Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 35 Records) |
Query Trace: Bowden B[original query] |
---|
Sociodemographic and occupational characteristics associated with early and continued COVID-19 vaccine uptake among healthcare personnel: Monroe County, NY
Russ S , Myers C , Licherdell E , Bowden A , Chinchilli E , Dahhan R , Van Wijngaarden E , Plumb ID , Dumyati G . Vaccine 2024 OBJECTIVE: Identify characteristics of healthcare personnel (HCP) who did not have timely initiation of the COVID-19 primary series, as well as HCP who did not receive a booster vaccine. METHODS: Characteristics of HCP enrolled in a COVID-19 vaccine effectiveness study between 12/28/2020-12/01/2022 were compared by timing of receipt of 1st mRNA dose, and by receipt of a booster dose. Data for this retrospective cohort analysis came from HCP working at a large healthcare system in Monroe County, New York, and included standardized questionnaires and verified vaccination status. HCP were categorized by whether they received their 1stmRNA COVID-19 vaccine between 12/14/2020-03/30/2021 (earlier) or 04/01/2021-09/28/2021 (later) based on timing of local vaccine eligibility and mandates, and by whether they received a 3rdmRNA booster dose by 12/01/22. Logistic regression models were run to identify characteristics of HCP who had later 1stdose receipt or did not receive a booster. RESULTS: 3,375 HCP were enrolled. Of these, 86.8 % had early initiation of their 1stCOVID-19 vaccine, and 85.0 % received a booster dose. Low education, low household income, younger age (<50), non-White race and public health insurance were all significant predictors of later receipt of 1stdose and lack of uptake of a booster. However, advanced professional role was only found to be a significant predictor of early 1stdose receipt. CONCLUSIONS: Continual monitoring of COVID-19 vaccine uptake among HCP to identify those less likely to receive new booster doses will be crucial to support targeted vaccine campaigns in this important population. |
Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs (preprint)
Bowden KE , Joseph SJ , Cartee JC , Ziklo N , Danavall D , Raphael BH , Read TD , Dean D . bioRxiv 2020 2020.09.04.282459 Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. U.S. cases have been steadily increasing for more than a decade in both the urogenital tract and rectum. C. trachomatis is an obligate intracellular bacterium that is not easily cultured, limiting the capacity for genome studies to understand strain diversity and emergence among various patient populations globally. While Agilent SureSelectXT target-enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival and rectal samples, efficiencies are only 60-80% for ≥95-100% genome coverage. We therefore re-designed and expanded the RNA bait library to augment enrichment of the organism from clinical samples to improve efficiency. We describe the expanded library, the limit of detection for C. trachomatis genome copy input, and the 100% efficiency and high-resolution of generated genomes where genomic recombination among paired vaginal and rectal specimens from four patients was identified. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, among geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.Importance Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, and there is limited information on rectal C. trachomatis transmission and its impact on morbidity. To improve efficiency of previous studies involving whole genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we expanded the RNA bait library to augment enrichment of the organism from clinical samples. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis. We show the new system is sensitive for near identical genomes of C. trachomatis from two body sites in four women. Further, we provide a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital and rectal infections, and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.Competing Interest StatementThe authors have declared no competing interest. |
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. |
Risk Factors for Ebola Virus Persistence in Semen of Survivors - Liberia.
Dyal J , Kofman A , Kollie JZ , Fankhauser J , Orone R , Soka MJ , Glaybo U , Kiawu A , Freeman E , Giah G , Tony HD , Faikai M , Jawara M , Kamara K , Kamara S , Flowers B , Kromah ML , Desamu-Thorpe R , Graziano J , Brown S , Morales-Betoulle ME , Cannon DL , Su K , Linderman SL , Plucinski M , Rogier E , Bradbury RS , Secor WE , Bowden KE , Phillips C , Carrington MN , Park YH , Martin MP , Del Pilar Aguinaga M , Mushi R , Haberling DL , Ervin ED , Klena JD , Massaquoi M , Nyenswah T , Nichol ST , Chiriboga DE , Williams DE , Hinrichs SH , Ahmed R , Vonhm BT , Rollin PE , Purpura LJ , Choi MJ . Clin Infect Dis 2022 76 (3) e849-e856 BACKGROUND: Long-term persistence of Ebola virus (EBOV) in immunologically-privileged sites has been implicated in recent outbreaks of Ebola Virus Disease (EVD) in Guinea and the Democratic Republic of Congo. This study was designed to understand how the acute course of EVD, convalescence, and host immune and genetic factors may play a role in prolonged viral persistence in semen. METHODS: A cohort of 131 male EVD survivors in Liberia were enrolled in a case-case study. "Early clearers" were defined as those with two consecutive negative EBOV semen tests by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) at least two weeks apart within 1 year after discharge from the Ebola Treatment Unit (ETU) or acute EVD. "Late clearers" had detectable EBOV RNA by rRT-PCR over one year following ETU discharge or acute EVD. Retrospective histories of their EVD clinical course were collected by questionnaire, followed by complete physical exams and blood work. RESULTS: Compared to early clearers, late clearers were older (median 42.5 years, p = 0.0001) and experienced fewer severe clinical symptoms (median 2, p = 0.006). Late clearers had more lens opacifications (OR 3.9, 95%CI 1.1-13.3, p = 0.03), after accounting for age, higher total serum IgG3 titers (p = 0.007) and increased expression of the HLA-C*03:04 allele (OR 0.14, 95% CI 0.02-0.70, p = 0.007). CONCLUSIONS: Older age, decreased illness severity, elevated total serum IgG3 and HLA-C*03:04 allele expression may be risk factors for the persistence of EBOV in the semen of EVD survivors. EBOV persistence in semen may also be associated with its persistence in other immunologically protected sites, such as the eye. |
Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC).
Lippa KA , Aristizabal-Henao JJ , Beger RD , Bowden JA , Broeckling C , Beecher C , Clay Davis W , Dunn WB , Flores R , Goodacre R , Gouveia GJ , Harms AC , Hartung T , Jones CM , Lewis MR , Ntai I , Percy AJ , Raftery D , Schock TB , Sun J , Theodoridis G , Tayyari F , Torta F , Ulmer CZ , Wilson I , Ubhi BK . Metabolomics 2022 18 (4) 24 INTRODUCTION: The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES: This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS: The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS: The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community. |
Costs and Consequences of Eliminating a Routine, Point-Of-Care HIV Screening Program in a High-Prevalence Jail
Hutchinson AB , MacGowan RJ , Margolis AD , Adee MG , Wen W , Bowden CJ , Spaulding AC . Am J Prev Med 2021 61 S32-s38 INTRODUCTION: This study aims to assess the public health impact of eliminating a longstanding routine HIV screening program and replacing it with targeted testing. In addition, costs, outcomes, and cost effectiveness of routine screening are compared with those of targeted testing in the Fulton County Jail, Atlanta, Georgia. METHODS: A published mathematical model was used to assess the cost effectiveness and public health impact of routine screening (March 2013-February 2014) compared with those of targeted testing (January 2018-December 2018) from a health system perspective. Costs, outcomes, and other model inputs were derived from the testing programs and the published literature, and the cost effectiveness analysis was conducted from 2019 to 2020. RESULTS: Routine screening identified 74 more new HIV infections over 1 year than targeted testing, resulting in an estimated 10 HIV transmissions averted and 45 quality-adjusted life-years saved, and was cost saving. The missed opportunity to diagnose infections because routine screening was eliminated resulted in an estimated 8.4 additional HIV transmissions and $3.7 million in additional costs to the healthcare system. CONCLUSIONS: Routine HIV screening in high-prevalence jails is cost effective and has a larger impact on public health than targeted testing. Prioritizing sustained funding for routine, jail-based HIV screening programs in high-prevalence areas may be important to realizing the national HIV prevention goals. |
Use of real-time PCR as an alternative to conventional genotyping methods for the laboratory detection of lymphogranuloma venereum (LGV).
Woodson EN , Katz SS , Mosley SS , Danavall DC , Bowden KE , Chi KH , Raphael BH . Diagn Microbiol Infect Dis 2021 101 (4) 115532 Lymphogranuloma venereum (LGV) can be differentiated from non-LGV chlamydial infection using Sanger sequencing or molecular assays, including those that are commercially-available internationally. Here, we describe the performance of a rapid real-time PCR (RT-PCR)-based strategy in differentiating Chlamydia trachomatis infections associated with LGV or non-LGV serovars. One hundred three rectal swabs, previously genotyped using Sanger sequencing of the ompA gene as a reference method, were tested in the RT-PCR assays. All non-LGV specimens were correctly identified, but the RT-PCR failed to detect 1 LGV specimen, resulting in a sensitivity of 87.5% for the non-LGV/LGV RT-PCR assay. Additional performance characteristics (e.g., specificity, accuracy, and reproducibility) were all between 93% and 100% with a limit of detection ≤100 copies/reaction. Thus, this rapid RT-PCR method for LGV detection in clinical specimens is comparable to the reference method. |
Development of a Multiplex Bead Assay To Detect Immunoglobulin G Antibodies to Babesia duncani in Human Serum.
Wang Y , Aderohunmu T , Bishop H , McAuliffe I , Rivera HN , Smith D , Wilkins PP , Bowden KE , Reed MS , Svoboda P , Stuchlik O , Pohl J , Wiegand RE , Handali S . J Clin Microbiol 2021 59 (11) Jcm0045821 Babesia duncani is the causative agent of babesiosis in the western United States. The indirect fluorescent antibody (IFA) assay is the diagnostic test of choice for detection of B. duncani specific antibodies. However, this test requires parasitized red blood cells harvested from infected hamsters and test results are often difficult to interpret. To simplify serological testing for B. duncani, a proteomics approach was employed to identify candidate immunodiagnostic antigens. Several proteins were identified by electrospray ionization (ESI) mass spectrometric analysis and four recombinant protein constructs were expressed and used in a multiplex bead assay (MBA) to detect B. duncani-specific antibodies. Two antigens, AAY83295.1 and AAY83296.1, performed well with high sensitivities and specificities. AAY83295.1 had a higher sensitivity (100%) but lower specificity (89%) in comparison to AAY83296.1, which had a sensitivity of 90% and a specificity of 96%. Combining these two antigens did not improve the performance of the assay. This MBA could be useful for diagnosis, serosurveillance, and blood donor screening for B. duncani infection. |
Assessment and utility of 2 Chlamydia trachomatis Pgp3 serological assays for seroprevalence studies among women in the United States
Danavall DC , Gwyn S , Anyalechi GE , Bowden KE , Hong J , Kirkcaldy RD , Bernstein KT , Kersh EN , Martin D , Raphael BH . Diagn Microbiol Infect Dis 2021 101 (2) 115480 Two plasmid gene protein (Pgp3)-based serological assays, the Pgp3-ELISA and multiplex bead assay (Pgp3-MBA), were compared and used to estimate seropositivity of Chlamydia trachomatis (CT) among females 14 to 39 years old participating in the National Health and Nutrition Examination Survey between 2013-2016. Of the 2,201 specimens tested, 502 (29.5%, 95% CI 27.6-31.5) were positive using Pgp3-ELISA and 624 (28.4%, 95% CI 26.5-30.3) were positive using Pgp3-MBA. The overall agreement between the assays was 87.7%. Corresponding nucleic acid amplification test (NAAT) results were available for 1,725 specimens (from women 18-39 years old); of these, 42 (2.4%, 95% CI 1.8-3.3) were CT NAAT-positive. Most of the CT NAAT-positive specimens had corresponding positive serological assay results; 33 (78.6%, 95% CI 62.8-89.2) were Pgp3-ELISA-positive and 36 (85.7%, 95% CI 70.8-94.1) were Pgp3-MBA-positive. Although Pgp3-ELISA and Pgp3-MBA demonstrated equivalent performance in this study, an advantage of the Pgp3-MBA over Pgp3-ELISA is that it is well suited for high sample throughput applications. |
Detection of Lymphogranuloma Venereum- associated Chlamydia trachomatis L2 Serovars in Remnant Rectal Specimens Collected from Seven United States Public Health Laboratories
Chi KH , de Voux A , Morris M , Katz SS , Pillay A , Danavall D , Bowden KE , Gaynor AM , Kersh EN . Sex Transm Dis 2021 49 (1) e26-e28 The frequency of lymphogranuloma venereum (LGV) or invasive Chlamydia trachomatis (CT) infection with serovar L1, L2 or L3 is unknown in the United States. While no diagnostic test is commercially available, we used a laboratory-developed test and detected LGV-associated serovar L2 in 14% of 132 remnant CT-positive rectal swabs. |
Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.
Bowden KE , Joseph SJ , Cartee JC , Ziklo N , Danavall D , Raphael BH , Read TD , Dean D . mSphere 2021 6 (2) Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelect(XT) target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity. |
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. |
Prevalence of urogenital Mycoplasma genitalium infection, United States, 2017-2018
Torrone E , Kruszon-Moran D , Philips C , Morris M , Bowden K , Papp J , Bachmann LH , Weinstock H , Kersh EN . Sex Transm Dis 2021 48 (11) e160-e162 During the 2017-2018 National Health and Nutrition Examination Survey, urine samples from participants aged 14-59 years were tested for Mycoplasma genitalium infection. Overall prevalence was 1.7% (95% CI: 1.1%, 2.7%). Prevalence was similar between males (1.8%, 95% CI: 0.9%, 3.1%) and females (1.7%, 95% CI: 0.8%, 3.0%). |
Modelling airport catchment areas to anticipate the spread of infectious diseases across land and air travel
Huber C , Watts A , Grills A , Yong JHE , Morrison S , Bowden S , Tuite A , Nelson B , Cetron M , Khan K . Spat Spatiotemporal Epidemiol 2021 36 100380 Air travel is an increasingly important conduit for the worldwide spread of infectious diseases. However, methods to identify which airports an individual may use to initiate travel, or where an individual may travel to upon arrival at an airport is not well studied. This knowledge gap can be addressed by estimating airport catchment areas: the geographic extent from which the airport derives most of its patronage. While airport catchment areas can provide a simple decision-support tool to help delineate the spatial extent of infectious disease spread at a local scale, observed data for airport catchment areas are rarely made publicly available. Therefore, we evaluated a probabilistic choice behavior model, the Huff model, as a potential methodology to estimate airport catchment areas in the United States in data-limited scenarios. We explored the impact of varying input parameters to the Huff model on estimated airport catchment areas: distance decay exponent, distance cut-off, and measures of airport attractiveness. We compared Huff model catchment area patterns for Miami International Airport (MIA) and Harrisburg International Airport (MDT). We specifically compared our model output to observed data sampled for MDT to align model parameters with an established, observed catchment area. Airport catchment areas derived using the Huff model were highly sensitive to changes in model parameters. We observed that a distance decay exponent of 2 and a distance cut-off of 500 km represented the most realistic spatial extent and heterogeneity of the MIA catchment area. When these parameters were applied to MDT, the Huff model produced similar spatial patterns to the observed MDT catchment area. Finally, our evaluation of airport attractiveness showed that travel volume to the specific international destinations of interest for infectious disease importation risks (i.e., Brazil) had little impact on the predicted choice of airport when compared to all international travel. Our work is a proof of concept for use of the Huff model to estimate airport catchment areas as a generalizable decision-support tool in data-limited scenarios. While our work represents an initial examination of the Huff model as a method to approximate airport catchment areas, an essential next step is to conduct a quantitative calibration and validation of the model based on multiple airports, possibly leveraging local human mobility data such as call detail records or online social network data collected from mobile devices. Ultimately, we demonstrate how the Huff model could be potentially helpful to improve the precision of early warning systems that anticipate infectious disease spread, or to incorporate when local public health decision makers need to identify where to mobilize screening infrastructure or containment strategies at a local level. |
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. |
Estimating recommended gonorrhea and chlamydia treatment rate using linked medical claims, prescription and laboratory data in US private settings
Tao G , Workowski K , Bowden KE , Pearson WS , Sullivan JM , Henk HJ , Gift TL . Sex Transm Dis 2020 48 (3) 167-173 BACKGROUND: The Centers for Disease Control and Prevention (CDC) recommends specific regimens for chlamydia and dual therapy for gonorrhea to mitigate antimicrobial resistant gonorrhea in the CDC 2015 STD Treatment Guidelines. Only limited studies examining adherence to these recommendations have been conducted at private practices in the United States. METHODS: We used the OptumLabs® Data Warehouse (OLDW), a comprehensive, longitudinal data asset with de-identified persons with linked commercial insurance claims and clinical information, to identify persons aged 15-60 years who had valid nucleic acid amplification testing results demonstrating urogenital or extragenital gonorrhea or chlamydia in 2016-2018. We defined valid lab results as positive or negative. We then assessed the time of their first positive test and the type of treatment within 30 days to determine if there was evidence in the claims record that the CDC-recommended treatment was provided. We defined presumed treatment if the date of treatment was before the date of the positive test within 30 days. RESULTS: Among 6,476 patients with positive gonorrhea tests and 26,847 patients with positive chlamydia tests only, 34.8% and 64.2% had evidence of receiving the CDC-recommended therapy, respectively. About 11.6% of patients with positive gonorrhea tests with recommended dual treatment and 7.1% of patients with positive chlamydia tests only with recommended chlamydia treatment were presumptively treated. CONCLUSION: Analysis of treatment claims and medical records from private settings indicated low rates of recommended gonorrhea and chlamydia treatment. Validation of treatment claims is needed to support further quality of care interventions based on these data. |
Impact of effective global tuberculosis control on health and economic outcomes in the United States
Menzies NA , Bellerose M , Testa C , Swartwood N , Malyuta Y , Cohen T , Marks SM , Hill AN , Date AA , Maloney SA , Bowden SE , Grills AW , Salomon JA . Am J Respir Crit Care Med 2020 202 (11) 1567-1575 RATIONALE: Most United States residents who develop tuberculosis were born abroad, and US TB incidence is increasingly driven by infection risks in other countries. OBJECTIVES: To estimate the potential impact of effective global TB control on health and economic outcomes in the United States. METHODS: We estimated outcomes using linked mathematical models of TB epidemiology in the United States and migrants' birth countries. A base-case scenario extrapolated country-specific TB incidence trends. We compared this to scenarios in which countries achieve 90% TB incidence reductions between 2015 and 2035, as targeted by the Global End TB Strategy ("effective global TB control"). We also considered pessimistic scenarios of flat TB incidence trends in individual countries. MEASUREMENTS AND MAIN RESULTS: We estimated TB cases, TB deaths, costs, and the total economic burden of TB in the US. Compared to the base-case, effective global TB control would avert 40,000 (95% uncertainty interval: 29,000-55,000) TB cases in the United States over 2020-2035. TB incidence rates in 2035 would be 43% (34-54) lower than the base-case, and 49% (44-55) lower than in 2020. Summed over 2020-2035, this represents $0.8 (0.6-1.0) billion dollars in averted healthcare costs and $2.5 (1.7-3.6) billion in productivity gains. The total US economic burden of TB (including the value of averted TB deaths) would be 21% (16-28) lower ($18 (8-32) billion). CONCLUSIONS: In addition to producing major health benefits for high-burden countries, strengthened efforts to achieve effective global TB control could produce substantial health and economic benefits for the United States. |
A review of efforts to improve lipid stability during sample preparation and standardization efforts to ensure accuracy in the reporting of lipid measurements
Ulmer CZ , Koelmel JP , Jones CM , Garrett TJ , Aristizabal-Henao JJ , Vesper HW , Bowden JA . Lipids 2020 56 (1) 3-16 Lipidomics is a rapidly growing field, fueled by developments in analytical instrumentation and bioinformatics. To date, most researchers and industries have employed their own lipidomics workflows without a consensus on best practices. Without a community-wide consensus on best practices for the prevention of lipid degradation and transformations through sample collection and analysis, it is difficult to assess the quality of lipidomics data and hence trust results. Clinical studies often rely on samples being stored for weeks or months until they are analyzed, but inappropriate sampling techniques, storage temperatures, and analytical protocols can result in the degradation of complex lipids and the generation of oxidized or hydrolyzed metabolite artifacts. While best practices for lipid stability are sample dependent, it is generally recommended that strategies during sample preparation capable of quenching enzymatic activity and preventing oxidation should be considered. In addition, after sample preparation, lipid extracts should be stored in organic solvents with antioxidants at -20 degrees C or lower in an airtight container without exposure to light or oxygen. This will reduce or eliminate sublimation, and chemically and physically induced molecular transformations such as oxidation, enzymatic transformation, and photon/heat-induced degradation. This review explores the available literature on lipid stability, with a particular focus on human health and/or clinical lipidomic applications. Specifically, this includes a description of known mechanisms of lipid degradation, strategies, and considerations for lipid storage, as well as current efforts for standardization and quality insurance of protocols. |
Prevalence of Mycoplasma genitalium infection, antimicrobial resistance mutations and symptom resolution following treatment of urethritis
Bachmann LH , Kirkcaldy RD , Geisler WM , Wiesenfeld HC , Manhart LE , Taylor SN , Sena AC , McNeil CJ , Newman L , Myler N , Fuchs R , Bowden KE . Clin Infect Dis 2020 71 (10) e624-e632 BACKGROUND: Antimicrobial resistance in Mycoplasma genitalium (MG), a cause of urethritis, is a growing concern. Yet little is known about the geographic distribution of MG resistance in the U.S. or associated clinical outcomes. We evaluated the frequency of MG among men with urethritis, resistance mutations, and post-treatment symptom persistence. METHODS: We enrolled men presenting with urethritis symptoms to 6 U.S. sexually transmitted disease (STD) clinics during June 2017-July 2018; men with urethritis were eligible for follow-up contact and (if persistent symptoms or MG) chart review. Urethral specimens were tested for MG and other bacterial STDs. Mutations in 23S rRNA loci (macrolide-associated mutations [MRMs]) and parC and gyrA (quinolone-associated mutations [QRMs]) were detected by targeted amplification/Sanger sequencing. RESULTS: Among 914 evaluable participants, 28.7% (95% CI 23.8-33.6) had MG. Men with MG were more often black (79.8% vs 66%), <30 years (72.9% vs 56.1%), and reported only female partners (83.7% vs 74.2%) than men without MG. Among MG-positive participants, 64.4% (95% CI 58.2%-70.3%) had MRM, 11.5% (95% CI 7.9-16.0%) had parC mutations, and 0% had gyrA mutations. Among participants treated with azithromycin-based therapy at enrollment and who completed the follow-up survey, persistent symptoms were reported by 25.8% of MG-positive/MRM-positive men, 13% of MG-positive/MRM-negative men, and 17.2% of MG-negative men. CONCLUSIONS: MG infection was common among men with urethritis; MRM prevalence was high among men with MG. Persistent symptoms following treatment were frequent among men with and without MG. |
Risk of yellow fever virus importation into the United States from Brazil, outbreak years 2016-2017 and 2017-2018
Dorigatti I , Morrison S , Donnelly CA , Garske T , Bowden S , Grills A . Sci Rep 2019 9 (1) 20420 Southeast Brazil has experienced two large yellow fever (YF) outbreaks since 2016. While the 2016-2017 outbreak mainly affected the states of Espirito Santo and Minas Gerais, the 2017-2018 YF outbreak primarily involved the states of Minas Gerais, Sao Paulo, and Rio de Janeiro, the latter two of which are highly populated and popular destinations for international travelers. This analysis quantifies the risk of YF virus (YFV) infected travelers arriving in the United States via air travel from Brazil, including both incoming Brazilian travelers and returning US travelers. We assumed that US travelers were subject to the same daily risk of YF infection as Brazilian residents. During both YF outbreaks in Southeast Brazil, three international airports-Miami, New York-John F. Kennedy, and Orlando-had the highest risk of receiving a traveler infected with YFV. Most of the risk was observed among incoming Brazilian travelers. Overall, we found low risk of YFV introduction into the United States during the 2016-2017 and 2017-2018 outbreaks. Decision makers can use these results to employ the most efficient and least restrictive actions and interventions. |
Orolabial lymphogranuloma venereum, Michigan, USA
Ilyas S , Richmond D , Burns G , Bowden KE , Workowski K , Kersh EN , Chandrasekar PH . Emerg Infect Dis 2019 25 (11) 2112-2114 Orolabial lymphogranuloma venereum was diagnosed for a man in Michigan, USA, who had sex with men, some infected with HIV. High index of suspicion for lymphogranuloma venereum led to accurate diagnosis, successful therapy, and description of an L2b variant with a unique genetic mutation. |
Systematic review and meta-analysis of tick-borne disease risk factors in residential yards, neighborhoods, and beyond
Fischhoff IR , Bowden SE , Keesing F , Ostfeld RS . BMC Infect Dis 2019 19 (1) 861 BACKGROUND: Exposure to blacklegged ticks Ixodes scapularis that transmit pathogens is thought to occur peri-domestically. However, the locations where people most frequently encounter infected ticks are not well characterized, leading to mixed messages from public health officials about where risk is highest. METHODS: We conducted a systematic review and meta-analysis on spatial risk factors for tick-borne disease and tick bites in eastern North America. We examined three scales: the residential yard, the neighborhood surrounding (but not including) the yard, and outside the neighborhood. Nineteen eligible studies represented 2741 cases of tick-borne illness and 1447 tick bites. Using random effects models, we derived pooled odds ratio (OR) estimates. RESULTS: The meta-analysis revealed significant disease risk factors at the scale of the yard (OR 2.60 95% CI 1.96 - 3.46), the neighborhood (OR 4.08 95% CI 2.49 - 6.68), and outside the neighborhood (OR 2.03 95% CI 1.59 - 2.59). Although significant risk exists at each scale, neighborhood scale risk factors best explained disease exposure. Analysis of variance revealed risk at the neighborhood scale was 57% greater than risk at the yard scale and 101% greater than risk outside the neighborhood. CONCLUSIONS: This analysis emphasizes the importance of understanding and reducing tick-borne disease risk at the neighborhood scale. Risk-reducing interventions applied at each scale could be effective, but interventions applied at the neighborhood scale are most likely to protect human health. TRIAL REGISTRATION: The study was registered with PROSPERO: CRD42017079169 . |
Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using Standard Reference Material 1950 metabolites in frozen human plasma
Bowden JA , Heckert A , Ulmer CZ , Jones CM , Koelmel JP , Abdullah L , Ahonen L , Alnouti Y , Armando A , Asara JM , Bamba T , Barr JR , Bergquist J , Borchers CH , Brandsma J , Breitkopf SB , Cajka T , Cazenave-Gassiot A , Checa A , Cinel MA , Colas RA , Cremers S , Dennis EA , Evans JE , Fauland A , Fiehn O , Gardner MS , Garrett TJ , Gotlinger KH , Han J , Huang Y , Neo AH , Hyotylainen T , Izumi Y , Jiang H , Jiang H , Jiang J , Kachman M , Kiyonami R , Klavins K , Klose C , Kofeler HC , Kolmert J , Koal T , Koster G , Kuklenyik Z , Kurland IJ , Leadley M , Lin K , Maddipati KR , McDougall D , Meikle PJ , Mellett NA , Monnin C , Moseley MA , Nandakumar R , Oresic M , Patterson RE , Peake D , Pierce JS , Post M , Postle AD , Pugh R , Qui Y , Quehenberger O , Ramrup P , Rees J , Rembiesa B , Reynaud D , Roth MR , Sales S , Schuhmann K , Schwartzman ML , Serhan CN , Shevchenko A , Somerville SE , St John-Williams L , Surma MA , Takeda H , Thakare R , Thompson JW , Torta F , Triebl A , Trötzmüller M , Ubhayasekera SJK , Vuckovic D , Weir JM , Welti R , Wenk MR , Wheelock CE , Yao L , Yuan M , Zhao XH , Zhou S . J Lipid Res 2017 58 (12) 2275-2288 As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950 Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each lab using a different lipidomics workflow. A total of 1527 unique lipids were measured across all laboratories, and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and inter-laboratory quality control and method validation. These analyses were performed using non-standardized laboratory-independent workflows. The consensus locations were also compared to a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement. |
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement.
Weigand MR , Peng Y , Loparev V , Batra D , Bowden KE , Burroughs M , Cassiday PK , Davis JK , Johnson T , Juieng P , Knipe K , Mathis MH , Pruitt AM , Rowe L , Sheth M , Tondella ML , Williams MM . J Bacteriol 2017 199 (8) Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genome structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine potential evolution of chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. Observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigation of disease resurgence and molecular epidemiology. IMPORTANCE: Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a high number of repetitive, mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-coding genes which otherwise exhibit little nucleotide sequence diversity. By comparing complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology. |
Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections.
Weigand MR , Peng Y , Loparev V , Batra D , Bowden KE , Cassiday PK , Davis JK , Johnson T , Juieng P , Miner CE , Rowe L , Sheth M , Tondella ML , Williams MM . Genome Announc 2016 4 (5) Species of the genus Bordetella associate with various animal hosts, frequently causing respiratory disease. Bordetella pertussis is the primary agent of whooping cough and other Bordetella species can cause similar cough illness. Here, we report four complete genome sequences from isolates of different Bordetella species recovered from human respiratory infections. |
Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics.
Bowden KE , Weigand MR , Peng Y , Cassiday PK , Sammons S , Knipe K , Rowe LA , Loparev V , Sheth M , Weening K , Tondella ML , Williams MM . mSphere 2016 1 (3) During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of pertussis with differences seen in the demographic affected, case clinical presentation, and molecular epidemiology of the circulating strains. To overcome limitations of the current molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader understanding of how current circulating strains are causing large epidemics. Through the use of combined next-generation sequencing technologies, this study compared de novo, single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final genome architecture assemblies were verified with whole-genome optical mapping. Sixteen distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which were distinct from the genome structures of the two resequenced vaccine strains. These rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number mobile genetic elements and rRNA operons. Additionally, novel and previously identified single nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates. Whole-genome variation analysis identified state-specific variants, and coding regions bearing nonsynonymous mutations were classified into functional annotated orthologous groups. Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis and develop novel tools to better characterize the molecular epidemiology of evolving B. pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled vaccine-preventable bacterial disease in the United States, which has experienced a resurgence for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains circulating during epidemics exhibit diversity visible on a genome structural level, previously undetectable by traditional sequence analysis using short-read technologies. For the first time, we combine short- and long-read sequencing platforms with restriction optical mapping for single-contig, de novo assembly of 31 isolates to investigate two geographically and temporally independent U.S. pertussis epidemics. These complete genomes reshape our understanding of B. pertussis evolution and strengthen molecular epidemiology toward one day understanding the resurgence of pertussis. |
Costs of rapid HIV screening in an urban emergency department and a nearby county jail in the southeastern United States
Spaulding AC , MacGowan RJ , Copeland B , Shrestha RK , Bowden CJ , Kim MJ , Margolis A , Mustaafaa G , Reid LC , Heilpern KL , Shah BB . PLoS One 2015 10 (6) e0128408 Emergency departments and jails provide medical services to persons at risk for HIV infection and are recommended venues for HIV screening. Our main objective in this study was to analyze the cost per new HIV diagnosis associated with the HIV screening program in these two venues. The emergency department's parallel testing program was conducted at Grady Memorial Hospital in Atlanta, Georgia starting in 2008; the jail's integrated testing program began at the Fulton County (GA) Jail in 2011. The two sites, four miles apart from one another, employed the same rapid HIV test. Ascertainment that cases were new differed by site; only the jail systematically checked identities against health department HIV registries. The program in the emergency department used dedicated HIV test counselors and made 242 diagnoses over a 40-month period at a cost of $2,981 per diagnosis. The jail program used staff nurses, and found 41 new HIV cases over 10.5 months at a cost of $6,688 per new diagnosis. Differences in methods for ascertainment of new diagnoses, previously undiagnosed HIV sero-positivity, and methodologies used for assessing program costs prevent concluding that one program was more economical than the other. Nonetheless, our findings show that testing in both venues yielded many new diagnoses, with the costs within the range reported in the literature. |
An evaluation of the level of agreement in Bordetella species identification in three United States laboratories during a period of increased pertussis.
Burgos-Rivera B , Lee AD , Bowden KE , Faulkner AE , Seaton BL , Lembke BD , Cartwright CP , Martin SW , Tondella ML . J Clin Microbiol 2015 53 (6) 1842-7 While PCR is the most common method used for detecting Bordetella pertussis in the US, most laboratories use insertion sequence 481 (IS481), which is not specific for B. pertussis; therefore, the relative contribution of other Bordetella species is not understood. The objectives of this study were to evaluate the proportion of other Bordetella spp. misidentified as B. pertussis during a period of increased pertussis incidence, determine the level of agreement in Bordetella species detection between US commercial laboratories and CDC, and assess the relative diagnostic sensitivity of CDC's PCR assay when using a different PCR master mix. Specimens collected between May 2012-2013 were tested at two US commercial laboratories for B. pertussis and B. parapertussis detection. Every fifth specimen positive for IS481 and/or IS1001 with Ct values ≤35 was sent to CDC for PCR testing that identifies Bordetella species. Specimens with CDC PCR indeterminate or negative results were tested using an alternate PCR master mix. Of 755 specimens, there was agreement in species identification for 83.4% (n=630). Of those with different identifications (n=125), 79.2% (n=99) were identified as indeterminate B. pertussis at CDC. Overall, 0.66% (n=5) of the specimens were identified as B. holmesii or B. bronchiseptica at CDC. Of 115 specimens with indeterminate or negative results, 46.1% (n=53) were B. pertussis positive when tested by an alternate master mix, suggesting possible increase in assay sensitivity. This study demonstrates good agreement between the two US commercial laboratories and CDC and little misidentification of Bordetella species during the 2012 US epidemic. |
Molecular epidemiology of the pertussis epidemic in Washington State in 2012.
Bowden KE , Williams MM , Cassiday PK , Milton A , Pawloski L , Harrison M , Martin SW , Meyer S , Qin X , DeBolt C , Tasslimi A , Syed N , Sorrell R , Tran M , Hiatt B , Tondella ML . J Clin Microbiol 2014 52 (10) 3549-57 Although pertussis disease is vaccine-preventable, Washington State experienced a substantial rise in pertussis incidence beginning in 2011. By June 2012, the reported cases reached 2,520 (37.5 cases per 100,000 residents), a 1,300% increase compared with the same period in 2011. We assessed the molecular epidemiology of this statewide epidemic using 240 isolates collected from case-patients reported from 19 of 39 Washington counties during 2012-2013. Typing methods included pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA), multilocus sequence typing (MLST), and pertactin gene (prn) mutational analysis. Using the scheme PFGE-MLVA-MLST-prn mutations-Prn deficiency, the 240 isolates comprised 65 distinct typing profiles. Thirty-one PFGE types were found, with the most common types, CDC013 (n=51), CDC237 (n=44), and CDC002 (n=42), accounting for 57% of them. Eleven MLVA types were observed, mainly comprising type 27 (n=183; 76%). Seven MLST types were identified, with the majority of the isolates typing as prn2-ptxP3-ptxA1-fim3-1 (n=157; 65%). Four different prn mutations accounted for the 76% of isolates exhibiting pertactin-deficiency. PFGE provided the highest discriminatory power (D=0.87) and was found to be a more powerful typing method than MLVA and MLST combined (D=0.67). This study provides evidence for the continued predominance of MLVA 27 and prn2-ptxP3-ptxA1, along with the reemergence of the fim3-1 allele. Our results indicate that the B. pertussis population causing this epidemic was diverse, with a few molecular types predominating. PFGE, MLVA, and MLST profiles were consistent with predominate types circulating in the US and other countries. For prn, several mutations were present in multiple molecular types. |
Workplace health: engaging business leaders to combat obesity
Lankford T , Lang J , Bowden B , Baun W . J Law Med Ethics 2013 41 Suppl 2 40-5 This article explores how employers can be part of the solution to obesity by offering workplace wellness programs and facilitating opportunities for physical activity, access to healthier foods and beverages, and incentives for disease management and prevention to help prevent weight gain among their employees. |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 06, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure