Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-30 (of 106 Records) |
Query Trace: Nicholas D[original query] |
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Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Njamkepo E , Fawal N , Tran-Dien A , Hawkey J , Strockbine N , Jenkins C , Talukder KA , Bercion R , Kuleshov K , Kolínská R , Russell JE , Kaftyreva L , Accou-Demartin M , Karas A , Vandenberg O , Mather AE , Mason CJ , Page AJ , Ramamurthy T , Bizet C , Gamian A , Carle I , Sow AG , Bouchier C , Wester AL , Lejay-Collin M , Fonkoua MC , Le Hello S , Blaser MJ , Jernberg C , Ruckly C , Mérens A , Page AL , Aslett M , Roggentin P , Fruth A , Denamur E , Venkatesan M , Bercovier H , Bodhidatta L , Chiou CS , Clermont D , Colonna B , Egorova S , Pazhani GP , Ezernitchi AV , Guigon G , Harris SR , Izumiya H , Korzeniowska-Kowal A , Lutyńska A , Gouali M , Grimont F , Langendorf C , Marejková M , Peterson LA , Perez-Perez G , Ngandjio A , Podkolzin A , Souche E , Makarova M , Shipulin GA , Ye C , Žemličková H , Herpay M , Grimont PA , Parkhill J , Sansonetti P , Holt KE , Brisse S , Thomson NR , Weill FX . Nat Microbiol 2016 1 16027 Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease. |
Nhumirim virus, a novel flavivirus isolated from mosquitoes from the Pantanal, Brazil.
Pauvolid-Corrêa A , Solberg O , Couto-Lima D , Kenney J , Serra-Freire N , Brault A , Nogueira R , Langevin S , Komar N . Arch Virol 2015 160 (1) 21-7 We describe the isolation of a novel flavivirus, isolated from a pool of mosquitoes identified as Culex (Culex) chidesteri collected in 2010 in the Pantanal region of west-central Brazil. The virus is herein designated Nhumirim virus (NHUV) after the name of the ranch from which the mosquito pool was collected. Flavivirus RNA was detected by real-time RT-PCR of homogenized mosquitoes and from the corresponding C6/36 culture supernatant. Based on full-genome sequencing, the virus isolate was genetically distinct from but most closely related to Barkedji virus (BJV), a newly described flavivirus from Senegal. Phylogenetic analysis demonstrated that NHUV grouped with mosquito-borne flaviviruses forming a clade with BJV. This clade may be genetically intermediate between the Culex-borne flaviviruses amplified by birds and the insect-only flaviviruses. |
Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study
Pneumonia Etiology Research for Child Health Study Group , O'Brien Katherine L , Levine Orin S , Knoll Maria Deloria , Feikin Daniel R , DeLuca Andrea N , Driscoll Amanda J , Fancourt Nicholas , Fu Wei , Haddix Meredith , Hammitt Laura L , Higdon Melissa M , Kagucia E Wangeci , Karron Ruth A , Li Mengying , Park Daniel E , Prosperi Christine , Shi Qiyuan , Wu Zhenke , Zeger Scott L , Watson Nora L , Crawley Jane , Murdoch David R , Brooks W Abdullah , Endtz Hubert P , Zaman Khalequ , Goswami Doli , Hossain Lokman , Jahan Yasmin , Chisti Mohammod Jobayer , Howie Stephen R C , Ebruke Bernard E , Antonio Martin , McLellan Jessica L , Machuka Eunice M , Shamsul Arifin , Zaman Syed M A , Mackenzie Grant , Scott J Anthony G , Awori Juliet O , Morpeth Susan C , Kamau Alice , Kazungu Sidi , Ominde Micah Silaba , Kotloff Karen L , Tapia Milagritos D , Sow Samba O , Sylla Mamadou , Tamboura Boubou , Onwuchekwa Uma , Kourouma Nana , Toure Aliou , Sissoko Seydou , Madhi Shabir A , Moore David P , Adrian Peter V , Baillie Vicky L , Kuwanda Locadiah , Mudau Azwifarwi , Groome Michelle J , Mahomed Nasreen , Simões Eric A F , Baggett Henry C , Thamthitiwat Somsak , Maloney Susan A , Bunthi Charatdao , Rhodes Julia , Sawatwong Pongpun , Akarasewi Pasakorn , Thea Donald M , Mwananyanda Lawrence , Chipeta James , Seidenberg Phil , Mwansa James , Somwe Somwe Wa , Kwenda Geoffrey , Anderson Trevor P , Mitchell Joanne L . Lancet 2019 394 (10200) 757-779 BACKGROUND: Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings. METHODS: We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1-59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data. FINDINGS: Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6-97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3-65·6) of causes, whereas bacteria accounted for 27·3% (23·3-31·6) and Mycobacterium tuberculosis for 5·9% (3·9-8·3). Viruses were less common (54·5%, 95% CrI 47·4-61·5 vs 68·0%, 62·7-72·7) and bacteria more common (33·7%, 27·2-40·8 vs 22·8%, 18·3-27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4-34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus-enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site's aetiological fraction. INTERPRETATION: In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes. FUNDING: Bill & Melinda Gates Foundation. |
Development of an empirically derived measure of food safety culture in restaurants
Kramer A , Hoover ER , Hedeen N , DiPrete L , Tuttle J , Irving DJ , Viveiros B , Nicholas D , Monroy JA , Moritz E , Brown L . J Food Prot 2023 86 (3) 100043 A poor food safety culture has been described as an emerging risk factor for foodborne illness outbreaks, yet there has been little research on this topic in the retail food industry. The purpose of this study was to identify and validate conceptual domains around food safety culture and develop an assessment tool that can be used to assess food workers' perceptions of their restaurant's food safety culture. The study, conducted from March 2018 through March 2019, surveyed restaurant food workers for their level of agreement with 28 statements. We received 579 responses from 331 restaurants spread across eight different health department jurisdictions. Factor analysis and structural equation modeling supported a model composed of four primary constructs. The highest rated construct was Resource Availability (x¯=4.69, sd=0.57), which assessed the availability of resources to maintain good hand hygiene. The second highest rated construct was Employee Commitment (x¯=4.49, sd=0.62), which assessed workers' perceptions of their coworkers' commitment to food safety. The last two constructs were related to management. Leadership (x¯=4.28, sd=0.69) assessed the existence of food safety policies, training, and information sharing. Management Commitment (x¯=3.94, sd=1.05) assessed whether food safety was a priority in practice. Finally, the model revealed one higher-order construct, Worker Beliefs about Food Safety Culture (x¯=4.35, sd=0.53). The findings from this study can support efforts by the restaurant industry, food safety researchers, and health departments to examine the influence and effects of food safety culture within restaurants. |
Incidence of chronic kidney disease among adults with diabetes, 2015-2020
Tuttle KR , Jones CR , Daratha KB , Koyama AK , Nicholas SB , Alicic RZ , Duru OK , Neumiller JJ , Norris KC , Ríos Burrows N , Pavkov ME . N Engl J Med 2022 387 (15) 1430-1431 The prevalence of kidney failure warranting dialysis or transplantation more than doubled between 2000 and 2019 to nearly 800,000 persons in the United States, with diabetes as the leading cause in 47% of those affected.1,2 The incidence of chronic kidney disease (CKD) among patients with diabetes is unknown, yet such data are vital for identifying high-risk populations, determining the effectiveness of interventions, and assessing the effects on health care delivery and public health responses. |
Multistate Outbreak of Listeria monocytogenes Infections Linked to Fresh, Soft Hispanic-Style Cheese - United States, 2021.
Palacios A , Otto M , Flaherty E , Boyle MM , Malec L , Holloman K , Low M , Wellman A , Newhart C , Gollarza L , Weeks T , Muyombwe A , Lozinak K , Kafka E , O'Halloran D , Rozza T , Nicholas D , Ivory S , Kreil K , Huffman J , Gieraltowski L , Conrad A . MMWR Morb Mortal Wkly Rep 2022 71 (21) 709-712 Listeriosis is a serious infection usually caused by eating food contaminated with the bacterium Listeria monocytogenes. An estimated 1,600 persons become ill with listeriosis each year, among whom approximately 260 die. Persons at higher risk for listeriosis include pregnant persons and their newborns, adults aged ≥65 years, and persons with weakened immune systems. Persons with invasive listeriosis usually report symptoms starting 1-4 weeks after eating food contaminated with L. monocytogenes; however, some persons who become infected have reported symptoms starting as late as 70 days after exposure or as early as the same day of exposure (1). On January 29, 2021, PulseNet, the national molecular subtyping surveillance network coordinated by CDC, identified a multistate cluster of three L. monocytogenes infections: two from Maryland and one from Connecticut (2). CDC, the Food and Drug Administration (FDA), and state and local partners began an investigation on February 1, 2021. A total of 13 outbreak-related cases were eventually identified from four states. All patients reported Hispanic ethnicity; 12 patients were hospitalized, and one died. Rapid food testing and record collection by regulatory agencies enabled investigators to identify a brand of queso fresco made with pasteurized milk as the likely source of the outbreak, leading to an initial product recall on February 19, 2021. Fresh, soft Hispanic-style cheeses made with pasteurized milk are a well-documented source of listeriosis outbreaks. These cheeses can be contaminated with L. monocytogenes unless stringent hygienic controls are implemented, and the processing environment is monitored for contamination (3). U.S. public health agencies should establish or improve communications, including new methods of disseminating information that also effectively reach Hispanic populations, to emphasize the risk from eating fresh, soft Hispanic-style cheeses, even those made with pasteurized milk. |
Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March-June 2020.
Lehnertz NB , Wang X , Garfin J , Taylor J , Zipprich J , VonBank B , Martin K , Eikmeier D , Medus C , Wiedinmyer B , Bernu C , Plumb M , Pung K , Honein MA , Carter R , MacCannell D , Smith KE , Como-Sabetti K , Ehresmann K , Danila R , Lynfield R . Emerg Infect Dis 2021 27 (8) 2052-2063 Coronavirus disease has disproportionately affected persons in congregate settings and high-density workplaces. To determine more about the transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings, we performed whole-genome sequencing and phylogenetic analysis on 319 (14.4%) samples from 2,222 SARS-CoV-2-positive persons associated with 8 outbreaks in Minnesota, USA, during March-June 2020. Sequencing indicated that virus spread in 3 long-term care facilities and 2 correctional facilities was associated with a single genetic sequence and that in a fourth long-term care facility, outbreak cases were associated with 2 distinct sequences. In contrast, cases associated with outbreaks in 2 meat-processing plants were associated with multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak. Early identification and cohorting (segregating) of virus-positive persons in these settings, along with continued vigilance with infection prevention and control measures, is imperative. |
Restaurant date-marking practices concerning ready-to-eat food requiring time and temperature control for safety
Brown LG , Ebrahim-Zadeh SD , Hoover ER , DiPrete L , Matis B , Viveiros B , Irving DJ , Copeland D , Nicholas D , Hedeen N , Tuttle J , Williams L , Liggans G , Kramer A . Foodborne Pathog Dis 2021 18 (11) 798-804 Certain foods are more vulnerable to foodborne pathogen growth and formation of toxins than others. Lack of time and temperature control for these foods can result in the growth of pathogens, such as Listeria monocytogenes, and lead to foodborne outbreaks. The Food and Drug Administration's (FDA) Food Code classifies these foods as time/temperature control for safety (TCS) foods and details safe cooking, holding, and storing temperatures for these foods. The FDA Food Code also includes a date-marking provision for ready-to-eat TCS foods that are held for >24 h. The provision states that these foods should not be held in refrigeration for >7 days and should be marked with the date or day by which the food should be "consumed on the premises, sold, or discarded." To learn more about restaurants' date-marking practices, the Centers for Disease Control and Prevention's Environmental Health Specialists Network (EHS-Net) conducted observations and manager interviews in 359 restaurants in 8 EHS-Net jurisdictions. Managers reported that they date marked ready-to-eat TCS foods more often than data collectors observed this practice (91% vs. 77%). Observation data showed almost a quarter of study restaurants did not date-mark ready-to-eat TCS foods. In addition, restaurants with an internal date-marking policy date marked 1.25 times more often than restaurants without such a policy and chain restaurants date marked 5.02 times more often than independently owned restaurants. These findings suggest that regulators and the retail food industry may improve food safety and lower the burden of foodborne illness in the United States if they target interventions to independent restaurants and encourage strong date-marking policies. |
Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios - United States, April-September 2021.
Borchering RK , Viboud C , Howerton E , Smith CP , Truelove S , Runge MC , Reich NG , Contamin L , Levander J , Salerno J , van Panhuis W , Kinsey M , Tallaksen K , Obrecht RF , Asher L , Costello C , Kelbaugh M , Wilson S , Shin L , Gallagher ME , Mullany LC , Rainwater-Lovett K , Lemaitre JC , Dent J , Grantz KH , Kaminsky J , Lauer SA , Lee EC , Meredith HR , Perez-Saez J , Keegan LT , Karlen D , Chinazzi M , Davis JT , Mu K , Xiong X , Pastore YPiontti A , Vespignani A , Srivastava A , Porebski P , Venkatramanan S , Adiga A , Lewis B , Klahn B , Outten J , Schlitt J , Corbett P , Telionis PA , Wang L , Peddireddy AS , Hurt B , Chen J , Vullikanti A , Marathe M , Healy JM , Slayton RB , Biggerstaff M , Johansson MA , Shea K , Lessler J . MMWR Morb Mortal Wkly Rep 2021 70 (19) 719-724 After a period of rapidly declining U.S. COVID-19 incidence during January-March 2021, increases occurred in several jurisdictions (1,2) despite the rapid rollout of a large-scale vaccination program. This increase coincided with the spread of more transmissible variants of SARS-CoV-2, the virus that causes COVID-19, including B.1.1.7 (1,3) and relaxation of COVID-19 prevention strategies such as those for businesses, large-scale gatherings, and educational activities. To provide long-term projections of potential trends in COVID-19 cases, hospitalizations, and deaths, COVID-19 Scenario Modeling Hub teams used a multiple-model approach comprising six models to assess the potential course of COVID-19 in the United States across four scenarios with different vaccination coverage rates and effectiveness estimates and strength and implementation of nonpharmaceutical interventions (NPIs) (public health policies, such as physical distancing and masking) over a 6-month period (April-September 2021) using data available through March 27, 2021 (4). Among the four scenarios, an accelerated decline in NPI adherence (which encapsulates NPI mandates and population behavior) was shown to undermine vaccination-related gains over the subsequent 2-3 months and, in combination with increased transmissibility of new variants, could lead to surges in cases, hospitalizations, and deaths. A sharp decline in cases was projected by July 2021, with a faster decline in the high-vaccination scenarios. High vaccination rates and compliance with public health prevention measures are essential to control the COVID-19 pandemic and to prevent surges in hospitalizations and deaths in the coming months. |
Interim Estimates of Vaccine Effectiveness of Pfizer-BioNTech and Moderna COVID-19 Vaccines Among Health Care Personnel - 33 U.S. Sites, January-March 2021.
Pilishvili T , Fleming-Dutra KE , Farrar JL , Gierke R , Mohr NM , Talan DA , Krishnadasan A , Harland KK , Smithline HA , Hou PC , Lee LC , Lim SC , Moran GJ , Krebs E , Steele M , Beiser DG , Faine B , Haran JP , Nandi U , Schrading WA , Chinnock B , Henning DJ , LoVecchio F , Nadle J , Barter D , Brackney M , Britton A , Marceaux-Galli K , Lim S , Phipps EC , Dumyati G , Pierce R , Markus TM , Anderson DJ , Debes AK , Lin M , Mayer J , Babcock HM , Safdar N , Fischer M , Singleton R , Chea N , Magill SS , Verani J , Schrag S . MMWR Morb Mortal Wkly Rep 2021 70 (20) 753-758 Throughout the COVID-19 pandemic, health care personnel (HCP) have been at high risk for exposure to SARS-CoV-2, the virus that causes COVID-19, through patient interactions and community exposure (1). The Advisory Committee on Immunization Practices recommended prioritization of HCP for COVID-19 vaccination to maintain provision of critical services and reduce spread of infection in health care settings (2). Early distribution of two mRNA COVID-19 vaccines (Pfizer-BioNTech and Moderna) to HCP allowed assessment of the effectiveness of these vaccines in a real-world setting. A test-negative case-control study is underway to evaluate mRNA COVID-19 vaccine effectiveness (VE) against symptomatic illness among HCP at 33 U.S. sites across 25 U.S. states. Interim analyses indicated that the VE of a single dose (measured 14 days after the first dose through 6 days after the second dose) was 82% (95% confidence interval [CI] = 74%-87%), adjusted for age, race/ethnicity, and underlying medical conditions. The adjusted VE of 2 doses (measured ≥7 days after the second dose) was 94% (95% CI = 87%-97%). VE of partial (1-dose) and complete (2-dose) vaccination in this population is comparable to that reported from clinical trials and recent observational studies, supporting the effectiveness of mRNA COVID-19 vaccines against symptomatic disease in adults, with strong 2-dose protection. |
Evaluating the Presence of Replication-Competent SARS-CoV-2 from Nursing Home Residents with Persistently Positive RT-PCR Results.
Lutgring JD , Tobolowsky FA , Hatfield KM , Lehnertz NB , Sullivan MM , Martin KG , Keaton A , Sexton DJ , Tamin A , Harcourt JL , Thornburg NJ , Reddy SC , Jernigan JA . Clin Infect Dis 2021 74 (3) 525-528 Replication-competent virus has not been detected in individuals with mild to moderate COVID-19 more than 10 days after symptom onset. It is unknown whether these findings apply to nursing home residents. Of 273 specimens collected from nursing home residents >10 days from the initial positive test, none were culture positive. |
Theoretical framework for retrospective studies of the effectiveness of SARS-CoV-2 vaccines.
Lewnard JA , Patel MM , Jewell NP , Verani JR , Kobayashi M , Tenforde MW , Dean NE , Cowling BJ , Lopman BA . Epidemiology 2021 32 (4) 508-517 Observational studies of the effectiveness of vaccines to prevent COVID-19 are needed to inform real-world use. Such studies are now underway amid the ongoing rollout of SARS-CoV-2 vaccines globally. Although traditional case-control and test-negative design studies feature prominently among strategies used to assess vaccine effectiveness, such studies may encounter important threats to validity. Here, we review the theoretical basis for estimation of vaccine direct effects under traditional case-control and test-negative design frameworks, addressing specific natural history parameters of SARS-CoV-2 infection and COVID-19 relevant to these designs. Bias may be introduced by misclassification of cases and controls, particularly when clinical case criteria include common, nonspecific indicators of COVID-19. When using diagnostic assays with high analytical sensitivity for SARS-CoV-2 detection, individuals testing positive may be counted as cases even if their symptoms are due to other causes. The traditional case-control design may be particularly prone to confounding due to associations of vaccination with healthcare-seeking behavior or risk of infection. The test-negative design reduces but may not eliminate this confounding, for instance, if individuals who receive vaccination seek care or testing for less-severe illness. These circumstances indicate the two study designs cannot be applied naively to datasets gathered through public health surveillance or administrative sources. We suggest practical strategies to reduce bias in vaccine effectiveness estimates at the study design and analysis stages. |
Symptoms of Anxiety, Burnout, and PTSD and the Mitigation Effect of Serologic Testing in Emergency Department Personnel During the COVID-19 Pandemic.
Rodriguez RM , Montoy JCC , Hoth KF , Talan DA , Harland KK , Eyck PT , Mower W , Krishnadasan A , Santibanez S , Mohr N . Ann Emerg Med 2021 78 (1) 35-43 e2 STUDY OBJECTIVE: Among a comprehensive range of frontline emergency department health care personnel, we assessed symptoms of anxiety and burnout, specific coronavirus disease 2019 (COVID-19) work-related stressors, and risk for post-traumatic stress disorder (PTSD). We also determined whether COVID-19 serologic testing of HCP decreased their self-reported anxiety. METHODS: In a prospective cohort study from May 13, 2020, to July 8, 2020, we used electronic surveys to capture participant self-reported symptoms before and after serologic testing for anti-SARS-CoV-2 immunoglobulin G antibodies. Participants were physicians, nurses, advanced practice providers, and nonclinical ED personnel at 20 geographically diverse United States EDs. We evaluated these domains: 1) the effects of the COVID-19 pandemic on overall stress and anxiety; 2) COVID-19-related work stressors; 3) burnout; and 4) PTSD risk (measured using the Primary Care-PTSD Screen for DSM-5, a 5-item screening instrument in which a score of ≥3 signifies high risk for PTSD). We also assessed perceptions of whether results of COVID-19 antibody testing decreased participants' self-reported anxiety. RESULTS: Of 1,606 participants, 100% and 88% responded to the baseline and follow-up surveys, respectively. At baseline, approximately half (46%) reported symptoms of emotional exhaustion and burnout from their work, and 308 (19.2%, 95% confidence interval [CI] 17.3% to 21.1%) respondents screened positive for increased PTSD risk. Female respondents were more likely than males to screen positive (odds ratio [OR] 2.03, 95% CI 1.49 to 2.78). Common concerns included exposing their family and the health of coworkers diagnosed with COVID-19. After receiving antibody test results, 54% (95% CI 51.8 to 56.7) somewhat agreed, agreed, or strongly agreed that knowledge of their immune status had decreased their anxiety. A positive serology result indicating prior SARS-CoV-2 infection was associated with a higher likelihood of reporting decreased anxiety (2.83, 95% CI 1.37 to 5.83). CONCLUSION: Symptoms of anxiety and burnout were prevalent across the spectrum of ED staff during the COVID-19 pandemic. One-fifth of ED personnel appeared to be at risk for PTSD. Increased provision of serologic testing may help to mitigate anxiety. |
A Comprehensive Approach to Ending an Outbreak of Rare bla OXA-72 gene-positive Carbapenem-resistant Acinetobacter baumannii at a Community Hospital, Kansas City, MO, 2018
McKinsey DS , Gasser C , McKinsey JP , Ditto G , Agard A , Zellmer B , Poteete C , Vagnone PS , Dale JL , Bos J , Hahn R , Turabelidze G , Poiry M , Franklin P , Vlachos N , McAllister GA , Halpin AL , Glowicz J , Ham DC , Epstein L . Am J Infect Control 2021 49 (9) 1183-1185 We identified a cluster of extensively drug-resistant, carbapenemase gene-positive, carbapenem-resistant Acinetobacter baumannii (CP-CRAB) at a teaching hospital in Kansas City. Extensively drug-resistant CRAB was identified from eight patients and 3% of environmental cultures. We used patient cohorting and targeted environmental disinfection to stop transmission. After implementation of these measures, no additional cases were identified. |
Diagnosed and Undiagnosed COVID-19 in US Emergency Department Health Care Personnel: A Cross-sectional Analysis.
Mohr NM , Harland KK , Krishnadasan A , Eyck PT , Mower WR , Willey J , Chisolm-Straker M , Lim SC , McDonald LC , Kutty PK , Hesse E , Santibanez S , Talan DA . Ann Emerg Med 2020 78 (1) 27-34 STUDY OBJECTIVE: We determine the percentage of diagnosed and undiagnosed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among a sample of US emergency department (ED) health care personnel before July 2020. METHODS: This was a cross-sectional analysis of ED health care personnel in 20 geographically diverse university-affiliated EDs from May 13, to July 8, 2020, including case counts of prior laboratory-confirmed coronavirus disease 2019 (COVID-19) diagnoses among all ED health care personnel, and then point-in-time serology (with confirmatory testing) and reverse transcriptase-polymerase chain reaction testing in a sample of volunteers without a previous COVID-19 diagnosis. Health care staff were categorized as clinical (physicians, advanced practice providers, and nurses) and nonclinical (clerks, social workers, and case managers). Previously undiagnosed infection was based on positive SARS-CoV-2 serology or reverse transcriptase-polymerase chain reaction result among health care personnel without prior diagnosis. RESULTS: Diagnosed COVID-19 occurred in 2.8% of health care personnel (193/6,788), and the prevalence was similar for nonclinical and clinical staff (3.8% versus 2.7%; odds ratio 1.5; 95% confidence interval 0.7 to 3.2). Among 1,606 health care personnel without previously diagnosed COVID-19, 29 (1.8%) had evidence of current or past SARS-CoV-2 infection. Most (62%; 18/29) who were seropositive did not think they had been infected, 76% (19/25) recalled COVID-19-compatible symptoms, and 89% (17/19) continued to work while symptomatic. Accounting for both diagnosed and undiagnosed infections, 4.6% (95% confidence interval 2.8% to 7.5%) of ED health care personnel were estimated to have been infected with SARS-CoV-2, with 38% of those infections undiagnosed. CONCLUSION: In late spring and early summer 2020, the estimated prevalence of severe acute respiratory syndrome coronavirus 2 infection was 4.6%, and greater than one third of infections were undiagnosed. Undiagnosed SARS-CoV-2 infection may pose substantial risk for transmission to other staff and patients. |
Establishment of Isolation and Noncongregate Hotels During COVID-19 and Symptom Evolution Among People Experiencing Homelessness-Atlanta, Georgia, 2020.
Montgomery MP , Paulin HN , Morris A , Cotton A , Speers A , Boyd AT , Buff AM , Mathews D , Wells A , Marchman C , Gaffga N , Bamrah Morris S , Cavanaugh SS . J Public Health Manag Pract 2021 27 (3) 285-294 CONTEXT: Local agencies across the United States have identified public health isolation sites for individuals with coronavirus disease 2019 (COVID-19) who are not able to isolate in residence. PROGRAM: We describe logistics of establishing and operating isolation and noncongregate hotels for COVID-19 mitigation and use the isolation hotel as an opportunity to understand COVID-19 symptom evolution among people experiencing homelessness (PEH). IMPLEMENTATION: Multiple agencies in Atlanta, Georgia, established an isolation hotel for PEH with COVID-19 and noncongregate hotel for PEH without COVID-19 but at risk of severe illness. PEH were referred to the isolation hotel through proactive, community-based testing and hospital-based testing. Daily symptoms were recorded prospectively. Disposition location was recorded for all clients. EVALUATION: During April 10 to September 1, 2020, 181 isolation hotel clients (77 community referrals; 104 hospital referrals) were admitted a median 3 days after testing. Overall, 32% of community referrals and 7% of hospital referrals became symptomatic after testing positive; 83% of isolation hotel clients reported symptoms at some point; 93% completed isolation. Among 302 noncongregate hotel clients, median stay was 18 weeks; 61% were discharged to permanent housing or had a permanent housing discharge plan. DISCUSSION: Overall, a high proportion of PEH completed isolation at the hotel, suggesting a high level of acceptability. Many PEH with COVID-19 diagnosed in the community developed symptoms after testing, indicating that proactive, community-based testing can facilitate early isolation. Noncongregate hotels can be a useful COVID-19 community mitigation strategy by bridging PEH at risk of severe illness to permanent housing. |
Ability of whole-genome sequencing to refine a salmonella i 4,[5],12:I:-cluster in New York state and detect a multistate outbreak linked to raw poultry
Huth P , Wirth SE , Baker D , Nicholas DC , Douris A , Freiman J , Kline KE , Devinney K , Glsker S , Schwensohn C . Food Prot Trends 2021 41 (2) 239-245 Whole-genome sequencing (WGS) has proven to be a more powerful tool than pulsed-field gel electrophoresis for foodborne illness cluster definition because of improved resolution. Between November 2017 and May 2018, the New York State (NYS) Dept. of Health investigated 10 cases of Salmonella I 4,[5],12:i:-with pulsed-field gel electrophoresis pattern JPXX01.0621; comparison of case exposures did not identify a common source of infection. In June 2018, the NYS Dept. of Healths Wadsworth Center analyzed the isolates using WGS and defined a subcluster of five isolates related within zero to six single-nucleotide polymorphisms. The National Center for Biotechnology Information Pathogen Detection browser advanced this investigation by identifying additional clinical and food (chicken) isolates related within zero to eight single-nucleotide polymorphisms to the original subcluster. Comparison of WGS-related isolates would support the hypothesis that illness was associated with exposure to a kosher poultry product. This outbreak ultimately consisted of 25 cases from six states. Of 20 cases interviewed, all reported chicken consumption, and of those able to recall brand information, 83% cited a brand produced at a facility linked to the WGS-related chicken isolates. This paper demonstrates how WGS was able to refine a Salmonella I 4,[5],12:i:-cluster in NYS to uncover a multistate outbreak linked to raw poultry. 2021, International Association for Food Protection 2900 100th Street, Suite 309, Des Moines, IA 50322-3855. |
Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses.
Kapuscinski ML , Bergren NA , Russell BJ , Lee JS , Borland EM , Hartman DA , King DC , Hughes HR , Burkhalter KL , Kading RC , Stenglein MD . PLoS Pathog 2021 17 (3) e1009315 Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention's Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses. |
Observed potential cross-contamination in retail delicatessens
Holst M , Brown LG , Viveiros B , Faw B , Hedeen N , McKelvey W , Nicholas D , Ripley D , Hammons S . J Food Prot 2021 84 (6) 1055-1059 Listeria monocytogenes (L. monocytogenes) is a persistent public health concern in the United States and is the third leading cause of death from foodborne illness. Cross-contamination of L. monocytogenes is common in delis (between contaminated and uncontaminated equipment, food and hands) and likely plays a role in the associated with retail deli meats. In 2012, EHS-Net conducted a study to describe deli characteristics related to cross-contamination with L. monocytogenes. The study included 298 retail delis in six state and local health departments' jurisdictions and assessed how well deli practices complied with the Food and Drug Administration (FDA) Food Code provisions. Among delis observed using wet wiping cloths for cleaning, 23.6% did not store the cloths in a sanitizing solution between uses. Observed potential cross-contamination of raw meats and ready-to-eat foods during preparation (e.g., same knife used on raw meats and ready-to-eat foods, without cleaning in between) was present in 9.4% of delis. In 24.6% of delis with a cold storage unit, raw meats were not stored separately from ready-to-eat products in containers, bins, or trays. A proper food safety management plan can reduce gaps in cross-contamination and include the adoption of procedures to minimize food safety risks, training with instructions and in-person demonstrations and certifying staff on those procedures, and monitoring to ensure procedures are followed. |
Investigation of a Large Diphtheria Outbreak and Co-circulation of Corynebacterium pseudodiphtheriticum among Forcibly Displaced Myanmar Nationals, 2017-2019.
Weil LM , Williams MM , Shirin T , Lawrence M , Habib ZH , Aneke JS , Tondella ML , Zaki Q , Cassiday PK , Lonsway D , Farrque M , Hossen T , Feldstein LR , Cook N , Maldonado-Quiles G , Alam AN , Muraduzzaman AKM , Akram A , Conklin L , Doan S , Friedman M , Acosta AM , Hariri S , Fox LM , Tiwari TSP , Flora MS . J Infect Dis 2020 224 (2) 318-325 BACKGROUND: Diphtheria, a life-threatening respiratory disease, is caused mainly by toxin-producing strains of Corynebacterium diphtheriae, while nontoxigenic Corynebacteria, such as C. pseudodiphtheriticum rarely causes diphtheria-like illness. Recently several global diphtheria outbreaks have resulted from the breakdown of healthcare infrastructures particularly in countries experiencing political conflict. This report summarizes a laboratory and epidemiological investigation of a diphtheria outbreak among Forcibly Displaced Myanmar Nationals in Bangladesh. METHODS: Specimens and clinical information were collected from patients presenting at Diphtheria Treatment Centers. Swabs were tested for toxin-gene (tox) bearing C. diphtheriae by real-time (RT) PCR and culture. The isolation of another Corynebacterium species prompted further laboratory investigation. RESULTS: Among 382 patients; 153 (40%) tested tox-positive for C. diphtheriae by RT-PCR; 31 (20%) PCR-positive swabs were culture-confirmed. RT-PCR revealed 78% (298/382) of patients tested positive for C. pseudodiphtheriticum. Of patients positive for only C. diphtheriae, 63% (17/27) had severe disease compared to 55% (69/126) positive for both Corynebacterium species, and 38% (66/172) for only C. pseudodiphtheriticum. CONCLUSIONS: We report the confirmation of a diphtheria outbreak and identification of a co-circulating Corynebacterium species. The high proportion of C. pseudodiphtheriticum co-detection may explain why many suspected patients testing negative for C. diphtheriae presented with diphtheria-like symptoms. |
Primary Swine Respiratory Epithelial Cell Lines for the Efficient Isolation and Propagation of Influenza A Viruses.
Meliopoulos V , Cherry S , Wohlgemuth N , Honce R , Barnard K , Gauger P , Davis T , Shult P , Parrish C , Schultz-Cherry S . J Virol 2020 94 (24) Influenza virus isolation from clinical samples is critical for the identification and characterization of circulating and emerging viruses. Yet efficient isolation can be difficult. In these studies, we isolated primary swine nasal and tracheal respiratory epithelial cells and immortalized swine nasal epithelial cells (siNEC) and tracheal epithelial cells (siTEC) that retained the abilities to form tight junctions and cilia and to differentiate at the air-liquid interface like primary cells. Critically, both human and swine influenza viruses replicated in the immortalized cells, which generally yielded higher-titer viral isolates from human and swine nasal swabs, supported the replication of isolates that failed to grow in Madin-Darby canine kidney (MDCK) cells, and resulted in fewer dominating mutations during viral passaging than MDCK cells.IMPORTANCE Robust in vitro culture systems for influenza virus are critically needed. MDCK cells, the most widely used cell line for influenza isolation and propagation, do not adequately model the respiratory tract. Therefore, many clinical isolates, both animal and human, are unable to be isolated and characterized, limiting our understanding of currently circulating influenza viruses. We have developed immortalized swine respiratory epithelial cells that retain the ability to differentiate and can support influenza replication and isolation. These cell lines can be used as additional tools to enhance influenza research and vaccine development. |
Characterization of COVID-19 in Assisted Living Facilities - 39 States, October 2020.
Yi SH , See I , Kent AG , Vlachos N , Whitworth JC , Xu K , Gouin KA , Zhang S , Slifka KJ , Sauer AG , Kutty PK , Perz JF , Stone ND , Stuckey MJ . MMWR Morb Mortal Wkly Rep 2020 69 (46) 1730-1735 The coronavirus disease 2019 (COVID-19) pandemic has highlighted the vulnerability of residents and staff members in long-term care facilities (LTCFs) (1). Although skilled nursing facilities (SNFs) certified by the Centers for Medicare & Medicaid Services (CMS) have federal COVID-19 reporting requirements, national surveillance data are less readily available for other types of LTCFs, such as assisted living facilities (ALFs) and those providing similar residential care. However, many state and territorial health departments publicly report COVID-19 surveillance data across various types of LTCFs. These data were systematically retrieved from health department websites to characterize COVID-19 cases and deaths in ALF residents and staff members. Limited ALF COVID-19 data were available for 39 states, although reporting varied. By October 15, 2020, among 28,623 ALFs, 6,440 (22%) had at least one COVID-19 case among residents or staff members. Among the states with available data, the proportion of COVID-19 cases that were fatal was 21.2% for ALF residents, 0.3% for ALF staff members, and 2.5% overall for the general population of these states. To prevent the introduction and spread of SARS-CoV-2, the virus that causes COVID-19, in their facilities, ALFs should 1) identify a point of contact at the local health department; 2) educate residents, families, and staff members about COVID-19; 3) have a plan for visitor and staff member restrictions; 4) encourage social (physical) distancing and the use of masks, as appropriate; 5) implement recommended infection prevention and control practices and provide access to supplies; 6) rapidly identify and properly respond to suspected or confirmed COVID-19 cases in residents and staff members; and 7) conduct surveillance of COVID-19 cases and deaths, facility staffing, and supply information (2). |
Coronavirus Disease among Workers in Food Processing, Food Manufacturing, and Agriculture Workplaces.
Waltenburg MA , Rose CE , Victoroff T , Butterfield M , Dillaha JA , Heinzerling A , Chuey M , Fierro M , Jervis RH , Fedak KM , Leapley A , Gabel JA , Feldpausch A , Dunne EM , Austin C , Pedati CS , Ahmed FS , Tubach S , Rhea C , Tonzel J , Krueger A , Crum DA , Vostok J , Moore MJ , Kempher H , Scheftel J , Turabelidze G , Stover D , Donahue M , Thomas D , Edge K , Gutierrez B , Berl E , McLafferty M , Kline KE , Martz N , Rajotte JC , Julian E , Diedhiou A , Radcliffe R , Clayton JL , Ortbahn D , Cummins J , Barbeau B , Carpenter S , Pringle JC , Murphy J , Darby B , Graff NR , Dostal TKH , Pray IW , Tillman C , Rose DA , Honein MA . Emerg Infect Dis 2020 27 (1) 243-9 We describe coronavirus disease (COVID-19) among US food manufacturing and agriculture workers and provide updated information on meat and poultry processing workers. Among 742 food and agriculture workplaces in 30 states, 8,978 workers had confirmed COVID-19; 55 workers died. Racial and ethnic minority workers could be disproportionately affected by COVID-19. |
Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks - Minnesota, April-June 2020.
Taylor J , Carter RJ , Lehnertz N , Kazazian L , Sullivan M , Wang X , Garfin J , Diekman S , Plumb M , Bennet ME , Hale T , Vallabhaneni S , Namugenyi S , Carpenter D , Turner-Harper D , Booth M , Coursey EJ , Martin K , McMahon M , Beaudoin A , Lifson A , Holzbauer S , Reddy SC , Jernigan JA , Lynfield R . MMWR Morb Mortal Wkly Rep 2020 69 (37) 1288-1295 SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), can spread rapidly in high-risk congregate settings such as skilled nursing facilities (SNFs) (1). In Minnesota, SNF-associated cases accounted for 3,950 (8%) of 48,711 COVID-19 cases reported through July 21, 2020; 35% of SNF-associated cases involved health care personnel (HCP*), including six deaths. Facility-wide, serial testing in SNFs has been used to identify residents with asymptomatic and presymptomatic SARS-CoV-2 infection to inform mitigation efforts, including cohorting of residents with positive test results and exclusion of infected HCP from the workplace (2,3). During April-June 2020, the Minnesota Department of Health (MDH), with CDC assistance, conducted weekly serial testing at two SNFs experiencing COVID-19 outbreaks. Among 259 tested residents, and 341 tested HCP, 64% and 33%, respectively, had positive reverse transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results. Continued SARS-CoV-2 transmission was potentially facilitated by lapses in infection prevention and control (IPC) practices, up to 12-day delays in receiving HCP test results (53%) at one facility, and incomplete HCP participation (71%). Genetic sequencing demonstrated that SARS-CoV-2 viral genomes from HCP and resident specimens were clustered by facility, suggesting facility-based transmission. Residents and HCP working in SNFs are at risk for infection with SARS-CoV-2. As part of comprehensive COVID-19 preparation and response, including early identification of cases, SNFs should conduct serial testing of residents and HCP, maximize HCP testing participation, ensure availability of personal protective equipment (PPE), and enhance IPC practices(†) (4-5). |
Modernizing the foodborne outbreak contributing factors: The key to prevention
Wittry B , Nicholas D . J Environ Health 2020 83 (2) 42-46 The article describes the revisions to the list of foodborne outbreak contributing factors (CF) that can be used to prevent future outbreaks and to improve food safety in the U.S. Topics mentioned include the categories of CF including poor personal hygiene and contaminated equipment, the proliferation factors that were added including the improper cooling of food, and the survival factors that were identified including the inadequate nontemperature dependent process like fermentation. |
COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April-May 2020.
Yoon JC , Montgomery MP , Buff AM , Boyd AT , Jamison C , Hernandez A , Schmit K , Shah S , Ajoku S , Holland DP , Prieto J , Smith S , Swancutt MA , Turner K , Andrews T , Flowers K , Wells A , Marchman C , Laney E , Bixler D , Cavanaugh S , Flowers N , Gaffga N , Ko JY , Paulin HN , Weng MK , Mosites E , Morris SB . Clin Infect Dis 2020 73 (9) e2978-e2984 BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies. METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7-May 6, 2020. A subset of PEH and staff was screened for symptoms. Shelter assessments were conducted concurrently at a convenience sample of shelters using a standardized questionnaire. RESULTS: Overall, 2,875 individuals at 24 shelters and nine unsheltered outreach events underwent SARS-CoV-2 testing and 2,860 (99.5%) had conclusive test results. SARS-CoV-2 prevalence was 2.1% (36/1,684) among PEH living sheltered, 0.5% (3/628) among PEH living unsheltered, and 1.3% (7/548) among staff. Reporting fever, cough, or shortness of breath in the last week during symptom screening was 14% sensitive and 89% specific for identifying COVID-19 cases compared with RT-PCR. Prevalence by shelter ranged 0%-27.6%. Repeat testing 3-4 weeks later at four shelters documented decreased SARS-CoV-2 prevalence (0%-3.9%). Nine of 24 shelters completed shelter assessments and implemented IPC measures as part of the COVID-19 response. CONCLUSIONS: PEH living in shelters experienced higher SARS-CoV-2 prevalence compared with PEH living unsheltered. Facility-wide testing in congregate settings allowed for identification and isolation of COVID-19 cases and is an important strategy to interrupt SARS-CoV-2 transmission. |
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alioto D , Alkhovsky SV , Amarasinghe GK , Anthony SJ , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bartonička T , Basler C , Bavari S , Beer M , Bente DA , Bergeron É , Bird BH , Blair C , Blasdell KR , Bradfute SB , Breyta R , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Buzkan N , Calisher CH , Cao M , Casas I , Chamberlain J , Chandran K , Charrel RN , Chen B , Chiumenti M , Choi IR , Clegg JCS , Crozier I , da Graça JV , Dal Bó E , Dávila AMR , de la Torre JC , de Lamballerie X , de Swart RL , Di Bello PL , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolja VV , Dolnik O , Drebot MA , Drexler JF , Dürrwald R , Dufkova L , Dundon WG , Duprex WP , Dye JM , Easton AJ , Ebihara H , Elbeaino T , Ergünay K , Fernandes J , Fooks AR , Formenty PBH , Forth LF , Fouchier RAM , Freitas-Astúa J , Gago-Zachert S , Gāo GF , García ML , García-Sastre A , Garrison AR , Gbakima A , Goldstein T , Gonzalez JJ , Griffiths A , Groschup MH , Günther S , Guterres A , Hall RA , Hammond J , Hassan M , Hepojoki J , Hepojoki S , Hetzel U , Hewson R , Hoffmann B , Hongo S , Höper D , Horie M , Hughes HR , Hyndman TH , Jambai A , Jardim R , Jiāng D , Jin Q , Jonson GB , Junglen S , Karadağ S , Keller KE , Klempa B , Klingström J , Kobinger G , Kondō H , Koonin EV , Krupovic M , Kurath G , Kuzmin IV , Laenen L , Lamb RA , Lambert AJ , Langevin SL , Lee B , Lemos ERS , Leroy EM , Li D , Lǐ J , Liang M , Liú W , Liú Y , Lukashevich IS , Maes P , Marciel de Souza W , Marklewitz M , Marshall SH , Martelli GP , Martin RR , Marzano SL , Massart S , McCauley JW , Mielke-Ehret N , Minafra A , Minutolo M , Mirazimi A , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki T , Navarro B , Navarro JA , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Nylund A , Økland AL , Oliveira RC , Palacios G , Pallas V , Pályi B , Papa A , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Payne S , Pérez DR , Pfaff F , Radoshitzky SR , Rahman AU , Ramos-González PL , Resende RO , Reyes CA , Rima BK , Romanowski V , Robles Luna G , Rota P , Rubbenstroth D , Runstadler JA , Ruzek D , Sabanadzovic S , Salát J , Sall AA , Salvato MS , Sarpkaya K , Sasaya T , Schwemmle M , Shabbir MZ , Shí X , Shí Z , Shirako Y , Simmonds P , Širmarová J , Sironi M , Smither S , Smura T , Song JW , Spann KM , Spengler JR , Stenglein MD , Stone DM , Straková P , Takada A , Tesh RB , Thornburg NJ , Tomonaga K , Tordo N , Towner JS , Turina M , Tzanetakis I , Ulrich RG , Vaira AM , van den Hoogen B , Varsani A , Vasilakis N , Verbeek M , Wahl V , Walker PJ , Wang H , Wang J , Wang X , Wang LF , Wèi T , Wells H , Whitfield AE , Williams JV , Wolf YI , Wú Z , Yang X , Yáng X , Yu X , Yutin N , Zerbini FM , Zhang T , Zhang YZ , Zhou G , Zhou X . Arch Virol 2020 165 (12) 3023-3072 In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Notes from the Field: Public Health Efforts to Mitigate COVID-19 Transmission During the April 7, 2020, Election - City of Milwaukee, Wisconsin, March 13-May 5, 2020.
Paradis H , Katrichis J , Stevenson M , Tomaro N , Mukai R , Torres G , Bhattacharyya S , Kowalik J , Schlanger K , Leidman E . MMWR Morb Mortal Wkly Rep 2020 69 (30) 1002-1003 Wisconsin was the first state to hold an election with in-person voting after stay-at-home orders were issued to limit transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). The statewide primary election, held on April 7, 2020, occurred fewer than 2 weeks after the statewide “Safer at Home” order* became effective on March 25. | | On March 3, 2020, CDC published interim guidance to prevent spread of SARS-CoV-2 at polling locations (1). Mitigation measures in line with the CDC guidance and additional measures were implemented in the city of Milwaukee (in Milwaukee County) to prevent the transmission of SARS-CoV-2 at in-person polling venues (Supplementary Table, https://stacks.cdc.gov/view/cdc/90768). In addition to the nearly 500 poll workers, election inspectors, and chief inspectors, Milwaukee city health department personnel and the Wisconsin National Guard were assigned to support mitigation efforts at each of five Milwaukee polling sites and the central count location. Mitigation measures implemented at the direction of the city health department complemented public messaging campaigns to encourage absentee voting. According to the Milwaukee Election Commission, comparing the number of persons voting in the spring of 2016 with those voting in the spring of 2020, the percentage of persons who voted by absentee mail-in ballots increased approximately fifteenfold, from 4.1% (6,874) to 68.0% (64,750) of voters; those who voted early (either in person or curbside [i.e., voting while remaining in their vehicle or at the voting place entrance]) increased by 160%, from 4.7% (7,949) to 12.2% (11,612). Although the proportion of those who voted in person on election day decreased 78%, from 91.2% (153,458) to 19.8% (18,806),† local news media reported long waiting times at Milwaukee voting locations on election day.§ Overall, the number of persons who voted decreased 43%, from 168,281 to 95,168, and the number of polling sites decreased from 181 to five. |
Estimated Community Seroprevalence of SARS-CoV-2 Antibodies - Two Georgia Counties, April 28-May 3, 2020.
Biggs HM , Harris JB , Breakwell L , Dahlgren FS , Abedi GR , Szablewski CM , Drobeniuc J , Bustamante ND , Almendares O , Schnall AH , Gilani Z , Smith T , Gieraltowski L , Johnson JA , Bajema KL , McDavid K , Schafer IJ , Sullivan V , Punkova L , Tejada-Strop A , Amiling R , Mattison CP , Cortese MM , Ford SE , Paxton LA , Drenzek C , Tate JE , CDC Field Surveyor Team , Brown Nicole , Chang Karen T , Deputy Nicholas P , Desamu-Thorpe Rodel , Gorishek Chase , Hanchey Arianna , Melgar Michael , Monroe Benjamin P , Nielsen Carrie F , Pellegrini Gerald JJr , Shamout Mays , Tison Laura I , Vagi Sara , Zacks Rachael . MMWR Morb Mortal Wkly Rep 2020 69 (29) 965-970 Transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is ongoing in many communities throughout the United States. Although case-based and syndromic surveillance are critical for monitoring the pandemic, these systems rely on persons obtaining testing or reporting a COVID-19-like illness. Using serologic tests to detect the presence of SARS-CoV-2 antibodies is an adjunctive strategy that estimates the prevalence of past infection in a population. During April 28-May 3, 2020, coinciding with the end of a statewide shelter-in-place order, CDC and the Georgia Department of Public Health conducted a serologic survey in DeKalb and Fulton counties in metropolitan Atlanta to estimate SARS-CoV-2 seroprevalence in the population. A two-stage cluster sampling design was used to randomly select 30 census blocks in each county, with a target of seven participating households per census block. Weighted estimates were calculated to account for the probability of selection and adjusted for age group, sex, and race/ethnicity. A total of 394 households and 696 persons participated and had a serology result; 19 (2.7%) of 696 persons had SARS-CoV-2 antibodies detected. The estimated weighted seroprevalence across these two metropolitan Atlanta counties was 2.5% (95% confidence interval [CI] = 1.4-4.5). Non-Hispanic black participants more commonly had SARS-CoV-2 antibodies than did participants of other racial/ethnic groups (p<0.01). Among persons with SARS-CoV-2 antibodies, 13 (weighted % = 49.9; 95% CI = 24.4-75.5) reported a COVID-19-compatible illness,* six (weighted % = 28.2; 95% CI = 11.9-53.3) sought medical care for a COVID-19-compatible illness, and five (weighted % = 15.7; 95% CI = 5.1-39.4) had been tested for SARS-CoV-2 infection, demonstrating that many of these infections would not have been identified through case-based or syndromic surveillance. The relatively low seroprevalence estimate in this report indicates that most persons in the catchment area had not been infected with SARS-CoV-2 at the time of the survey. Continued preventive measures, including social distancing, consistent and correct use of face coverings, and hand hygiene, remain critical in controlling community spread of SARS-CoV-2. |
Risk Factors for Healthcare Personnel Infection with Endemic Coronaviruses (HKU1, OC43, NL63, 229E): Results from the Respiratory Protection Effectiveness Clinical Trial (ResPECT).
Cummings DAT , Radonovich LJ , Gorse GJ , Gaydos CA , Bessesen MT , Brown AC , Gibert CL , Hitchings MDT , Lessler J , Nyquist AC , Rattigan SM , Rodriguez-Barradas MC , Price CS , Reich NG , Simberkoff MS , Perl TM . Clin Infect Dis 2020 73 (11) e4428-e4432 BACKGROUND: SARS-CoV-2 presents a large risk to healthcare personnel. Quantifying the risk of coronavirus infection associated with workplace activities is an urgent need. METHODS: We assessed the association of worker characteristics, occupational roles and behaviors, and participation in procedures with the risk of endemic coronavirus infection among healthcare personnel who participated in the Respiratory Protection Effectiveness Trial (ResPECT), a cluster randomized trial to assess personal protective equipment to prevent respiratory infections and illness conducted from 2011 to 2016. RESULTS: Among 4,689 HCP-seasons, we detected coronavirus infection in 387 (8%). HCP who participated in an aerosol generation procedure (AGP) at least once during the viral respiratory season were 105% (95% CI 21%, 240%) more likely to be diagnosed with a laboratory-confirmed coronavirus infection. Younger individuals, those who saw pediatric patients and those with household members under the age of five were at increased risk of coronavirus infection. CONCLUSIONS: Our analysis suggests the risk of HCP becoming infected with an endemic coronavirus increases approximately two-fold with exposures to AGP. Our findings may be relevant to the Coronavirus Disease 2019 (COVID-19) pandemic; however, SARS-COV-2, the virus that causes COVID-19, may differ from endemic coronaviruses in important ways. |
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