≥5 years ago. The outcome variable was underscreened versus not underscreened. Other predictor variables included age, household income as a percent of federal poverty level, previous live birth, primary care provider, and insurance status. Results: Prevalence of tubal sterilization completed 5 or more years ago was 12.5% and varied by most measured characteristics in univariate analyses. Approximately 8% of women were underscreened for cervical cancer. In multivariable analyses, women with a tubal sterilization 5 or more years ago had 2.64 times the odds (95% confidence interval = 1.75-4.00) of being underscreened for cervical cancer compared with women who did not have a tubal sterilization. Conclusions: Approximately 4.3 million women ages 22-49 in the United States are potentially underscreened for cervical cancer and women with previous tubal ligation ≥5 years ago are more likely to be underscreened. These results may inform the need for culturally sensitive public health messages informing people who have had these procedures about the need for continued screening. |
Equivalency of PDM3700 and PDM3600 dust monitors
Tuchman DP , Mischler SE , Cauda EG , Colinet JF , Rubinstein EN . Min Metall Explor 2024 The PDM3600 and PDM3700 are two closely related person-wearable dust monitors manufactured by Thermo Fisher Scientific. Both are based on tapered element oscillating microbalance technology and provide nearly real-time, mass-based readings of respirable dust concentrations. From a monitoring perspective, the primary difference between the models is the PDM3600 has an integrated cap lamp with attached inlet, while the PDM3700 has no cap lamp and a revised inlet attaches to the worker’s lapel. Using coals of varied origin and employing a wide range of concentrations, side-by-side measurements from these instruments were collected under controlled laboratory conditions and then compared. By use of ordinary least squares and weighted least squares regression methods, followed by mixed model analysis, results suggest there is no statistically significant or practical difference in instrument performance. The two monitors are equivalent for the field dust concentration measurements for which they were designed. © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024. |
Cost-effectiveness of expanded latent TB infection testing and treatment: Lynn City, Massachusetts, USA
Beeler Asay GR , Woodruff R , Sanderson DM , Fisher CF , Marks SM , Green VD , Tibbs AM , Hill AN , Haptu HH , McManus D , Paradise RK , Auguste-Nelson C , Cochran JJ . Int J Tuberc Lung Dis 2024 28 (1) 21-28 BACKGROUND: Between October 2016 and March 2019, Lynn Community Health Center in Massachusetts implemented a targeted latent TB infection testing and treatment (TTT) program, increasing testing from a baseline of 1,200 patients tested to an average of 3,531 patients tested, or 9% of the population per year.METHODS: We compared pre-implementation TTT, represented by the first two quarters of implementation data, to TTT, represented by 12 quarters of data. Time, diagnostic, and laboratory resources were estimated using micro-costing. Other cost and testing data were obtained from the electronic health record, pharmaceutical claims, and published reimbursement rates. A Markov cohort model estimated future health outcomes and cost-effectiveness from a societal perspective in 2020 US dollars. Monte Carlo simulation generated 95% uncertainty intervals.RESULTS: The TTT program exhibited extended dominance over baseline pre-intervention testing and had an incremental cost-effectiveness ratio (ICER) of US$52,603 (US$22,008â-"US$95,360). When compared to baseline pre-TTT testing, the TTT program averted an estimated additional 7.12 TB cases, 3.49 hospitalizations, and 0.16 deaths per lifetime cohort each year.CONCLUSIONS: TTT was more cost-effective than baseline pre-implementation testing. Lynn Community Health Centerâ-™s experience can help inform other clinics considering expanding latent TB infection testing. |
2022 American College of Rheumatology Guideline for Exercise, Rehabilitation, Diet, and Additional Integrative Interventions for Rheumatoid Arthritis
England BR , Smith BJ , Baker NA , Barton JL , Oatis CA , Guyatt G , Anandarajah A , Carandang K , Chan KK , Constien D , Davidson E , Dodge CV , Bemis-Dougherty A , Everett S , Fisher N , Fraenkel L , Goodman SM , Lewis J , Menzies V , Moreland LW , Navarro-Millan I , Patterson S , Phillips LR , Shah N , Singh N , White D , AlHeresh R , Barbour KE , Bye T , Guglielmo D , Haberman R , Johnson T , Kleiner A , Lane CY , Li LC , Master H , Pinto D , Poole JL , Steinbarger K , Sztubinski D , Thoma L , Tsaltskan V , Turgunbaev M , Wells C , Turner AS , Treadwell JR . Arthritis Rheumatol 2023 75 (8) 1299-1311 OBJECTIVE: To develop initial American College of Rheumatology (ACR) guidelines on the use of exercise, rehabilitation, diet, and additional interventions in conjunction with disease-modifying antirheumatic drugs (DMARDs) as part of an integrative management approach for people with rheumatoid arthritis (RA). METHODS: An interprofessional guideline development group constructed clinically relevant Population, Intervention, Comparator, and Outcome (PICO) questions. A literature review team then completed a systematic literature review and applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate the certainty of evidence. An interprofessional Voting Panel (n = 20 participants) that included 3 individuals with RA achieved consensus on the direction (for or against) and strength (strong or conditional) of recommendations. RESULTS: The Voting Panel achieved consensus on 28 recommendations for the use of integrative interventions in conjunction with DMARDs for the management of RA. Consistent engagement in exercise received a strong recommendation. Of 27 conditional recommendations, 4 pertained to exercise, 13 to rehabilitation, 3 to diet, and 7 to additional integrative interventions. These recommendations are specific to RA management, recognizing that other medical indications and general health benefits may exist for many of these interventions. CONCLUSION: This guideline provides initial ACR recommendations on integrative interventions for the management of RA to accompany DMARD treatments. The broad range of interventions included in these recommendations illustrates the importance of an interprofessional, team-based approach to RA management. The conditional nature of most recommendations requires clinicians to engage persons with RA in shared decision-making when applying these recommendations. |
Mortality among children aged <5 years living with HIV who are receiving antiretroviral treatment - U.S. President's Emergency Plan for AIDS Relief, 28 supported countries and regions, October 2020-September 2022
Agathis NT , Faturiyele I , Agaba P , Fisher KA , Hackett S , Agyemang E , Mehta N , Kindra G , Morof DF , Mutisya I , Nyabiage L , Battey KA , Olotu E , Maphosa T , Motswere-Chirwa C , Ketlogetswe AT , Mafa-Setswalo J , Mazibuko S , de Deus MIT , Nhaguiombe HG , Machage EM , Mugisa B , Ogundehin DT , Mbelwa C , Birabwa E , Etima M , Adamu Y , Lawal I , Maswai J , Njeru D , Mwambona J , Nguhuni B , Mrina R , Hrapcak S , Siberry GK , Godfrey C , Wolf HT . MMWR Morb Mortal Wkly Rep 2023 72 (48) 1293-1299 Globally, children aged <5 years, including those living with HIV who are not receiving antiretroviral treatment (ART), experience disproportionately high mortality. Global mortality among children living with HIV aged <5 years receiving ART is not well described. This report compares mortality and related clinical measures among infants aged <1 year and children aged 1-4 years living with HIV with those among older persons aged 5-14, 15-49, and ≥50 years living with HIV receiving ART services at all clinical sites supported by the U.S. President's Emergency Plan for AIDS Relief. During October 2020-September 2022, an average of 11,980 infants aged <1 year and 105,510 children aged 1-4 years were receiving ART each quarter; among these infants and children receiving ART, 586 (4.9%) and 2,684 (2.5%), respectively, were reported to have died annually. These proportions of infants and children who died ranged from four to nine times higher in infants aged <1 year, and two to five times higher in children aged 1-4 years, than the proportions of older persons aged ≥5 years receiving ART. Compared with persons aged ≥5 years living with HIV, the proportions of children aged <5 years living with HIV who experienced interruptions in treatment were also higher, and the proportions who had a documented HIV viral load result or a suppressed viral load were lower. Prioritizing and optimizing HIV and general health services for children aged <5 years living with HIV receiving ART, including those recommended in the WHO STOP AIDS Package, might help address these disproportionately poorer outcomes. |
Comparison of serum PFAS concentrations in incumbent and recruit firefighters and longitudinal assessment in recruits
Nematollahi AJ , Fisher JM , Furlong MA , Beamer PI , Goodrich JM , Graber JM , Calafat AM , Botelho JC , Beitel SC , Littau SR , Gulotta JJ , Wallentine DD , Burgess JL . J Occup Environ Med 2023 OBJECTIVE: Firefighters are occupationally exposed to per- and polyfluoroalkyl substances (PFAS). This study objective was to compare serum PFAS concentrations in incumbent and recruit firefighters and evaluate temporal trends among recruits. METHODS: Serum PFAS concentrations were measured in 99 incumbent and 55 recruit firefighters at enrollment in 2015-2016, with follow-up 20-37 months later for recruits. Linear and logistic regression and linear mixed-effects models were used for analyses. Fireground exposure impact on PFAS concentrations was investigated using adjusted linear and logistic regression models. RESULTS: Incumbents had lower n-PFOA and PFNA than recruits and most PFAS significantly decreased over time among male recruits. No significant links were found between cumulative fireground exposures and PFAS concentrations. CONCLUSIONS: Serum PFAS concentrations were not increased in incumbent firefighters compared with recruits and were not associated with cumulative fireground exposures. |
Serum per- and polyfluoroalkyl substance concentrations and longitudinal change in post-infection and post-vaccination SARS-CoV-2 antibodies
Hollister J , Caban-Martinez AJ , Ellingson KD , Beitel S , Fowlkes AL , Lutrick K , Tyner H , Naleway AL , Yoon SK , Gaglani M , Hunt D , Meece J , Mayo Lamberte J , Schaefer Solle N , Rose S , Dunnigan K , Khan SM , Kuntz JL , Fisher JM , Coleman A , Britton A , Thiese M , Hegmann K , Pavuk M , Ramadan F , Fuller S , Nematollahi A , Sprissler R , Burgess JL . Environ Res 2023 239 117297 Per- and polyfluoroalkyl substances (PFAS) are ubiquitous throughout the United States. Previous studies have shown PFAS exposure to be associated with a reduced immune response. However, the relationship between serum PFAS and antibody levels following SARS-CoV-2 infection or COVID-19 vaccination has not been examined. We examined differences in peak immune response and the longitudinal decline of antibodies following SARS-CoV-2 infection and COVID-19 vaccination by serum PFAS levels in a cohort of essential workers in the United States. We measured serum antibodies using an in-house semi-quantitative enzyme-linked immunosorbent assay (ELISA). Two cohorts contributed blood samples following SARS-CoV-2 infection or COVID-19 vaccination. We used linear mixed regression models, adjusting for age, race/ethnicity, gender, presence of chronic conditions, location, and occupation, to estimate differences in immune response with respect to serum PFAS levels. Our study populations included 153 unvaccinated participants that contributed 316 blood draws over a 14-month period following infection, and 860 participants and 2451 blood draws over a 12-month period following vaccination. Higher perfluorooctane sulfonic acid (PFOS), perfluorohexane sulfonic acid (PFHxS), and perfluorononanoic acid (PFNA) concentrations were associated with a lower peak antibody response after infection (p = 0.009, 0.031, 0.015). Higher PFOS, perfluorooctanoic acid (PFOA), PFHxS, and PFNA concentrations were associated with slower declines in antibodies over time after infection (p = 0.003, 0.014, 0.026, 0.025). PFOA, PFOS, PFHxS, and PFNA serum concentrations prior to vaccination were not associated with differences in peak antibody response after vaccination or with differences in decline of antibodies over time after vaccination. These results suggest that elevated PFAS may impede potential immune response to SARS-CoV-2 infection by blunting peak antibody levels following infection; the same finding was not observed for immune response to vaccination. |
Total outward leakage of half-mask respirators and surgical masks used for source control
Myers WR , Yang W , Ryan KJ , Bergman M , Fisher E , Soo JC , Zhuang Z . J Occup Environ Hyg 2023 1-15 Both respirators and surgical masks (SM) are used as source control devices. During the COVID-19 pandemic, there was much interest in understanding the extent of particle total outward leakage (TOL) from these devices. The objective of this study was to quantify the TOL for five categories of devices: SMs, National Institute for Occupational Safety and Health (NIOSH®) Approved N95(®) filtering facepiece respirators (FFRs) without exhalation valves, NIOSH Approved N95 FFRs with exhalation valves (N95 FFRV), NIOSH Approved elastomeric half-mask respirators (EHMRs) with exhalation valves, and NIOSH Approved EHMRs with an SM covering the exhalation valve (EHMRSM). A benchtop test system was designed to test two models of each device category. Each device was mounted on a headform at three faceseal levels (0% faceseal, 50% faceseal, and 100% faceseal). At each faceseal level, the TOL was assessed at three flowrates of minute ventilations of 17, 28, and 39 L/min. The experimental design was a split-split-plot configuration. Device type, faceseal level, flowrate, and the interaction of device type and faceseal level were found to have a significant effect ( P - Value <0.05) on the TOL.This study found that the N95 FFRs without exhalation valves had the lowest mean TOL. The SMs had about three times higher TOL than the N95 FFRs without exhalation valves. The TOL of the N95 FFRV was comparable to that of the SM at 0% and 50% faceseal on average over all conditions, but the N95 FFRV had a significantly higher TOL than the SM at a 100% faceseal. The EHMRs had the highest TOL because of the exhalation valve. Using an SM to cover the exhalation valve did not improve the EHMRs' efficiency in mitigating the TOL. Caution should be exercised when using N95 FFRVs as a source control measure against respiratory activities with heavy work rates, such as performing CPR. Results of this study showed that reduced faceseal leakage for N95 FFRs and SMs improves source control. |
Adjunctive diagnostic studies completed following detection of candidemia in children: Secondary analysis of observed practice from a multicenter cohort study conducted by The Pediatric Fungal Network
Wattier RL , Bucayu RFT , Boge CLK , Ross RK , Yildirim I , Zaoutis TE , Palazzi DL , Vora SB , Castagnola E , Avilés-Robles M , Danziger-Isakov L , Tribble AC , Sharma TS , Arrieta AC , Maron G , Berman DM , Yin DE , Sung L , Green M , Roilides E , Belani K , Romero J , Soler-Palacin P , López-Medina E , Nolt D , Bin Hussain IZ , Muller WJ , Hauger SB , Halasa N , Dulek D , Pong A , Gonzalez BE , Abzug MJ , Carlesse F , Huppler AR , Rajan S , Aftandilian C , Ardura MI , Chakrabarti A , Hanisch B , Salvatore CM , Klingspor L , Knackstedt ED , Lutsar I , Santolaya ME , Shuster S , Johnson SK , Steinbach WJ , Fisher BT . J Pediatric Infect Dis Soc 2023 12 (9) 487-495 BACKGROUND: Adjunctive diagnostic studies (aDS) are recommended to identify occult dissemination in patients with candidemia. Patterns of evaluation with aDS across pediatric settings are unknown. METHODS: Candidemia episodes were included in a secondary analysis of a multicenter comparative effectiveness study that prospectively enrolled participants age 120 days -17 years with invasive candidiasis (predominantly candidemia) from 2014-2017. Ophthalmologic examination, abdominal imaging, echocardiogram, neuroimaging, and lumbar puncture were performed per clinician discretion. aDS performance and positive results were determined per episode, within 30 days from candidemia onset. Associations of aDS performance with episode characteristics were evaluated via mixed effects logistic regression. RESULTS: In 662 pediatric candidemia episodes, 490 (74%) underwent abdominal imaging, 450 (68%) ophthalmologic examination, 426 (64%) echocardiogram, 160 (24%) neuroimaging, and 76 (11%) lumbar puncture; performance of each aDS per episode varied across sites up to 16-fold. Longer durations of candidemia were associated with undergoing ophthalmologic examination, abdominal imaging, and echocardiogram. Immunocompromised status (58% of episodes) was associated with undergoing abdominal imaging (aOR 2.38; 95% CI 1.51-3.74). Intensive care at candidemia onset (30% of episodes) was associated with undergoing echocardiogram (aOR 2.42; 95% CI 1.51-3.88). Among evaluated episodes, positive ophthalmologic examination was reported in 15 (3%), abdominal imaging in 30 (6%), echocardiogram in 14 (3%), neuroimaging in 9 (6%) and lumbar puncture in 3 (4%). CONCLUSIONS: Our findings show heterogeneity in practice, with some clinicians performing aDS selectively, potentially influenced by clinical factors. The low frequency of positive results suggests that targeted application of aDS is warranted. |
Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan
Crawford MA , Lascols C , Lomonaco S , Timme RE , Fisher DJ , Anderson K , Hodge DR , Morse SA , Pillai SP , Sharma SK , Khan E , Allard MW , Hughes MA . Microbiol Resour Announc 2023 12 (9) e0016323 The continued emergence and spread of antimicrobial resistance among pathogenic bacteria are ever-growing threats to health and economy. Here, we report the draft genomes for 45 Enterobacterales clinical isolates, including historical and contemporary drug-resistant organisms, obtained in Pakistan between 1998 and 2016: 5 Serratia, 3 Salmonella, 3 Enterobacter, and 34 Klebsiella. |
High-level colonization with antibiotic-resistant enterobacterales among individuals in a semi-urban setting in South India: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study
Kumar CPG , Bhatnagar T , Sathya Narayanan G , Swathi SS , Sindhuja V , Siromany VA , VanderEnde D , Malpiedi P , Smith RM , Bollinger S , Babiker A , Styczynski A . Clin Infect Dis 2023 77 S111-7 BACKGROUND: Antimicrobial resistance poses a significant threat to public health globally. We studied the prevalence of colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), carbapenem-resistant Enterobacterales (CRE), and colistin-resistant Enterobacterales (Col-RE) in hospitals and the surrounding community in South India. METHODS: Adults from 2 hospitals and the catchment community who consented to provide stool specimens were enrolled. Stools were plated on CHROMagar selective for ESCrE, CRE, and Col-RE. Bacterial identification and antibiotic susceptibility testing were done using Vitek 2 Compact and disc diffusion testing. Colistin broth microdilution was performed for a subset of isolates. Prevalence estimates were calculated with 95% confidence intervals (CIs), and differences were compared across populations using the Pearson χ(2) or Fisher exact test. RESULTS: Between November 2020 and March 2022, 757 adults in the community and 556 hospitalized adults were enrolled. ESCrE colonization prevalence was 71.5% (95% CI, 68.1%–74.6%) in the community and 81.8% (95% CI, 78.4%–84.8%) in the hospital, whereas CRE colonization prevalence was 15.1% (95% CI, 12.7%–17.8%) in the community and 22.7% (95% CI, 19.4%–26.3%) in the hospital. Col-RE colonization prevalence was estimated to be 1.1% (95% CI, .5%–2.1%) in the community and 0.5% (95% CI, .2%–1.6%) in the hospital. ESCrE and CRE colonization in hospital participants was significantly higher compared with community participants (P < .001 for both). CONCLUSIONS: High levels of colonization with antibiotic-resistant Enterobacterales were found in both community and hospital settings. This study highlights the importance of surveillance of colonization in these settings for understanding the burden of antimicrobial resistance. |
Rapid Evolution of Knockdown Resistance Haplotypes in Response to Pyrethroid Selection in Aedes aegypti (preprint)
Baltzegar J , Vella M , Gunning C , Vasquez G , Astete H , Stell F , Fisher M , Scott TW , Lenhart A , Lloyd AL , Morrison A , Gould F . bioRxiv 2021 2021.04.02.438212 This study describes the evolution of knockdown resistance (kdr) haplotypes in Aedes aegypti in response to pyrethroid insecticide use over the course of 18 years in Iquitos, Peru. Based on the duration and intensiveness of sampling (∼10,000 samples), this is the most thorough study of kdr population genetics in Ae. aegypti to date within a city. We provide evidence for the direct connection between programmatic citywide pyrethroid spraying and the increase in frequency of specific kdr haplotypes by identifying two evolutionary events in the population. The relatively high selection coefficients, even under infrequent insecticide pressure, emphasizes how quickly populations can evolve. The observed rapid increase in frequency of resistance alleles might have been aided by the incomplete dominance of resistance-conferring alleles over corresponding susceptibility alleles. In addition to dramatic temporal shifts, spatial suppression experiments reveal that genetic heterogeneity existed not only at the citywide scale, but also on a very fine scale within the city.Competing Interest StatementThe authors have declared no competing interest. |
Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States (preprint)
Burke RM , Balter S , Barnes E , Barry V , Bartlett K , Beer KD , Benowitz I , Biggs HM , Bruce H , Bryant-Genevier J , Cates J , Chatham-Stephens K , Chea N , Chiou H , Christiansen D , Chu VT , Clark S , Cody SH , Cohen M , Conners EE , Dasari V , Dawson P , DeSalvo T , Donahue M , Dratch A , Duca L , Duchin J , Dyal JW , Feldstein LR , Fenstersheib M , Fischer M , Fisher R , Foo C , Freeman-Ponder B , Fry AM , Gant J , Gautom R , Ghinai I , Gounder P , Grigg CT , Gunzenhauser J , Hall AJ , Han GS , Haupt T , Holshue M , Hunter J , Ibrahim MB , Jacobs MW , Jarashow MC , Joshi K , Kamali T , Kawakami V , Kim M , Kirking HL , Kita-Yarbro A , Klos R , Kobayashi M , Kocharian A , Lang M , Layden J , Leidman E , Lindquist S , Lindstrom S , Link-Gelles R , Marlow M , Mattison CP , McClung N , McPherson TD , Mello L , Midgley CM , Novosad S , Patel MT , Pettrone K , Pillai SK , Pray IW , Reese HE , Rhodes H , Robinson S , Rolfes M , Routh J , Rubin R , Rudman SL , Russell D , Scott S , Shetty V , Smith-Jeffcoat SE , Soda EA , Spitters C , Stierman B , Sunenshine R , Terashita D , Traub E , Vahey GM , Verani JR , Wallace M , Westercamp M , Wortham J , Xie A , Yousaf A , Zahn M . medRxiv 2020 2020.04.27.20081901 Background Coronavirus disease 2019 (COVID-19), the respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. As part of initial response activities in the United States, enhanced contact investigations were conducted to enable early identification and isolation of additional cases and to learn more about risk factors for transmission.Methods Close contacts of nine early travel-related cases in the United States were identified. Close contacts meeting criteria for active monitoring were followed, and selected individuals were targeted for collection of additional exposure details and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (RT-PCR) at the Centers for Disease Control and Prevention.Results There were 404 close contacts who underwent active monitoring in the response jurisdictions; 338 had at least basic exposure data, of whom 159 had ≥1 set of respiratory samples collected and tested. Across all known close contacts under monitoring, two additional cases were identified; both secondary cases were in spouses of travel-associated case patients. The secondary attack rate among household members, all of whom had ≥1 respiratory sample tested, was 13% (95% CI: 4 – 38%).Conclusions The enhanced contact tracing investigations undertaken around nine early travel-related cases of COVID-19 in the United States identified two cases of secondary transmission, both spouses. Rapid detection and isolation of the travel-associated case patients, enabled by public awareness of COVID-19 among travelers from China, may have mitigated transmission risk among close contacts of these cases.Competing Interest StatementThe authors have declared no competing interest.Funding StatementNo external funding was sought or received.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll 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 may be available upon reasonable request. |
Residential social vulnerability among healthcare personnel with and without severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in Five US states, May-December 2020
Zlotorzynska M , Chea N , Eure T , Alkis Ramirez R , Blazek GT , Czaja CA , Johnston H , Barter D , Kellogg M , Emanuel C , Lynfield R , Fell A , Lim S , Lovett S , Phipps EC , Shrum Davis S , Sievers M , Dumyati G , Concannon C , Myers C , McCullough K , Woods A , Hurley C , Licherdell E , Pierce R , Ocampo VLS , Hall E , Magill SS , Grigg CT . Infect Control Hosp Epidemiol 2023 1-7 OBJECTIVE: To characterize residential social vulnerability among healthcare personnel (HCP) and evaluate its association with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection. DESIGN: Case-control study. SETTING: This study analyzed data collected in May-December 2020 through sentinel and population-based surveillance in healthcare facilities in Colorado, Minnesota, New Mexico, New York, and Oregon. PARTICIPANTS: Data from 2,168 HCP (1,571 cases and 597 controls from the same facilities) were analyzed. METHODS: HCP residential addresses were linked to the social vulnerability index (SVI) at the census tract level, which represents a ranking of community vulnerability to emergencies based on 15 US Census variables. The primary outcome was SARS-CoV-2 infection, confirmed by positive antigen or real-time reverse-transcriptase- polymerase chain reaction (RT-PCR) test on nasopharyngeal swab. Significant differences by SVI in participant characteristics were assessed using the Fisher exact test. Adjusted odds ratios (aOR) with 95% confidence intervals (CIs) for associations between case status and SVI, controlling for HCP role and patient care activities, were estimated using logistic regression. RESULTS: Significantly higher proportions of certified nursing assistants (48.0%) and medical assistants (44.1%) resided in high SVI census tracts, compared to registered nurses (15.9%) and physicians (11.6%). HCP cases were more likely than controls to live in high SVI census tracts (aOR, 1.76; 95% CI, 1.37-2.26). CONCLUSIONS: These findings suggest that residing in more socially vulnerable census tracts may be associated with SARS-CoV-2 infection risk among HCP and that residential vulnerability differs by HCP role. Efforts to safeguard the US healthcare workforce and advance health equity should address the social determinants that drive racial, ethnic, and socioeconomic health disparities. |
Occupational safety and health equity impacts of artificial intelligence: A scoping review
Fisher E , Flynn MA , Pratap P , Vietas JA . Int J Environ Res Public Health 2023 20 (13) Artificial intelligence (AI) has the potential to either reduce or exacerbate occupational safety and health (OSH) inequities in the workplace, and its impact will be mediated by numerous factors. This paper anticipates challenges to ensuring that the OSH benefits of technological advances are equitably distributed among social groups, industries, job arrangements, and geographical regions. A scoping review was completed to summarize the recent literature on AI's role in promoting OSH equity. The scoping review was designed around three concepts: artificial intelligence, OSH, and health equity. Scoping results revealed 113 articles relevant for inclusion. The ways in which AI presents barriers and facilitators to OSH equity are outlined along with priority focus areas and best practices in reducing OSH disparities and knowledge gaps. The scoping review uncovered priority focus areas. In conclusion, AI's role in OSH equity is vastly understudied. An urgent need exists for multidisciplinary research that addresses where and how AI is being adopted and evaluated and how its use is affecting OSH across industries, wage categories, and sociodemographic groups. OSH professionals can play a significant role in identifying strategies that ensure the benefits of AI in promoting workforce health and wellbeing are equitably distributed. |
Investigation of multidrug-resistant plasmids from carbapenemase-producing Klebsiella pneumoniae clinical isolates from Pakistan
Lascols C , Cherney B , Conley AB , Rishishwar L , Crawford MA , Morse SA , Fisher DJ , Anderson K , Hodge DR , Pillai SP , Hughes MA , Khan E , Sue D . Front Microbiol 2023 14 1192097 OBJECTIVES: The study aim was to investigate multidrug-resistant (MDR) plasmids from a collection of 10 carbapenemase-producing Klebsiella pneumoniae clinical isolates identified within the same healthcare institution in Pakistan. Full characterization of the MDR plasmids including structure, typing characteristics, and AMR content as well as determination of their plasmid-based antimicrobial susceptibility profiles were carried out. METHODS: Plasmids were isolated from 10 clinical isolates of Klebsiella pneumoniae, and from a corresponding set of Escherichia coli transconjugants, then sequenced using Nanopore/Illumina technology to generate plasmid hybrid assemblies. Full characterization of MDR plasmids, including determination of next generation sequencing (NGS)-based AMR profiles, plasmid incompatibility groups, and types, was carried out. The structure of MDR plasmids was analyzed using the Galileo AMR platform. For E. coli transconjugants, the NGS-based AMR profiles were compared to NGS-predicted AMR phenotypes and conventional broth microdilution (BMD) antimicrobial susceptibility testing (AST) results. RESULTS: All carbapenemase-producing K. pneumoniae isolates (carrying either bla(NDM-1), or/and bla(OXA-48)) carried multiple AMR plasmids encoding 34 antimicrobial resistance genes (ARGs) conferring resistance to antimicrobials from 6 different classes. The plasmid incompatibility groups and types identified were: IncC (types 1 and 3), IncFIA (type 26) IncFIB, IncFII (types K1, K2, K7, and K9), IncHI1B, and IncL. None of the bla(NDM-1) and bla(ESBL)-plasmids identified in this study were previously described. Most bla(NDM-1-)plasmids shared identical AMR regions suggesting potential genetic material/plasmid exchange between K. pneumoniae isolates of this collection. The majority of NGS-based AMR profiles from the E. coli transconjugants correlated well with both NGS-based predicted and conventional AST results. CONCLUSION: This study highlights the complexity and diversity of the plasmid-based genetic background of carbapenemase-producing clinical isolates from Pakistan. This study emphasizes the need for characterization of MDR plasmids to determine their complete molecular background and monitor AMR through plasmid transmission between multi-resistant bacterial pathogens. |
Maternal exposure to zolpidem and risk of specific birth defects
Howley MM , Werler MM , Fisher SC , Tracy M , Van Zutphen AR , Papadopoulos EA , Hansen C , Ailes EC , Reefhuis J , Wood ME , Browne ML . J Sleep Res 2023 e13958 Zolpidem is a non-benzodiazepine agent indicated for treatment of insomnia. While zolpidem crosses the placenta, little is known about its safety in pregnancy. We assessed associations between self-reported zolpidem use 1 month before pregnancy through to the end of the third month ("early pregnancy") and specific birth defects using data from two multi-site case-control studies: National Birth Defects Prevention Study and Slone Epidemiology Center Birth Defects Study. Analysis included 39,711 birth defect cases and 23,035 controls without a birth defect. For defects with ≥ 5 exposed cases, we used logistic regression with Firth's penalised likelihood to estimate adjusted odds ratios and 95% confidence intervals, considering age at delivery, race/ethnicity, education, body mass index, parity, early-pregnancy antipsychotic, anxiolytic, antidepressant use, early-pregnancy opioid use, early-pregnancy smoking, and study as potential covariates. For defects with three-four exposed cases, we estimated crude odds ratios and 95% confidence intervals. Additionally, we explored differences in odds ratios using propensity score-adjustment and conducted a probabilistic bias analysis of exposure misclassification. Overall, 84 (0.2%) cases and 46 (0.2%) controls reported early-pregnancy zolpidem use. Seven defects had sufficient sample size to calculate adjusted odds ratios, which ranged from 0.76 for cleft lip to 2.18 for gastroschisis. Four defects had odds ratios > 1.8. All confidence intervals included the null. Zolpidem use was rare. We could not calculate adjusted odds ratios for most defects and estimates are imprecise. Results do not support a large increase in risk, but smaller increases in risk for certain defects cannot be ruled out. |
2022 American College of Rheumatology Guideline for exercise, rehabilitation, diet, and additional integrative interventions for rheumatoid arthritis
England BR , Smith BJ , Baker NA , Barton JL , Oatis CA , Guyatt G , Anandarajah A , Carandang K , Chan KK , Constien D , Davidson E , Dodge CV , Bemis-Dougherty A , Everett S , Fisher N , Fraenkel L , Goodman SM , Lewis J , Menzies V , Moreland LW , Navarro-Millan I , Patterson S , Phillips LR , Shah N , Singh N , White D , AlHeresh R , Barbour KE , Bye T , Guglielmo D , Haberman R , Johnson T , Kleiner A , Lane CY , Li LC , Master H , Pinto D , Poole JL , Steinbarger K , Sztubinski D , Thoma L , Tsaltskan V , Turgunbaev M , Wells C , Turner AS , Treadwell JR . Arthritis Care Res (Hoboken) 2023 75 (8) 1603-1615 OBJECTIVE: To develop initial American College of Rheumatology (ACR) guidelines on the use of exercise, rehabilitation, diet, and additional interventions in conjunction with disease-modifying antirheumatic drugs (DMARDs) as part of an integrative management approach for people with rheumatoid arthritis (RA). METHODS: An interprofessional guideline development group constructed clinically relevant Population, Intervention, Comparator, and Outcome (PICO) questions. A literature review team then completed a systematic literature review and applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate the certainty of evidence. An interprofessional Voting Panel (n = 20 participants) that included 3 individuals with RA achieved consensus on the direction (for or against) and strength (strong or conditional) of recommendations. RESULTS: The Voting Panel achieved consensus on 28 recommendations for the use of integrative interventions in conjunction with DMARDs for the management of RA. Consistent engagement in exercise received a strong recommendation. Of 27 conditional recommendations, 4 pertained to exercise, 13 to rehabilitation, 3 to diet, and 7 to additional integrative interventions. These recommendations are specific to RA management, recognizing that other medical indications and general health benefits may exist for many of these interventions. CONCLUSION: This guideline provides initial ACR recommendations on integrative interventions for the management of RA to accompany DMARD treatments. The broad range of interventions included in these recommendations illustrates the importance of an interprofessional, team-based approach to RA management. The conditional nature of most recommendations requires clinicians to engage persons with RA in shared decision-making when applying these recommendations. |
Attitudes, beliefs, and perceptions associated with mask wearing within four racial and ethnic groups early in the COVID-19 pandemic
Earle-Richardson G , Nestor C , Fisher KA , Soelaeman RH , Calanan RM , Yee D , Craig C , Reese P , Prue CE . J Racial Ethn Health Disparities 2023 1-15 BACKGROUND: While previous studies have identified a range of factors associated with mask wearing in the US, little is known about drivers of mask-wearing among racial and ethnic minority groups. This analysis assessed whether factors positively associated with wearing a mask early in the pandemic differed between participants grouped by race/ethnicity (Hispanic, non-Hispanic Black, non-Hispanic Asian, and non-Hispanic White). METHOD: Data were obtained from a US internet panel survey of 3217 respondents during May-November 2020 (weighted by race/ethnicity, age, gender, and education to the US national population). Within each of the four available racial/ethnic groups, crude and adjusted odds ratios (COR and AOR) were calculated using logistic regression to assess factors positively associated with wearing a mask. Adjusted models were controlled for age, gender, education, county COVID-19 case count, presence of a state-issued mask mandate, and interview month. RESULTS: The following variables were most strongly positively associated with mask wearing (p<0.05) in each racial/ethnic group: Hispanic-seeing others wearing masks (AOR: 6.7), importance of wearing a mask combined with social distancing (AOR: 3.0); non-Hispanic Black-belief that wearing a mask would protect others from coronavirus (AOR: 5.1), reporting hearing that one should wear a mask (AOR: 3.6); non-Hispanic Asian-belief that people important to them believe they should wear a mask (COR: 5.1, not statistically significant); and non-Hispanic White-seeing others wearing masks (AOR: 3.1), importance of wearing a mask (AOR: 2.3). CONCLUSION: Public health efforts to encourage mask wearing should consider the diversity of behavioral influences within different population groups. |
Engaging transgender women in HIV research in South Africa
van der Merwe LLA , Cloete A , Savva H , Skinner D , November G , Fisher ZZ . BMC Public Health 2023 23 (1) 990 The Botshelo Ba Trans study was the first HIV bio-behavioral survey conducted with transgender women in South Africa. Engaging research with marginalized communities requires clear points of entry, reference points for understanding the internal culture, and establishing trust and understanding. The community-based participatory research approach guided the development and implementation of this study. We conducted a rapid qualitative and pre-surveillance formative assessment between August 2017 to January 2018 and a bio-behavioral survey between July 2018 and March 2019. At the start, a Steering Committee, comprising primarily of transgender women, was established and subsequently provided substantial input into the mixed methods study conducted in Buffalo City, Cape Town, and Johannesburg. Key to the study's success was building trust and establishing ownership of the survey by transgender women recognized as expert knowledge holders. Thus, a community-based participatory research-informed approach enhanced the validity of the data and ensured that we addressed relevant issues. |
Estimated effectiveness of JYNNEOS vaccine in preventing Mpox: A Multijurisdictional Case-Control Study - United States, August 19, 2022-March 31, 2023
Dalton AF , Diallo AO , Chard AN , Moulia DL , Deputy NP , Fothergill A , Kracalik I , Wegner CW , Markus TM , Pathela P , Still WL , Hawkins S , Mangla AT , Ravi N , Licherdell E , Britton A , Lynfield R , Sutton M , Hansen AP , Betancourt GS , Rowlands JV , Chai SJ , Fisher R , Danza P , Farley M , Zipprich J , Prahl G , Wendel KA , Niccolai L , Castilho JL , Payne DC , Cohn AC , Feldstein LR . MMWR Morb Mortal Wkly Rep 2023 72 (20) 553-558 As of March 31, 2023, more than 30,000 monkeypox (mpox) cases had been reported in the United States in an outbreak that has disproportionately affected gay, bisexual, and other men who have sex with men (MSM) and transgender persons (1). JYNNEOS vaccine (Modified Vaccinia Ankara vaccine, Bavarian Nordic) was approved by the Food and Drug Administration (FDA) in 2019 for the prevention of smallpox and mpox via subcutaneous injection as a 2-dose series (0.5 mL per dose, administered 4 weeks apart) (2). To expand vaccine access, an Emergency Use Authorization was issued by FDA on August 9, 2022, for dose-sparing intradermal injection of JYNNEOS as a 2-dose series (0.1 mL per dose, administered 4 weeks apart) (3). Vaccination was available to persons with known or presumed exposure to a person with mpox (postexposure prophylaxis [PEP]), as well as persons at increased risk for mpox or who might benefit from vaccination (preexposure mpox prophylaxis [PrEP]) (4). Because information on JYNNEOS vaccine effectiveness (VE) is limited, a matched case-control study was conducted in 12 U.S. jurisdictions,(†) including nine Emerging Infections Program sites and three Epidemiology and Laboratory Capacity sites,(§) to evaluate VE against mpox among MSM and transgender adults aged 18-49 years. During August 19, 2022-March 31, 2023, a total of 309 case-patients were matched to 608 control patients. Adjusted VE was 75.2% (95% CI = 61.2% to 84.2%) for partial vaccination (1 dose) and 85.9% (95% CI = 73.8% to 92.4%) for full vaccination (2 doses). Adjusted VE for full vaccination by subcutaneous, intradermal, and heterologous routes of administration was 88.9% (95% CI = 56.0% to 97.2%), 80.3% (95% CI = 22.9% to 95.0%), and 86.9% (95% CI = 69.1% to 94.5%), respectively. Adjusted VE for full vaccination among immunocompromised participants was 70.2% (95% CI = -37.9% to 93.6%) and among immunocompetent participants was 87.8% (95% CI = 57.5% to 96.5%). JYNNEOS is effective at reducing the risk for mpox. Because duration of protection of 1 versus 2 doses remains unknown, persons at increased risk for mpox exposure should receive the 2-dose series as recommended by the Advisory Committee on Immunization Practices (ACIP),(¶) regardless of administration route or immunocompromise status. |
Lessons Learned through Implementing SARS-CoV-2 Testing and Isolation for People Experiencing Homelessness in Congregate Shelters.
Scott E , Rowan S , Chandler K , Fisher A , Hill B , Hill J , Marx GE , Farrell E , Wendel K , Stella SA . Prog Community Health Partnersh 2022 16 13-22 BACKGROUND: The Denver COVID-19 Joint Task Force is a multisector community partnership which formed to coordinate Denver's pandemic response in people experiencing homelessness (PEH). OBJECTIVES: Describe how interdisciplinary community partners collaborated to develop, implement, and pilot severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing and isolation protocols in congregate shelters, and discuss lessons learned and subsequently applied. METHODS: In March through May 2020, community partners collaborated to design, implement and conduct pilot testing paired with isolation in a subset of PEH at a congregate shelter to assess feasibility and inform protocol development.Results and Lessons Learned: We performed SARS-CoV-2 testing in 52 PEH with 14 (27%) testing positive or inconclusive. Thirteen (93%) positive or inconclusive participants were transferred to isolation hotels with 9 of 13 (69%) transferred within 72 hours of testing. CONCLUSIONS: Our findings informed development of coronavirus disease 2019 surveillance testing and isolation protocols for PEH and highlight the value of community partnerships in nimbly responding to the pandemic. |
Knowledge, attitudes, and behaviors with mask use and vaccines forCOVID-19 prevention at 13 colleges and universities, April 2021
Riggs MA , Madni SA , Cornelius J , Zhang A , Czarnik M , Zullig K , Bensley RJ , Gibson-Young L , Gardner M , Waggett CE , Grabeel V , Pettyjohn SJ , Fisher C , Jones RM , Maniccia DM , Doyle J , Treuth M , Neatherlin J , Thomas E , Barrios L . J Am Coll Health 2023 1-11 Objectives: To understand college and university student knowledge, attitudes, and behaviors (KAB) regarding COVID-19 prevention strategies. Methods: Thirteen colleges and universities volunteered to conduct an anonymous electronic survey in April 2021 to assess students' KAB about mask use and vaccination to prevent COVID-19. Results: Three-quarters of students indicated they "Always" wore a mask correctly when in public indoor places. Of those not yet vaccinated, 55% expressed concern about unknown side effects. Over half of students were unsure or believe they do not need to continue wearing masks after vaccination and older students more likely to be vaccinated. There was a significant inverse correlation between intention of getting vaccinated and intention to attend a large indoor party without a mask. Conclusions: Colleges and universities are important to community efforts to slow the COVID-19 pandemic. The KAB findings can inform approaches to increase overall mask use and vaccination uptake among young students. |
Comparing genomic variant identification protocols for Candida auris
Li X , Muñoz JF , Gade L , Argimon S , Bougnoux ME , Bowers JR , Chow NA , Cuesta I , Farrer RA , Maufrais C , Monroy-Nieto J , Pradhan D , Uehling J , Vu D , Yeats CA , Aanensen DM , d'Enfert C , Engelthaler DM , Eyre DW , Fisher MC , Hagen F , Meyer W , Singh G , Alastruey-Izquierdo A , Litvintseva AP , Cuomo CA . Microb Genom 2023 9 (4) Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies. |
Validation of the Diagnostic Interview Schedule For Children (DISC-5) tic disorder and attention-deficit/hyperactivity disorder modules
Bitsko RH , Holbrook JR , Fisher PW , Lipton C , van Wijngaarden E , Augustine EF , Mink JW , Vierhile A , Piacentini J , Walkup J , Firchow B , Ali AR , Badgley A , Adams HR . Evid Based Pract Child Adolesc Mental Heal 2023 Effective methods to assess mental disorders in children are necessary for accurate prevalence estimates and to monitor prevalence over time. This study assessed updates of the tic disorder and attention-deficit/hyperactivity disorder (ADHD) modules of the Diagnostic Interview Schedule for Children, Version 5 (DISC-5) that reflect changes in diagnostic criteria in the Diagnostic and Statistical Manual of Mental Disorders (Fifth edition, DSM-5). The DISC-5 tic disorder and ADHD parent- and child-report modules were compared to expert clinical assessment for 100 children aged 6–17 years (40 with tic disorder alone, 17 with tic disorder and ADHD, 9 with ADHD alone, and 34 with neither) for validation. For the tic disorder module, parent-report had high (>90%) sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy, while the youth-report had high specificity and PPV, moderate accuracy (81.4%), and lower sensitivity (69.8%) and NPV (67.3%). The ADHD module performed less well: parent-report had high NPV (91.4%), moderate sensitivity (80.8%), and lower specificity (71.6%), PPV (50.0%), and accuracy (74.0%); youth-report had moderate specificity (82.8%) and NPV (88.3%), and lower sensitivity (65.0%), PPV (54.2%), and accuracy (78.6%). Adding teacher-report of ADHD symptoms to DISC-5 parent-report of ADHD increased sensitivity (94.7%) and NPV (97.1%), but decreased specificity (64.2%), PPV (48.7%), and accuracy (72.2%). These findings support the use of the parent-report tic disorder module alone or in combination with the child report module in future research and epidemiologic studies; additional validation studies are warranted for the ADHD module. © 2023 Society of Clinical Child & Adolescent Psychology. |
Maternal cyclobenzaprine exposure and risk of birth defects in the National Birth Defects Prevention Study (1997-2011) and Birth Defects Study to Evaluate Pregnancy Exposures (2014-2018)
Fisher SC , Howley MM , Tran EL , Ailes EC , Papadopoulos EA , Nembhard WN , Browne ML . Pharmacoepidemiol Drug Saf 2023 32 (8) 855-862 PURPOSE: Cyclobenzaprine is a muscle relaxant indicated for acute pain. Little is known about cyclobenzaprine's safety during pregnancy. We explored the association between maternal cyclobenzaprine exposure and risk of birth defects among offspring. METHODS: We combined data from two large, multi-site, population-based case-control studies in the US. Cases were identified from birth defects registries across 10 states; controls were liveborn infants without birth defects randomly selected from the same catchment areas. Participants reported cyclobenzaprine use during the month before conception through the third month of pregnancy ("periconception") via computer-assisted telephone interview. We used logistic regression to assess associations between periconceptional cyclobenzaprine exposure and selected structural birth defects. We calculated crude odds ratios (OR) with corresponding 95% confidence intervals (CI). RESULTS: Our study included 33,615 cases and 13,110 controls. Overall, 51 case (0.15%) and 9 control (0.07%) participants reported periconceptional cyclobenzaprine use. We observed increased risk for all seven defects with >3 exposed cases: cleft palate (OR=4.79, 95% CI 1.71-13.44), cleft lip (OR=2.50, 95% CI 0.89-7.02), anorectal atresia/stenosis (OR=6.91, 95% CI 1.67, 28.65), d-transposition of the great arteries (OR=6.97, 95% CI 2.17-22.36), coarctation of the aorta (OR=5.58, 95% CI 1.88-16.58), pulmonary valve stenosis (OR=4.55, 95% CI 1.10-18.87), and secundum atrial septal defect (OR=3.08, 95% CI 0.83-11.45). CONCLUSIONS: Even in our large sample, cyclobenzaprine use was rare. Our estimates are unadjusted and imprecise so should be interpreted cautiously. These hypothesis-generating results warrant confirmation and further research to explore possible mechanisms. |
Maternal dietary caffeine consumption and risk of birth defects in the National Birth Defects Prevention Study, 1997-2011
Williford EM , Howley MM , Fisher SC , Conway KM , Romitti PA , Reeder MR , Olshan AF , Reefhuis J , Browne ML . Birth Defects Res 2023 115 (9) 921-932 BACKGROUND: Caffeine consumption is common during pregnancy, but published associations with birth defects are mixed. We updated estimates of associations between prepregnancy caffeine consumption and 48 specific birth defects from the National Birth Defects Prevention Study (NBDPS) for deliveries from 1997 to 2011. METHODS: NBDPS was a large population-based case-control study conducted in 10 U.S. states. We categorized self-reported total dietary caffeine consumption (mg/day) from coffee, tea, soda, and chocolate as: <10, 10 to <100, 100 to <200, 200 to <300, and ≥ 300. We used logistic regression to estimate adjusted odds ratios (aORs [95% confidence intervals]). Analyses for defects with ≥5 exposed case children were adjusted for maternal race/ethnicity, age at delivery, body mass index, early pregnancy cigarette smoking and alcohol use, and study site. RESULTS: Our analysis included 30,285 case and 11,502 control children, with mothers of 52% and 54%, respectively, reporting consuming <100 mg caffeine, and 11% of mothers of both cases and controls reported consuming ≥300 mg per day. Low (10 to <100 mg/day) levels of prepregnancy caffeine consumption were associated with statistically significant increases in aORs (1.2-1.7) for 10 defects. Associations with high (≥300 mg/day) levels of caffeine were generally weaker, except for craniosynostosis and aortic stenosis (aORs = 1.3 [1.1-1.6], 1.6 [1.1-2.3]). CONCLUSIONS: Given the large number of estimates generated, some of the statistically significant results may be due to chance and thus the weakly increased aORs should be interpreted cautiously. This study supports previous observations suggesting lack of evidence for meaningful associations between caffeine consumption and the studied birth defects. |
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