Last data update: Sep 16, 2024. (Total: 47680 publications since 2009)
Records 1-30 (of 46 Records) |
Query Trace: Morse D [original query] |
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Influenza A(H5N1) virus infection in two dairy farm workers in Michigan
Morse J , Coyle J , Mikesell L , Stoddard B , Eckel S , Weinberg M , Kuo J , Riner D , Margulieux K , Stricklen J , Dover M , Kniss KL , Jang Y , Kirby MK , Frederick JC , Lacek KA , Davis CT , Uyeki TM , Lyon-Callo S , Bagdasarian N . N Engl J Med 2024 |
Comparative diagnostic utility of SARS-CoV-2 rapid antigen and molecular testing in a community setting
Kim AE , Bennett JC , Luiten K , O'Hanlon JA , Wolf CR , Magedson A , Han PD , Acker Z , Regelbrugge L , McCaffrey KM , Stone J , Reinhart D , Capodanno BJ , Morse SS , Bedford T , Englund JA , Boeckh M , Starita LM , Uyeki TM , Carone M , Weil A , Chu HY . J Infect Dis 2024 BACKGROUND: SARS-CoV-2 antigen-detection rapid diagnostic tests (Ag-RDTs) have become widely utilized but longitudinal characterization of their community-based performance remains incompletely understood. METHODS: This prospective longitudinal study at a large public university in Seattle, WA utilized remote enrollment, online surveys, and self-collected nasal swab specimens to evaluate Ag-RDT performance against real-time reverse transcription polymerase chain reaction (rRT-PCR) in the context of SARS-CoV-2 Omicron. Ag-RDT sensitivity and specificity within 1 day of rRT-PCR were evaluated by symptom status throughout the illness episode and Orf1b cycle threshold (Ct). RESULTS: From February to December 2022, 5,757 participants reported 17,572 Ag-RDT results and completed 12,674 rRT-PCR tests, of which 995 (7.9%) were rRT-PCR-positive. Overall sensitivity and specificity were 53.0% (95% CI: 49.6-56.4%) and 98.8% (98.5-99.0%), respectively. Sensitivity was comparatively higher for Ag-RDTs used 1 day after rRT-PCR (69.0%), 4 to 7 days post-symptom onset (70.1%), and Orf1b Ct ≤20 (82.7%). Serial Ag-RDT sensitivity increased with repeat testing ≥2 (68.5%) and ≥4 (75.8%) days after an initial Ag-RDT-negative result. CONCLUSION: Ag-RDT performance varied by clinical characteristics and temporal testing patterns. Our findings support recommendations for serial testing following an initial Ag-RDT-negative result, especially among recently symptomatic persons or those at high-risk for SARS-CoV-2 infection. |
Prevalence of symptoms 12 months after acute illness, by COVID-19 testing status among adults - United States, December 2020-March 2023
Montoy JCC , Ford J , Yu H , Gottlieb M , Morse D , Santangelo M , O'Laughlin KN , Schaeffer K , Logan P , Rising K , Hill MJ , Wisk LE , Salah W , Idris AH , Huebinger RM , Spatz ES , Rodriguez RM , Klabbers RE , Gatling K , Wang RC , Elmore JG , McDonald SA , Stephens KA , Weinstein RA , Venkatesh AK , Saydah S . MMWR Morb Mortal Wkly Rep 2023 72 (32) 859-865 To further the understanding of post-COVID conditions, and provide a more nuanced description of symptom progression, resolution, emergence, and reemergence after SARS-CoV-2 infection or COVID-like illness, analysts examined data from the Innovative Support for Patients with SARS-CoV-2 Infections Registry (INSPIRE), a prospective multicenter cohort study. This report includes analysis of data on self-reported symptoms collected from 1,296 adults with COVID-like illness who were tested for SARS-CoV-2 using a Food and Drug Administration-approved polymerase chain reaction or antigen test at the time of enrollment and reported symptoms at 3-month intervals for 12 months. Prevalence of any symptom decreased substantially between baseline and the 3-month follow-up, from 98.4% to 48.2% for persons who received a positive SARS-CoV-2 test results (COVID test-positive participants) and from 88.2% to 36.6% for persons who received negative SARS-CoV-2 test results (COVID test-negative participants). Persistent symptoms decreased through 12 months; no difference between the groups was observed at 12 months (prevalence among COVID test-positive and COVID test-negative participants = 18.3% and 16.1%, respectively; p>0.05). Both groups reported symptoms that emerged or reemerged at 6, 9, and 12 months. Thus, these symptoms are not unique to COVID-19 or to post-COVID conditions. Awareness that symptoms might persist for up to 12 months, and that many symptoms might emerge or reemerge in the year after COVID-like illness, can assist health care providers in understanding the clinical signs and symptoms associated with post-COVID-like conditions. |
Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan
Crawford MA , Lascols C , Lomonaco S , Timme RE , Fisher DJ , Anderson K , Hodge DR , Morse SA , Pillai SP , Sharma SK , Khan E , Allard MW , Hughes MA . Microbiol Resour Announc 2023 12 (9) e0016323 The continued emergence and spread of antimicrobial resistance among pathogenic bacteria are ever-growing threats to health and economy. Here, we report the draft genomes for 45 Enterobacterales clinical isolates, including historical and contemporary drug-resistant organisms, obtained in Pakistan between 1998 and 2016: 5 Serratia, 3 Salmonella, 3 Enterobacter, and 34 Klebsiella. |
Investigation of multidrug-resistant plasmids from carbapenemase-producing Klebsiella pneumoniae clinical isolates from Pakistan
Lascols C , Cherney B , Conley AB , Rishishwar L , Crawford MA , Morse SA , Fisher DJ , Anderson K , Hodge DR , Pillai SP , Hughes MA , Khan E , Sue D . Front Microbiol 2023 14 1192097 OBJECTIVES: The study aim was to investigate multidrug-resistant (MDR) plasmids from a collection of 10 carbapenemase-producing Klebsiella pneumoniae clinical isolates identified within the same healthcare institution in Pakistan. Full characterization of the MDR plasmids including structure, typing characteristics, and AMR content as well as determination of their plasmid-based antimicrobial susceptibility profiles were carried out. METHODS: Plasmids were isolated from 10 clinical isolates of Klebsiella pneumoniae, and from a corresponding set of Escherichia coli transconjugants, then sequenced using Nanopore/Illumina technology to generate plasmid hybrid assemblies. Full characterization of MDR plasmids, including determination of next generation sequencing (NGS)-based AMR profiles, plasmid incompatibility groups, and types, was carried out. The structure of MDR plasmids was analyzed using the Galileo AMR platform. For E. coli transconjugants, the NGS-based AMR profiles were compared to NGS-predicted AMR phenotypes and conventional broth microdilution (BMD) antimicrobial susceptibility testing (AST) results. RESULTS: All carbapenemase-producing K. pneumoniae isolates (carrying either bla(NDM-1), or/and bla(OXA-48)) carried multiple AMR plasmids encoding 34 antimicrobial resistance genes (ARGs) conferring resistance to antimicrobials from 6 different classes. The plasmid incompatibility groups and types identified were: IncC (types 1 and 3), IncFIA (type 26) IncFIB, IncFII (types K1, K2, K7, and K9), IncHI1B, and IncL. None of the bla(NDM-1) and bla(ESBL)-plasmids identified in this study were previously described. Most bla(NDM-1-)plasmids shared identical AMR regions suggesting potential genetic material/plasmid exchange between K. pneumoniae isolates of this collection. The majority of NGS-based AMR profiles from the E. coli transconjugants correlated well with both NGS-based predicted and conventional AST results. CONCLUSION: This study highlights the complexity and diversity of the plasmid-based genetic background of carbapenemase-producing clinical isolates from Pakistan. This study emphasizes the need for characterization of MDR plasmids to determine their complete molecular background and monitor AMR through plasmid transmission between multi-resistant bacterial pathogens. |
Application of multi-criteria decision analysis techniques and decision support framework for informing select agent designation for agricultural animal pathogens
Pillai SP , West T , Anderson K , Fruetel JA , McNeil C , Hernandez P , Ball C , Beck N , Morse SA . Front Bioeng Biotechnol 2023 11 1185743 The United States Department of Agriculture (USDA), Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents and toxins (Select Agent List) that potentially threaten agricultural health and safety, the procedures governing the transfer of those agents, and training requirements for entities working with them. Every 2 years the USDA DASAT reviews the Select Agent List, using subject matter experts (SMEs) to perform an assessment and rank the agents. To assist the USDA DASAT biennial review process, we explored the applicability of multi-criteria decision analysis (MCDA) techniques and a Decision Support Framework (DSF) in a logic tree format to identify pathogens for consideration as select agents, applying the approach broadly to include non-select agents to evaluate its robustness and generality. We conducted a literature review of 41 pathogens against 21 criteria for assessing agricultural threat, economic impact, and bioterrorism risk and documented the findings to support this assessment. The most prominent data gaps were those for aerosol stability and animal infectious dose by inhalation and ingestion routes. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for accuracy, particularly for pathogens with very few known cases, or where proxy data (e.g., from animal models or similar organisms) were used to address data gaps. The MCDA analysis supported the intuitive sense that select agents should rank high on the relative risk scale when considering agricultural health consequences of a bioterrorism attack. However, comparing select agents with non-select agents indicated that there was not a clean break in scores to suggest thresholds for designating select agents, requiring subject matter expertise collectively to establish which analytical results were in good agreement to support the intended purpose in designating select agents. The DSF utilized a logic tree approach to identify pathogens that are of sufficiently low concern that they can be ruled out from consideration as a select agent. In contrast to the MCDA approach, the DSF rules out a pathogen if it fails to meet even one criteria threshold. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making. |
Editorial: Biosafety and biosecurity approaches to counter SARS-CoV-2: From detection to best practices and risk assessment Volume 2
Pillai SP , Morse SA . Front Bioeng Biotechnol 2022 10 1118544 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is the causative agent of Coronavirus Disease-19, commonly referred to as COVID-19. SARS-CoV- 2 was discovered in 2019 and is currently responsible for a global pandemic that has resulted in more than 642.7 million cases and 6.625 million deaths worldwide as of 19 November 2022. However, there have been a large number of asymptomatic cases that have gone unreported, which likely results in an overestimation of the case fatality rate of 1.03%. It is also important to note that many deaths due to SARS-CoV-2 have gone unreported. |
The development and use of decision support framework for informing selection of select agent toxins with modelling studies to inform permissible toxin amounts
Pillai SP , West T , Levinson R , Fruetel JA , Anderson K , Edwards D , Morse SA . Front Bioeng Biotechnol 2022 10 1003127 Many countries have worked diligently to establish and implement policies and processes to regulate high consequence pathogens and toxins that could have a significant public health impact if misused. In the United States, the Antiterrorism and Effective Death Penalty Act of 1996 (Public Law 104-132, 1996), as amended by the Bioterrorism Preparedness and Response Act of 2002 (Public Law 107-188, 2002) requires that the Department of Health and Human Services (HHS) [through the Centers for Disease Control and Prevention (CDC)] establish a list of bacteria, viruses, and toxins that have the potential to pose a severe threat to public health and safety. Currently, this list is reviewed and updated on a biennial basis using input from subject matter experts (SMEs). We have developed decision support framework (DSF) approaches to facilitate selection of select toxins and, where toxicity data are known, conducted modelling studies to inform selection of toxin amounts that should be excluded from select agent regulations. Exclusion limits allow laboratories to possess toxins under an established limit to support their research or teaching activities without the requirement to register with the Federal Select Agent Program. Fact sheets capturing data from a previously vetted SME workshop convened by CDC, literature review and SME input were developed to assist in evaluating toxins using the DSF approach. The output of the DSF analysis agrees with the current select toxin designations, and no other toxins evaluated in this study were recommended for inclusion on the select agent and toxin list. To inform the selection of exclusion limits, attack scenarios were developed to estimate the amount of toxin needed to impact public health. Scenarios consisted of simulated aerosol releases of a toxin in high-population-density public facilities and the introduction of a toxin into a daily consumable product supply chain. Using published inhalation and ingestion median toxic dose (TD(50)) and median lethal dose (LD(50)) values, where available, a range of toxin amounts was examined to estimate the number of people exposed to these amounts in these scenarios. Based on data generated by these models, we proposed toxin exclusion values corresponding to levels below those that would trigger a significant public health response (i.e., amounts estimated to expose up to ten people by inhalation or one hundred people by ingestion to LD(50) or TD(50) levels of toxin in the modeled scenarios). |
Manipulation of menthol and nicotine content in cigarettes: Effects on smoking behavior and toxicant exposure in women menthol smokers
Oncken C , Litt MD , Thurlow S , Mead-Morse EL , Wang L , Hatsukami DK . Nicotine Tob Res 2022 25 (4) 665-673 BACKGROUND: The purpose of this study was to determine the effects on smoking and other outcomes of assigning cigarettes with reduced nicotine and/or no menthol to female menthol smokers. METHODS: Non-treatment seeking female menthol smokers (N=263) participated in a randomized controlled trial in which levels of menthol and nicotine in cigarettes were manipulated using experimental cigarettes. After a baseline period, participants were assigned to the following conditions for 6 weeks: 1) their own brand of cigarette (conventional nicotine with menthol); 2) a conventional nicotine cigarette with no menthol; 3) a cigarette with reduced nicotine (RNC) with menthol; or 4) a RNC cigarette and no menthol. Participants then returned to using their own brand and were followed for another 6 weeks. Outcomes included cigarettes smoked, biomarkers of exposure, and dependence measures. RESULTS: Results indicated that, after an initial increase, rates of smoking of all three experimental cigarettes were at or below baseline rates of smoking of one's own brand. Levels of biomarkers also decreased during the experimental phase, but rebounded somewhat after participants resumed smoking their own brand. There was evidence that overall amount of smoking decreased similarly among women switched to non-menthol and/or RNC cigarettes. CONCLUSIONS: These results suggest that no detrimental effect will occur in nicotine or toxicant exposure levels with a ban on characterizing menthol and/or a product standard on nicotine content in cigarettes. IMPLICATIONS: The implication of this work is that there would be no risk to women menthol smokers associated with regulations restricting nicotine and eliminating menthol in cigarettes. |
Community outbreak of legionellosis associated with an indoor hot tub, New Hampshire, 2018
Daly ER , Talbot EA , Smith JC , Ritter T , McCormic ZD , Fay K , Raphael BH , Kozak-Muiznieks NA , Levinson KJ , Bean CL , Wilson RT , Morse D , Scacheri A , Linxweiler J , Chan BP . J Environ Health 2022 84 (10) 16-25 Legionellosis is an infection acquired through inhalation of aerosolized water droplets containing Legionella bacteria. In August 2018, public health officials in New Hampshire launched an investigation into a legionellosis outbreak. They identified 49 illnesses likely associated with the outbreak and implicated an improperly maintained hot tub at a hotel. The same strain of Legionella pneumophila serogroup 1 was found in both the hot tub and in samples from two patients with Legionnaires disease. The indoor hot tub vented to the outdoors, which is how some patients with confirmed legionellosis likely acquired the infection despite not entering the hotel during the incubation period. This outbreak is notable for 1) likely illness acquisition through the exterior vent of the hot tub room and 2) use of whole genome sequencing to link environmental and patient specimens. Collaboration among public health and environmental officials, laboratorians, and building managers was essential to determining the source of the outbreak and preventing further illness. 2022, National Environmental Health Association. All rights reserved. |
Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab.
Solomon IH , Ganesh VS , Yu G , Deng XD , Wilson MR , Miller S , Milligan TA , Mukerji SS , Mathewson A , Linxweiler J , Morse D , Ritter JM , Staples JE , Hughes H , Gould CV , Sabeti PC , Chiu CY , Piantadosi A . Emerg Infect Dis 2021 27 (1) 238-42 A 56-year-old man receiving rituximab who had months of neurologic symptoms was found to have Jamestown Canyon virus in cerebrospinal fluid by clinical metagenomic sequencing. The patient died, and postmortem examination revealed extensive neuropathologic abnormalities. Deep sequencing enabled detailed characterization of viral genomes from the cerebrospinal fluid, cerebellum, and cerebral cortex. |
Patterns of tobacco use and nicotine dependence among youth, United States, 2017-2018
Gomez Y , Creamer M , Trivers KF , Anic G , Morse AL , Reissig C , Agaku I . Prev Med 2020 141 106284 This study examined patterns of tobacco product use and its influence on nicotine dependence among U.S. youth. Combined data from the 2017-2018 National Youth Tobacco Surveys were analyzed for students that reported current (past-30-day) use of e-cigarettes, cigarettes, cigars, smokeless tobacco, or hookah (n = 6106). Analyses assessed multiple product use (≥2 tobacco products) overall and by sex, school level, race/ethnicity, current use, and frequent use (use of a product for ≥20 of the preceding 30 days). Multivariable logistic regression was used to identify correlates of nicotine dependence. During 2017-2018, 40.8% of tobacco product users reported use of multiple products. Multiple product use ranged from 47.0% among e-cigarette users to 80.7% among cigarette users. Among frequent users of each respective product, 80.0% of cigarette smokers, 74.9% of cigar smokers, 73.6% of smokeless tobacco users, 70.7% of hookah smokers, and 40.3% of e-cigarette users reported use of multiple products. Most youth who reported nicotine dependence (64.0%) were multiple product users. E-cigarettes were the most common single product used (36.3%) and the product most commonly used in combination with other products; ecigarettes plus cigarettes (6.7%) was the most common product combination. Combustible product use, smokeless tobacco use, multiple product use and frequent use were associated with greater odds of nicotine dependence. Nicotine dependence among youth is especially influenced by cigarette use, smokeless tobacco use, frequent use of any tobacco product, and multiple product use. Proven tobacco control interventions in coordination with regulatory efforts can reduce youth tobacco product use. |
Comprehensive laboratory evaluation of a specific lateral flow assay for the presumptive identification of Francisella tularensis in suspicious white powders and aerosol samples
Pillai SP , DePalma L , Prentice KW , Ramage JG , Chapman C , Sarwar J , Parameswaran N , Petersen J , Yockey B , Young J , Singh A , Pillai CA , Manickam G , Thirunavkkarasu N , Avila JR , Sharma S , Morse SA , Venkateswaran K , Anderson K , Hodge DR . Health Secur 2020 18 (2) 83-95 We conducted a comprehensive, multi-phase laboratory evaluation of the Tularemia BioThreat Alert(®) (BTA) test, a lateral flow assay (LFA) for the rapid detection of Francisella tularensis. The study, conducted at 2 sites, evaluated the limit of detection (LOD) of this assay using the virulent SchuS4 strain and the avirulent LVS strain of F. tularensis. In 6-phase evaluation (linear dynamic range and reproducibility, inclusivity, near-neighbor, environmental background, white powder, and environmental filter extract), 13 diverse strains of F. tularensis, 8 Francisella near neighbors, 61 environmental background organisms, 26 white powders, and a pooled aerosol extract were tested. In the 937 tests performed, the Tularemia BTA demonstrated an LOD of 10(7) to 10(8) cfu/mL, with a sensitivity of 100.00%, specificity of 98.08%, and accuracy of 98.84%. These performance data are important for accurate interpretation of qualitative results arising from screening suspicious white powders in the field. |
Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Acinetobacter baumannii Isolated from Clinical Samples in Pakistan.
Lomonaco S , Crawford MA , Lascols C , Fisher DJ , Anderson K , Hodge DR , Pillai SP , Morse SA , Khan E , Hughes MA , Allard MW , Sharma SK . Microbiol Resour Announc 2020 9 (20) Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan. |
Comprehensive laboratory evaluation of a lateral flow assay for the detection of Yersinia pestis
Prentice KW , DePalma L , Ramage JG , Sarwar J , Parameswaran N , Petersen J , Yockey B , Young J , Joshi M , Thirunavvukarasu N , Singh A , Chapman C , Avila JR , Pillai CA , Manickam G , Sharma SK , Morse SA , Venkateswaran KV , Anderson K , Hodge DR , Pillai SP . Health Secur 2019 17 (6) 439-453 We conducted a comprehensive, multiphase laboratory evaluation of the Plague BioThreat Alert((R)) (BTA) test, a lateral flow immunoassay (LFA), for the rapid detection of Yersinia pestis. The study was conducted in 7 phases at 2 sites to assess the performance of the LFA. The limit of detection (LOD) was determined using both a virulent and avirulent strain of Y. pestis, CO99-3015 (10(5) CFU/ml) and A1122 (10(4) CFU/ml), respectively. In the other phases, 18 Y. pestis strains, 20 phylogenetic near-neighbor strains, 61 environmental background microorganisms, 26 white powders, and a pooled aerosol sample were also tested. A total of 1,110 LFA test results were obtained, and their analysis indicates that this LFA had a sensitivity of 97.65% and specificity of 96.57%. These performance data are important for accurate interpretation of qualitative results arising from testing suspicious white powders and aerosol samples in the field. Any positive specimen in this assay is considered presumptive positive and should be referred to the Centers for Disease Control and Prevention Laboratory Response Network for additional testing, confirmation, and characterization for an appropriate public health response. |
Rapid presumptive identification of Bacillus anthracis Isolates using the Tetracore RedLine Alert Test
Pillai SP , Prentice KW , Ramage JG , DePalma L , Sarwar J , Parameswaran N , Bell M , Plummer A , Santos A , Singh A , Pillai CA , Thirunavvukarasu N , Manickam G , Avila JR , Sharma SK , Hoffmaster A , Anderson K , Morse SA , Venkateswaran KV , Hodge DR . Health Secur 2019 17 (4) 334-343 A comprehensive laboratory evaluation of the Tetracore RedLine Alert test, a lateral flow immunoassay (LFA) for the rapid presumptive identification of Bacillus anthracis, was conducted at 2 different test sites. The study evaluated the sensitivity of this assay using 16 diverse strains of B. anthracis grown on sheep blood agar (SBA) plates. In addition, 83 clinically relevant microorganisms were tested to assess the specificity of the RedLine Alert test. The results indicated that the RedLine Alert test for the presumptive identification of B. anthracis is highly robust, specific, and sensitive. RedLine Alert is a rapid test that has applicability for use in a clinical setting for ruling-in or ruling-out nonhemolytic colonies of Bacillus spp. grown on SBA medium as presumptive isolates of B. anthracis. |
Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.
Lomonaco S , Lascols C , Crawford MA , Anderson K , Hodge DR , Fisher DJ , Pillai SP , Morse SA , Khan E , Hughes MA , Allard MW , Sharma SK . Microbiol Resour Announc 2019 8 (30) Shigella spp. are the most common cause of dysentery in developing countries and the second leading cause of diarrheal deaths worldwide. Multidrug-resistant (MDR) Shigella spp. are a serious threat to global health. Herein, we report draft genome sequences for three MDR Shigella isolates from Pakistan, two Shigella flexneri isolates and one Shigella sonnei isolate. |
Perspective on improving environmental monitoring of biothreats
Dunbar J , Pillai S , Wunschel D , Dickens M , Morse SA , Franz D , Bartko A , Challacombe J , Persons T , Hughes MA , Blanke SR , Holland R , Hutchison J , Merkley ED , Campbell K , Branda CS , Sharma S , Lindler L , Anderson K , Hodge D . Front Bioeng Biotechnol 2018 6 147 For more than a decade, the United States has performed environmental monitoring by collecting and analyzing air samples for a handful of biological threat agents (BTAs) in order to detect a possible biological attack. This effort has faced numerous technical challenges including timeliness, sampling efficiency, sensitivity, specificity, and robustness. The cost of city-wide environmental monitoring using conventional technology has also been a challenge. A large group of scientists with expertise in bioterrorism defense met to assess the objectives and current efficacy of environmental monitoring and to identify operational and technological changes that could enhance its efficacy and cost-effectiveness, thus enhancing its value. The highest priority operational change that was identified was to abandon the current concept of city-wide environmental monitoring because the operational costs were too high and its value was compromised by low detection sensitivity and other environmental factors. Instead, it was suggested that the focus should primarily be on indoor monitoring and secondarily on special-event monitoring because objectives are tractable and these operational settings are aligned with likelihood and risk assessments. The highest priority technological change identified was the development of a reagent-less, real-time sensor that can identify a potential airborne release and trigger secondary tests of greater sensitivity and specificity for occasional samples of interest. This technological change could be transformative with the potential to greatly reduce operational costs and thereby create the opportunity to expand the scope and effectiveness of environmental monitoring. |
Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates.
Lomonaco S , Crawford MA , Lascols C , Timme RE , Anderson K , Hodge DR , Fisher DJ , Pillai SP , Morse SA , Khan E , Hughes MA , Allard MW , Sharma SK . PLoS One 2018 13 (6) e0198526 The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most beta-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health. |
Francisella tularensis: Understanding reported occupational exposures and laboratory methods used for the identification of Francisella tularensis
Morse S , Henkel R . Appl Biosaf 2018 23 (1) 11-18 Francisella tularensis, the causative agent of tularemia, is a HHS Tier 1 select agent. Tularemia is the most commonly reported human and animal infection caused by a bacterial select agent in the United States. Because of the rarity of disease, low clinical suspicion, and the organism’s low infectious dose, F. tularensis poses a hazard for unsuspecting laboratorians, particularly those who handle cultures outside a biological safety cabinet or without use of appropriate personal protective equipment (PPE). We examined Form 4s and Form 3s submitted to the Federal Select Agent Program between 2011 and 2015 to assess laboratory methods used in the identification of F. tularensis and categorize reported occupational exposures. Culture, which is used in a confirmatory identification, was the primary method used in clinical laboratories. Reported occupational exposures in clinical, veterinary, and reference laboratories occurred at a rate of 33.8, 14.0, and 0.4/100 isolates, respectively. The number of exposed workers in clinical, reference, veterinary, and research laboratories was 3.2, 2.4, 5.1, and 0.9 workers per reported incident, respectively. Most reported occupational exposures occurred in clinical laboratorians working on the bench at BSL-2 conditions with isolated cultures with no suspicion that the organism was F. tularensis; the fewest occurred in research laboratories at BSL-3 where occupational exposures were prevented by prior knowledge that the organism was F. tularensis and the PPE that was used in these laboratories. |
AOAC SMPR 2016.010: Standard Method Performance Requirements (SMPRs) for DNA-based methods of detecting Burkholderia pseudomallei in field-deployable, Department of Defense aerosol collection devices
Gee J , Arce J , Beck LC , Blank TR , Blyn L , Cahall R , Clark AJ , Currie B , Damer K , Davenport M , DeShazer D , Johns M , Keim PS , Kiss K , Lesho M , Lin N , Morse SA , Naraghi-Arani P , Ozanich R , Roberto F , Rozak D , Sahl J , Schaefer F , Schutzer S , Schweizer HP , Sozhamannan S , Tuanyok A , Coates S . J AOAC Int 2017 100 (1) 261-265 Intended Use: Field-deployed use for analysis of | aerosol collection filters and/or liquids | 1 Applicability | Detection of Burkholderia pseudomallei in collection buffers | from aerosol collection devices. Field-deployable assays are | preferred. | 2 Analytical Technique | Molecular detection of nucleic acid. | 3 Definitions | Acceptable minimum detection level (AMDL).— | Predetermined minimum level of an analyte, as specified by | an expert committee which must be detected by the candidate | method at a specified probability of detection (POD). | Exclusivity.—Study involving pure nontarget strains, which | are potentially cross-reactive, that shall not be detected or | enumerated by the candidate method. | Inclusivity.—Study involving pure target strains that shall be | detected or enumerated by the candidate method. | Maximum time-to-result.—Maximum time to complete an | analysis starting from the collection buffer to assay result. | Probability of detection (POD).—Proportion of positive | analytical outcomes for a qualitative method for a given matrix | at a specified analyte level or concentration with a ≥0.95 | confidence interval. | System false-negative rate.—Proportion of test results that | are negative contained within a population of known positives. | System false-positive rate.—Proportion of test results that are | positive contained within a population of known negatives. | 4 Method Performance Requirements | See Table 1. | 5 System Suitability Tests and/or Analytical Quality Control | The controls listed in Table 2 shall be embedded in assays as | appropriate. Manufacturer must provide written justification if | controls are not embedded in the assay. |
Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.
Crawford MA , Timme R , Lomonaco S , Lascols C , Fisher DJ , Sharma SK , Strain E , Allard MW , Brown EW , McFarland MA , Croley T , Hammack TS , Weigel LM , Anderson K , Hodge DR , Pillai SP , Morse SA , Khan E , Hughes MA . Genome Announc 2016 4 (6) The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella pneumoniae represent a critical threat to global health. Here, we report the complete genome sequences of 10 MDR, colistin-susceptible and -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and 2013. |
Comprehensive laboratory evaluation of a highly specific lateral flow assay for the presumptive identification of Bacillus anthracis spores in suspicious white powders and environmental samples
Ramage JG , Prentice KW , DePalma L , Venkateswaran KS , Chivukula S , Chapman C , Bell M , Datta S , Singh A , Hoffmaster A , Sarwar J , Parameswaran N , Joshi M , Thirunavkkarasu N , Krishnan V , Morse S , Avila JR , Sharma S , Estacio PL , Stanker L , Hodge DR , Pillai SP . Health Secur 2016 14 (5) 351-65 We conducted a comprehensive, multiphase laboratory evaluation of the Anthrax BioThreat Alert((R)) test strip, a lateral flow immunoassay (LFA) for the rapid detection of Bacillus anthracis spores. The study, conducted at 2 sites, evaluated this assay for the detection of spores from the Ames and Sterne strains of B. anthracis, as well as those from an additional 22 strains. Phylogenetic near neighbors, environmental background organisms, white powders, and environmental samples were also tested. The Anthrax LFA demonstrated a limit of detection of about 10(6) spores/mL (ca. 1.5 x 10(5) spores/assay). In this study, overall sensitivity of the LFA was 99.3%, and the specificity was 98.6%. The results indicated that the specificity, sensitivity, limit of detection, dynamic range, and repeatability of the assay support its use in the field for the purpose of qualitatively evaluating suspicious white powders and environmental samples for the presumptive presence of B. anthracis spores. |
Culture-independent diagnostics for health security
Doggett NA , Mukundan H , Lefkowitz EJ , Slezak TR , Chain PS , Morse S , Anderson K , Hodge DR , Pillai S . Health Secur 2016 14 (3) 122-42 The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop. |
Evaluation of standardized sample collection, packaging, and decontamination procedures to assess cross-contamination potential during Bacillus anthracis incident response operations
Calfee MW , Tufts J , Meyer K , McConkey K , Mickelsen L , Rose L , Dowell C , Delaney L , Weber A , Morse S , Chaitram J , Gray M . J Occup Environ Hyg 2016 13 (12) 0 Sample collection procedures and primary receptacle (sample container and bag) decontamination methods should prevent contaminant transfer between contaminated and non-contaminated surfaces and areas during bio-incident operations. Cross-contamination of personnel, equipment, or sample containers may result in the exfiltration of biological agent from the exclusion (hot) zone and have unintended negative consequences on response resources, activities and outcomes. The current study was designed to 1) evaluate currently recommended sample collection and packaging procedures to identify procedural steps that may increase the likelihood of spore exfiltration or contaminant transfer, 2) evaluate the efficacy of currently recommended primary receptacle decontamination procedures, and 3) evaluate the efficacy of outer packaging decontamination methods. Wet- and dry-deposited fluorescent tracer powder was used in contaminant transfer tests to qualitatively evaluate the currently-recommended sample collection procedures. Bacillus atrophaeus spores, a surrogate for Bacillus anthracis, were used to evaluate the efficacy of spray- and wipe-based decontamination procedures. Both decontamination procedures were quantitatively evaluated on three types of sample packaging materials (corrugated fiberboard, polystyrene foam, and polyethylene plastic), and two contamination mechanisms (wet or dry inoculums). Contaminant transfer results suggested that size-appropriate gloves should be worn by personnel, templates should not be taped to or removed from surfaces, and primary receptacles should be selected carefully. The decontamination tests indicated that wipe-based decontamination procedures may be more effective than spray-based procedures; efficacy was not influenced by material type but was affected by the inoculation method. Incomplete surface decontamination was observed in all tests with dry inoculums. This study provides a foundation for optimizing current B. anthracis response procedures to minimize contaminant exfiltration. |
The association of health-related quality of life with severity of visual impairment among people aged 40-64 years: Findings from the 2006-2010 Behavioral Risk Factor Surveillance System
Crews JE , Chou CF , Zack MM , Zhang X , Bullard KM , Morse AR , Saaddine JB . Ophthalmic Epidemiol 2016 23 (3) 145-53 PURPOSE: To examine the association of health-related quality of life (HRQoL) with severity of visual impairment among people aged 40-64 years. METHODS: We used cross-sectional data from the 2006-2010 Behavioral Risk Factor Surveillance System to examine six measures of HRQoL: self-reported health, physically unhealthy days, mentally unhealthy days, activity limitation days, life satisfaction, and disability. Visual impairment was categorized as no, a little, or moderate/severe. We examined the association between visual impairment and HRQoL using logistic regression accounting for the survey's complex design. RESULTS: Overall, 23.0% of the participants reported a little difficult seeing, while 16.8% reported moderate/severe difficulty seeing. People aged 40-64 years with moderate/severe visual impairment had more frequent (≥14) physically unhealthy days, mentally unhealthy days, and activity limitation days in the last 30 days, as well as greater life dissatisfaction, greater disability, and poorer health compared to people reporting no or a little visual impairment. After controlling for covariates (age, sex, marital status, race/ethnicity, education, income, state, year, health insurance, heart disease, stroke, heart attack, body mass index, leisure-time activity, smoking, and medical care costs), and compared to people with no visual impairment, those with moderate/severe visual impairment were more likely to have fair/poor health (odds ratio, OR, 2.01, 95% confidence interval, CI, 1.82-2.23), life dissatisfaction (OR 2.06, 95% CI 1.80-2.35), disability (OR 1.95, 95% CI 1.80-2.13), and frequent physically unhealthy days (OR 1.69, 95% CI 1.52-1.88), mentally unhealthy days (OR 1.84, 95% CI 1.66-2.05), and activity limitation days (OR 1.94, 95% CI 1.71-2.20; all p < 0.0001). CONCLUSION: Poor HRQoL was strongly associated with moderate/severe visual impairment among people aged 40-64 years. |
Reportable Bacterial Infections among New York City-Born Infants, 2001-2009
Isaac BM , Masonbrink A , Kennedy J , Greene SK , Hennessy RR , Rosen JB , Trieu L , Ngai S , Morse SS , Weiss D . J Pediatr 2016 174 218-225.e4 OBJECTIVE: To determine rates of reportable bacterial infections among infants in New York City and identify populations at risk and preventable causes of morbidity. STUDY DESIGN: This retrospective cohort study matched live births in New York City from 2001-2009 to reported cases of bacterial infections among infants less than 1 year of age. Characteristics recorded on birth certificates were compared between infants with bacterial enteric infection, bacterial nonenteric infection, and no reportable bacterial infection. Multinomial logistic regression and multivariable logistic regression were used to identify risk factors for infection. RESULTS: Bacterial infection was reported in 4.6 cases per 1000 live births. Of 4524 infants with a reportable infection, the majority (2880, 63%) had an enteric infection. Asian/Pacific Islanders in Brooklyn were the borough-level race/ethnic group with the highest enteric infection rate (8.5 per 1000 live births). Citywide, infants with enteric infections were disproportionately male, from higher poverty neighborhoods, born to foreign-born mothers, and enrolled in Special Supplemental Food Program for Women, Infants, and Children or Medicaid. In contrast, infants with nonenteric infections were more likely to have low birthweight and mothers characterized by US birth and black race or white Hispanic race/ethnicity. CONCLUSIONS: Distinct patterns of risk factors for enteric and nonenteric bacterial infections among infants were identified. The results suggest that infants born to Asian/Pacific Islander mothers residing in Brooklyn should be a focus of enteric disease prevention. More research is necessary to better understand what behaviors increase the risk of enteric disease in this population. |
Pathogen security-help or hindrance?
Morse SA . Front Bioeng Biotechnol 2014 2 83 Events over the past 15 years have resulted in the promulgation of regulations in the United States to enhance biosecurity by restricting the access to pathogens and toxins (i.e., biological select agents and toxins [BSATs]), which pose a severe threat to human being, animal, or plant health or to animal or plant products, to qualified institutions, laboratories, and scientists. These regulations also reduce biosafety concerns by imposing specific requirements on laboratories working with BSATs. Furthermore, they provide a legal framework for prosecuting someone who possesses a BSAT illegally. With the implementation of these regulations has come discussion in the scientific community about the potential of these regulations to affect the cost of doing BSAT research, hamper research and international collaborations, or whether it would stop someone with a microbiological background from isolating many of the select agents from nature. |
Quantification of ricin, RCA and comparison of enzymatic activity in 18 Ricinus communis cultivars by isotope dilution mass spectrometry
Schieltz DM , McWilliams LG , Kuklenyik Z , Prezioso SM , Carter AJ , Williamson YM , McGrath SC , Morse SA , Barr JR . Toxicon 2015 95 72-83 The seeds of the Ricinus communis (Castor bean) plant are the source of the economically important commodity castor oil. Castor seeds also contain the proteins ricin and R. communis agglutinin (RCA), two toxic lectins that are hazardous to human health. Radial immunodiffusion (RID) and the enzyme linked immunosorbent assay (ELISA) are two antibody-based methods commonly used to quantify ricin and RCA; however, antibodies currently used in these methods cannot distinguish between ricin and RCA due to the high sequence homology of the respective proteins. In this study, a technique combining antibody-based affinity capture with liquid chromatography and multiple reaction monitoring (MRM) mass spectrometry (MS) was used to quantify the amounts of ricin and RCA independently in extracts prepared from the seeds of eighteen representative cultivars of R. communis which were propagated under identical conditions. Additionally, liquid chromatography and MRM-MS was used to determine rRNA N-glycosidase activity for each cultivar and the overall activity in these cultivars was compared to a purified ricin standard. Of the cultivars studied, the average ricin content was 9.3 mg/g, the average RCA content was 9.9 mg/g, and the enzymatic activity agreed with the activity of a purified ricin reference within 35% relative activity. |
Integrating active tuberculosis case finding in antenatal services in Zambia
Kancheya N , Luhanga D , Harris JB , Morse J , Kapata N , Bweupe M , Henostroza G , Reid SE . Int J Tuberc Lung Dis 2014 18 (12) 1466-72 SETTING: Three out-patient antenatal care (ANC) clinics in Lusaka, Zambia. OBJECTIVE: To estimate tuberculosis (TB) prevalence in human immunodeficiency virus (HIV) infected and symptomatic, non-HIV-infected pregnant women and explore the feasibility of routine TB screening in ANC settings. DESIGN: Peer educators administered TB symptom questionnaires to pregnant women attending their first ANC clinic visit. Presumptive TB patients were defined as all HIV-infected women and symptomatic non-HIV-infected women. Sputum samples were tested using smear microscopy and culture to estimate TB prevalence. RESULTS: All 5033 (100%) women invited to participate in the study agreed, and 17% reported one or more TB symptoms. Among 1152 presumed TB patients, 17 (1.5%) had previously undiagnosed culture-confirmed TB; 2 (12%) were smear-positive. Stratified by HIV status, TB prevalence was 10/664 (1.5%, 95%CI 0. 7-2.8) among HIV-infected women and 7/488 (1.4%, 95%CI 0.6-2.9) among symptomatic non-HIV-infected women. In HIV-infected women, the only symptom significantly associated with TB was productive cough; symptom screening was only 50% sensitive. CONCLUSION: There is a sizable burden of TB in pregnant women in Zambia, which may lead to adverse maternal and infant outcomes. TB screening in ANC settings in Zambia is acceptable and feasible. More sensitive diagnostics are needed. |
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