Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 81 Records) |
Query Trace: Peng Y[original query] |
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Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens
Peng Y , Williams MM , Xiaoli L , Simon A , Fueston H , Tondella ML , Weigand MR . J Clin Microbiol 2024 e0165323 Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization. |
A Community Guide Systematic Review: Digital HIV pre-exposure prophylaxis interventions
Kamitani E , Peng Y , Hopkins D , Higa DH , Mullins MM . Am J Prev Med 2024 INTRODUCTION: HIV preexposure prophylaxis (PrEP) is highly effective when taken as prescribed. Digital health adherence interventions have been identified as effective for improving antiretroviral therapy adherence among people with HIV, but limited evidence exists for PrEP adherence interventions among people without HIV. The purpose of this Community Guide systematic review was to present the characteristics and effectiveness of digital PrEP adherence interventions. METHODS: The author searched the CDC HIV Prevention Research Synthesis cumulative database for digital health interventions with PrEP adherence outcomes published in peer-reviewed journals from 2000-2022. Studies with comparison arms or pre-post data evaluating interventions in high-income countries were included. Two reviewers independently screened citations, extracted data, conducted risk of bias assessment, and resolved discrepancies through discussion. Summary effect estimates were calculated using median and interquartile interval. RESULTS: Nine studies were included and all focused on gay, bisexual, and other men who have sex with men. Eight studies were U.S.-based while the other was conducted in the Netherlands. Five were randomized control trials and four were pre-/post studies. All studies showed improved adherence in the intervention arms compared with comparison groups or pre-intervention data. One study also reported improvement in PrEP care retention. DISCUSSION: Digital health adherence interventions with different strategies to improve PrEP and HIV-related outcomes were identified. The small number of studies identified is a limitation. Findings from this review served as the basis for the Community Preventive Services Task Force recommendation to use these interventions to increase PrEP adherence to prevent HIV infection. |
Genomic characterization of Bordetella pertussis in South Africa, 2015-2019
Moosa F , du Plessis M , Weigand MR , Peng Y , Mogale D , de Gouveia L , Nunes MC , Madhi SA , Zar HJ , Reubenson G , Ismail A , Tondella ML , Cohen C , Walaza S , von Gottberg A , Wolter N . Microb Genom 2023 9 (12) Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps. |
Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple Bordetella species
Natrajan MS , Hall JM , Weigand MR , Peng Y , Williams MM , Momin M , Damron FH , Dubey P , Tondella ML , Pawloski LC . Microbiol Spectr 2023 e0352723 Pertussis, caused by Bordetella pertussis, can cause debilitating respiratory symptoms, so whole-cell pertussis vaccines (wPVs) were introduced in the 1940s. However, reactogenicity of wPV necessitated the development of acellular pertussis vaccines (aPVs) that were introduced in the 1990s. Since then, until the COVID-19 pandemic began, reported pertussis incidence was increasing, suggesting that aPVs do not induce long-lasting immunity and may not effectively prevent transmission. Additionally, aPVs do not provide protection against other Bordetella species that are observed during outbreaks. The significance of this work is in determining potential new vaccine antigens for multiple Bordetella species that are predicted to elicit long-term immune responses. Genome-based approaches have aided the development of novel vaccines; here, these methods identified Bordetella vaccine candidates that may be cross-protective and predicted to induce strong memory responses. These targets can lead to an improved vaccine with a strong safety profile while also strengthening the longevity of the immune response. |
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017-2019
Xiaoli L , Peng Y , Williams MM , Lawrence M , Cassiday PK , Aneke JS , Pawloski LC , Shil SR , Rashid MO , Bhowmik P , Weil LM , Acosta AM , Shirin T , Habib ZH , Tondella ML , Weigand MR . Microb Genom 2023 9 (9) Respiratory diphtheria is a serious infection caused by toxigenic Corynebacterium diphtheriae, and disease transmission mainly occurs through respiratory droplets. Between 2017 and 2019, a large diphtheria outbreak among forcibly displaced Myanmar nationals densely settled in Bangladesh was investigated. Here we utilized whole-genome sequencing (WGS) to characterize recovered isolates of C. diphtheriae and two co-circulating non-diphtheritic Corynebacterium (NDC) species - C. pseudodiphtheriticum and C. propinquum. C. diphtheriae isolates recovered from all 53 positive cases in this study were identified as toxigenic biovar mitis, exhibiting intermediate resistance to penicillin, and formed four phylogenetic clusters circulating among multiple refugee camps. Additional sequenced isolates collected from two patients showed co-colonization with non-toxigenic C. diphtheriae biovar gravis, one of which exhibited decreased susceptibility to the first-line antibiotics and harboured a novel 23-kb multidrug resistance plasmid. Results of phylogenetic reconstruction and virulence-related gene contents of the recovered NDC isolates indicated they were likely commensal organisms, though 80.4 %(45/56) were not susceptible to erythromycin, and most showed high minimum inhibition concentrations against azithromycin. These results demonstrate the high resolution with which WGS can aid molecular investigation of diphtheria outbreaks, through the quantification of bacterial genetic relatedness, as well as the detection of virulence factors and antibiotic resistance markers among case isolates. |
Genomic surveillance and improved molecular typing of Bordetella pertussis using wgMLST (preprint)
Weigand MR , Peng Y , Pouseele H , Kania D , Bowden KE , Williams MM , Tondella ML . bioRxiv 2020 2020.10.28.360149 Multi-Locus Sequence Typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, current MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 214 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphisms (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a re-analysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core-genome (cgMLST) scheme highlights the genomic stability of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence. |
Deep learning-based estimation of whole-body kinematics from multi-view images
Nguyen KX , Zheng L , Hawke AL , Carey RE , Breloff SP , Li K , Peng X . Comput Vision Image Understanding 2023 235 It is necessary to analyze the whole-body kinematics (including joint locations and joint angles) to assess risks of fatal and musculoskeletal injuries in occupational tasks. Human pose estimation has gotten more attention in recent years as a method to minimize the errors in determining joint locations. However, the joint angles are not often estimated, nor is the quality of joint angle estimation assessed. In this paper, we presented an end-to-end approach on direct joint angle estimation from multi-view images. Our method leveraged the volumetric pose representation and mapped the rotation representation to a continuous space where each rotation was uniquely represented. We also presented a new kinematic dataset in the domain of residential roofing with a data processing pipeline to generate necessary annotations for the supervised training procedure on direct joint angle estimation. We achieved a mean angle error of 7.19° on the new Roofing dataset and 8.41° on the Human3.6M dataset, paving the way for employment of on-site kinematic analysis using multi-view images. © 2023 Elsevier Inc. |
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. |
Distinct In Vitro and In Vivo Neutralization Profiles of Monoclonal Antibodies Elicited by the Receptor Binding Domain of the Ancestral SARS-CoV-2.
Kwon HJ , Zhang J , Kosikova M , Tang W , Ortega-Rodriguez U , Peng H , Meseda CA , Pedro CL , Schmeisser F , Lu J , Kang I , Zhou B , Davis CT , Wentworth DE , Chen WH , Shriver MC , Barnes RS , Pasetti MF , Weir JP , Chen B , Xie H . J Med Virol 2023 95 (3) e28673 Broadly neutralizing antibodies against SARS-CoV-2 variants are sought to curb COVID-19 infections. Here we produced and characterized a set of mouse monoclonal antibodies (mAbs) specific for the ancestral SARS-CoV-2 receptor binding domain (RBD). Two of them, 17A7 and 17B10, were highly potent in microneutralization assay with 50% inhibitory concentration (IC(50) ) ≤ 135 ng/ml against infectious SARS-CoV-2 variants, including G614, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Kappa, Lambda, B.1.1.298, B.1.222, B.1.5 and R.1. Both mAbs (especially 17A7) also exhibited strong in vivo efficacy in protecting K18-hACE2 transgenic mice from the lethal infection with G614, Alpha, Beta, Gamma and Delta viruses. Structural analysis indicated that 17A7 and 17B10 target the tip of the receptor binding motif (RBM) in the RBD-up conformation. A third RBD-reactive mAb (3A6) although escaped by Beta and Gamma, was highly effective in cross-neutralizing Delta and Omicron BA.1 variants in vitro and in vivo. In competition experiments, antibodies targeting epitopes similar to these 3 mAbs were rarely enriched in human COVID-19 convalescent sera or post-vaccination sera. These results are helpful to inform new antibody/vaccine design and these mAbs can be useful tools for characterizing SARS-CoV-2 variants and elicited antibody responses. This article is protected by copyright. All rights reserved. |
Community health workers to increase cancer screening: 3 Community Guide systematic reviews
Okasako-Schmucker DL , Peng Y , Cobb J , Buchanan LR , Xiong KZ , Mercer SL , Sabatino SA , Melillo S , Remington PL , Kumanyika SK , Glenn B , Breslau ES , Escoffery C , Fernandez ME , Coronado GD , Glanz K , Mullen PD , Vernon SW . Am J Prev Med 2022 INTRODUCTION: Many in the U.S. are not up to date with cancer screening. This systematic review examined the effectiveness of interventions engaging community health workers to increase breast, cervical, and colorectal cancer screening. METHODS: Authors identified relevant publications from previous Community Guide systematic reviews of interventions to increase cancer screening (1966 through 2013) and from an update search (January 2014-November 2021). Studies written in English and published in peer-reviewed journals were included if they assessed interventions implemented in high-income countries; reported screening for breast, cervical, or colorectal cancer; and engaged community health workers to implement part or all of the interventions. Community health workers needed to come from or have close knowledge of the intervention community. RESULTS: The review included 76 studies. Interventions engaging community health workers increased screening use for breast (median increase=11.5 percentage points, interquartile interval=5.523.5), cervical (median increase=12.8 percentage points, interquartile interval=6.421.0), and colorectal cancers (median increase=10.5 percentage points, interquartile interval=4.517.5). Interventions were effective whether community health workers worked alone or as part of a team. Interventions increased cancer screening independent of race or ethnicity, income, or insurance status. DISCUSSION: Interventions engaging community health workers are recommended by the Community Preventive Services Task Force to increase cancer screening. These interventions are typically implemented in communities where people are underserved to improve health and can enhance health equity. Further training and financial support for community health workers should be considered to increase cancer screening uptake. |
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. |
Complete Genome Sequences of Four Macrolide-Resistant Nondiphtheritic Corynebacterium Isolates.
Xiaoli L , Peng Y , Williams MM , Cassiday PK , Nobles S , Unoarumhi Y , Weil LM , Shirin T , Habib ZH , Tondella ML , Weigand MR . Microbiol Resour Announc 2022 11 (9) e0049222 This report describes the complete genome sequences of four isolates of the nondiphtheritic Corynebacterium (NDC) species Corynebacterium pseudodiphtheriticum and Corynebacterium propinquum, recovered during investigation of a large diphtheria outbreak in Bangladesh. These data will assist in better delineating the boundary between these related species and understanding their virulence potential. |
Video-Based 3D pose estimation for residential roofing
Wang R , Zheng L , Hawke AL , Carey RE , Breloff SP , Li K , Peng X . Comput Methods Biomech Biomed Eng Imaging Vis 2022 1-9 Residential roofers are often exposed to awkward postures and motions in a prolonged time, which may not only reduce their body stability and increase fall potential, but also increase the risk of musculoskeletal disorders (MSDs). To assess their risks of fatal and musculoskeletal injuries, it is crucial to capture 3D body poses of workers during roofing tasks. In this paper, we proposed a novel two-stage motion estimation approach based on a convolution neural network to estimate residential roofer’s body poses using three-view video data. Our approach includes two stages: (1) use of an offline multi-view model to estimate the 3D pose in a single frame; (2) use of a multi-frame model to apply temporal convolutions to refine the multi-view outputs. The performance of the approach was evaluated by comparing our estimation with the gold-standard marker-based 3D human pose during one of the common residential roofing tasks–shingle installation. The evaluation results show that the proposed multi-frame model can effectively improve the accuracy of the coordinate sequence. Moreover, these results prove that the proposed video-based motion estimation approach can efficiently and accurately locate 3D body joints and pave the way for future onsite motion analysis during roofing activities. © This work was authored as part of the Contributor’s official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law. |
Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis.
Abrahams JS , Weigand MR , Ring N , MacArthur I , Etty J , Peng S , Williams MM , Bready B , Catalano AP , Davis JR , Kaiser MD , Oliver JS , Sage JM , Bagby S , Tondella ML , Gorringe AR , Preston A . Microb Genom 2022 8 (2) Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis. We found 590 amplifications in M. tuberculosis, and like B. pertussis, these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis. This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis, highlighting the need for a more holistic understanding of bacterial genetics. |
Permanent Supportive Housing With Housing First: Findings From a Community Guide Systematic Economic Review
Jacob V , Chattopadhyay SK , Attipoe-Dorcoo S , Peng Y , Hahn RA , Finnie R , Cobb J , Cuellar AE , Emmons KM , Remington PL . Am J Prev Med 2021 62 (3) e188-e201 INTRODUCTION: The annual economic burden of chronic homelessness in the U.S. is estimated to be as high as $3.4 billion. The Permanent Supportive Housing with Housing First (Housing First) program, implemented to address the problem, has been shown to be effective. This paper examines the economic cost and benefit of Housing First Programs. METHODS: The search of peer-reviewed and gray literature from inception of databases through November 2019 yielded 20 evaluation studies of Housing First Programs, 17 from the U.S. and 3 from Canada. All analyses were conducted from March 2019 through July 2020. Monetary values are reported in 2019 U.S. dollars. RESULTS: Evidence from studies conducted in the U.S. was separated from those conducted in Canada. The median intervention cost per person per year for U.S. studies was $16,479, and for all studies, including those from Canada, it was $16,336. The median total benefit for the U.S. studies was $18,247 per person per year, and it was $17,751 for all studies, including those from Canada. The benefit-to-cost ratio for U.S. studies was 1.80:1, and for all studies, including those from Canada, it was 1.06:1. DISCUSSION: The evidence from this review shows that economic benefits exceed the cost of Housing First Programs in the U.S. There were too few studies to determine cost-benefit in the Canadian context. |
Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis).
Yang Y , Gardner C , Gupta P , Peng Y , Piasecki C , Millwood RJ , Ahn TH , Stewart CN Jr . Genes (Basel) 2021 12 (10) The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis. |
Randomized clinical trial of air cleaners to improve indoor air quality and COPD health: results of the Clean Air Study
Hansel NN , Putcha N , Woo H , Peng R , Diette GB , Fawzy A , Wise RA , Romero K , Davis MF , Rule AM , Eakin MN , Breysse PN , McCormack MC , Koehler K . Am J Respir Crit Care Med 2021 205 (4) 421-430 RATIONALE: Indoor particulate matter is associated with worse COPD outcomes. It remains unknown whether reductions of indoor pollutants improve respiratory morbidity. METHODS: Eligible former smokers with moderate-severe COPD received active or sham portable HEPA air cleaners and followed for six months in this blinded randomized controlled trial. The primary outcome was six-month change in Saint George's Respiratory Questionnaire (SGRQ). Secondary outcomes were exacerbation risk, respiratory symptoms, rescue medication use and 6MWD. Intention to treat analysis included all subjects and per protocol analysis included adherent participants (greater than 80% use of air cleaner). MAIN RESULTS: 116 participants were randomized of which 84.5% completed study. There was no statistically significant difference in total SGRQ score, but the active filter group had greater reduction in SGRQ symptom subscale (ß -7.7 [95% CI, -15.0 to -0.37]) and respiratory symptoms (BCSS, ß -0.8 [95% CI, -1.5 to -0.1); and lower rate of moderate exacerbations (IRR 0.32 [95% CI, 0.12-0.91]) and rescue medication use (IRR 0.54 [95% CI, 0.33-0.86]) compared to sham group (all p<0.05). In per protocol analysis, there was statistically significant difference in primary outcome between the active filter vs. sham group (SGRQ β-4.76 [95% CI, -9.2 to -0.34]) and in moderate exacerbation risk, BCSS and 6MWD. Participants spending more time indoors were more likely to have treatment benefit. CONCLUSIONS: This is the first environmental intervention study conducted among former smokers with COPD showing potential health benefits of portable HEPA air cleaners, particularly among those with greater adherence and spending a greater time indoors. Clinical trial registration available at www.clinicaltrials.gov, ID: NCT02236858. |
Diagnostic Utility of Serum and Urinary Metabolite Analysis in Patients with Interstitial Cystitis/Painful Bladder Syndrome.
Kim J , De Hoedt A , Wiggins E , Haywood K , Jin P , Greenwood B , Narain NR , Tolstikov V , Bussberg V , Barbour KE , Kiebish MA , Freedland S , Anger JT . Urology 2021 157 85-92 OBJECTIVE: To identify the potential biomarkers of interstitial cystitis/painful bladder syndrome (IC), a chronic syndrome of bladder-centric pain with unknown etiology that has an adverse impact on quality of life, we analyzed the urine and serum metabolomes of a cohort of IC patients and non-disease controls (NC). METHODS: Home collection of serum and urine samples was obtained from 19 IC and 20 NC females in the Veterans Affairs (VA) Health Care System. IC was diagnosed independently by thorough review of medical records using established criteria. Biostatistics and bioinformatics analyses, including univariate analysis, unsupervised clustering, random forest analysis, and metabolite set enrichment analysis (MSEA), were then utilized to identify potential IC biomarkers. RESULTS: Metabolomics profiling revealed distinct expression patterns between NC and IC. Random forest analysis of urine samples suggested discriminators specific to IC; these include phenylalanine, purine, 5-oxoproline, and 5-hydroxyindoleacetic acid. When these urinary metabolomics-based analytes were combined into a single model, the AUC was 0.92, suggesting strong potential clinical value as a diagnostic signature. Serum-based metabolomics did not provide potential IC discriminators. CONCLUSIONS: Analysis of serum and urine revealed that women with IC have distinct metabolomes, highlighting key metabolic pathways that may provide insight into the pathophysiology of IC. The findings from this pilot study suggest that integrated analyses of urinary metabolites, purine, phenylalanine, 5-oxoproline, and 5-HIAA, can lead to promising IC biomarkers for pathophysiology of IC. Validation of these results using a larger dataset is currently underway. |
Iterative guided machine learning-assisted systematic literature reviews: a diabetes case study.
Zimmerman J , Soler RE , Lavinder J , Murphy S , Atkins C , Hulbert L , Lusk R , Ng BP . Syst Rev 2021 10 (1) 97 BACKGROUND: Systematic Reviews (SR), studies of studies, use a formal process to evaluate the quality of scientific literature and determine ensuing effectiveness from qualifying articles to establish consensus findings around a hypothesis. Their value is increasing as the conduct and publication of research and evaluation has expanded and the process of identifying key insights becomes more time consuming. Text analytics and machine learning (ML) techniques may help overcome this problem of scale while still maintaining the level of rigor expected of SRs. METHODS: In this article, we discuss an approach that uses existing examples of SRs to build and test a method for assisting the SR title and abstract pre-screening by reducing the initial pool of potential articles down to articles that meet inclusion criteria. Our approach differs from previous approaches to using ML as a SR tool in that it incorporates ML configurations guided by previously conducted SRs, and human confirmation on ML predictions of relevant articles during multiple iterative reviews on smaller tranches of citations. We applied the tailored method to a new SR review effort to validate performance. RESULTS: The case study test of the approach proved a sensitivity (recall) in finding relevant articles during down selection that may rival many traditional processes and show ability to overcome most type II errors. The study achieved a sensitivity of 99.5% (213 out of 214) of total relevant articles while only conducting a human review of 31% of total articles available for review. CONCLUSIONS: We believe this iterative method can help overcome bias in initial ML model training by having humans reinforce ML models with new and relevant information, and is an applied step towards transfer learning for ML in SR. |
Global burden of influenza-associated lower respiratory tract infections and hospitalizations among adults: A systematic review and meta-analysis
Lafond KE , Porter RM , Whaley MJ , Suizan Z , Ran Z , Aleem MA , Thapa B , Sar B , Proschle VS , Peng Z , Feng L , Coulibaly D , Nkwembe E , Olmedo A , Ampofo W , Saha S , Chadha M , Mangiri A , Setiawaty V , Ali SS , Chaves SS , Otorbaeva D , Keosavanh O , Saleh M , Ho A , Alexander B , Oumzil H , Baral KP , Huang QS , Adebayo AA , Al-Abaidani I , von Horoch M , Cohen C , Tempia S , Mmbaga V , Chittaganpitch M , Casal M , Dang DA , Couto P , Nair H , Bresee JS , Olsen SJ , Azziz-Baumgartner E , Nuorti JP , Widdowson MA . PLoS Med 2021 18 (3) e1003550 BACKGROUND: Influenza illness burden is substantial, particularly among young children, older adults, and those with underlying conditions. Initiatives are underway to develop better global estimates for influenza-associated hospitalizations and deaths. Knowledge gaps remain regarding the role of influenza viruses in severe respiratory disease and hospitalizations among adults, particularly in lower-income settings. METHODS AND FINDINGS: We aggregated published data from a systematic review and unpublished data from surveillance platforms to generate global meta-analytic estimates for the proportion of acute respiratory hospitalizations associated with influenza viruses among adults. We searched 9 online databases (Medline, Embase, CINAHL, Cochrane Library, Scopus, Global Health, LILACS, WHOLIS, and CNKI; 1 January 1996-31 December 2016) to identify observational studies of influenza-associated hospitalizations in adults, and assessed eligible papers for bias using a simplified Newcastle-Ottawa scale for observational data. We applied meta-analytic proportions to global estimates of lower respiratory infections (LRIs) and hospitalizations from the Global Burden of Disease study in adults ≥20 years and by age groups (20-64 years and ≥65 years) to obtain the number of influenza-associated LRI episodes and hospitalizations for 2016. Data from 63 sources showed that influenza was associated with 14.1% (95% CI 12.1%-16.5%) of acute respiratory hospitalizations among all adults, with no significant differences by age group. The 63 data sources represent published observational studies (n = 28) and unpublished surveillance data (n = 35), from all World Health Organization regions (Africa, n = 8; Americas, n = 11; Eastern Mediterranean, n = 7; Europe, n = 8; Southeast Asia, n = 11; Western Pacific, n = 18). Data quality for published data sources was predominantly moderate or high (75%, n = 56/75). We estimate 32,126,000 (95% CI 20,484,000-46,129,000) influenza-associated LRI episodes and 5,678,000 (95% CI 3,205,000-9,432,000) LRI hospitalizations occur each year among adults. While adults <65 years contribute most influenza-associated LRI hospitalizations and episodes (3,464,000 [95% CI 1,885,000-5,978,000] LRI hospitalizations and 31,087,000 [95% CI 19,987,000-44,444,000] LRI episodes), hospitalization rates were highest in those ≥65 years (437/100,000 person-years [95% CI 265-612/100,000 person-years]). For this analysis, published articles were limited in their inclusion of stratified testing data by year and age group. Lack of information regarding influenza vaccination of the study population was also a limitation across both types of data sources. CONCLUSIONS: In this meta-analysis, we estimated that influenza viruses are associated with over 5 million hospitalizations worldwide per year. Inclusion of both published and unpublished findings allowed for increased power to generate stratified estimates, and improved representation from lower-income countries. Together, the available data demonstrate the importance of influenza viruses as a cause of severe disease and hospitalizations in younger and older adults worldwide. |
Genomic surveillance and improved molecular typing of Bordetella pertussis using wgMLST
Weigand MR , Peng Y , Pouseele H , Kania D , Bowden KE , Williams MM , Tondella ML . J Clin Microbiol 2021 59 (5) Multi-Locus Sequence Typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphisms (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a re-analysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core-genome (cgMLST) scheme highlights the stable gene content of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence. |
Engaging community health workers to increase cancer screening: A Community Guide Systematic Economic Review
Attipoe-Dorcoo S , Chattopadhyay SK , Verughese J , Ekwueme DU , Sabatino SA , Peng Y . Am J Prev Med 2020 60 (4) e189-e197 CONTEXT: The Community Preventive Services Task Force recommends engaging community health workers to increase breast, cervical, and colorectal cancer screenings on the basis of strong evidence of effectiveness. This systematic review examines the economic evidence of these interventions. EVIDENCE ACQUISITION: A systematic literature search was performed with a search period through April 2019 to identify relevant economic evaluation studies. All monetary values were adjusted to 2018 U.S. dollars, and the analysis was completed in 2019. EVIDENCE SYNTHESIS: A total of 19 studies were included in the final analysis with 3 on breast cancer, 5 on cervical cancer, 9 on colorectal cancer, and 2 that combined costs for breast and cervical cancers and for breast, cervical, and colorectal cancers. For cervical cancer screening, 2 U.S. studies reported incremental cost per quality-adjusted life year saved of $762 and $34,405. For colorectal cancer screening, 2 U.S. studies reported both a negative incremental cost and an increase in quality-adjusted life years saved with colonoscopy screening. CONCLUSIONS: Engaging community health workers to increase cervical and colorectal cancer screenings is cost effective on the basis of estimated incremental cost-effectiveness ratios that were less than the conservative $50,000 per quality-adjusted life year threshold. In addition, quality-adjusted life years saved from colorectal screening with colonoscopy were associated with net healthcare cost savings. |
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019.
Xiaoli L , Benoliel E , Peng Y , Aneke J , Cassiday PK , Kay M , McKeirnan S , Duchin JS , Kawakami V , Lindquist S , Acosta AM , DeBolt C , Tondella ML , Weigand MR . Microb Genom 2020 6 (12) Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available C. diphtheriae genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic C. diphtheriae. |
Detection and characterization of diphtheria toxin gene-bearing Corynebacterium species through a new real-time PCR assay.
Williams MM , Waller JL , Aneke JS , Weigand MR , Diaz MH , Bowden KE , Simon AK , Peng Y , Xiaoli L , Cassiday PK , Winchell J , Tondella ML . J Clin Microbiol 2020 58 (10) Respiratory diphtheria, characterized by a firmly adherent pseudomembrane, is caused by toxin-producing strains of Corynebacterium diphtheriae, with similar illness produced occasionally by toxigenic Corynebacterium ulcerans or, rarely, Corynebacterium pseudotuberculosis While diphtheria laboratory confirmation requires culture methods to determine toxigenicity, real-time PCR (RT-PCR) provides a faster method to detect the toxin gene (tox). Nontoxigenic tox-bearing (NTTB) Corynebacterium isolates have been described, but impact of these isolates on the accuracy of molecular diagnostics is not well characterized. Here, we describe a new triplex RT-PCR assay to detect tox and distinguish C. diphtheriae from the closely related species C. ulcerans and C. pseudotuberculosis Analytical sensitivity and specificity of the assay were assessed in comparison to culture using 690 previously characterized microbial isolates. The new triplex assay characterized Corynebacterium isolates accurately, with 100% analytical sensitivity for all targets. Analytical specificity with isolates was 94.1%, 100%, and 99.5% for tox, Diph_rpoB, and CUP_rpoB targets, respectively. Twenty-nine NTTB Corynebacterium isolates, representing 5.9% of 494 nontoxigenic isolates tested, were detected by RT-PCR. Whole-genome sequencing of NTTB isolates revealed varied mutations putatively underlying their lack of toxin production, as well as eight isolates with no mutation in tox or the promoter region. This new Corynebacterium RT-PCR method provides a rapid tool to screen isolates and identify probable diphtheria cases directly from specimens. However, the sporadic occurrence of NTTB isolates reinforces the viewpoint that diphtheria culture diagnostics continue to provide the most accurate case confirmation. |
Permanent supportive housing with housing first to reduce homelessness and promote health among homeless populations with disability: A Community Guide systematic review
Peng Y , Hahn RA , Finnie RKC , Cobb J , Williams SP , Fielding JE , Johnson RL , Montgomery AE , Schwartz AF , Muntaner C , Garrison VH , Jean-Francois B , Truman BI , Fullilove MT . J Public Health Manag Pract 2020 26 (5) 404-411 CONTEXT: Poor physical and mental health and substance use disorder can be causes and consequences of homelessness. Approximately 2.1 million persons per year in the United States experience homelessness. People experiencing homelessness have high rates of emergency department use, hospitalization, substance use treatment, social services use, arrest, and incarceration. OBJECTIVES: A standard approach to treating homeless persons with a disability is called Treatment First, requiring clients be "housing ready"-that is, in psychiatric treatment and substance-free-before and while receiving permanent housing. A more recent approach, Housing First, provides permanent housing and health, mental health, and other supportive services without requiring clients to be housing ready. To determine the relative effectiveness of these approaches, this systematic review compared the effects of both approaches on housing stability, health outcomes, and health care utilization among persons with disabilities experiencing homelessness. DESIGN: A systematic search (database inception to February 2018) was conducted using 8 databases with terms such as "housing first," "treatment first," and "supportive housing." Reference lists of included studies were also searched. Study design and threats to validity were assessed using Community Guide methods. Medians were calculated when appropriate. ELIGIBILITY CRITERIA: Studies were included if they assessed Housing First programs in high-income nations, had concurrent comparison populations, assessed outcomes of interest, and were written in English and published in peer-reviewed journals or government reports. MAIN OUTCOME MEASURES: Housing stability, physical and mental health outcomes, and health care utilization. RESULTS: Twenty-six studies in the United States and Canada met inclusion criteria. Compared with Treatment First, Housing First programs decreased homelessness by 88% and improved housing stability by 41%. For clients living with HIV infection, Housing First programs reduced homelessness by 37%, viral load by 22%, depression by 13%, emergency departments use by 41%, hospitalization by 36%, and mortality by 37%. CONCLUSIONS: Housing First programs improved housing stability and reduced homelessness more effectively than Treatment First programs. In addition, Housing First programs showed health benefits and reduced health services use. Health care systems that serve homeless patients may promote their health and well-being by linking them with effective housing services. |
Exposure to bisphenols and asthma morbidity among low-income urban children with asthma
Quiros-Alcala L , Hansel NN , McCormack M , Calafat AM , Ye X , Peng RD , Matsui EC . J Allergy Clin Immunol 2020 147 (2) 577-586 e7 BACKGROUND: Bisphenol A (BPA) has been linked with pediatric asthma development and allergic airway inflammation in animal models. Whether exposure to BPA or its structural analogs bisphenol S (BPS) and bisphenol F (BPF) is associated with asthma morbidity remains unknown. OBJECTIVE: We examined associations between bisphenols and morbidity due to pediatric asthma. METHODS: We quantified concentrations of BPA, BPS, and BPF in 660 urine samples from 148 predominantly low-income, African American children (aged 5-17 years) with established asthma. We used biobanked biospecimens and data on symptoms, health care utilization, and pulmonary function and inflammation that were collected every 3 months over the course of a year. We used generalized estimating equations to examine associations between concentrations or detection of urinary bisphenols and morbidity outcomes and assessed heterogeneity of associations by sex. RESULTS: We observed consistent positive associations between BPA exposure and measures of asthma morbidity. For example, we observed increased odds of general symptom days (adjusted odds ratio [aOR] = 1.40 [95% C = 1.02-1.92]), maximal symptom days (aOR = 1.36 [95% CI = 1.00-1.83]), and emergency department visits (aOR = 2.12 [95% CI =1.28-3.51]) per 10-fold increase in BPA concentration. We also observed evidence of sexually dimorphic effects; BPA concentrations were associated with increased odds of symptom days and health care utilization only among boys. Findings regarding BPS and BPF did not consistently point to associations with asthma symptoms or health care utilization. CONCLUSION: We found evidence to suggest that BPA exposure in a predominantly low-income, minority pediatric cohort is associated with asthma morbidity and that associations may differ by sex. Our findings support additional studies, given the high pediatric asthma burden and widespread exposure to BPA in the United States. |
Association of long-term ambient ozone exposure with respiratory morbidity in smokers
Paulin LM , Gassett AJ , Alexis NE , Kirwa K , Kanner RE , Peters S , Krishnan JA , Paine R3rd , Dransfield M , Woodruff PG , Cooper CB , Barr RG , Comellas AP , Pirozzi CS , Han M , Hoffman EA , Martinez FJ , Woo H , Peng RD , Fawzy A , Putcha N , Breysse PN , Kaufman JD , Hansel NN . JAMA Intern Med 2019 180 (1) 106-115 Importance: Few studies have investigated the association of long-term ambient ozone exposures with respiratory morbidity among individuals with a heavy smoking history. Objective: To investigate the association of historical ozone exposure with risk of chronic obstructive pulmonary disease (COPD), computed tomography (CT) scan measures of respiratory disease, patient-reported outcomes, disease severity, and exacerbations in smokers with or at risk for COPD. Design, Setting, and Participants: This multicenter cross-sectional study, conducted from November 1, 2010, to July 31, 2018, obtained data from the Air Pollution Study, an ancillary study of SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study). Data analyzed were from participants enrolled at 7 (New York City, New York; Baltimore, Maryland; Los Angeles, California; Ann Arbor, Michigan; San Francisco, California; Salt Lake City, Utah; and Winston-Salem, North Carolina) of the 12 SPIROMICS clinical sites. Included participants had historical ozone exposure data (n = 1874), were either current or former smokers (>/=20 pack-years), were with or without COPD, and were aged 40 to 80 years at baseline. Healthy persons with a smoking history of 1 or more pack-years were excluded from the present analysis. Exposures: The 10-year mean historical ambient ozone concentration at participants' residences estimated by cohort-specific spatiotemporal modeling. Main Outcomes and Measures: Spirometry-confirmed COPD, chronic bronchitis diagnosis, CT scan measures (emphysema, air trapping, and airway wall thickness), 6-minute walk test, modified Medical Research Council (mMRC) Dyspnea Scale, COPD Assessment Test (CAT), St. George's Respiratory Questionnaire (SGRQ), postbronchodilator forced expiratory volume in the first second of expiration (FEV1) % predicted, and self-report of exacerbations in the 12 months before SPIROMICS enrollment, adjusted for demographics, smoking, and job exposure. Results: A total of 1874 SPIROMICS participants were analyzed (mean [SD] age, 64.5 [8.8] years; 1479 [78.9%] white; and 1013 [54.1%] male). In adjusted analysis, a 5-ppb (parts per billion) increase in ozone concentration was associated with a greater percentage of emphysema (beta = 0.94; 95% CI, 0.25-1.64; P = .007) and percentage of air trapping (beta = 1.60; 95% CI, 0.16-3.04; P = .03); worse scores for the mMRC Dyspnea Scale (beta = 0.10; 95% CI, 0.03-0.17; P = .008), CAT (beta = 0.65; 95% CI, 0.05-1.26; P = .04), and SGRQ (beta = 1.47; 95% CI, 0.01-2.93; P = .048); lower FEV1% predicted value (beta = -2.50; 95% CI, -4.42 to -0.59; P = .01); and higher odds of any exacerbation (odds ratio [OR], 1.37; 95% CI, 1.12-1.66; P = .002) and severe exacerbation (OR, 1.37; 95% CI, 1.07-1.76; P = .01). No association was found between historical ozone exposure and chronic bronchitis, COPD, airway wall thickness, or 6-minute walk test result. Conclusions and Relevance: This study found that long-term historical ozone exposure was associated with reduced lung function, greater emphysema and air trapping on CT scan, worse patient-reported outcomes, and increased respiratory exacerbations for individuals with a history of heavy smoking. The association between ozone exposure and adverse respiratory outcomes suggests the need for continued reevaluation of ambient pollution standards that are designed to protect the most vulnerable members of the US population. |
Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens.
Weigand MR , Peng Y , Batra D , Burroughs M , Davis JK , Knipe K , Loparev VN , Johnson T , Juieng P , Rowe LA , Sheth M , Tang K , Unoarumhi Y , Williams MM , Tondella ML . mSystems 2019 4 (6) Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens.IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species. |
The epidemiological signature of influenza B virus and its B/Victoria and B/Yamagata lineages in the 21st century
Caini S , Kusznierz G , Garate VV , Wangchuk S , Thapa B , de Paula Junior FJ , Ferreira de Almeida WA , Njouom R , Fasce RA , Bustos P , Feng L , Peng Z , Araya JL , Bruno A , de Mora D , Barahona de Gamez MJ , Pebody R , Zambon M , Higueros R , Rivera R , Kosasih H , Castrucci MR , Bella A , Kadjo HA , Daouda C , Makusheva A , Bessonova O , Chaves SS , Emukule GO , Heraud JM , Razanajatovo NH , Barakat A , El Falaki F , Meijer A , Donker GA , Huang QS , Wood T , Balmaseda A , Palekar R , Arevalo BM , Rodrigues AP , Guiomar R , Lee VJM , Ang LW , Cohen C , Treurnicht F , Mironenko A , Holubka O , Bresee J , Brammer L , Le MTQ , Hoang PVM , El Guerche-Seblain C , Paget J . PLoS One 2019 14 (9) e0222381 We describe the epidemiological characteristics, pattern of circulation, and geographical distribution of influenza B viruses and its lineages using data from the Global Influenza B Study. We included over 1.8 million influenza cases occurred in thirty-one countries during 2000-2018. We calculated the proportion of cases caused by influenza B and its lineages; determined the timing of influenza A and B epidemics; compared the age distribution of B/Victoria and B/Yamagata cases; and evaluated the frequency of lineage-level mismatch for the trivalent vaccine. The median proportion of influenza cases caused by influenza B virus was 23.4%, with a tendency (borderline statistical significance, p = 0.060) to be higher in tropical vs. temperate countries. Influenza B was the dominant virus type in about one every seven seasons. In temperate countries, influenza B epidemics occurred on average three weeks later than influenza A epidemics; no consistent pattern emerged in the tropics. The two B lineages caused a comparable proportion of influenza B cases globally, however the B/Yamagata was more frequent in temperate countries, and the B/Victoria in the tropics (p = 0.048). B/Yamagata patients were significantly older than B/Victoria patients in almost all countries. A lineage-level vaccine mismatch was observed in over 40% of seasons in temperate countries and in 30% of seasons in the tropics. The type B virus caused a substantial proportion of influenza infections globally in the 21st century, and its two virus lineages differed in terms of age and geographical distribution of patients. These findings will help inform health policy decisions aiming to reduce disease burden associated with seasonal influenza. |
Economics of multicomponent interventions to increase breast, cervical, and colorectal cancer screening: A Community Guide Systematic Review
Mohan G , Chattopadhyay SK , Ekwueme DU , Sabatino SA , Okasako-Schmucker DL , Peng Y , Mercer SL , Thota AB . Am J Prev Med 2019 57 (4) 557-567 CONTEXT: The Community Preventive Services Task Force recently recommended multicomponent interventions to increase breast, cervical, and colorectal cancer screening based on strong evidence of effectiveness. This systematic review examines the economic evidence to guide decisions on the implementation of these interventions. EVIDENCE ACQUISITION: A systematic literature search for economic evidence was performed from January 2004 to January 2018. All monetary values were reported in 2016 US dollars, and the analysis was completed in 2018. EVIDENCE SYNTHESIS: Fifty-three studies were included in the body of evidence from a literature search yield of 8,568 total articles. For multicomponent interventions to increase breast cancer screening, the median intervention cost per participant was $26.69 (interquartile interval [IQI]=$3.25, $113.72), and the median incremental cost per additional woman screened was $147.64 (IQI=$32.92, $924.98). For cervical cancer screening, the median costs per participant and per additional woman screened were $159.80 (IQI=$117.62, $214.73) and $159.49 (IQI=$64.74, $331.46), respectively. Two studies reported incremental cost per quality-adjusted life year gained of $748 and $33,433. For colorectal cancer screening, the median costs per participant and per additional person screened were $36.63 (IQI=$7.70, $139.23) and $582.44 (IQI=$91.10, $1,452.12), respectively. Two studies indicated a decline in incremental cost per quality-adjusted life year gained of $1,651 and $3,817. CONCLUSIONS: Multicomponent interventions to increase cervical and colorectal cancer screening were cost effective based on a very conservative threshold. Additionally, multicomponent interventions for colorectal cancer screening demonstrated net cost savings. Cost effectiveness for multicomponent interventions to increase breast cancer screening could not be determined owing to the lack of studies reporting incremental cost per quality-adjusted life year gained. Future studies estimating this outcome could assist implementers with decision making. |
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