scholarly journals 432. An Outbreak of Coronavirus Disease, 2019 (COVID-19) in a Skilled Nursing Facility – California, 2021: Description, Mitigation, Challenges, and Opportunities

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S318-S319
Author(s):  
Anastasia Maletz ◽  
Grace Kang ◽  
Raymond Y Chinn ◽  
John D Malone ◽  
Hosniyeh Bagheri ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Skilled Nursing Facility ◽  
Geographic Location ◽  
The United States ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Nursing Facility ◽  
Skilled Nursing ◽  
Increased Risk

Abstract Background Skilled nursing facility (SNF) residents comprised 11% of all COVID-19 cases in the United States; however, they account for 43% of deaths with case fatality rates (CFR) of 26.0-33.7%. Methods We report an outbreak of COVID-19, from June 15 to July 21, 2020 in a 159-bed SNF with a staff of 172 that resulted in an infection rate of 97% in residents and 23% in HCWs (Figure 1). A retroactive review outlined mitigation efforts, discussed challenges, identified risk factors among residents and health care workers (HCW) for acquisition of COVID-19, and reviewed opportunities for improvement (Figure 2). Figure 1. Epi Curve of COVID-19 Outbreak in a Skilled Nursing Facility Figure 2. Timeline of COVID-19 Outbreak in a Skilled Nursing Facility Results Factors that contributed to the outbreak: delay in test results had an impact on cohorting; suboptimal adherence to the principles of infection prevention and control (IPC) and minimal adherence monitoring; strict criteria were used to screen for infection; the underappreciated transmissibility of COVID-19 from presymptomatic and asymptomatic persons; symptomatic HCWs who continued to work; the changing guidance on, the suboptimal use of, and an inadequate supply of personal protective equipment; poor indoor air quality due to ventilation challenges; and the important role of community/family/interfacility spread on the outbreak. Whole genome sequencing, performed in 52 samples, identified a common strain that was also found in clusters of 2 other facilities: 1 in the same geographic location, the other in a different geographic location but whose HCWs had the same zip codes as the facility (Figure 3). Certified nursing and restorative nursing assistants had the highest risk of infection with an odds ratio (OR) of 4.02 (confidence interval 1.29-12.55, p value: 0.02) when compared to registered and licensed vocational nurses. The residents’ CFR was 24%. The OR for death was increased by 10.5 (10.20-11.00) for every decade of life as was morbid obesity (BMI > 35) with an OR of 8.50. BMI as a continuous variable increased risk of mortality for every additional unit, OR 1.07 (Tables 1, 2). Whole Genome Sequencing of Isolates from a Skilled Nursing Facility Outbreak Univariate Analysis of Selected Variables Associated with Mortality among Residents at Facility A during COVID-19 Outbreak, June 19 - July 21, 2021 Multivariate Analysis of Factors Associated with Mortality from COVID-19 after Adjusting for Age among Residents (N =124) of Facility A, June 15 - July 21, 2020 Conclusion While implementation of optimal IPC measures in the pre-COVID-19 vaccination era had no impact on the infections in residents who were likely already infected or exposed at the onset of the outbreak, these measures along with non-pharmacologic strategies were effective in halting the spread among HCWs. Disclosures All Authors: No reported disclosures

scholarly journals Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1

2017 ◽  
Vol 13 (11) ◽  
pp. e1006703 ◽  
Author(s):  
Romel D. Mackelprang ◽  
Michael J. Bamshad ◽  
Jessica X. Chong ◽  
Xuanlin Hou ◽  
Kati J. Buckingham ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Increased Risk ◽  
Extreme Phenotypes ◽  
Hiv 1

scholarly journals Clinical Courses and Characteristics of Residents During a SARS-CoV-2 Outbreak at a Central Indiana Skilled Nursing Facility

2020 ◽  
Vol 3 ◽  
Author(s):  
Lauren Albert ◽  
Kristi Lieb ◽  
Laramie Mack ◽  
Kathleen Unroe
Keyword(s):  
Older Adults ◽  
Case Reports ◽  
Skilled Nursing Facility ◽  
Nursing Facilities ◽  
Retrospective Case ◽  
Nursing Facility ◽  
Skilled Nursing ◽  
Increased Risk ◽  
Symptom Load ◽  
Retrospective Case Study

Background/Objective: Older adults such as skilled nursing facility residents have increased risk of serious SARS-CoV-2 infection and comprise a large proportion of the COVID-19 pandemic’s deceased—the US Centers for Medicare & Medicaid Services report 232,831 cases and 38,518 resident deaths to date. Recent case reports reveal, as in other diseases, older adults may experience atypical symptomology, complicating identification of ill residents and efforts to slow transmission. While a few facility outbreaks have been characterized epidemiologically, little research exists regarding clinical timelines and trajectories which residents experience during COVID-19 illness.   Methods: From May 9, 2020-June 1, 2020, daily notes on each COVID-19 positive resident’s status (n = 69) were taken by the medical director of a central Indiana nursing facility. Combined with a retrospective resident chart review of this same period, these notes were examined for COVID-19 infection symptoms and illness timelines to descriptively categorize a number of common illness trajectories and symptoms seen in residents with SARS-CoV-2 infection.  Results: Residents fit four descriptive clinical timelines: concurrent symptom load with quick death (Avg 5.6 days) (n = 5), accumulating symptom load with gradual decline (Avg. 13.9 days) (n = 9), prolonged active symptom load with periods of stabilization and symptom reoccurrence (n = 42), and asymptomatic or atypical symptom load (n = 12). Most common symptoms were fever, hypoxia, anorexia, and fatigue/malaise. Of the 14 residents who died (20.3% of infected), 8 died in the facility and 6 died in the hospital.  Conclusion and Implications: This retrospective case study adds to literature describing the presentation and symptomology of SARS-CoV-2 infection in residents of skilled nursing facilities and aids efforts to evaluate resident presentation, prognosis, and disease course. Robust descriptions of expected clinical courses may support realistic expectations of disease progression for residents and their family members experiencing future outbreaks.

scholarly journals Whole Genome Sequencing Resource of the European Larch Canker Pathogen Lachnellula willkommii for Molecular Diagnostic Marker Development

2020 ◽  
Vol 110 (7) ◽  
pp. 1255-1259
Author(s):  
Emily Giroux ◽  
Guillaume J. Bilodeau
Keyword(s):  
United States ◽  
North America ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
The United States ◽  
Molecular Diagnostic ◽  
Whole Genome ◽  
European Larch ◽  
The North

The filamentous ascomycete fungus Lachnellula willkommii is the causal agent of European larch canker (ELC), one of the most destructive diseases of larch in Europe and a regulated plant pathogen of quarantine significance in Canada and the United States. L. willkommii was first detected in Massachusetts, North America in 1927 on a larch plantation cultivated with nursery stock imported from Great Britain. Despite the decades of practices aimed at eliminating the pathogen, it has reappeared in coastal areas of Canada and the United States. There is concern ELC could spread throughout the range of eastern larch, a transcontinental species typical of the Boreal forest that spans the North American landscape. There is geographic range overlap between several nonpathogenic indigenous Lachnellula species and the reported distribution of L. willkommii in North America. Morphological and biological methods to distinguish L. willkommii are often inadequate as the fungus does not always produce the phenotypic structures that distinguish it from these other saprophytic Lachnellula species. Whole genome sequencing technologies were used to obtain the draft genome sequences of L. willkommii and six other Lachnellula species. Molecular markers identified from the genomic data may be used to discriminate L. willkommii from its nonpathogenic relatives.

scholarly journals Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States

2019 ◽  
Vol 16 (7) ◽  
pp. 441-450 ◽  
Author(s):  
Eric Brown ◽  
Uday Dessai ◽  
Sherri McGarry ◽  
Peter Gerner-Smidt
Keyword(s):  
Public Health ◽  
United States ◽  
Food Safety ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome

scholarly journals Comparison of whole genome sequencing to restriction endonuclease analysis and gel diffusion precipitin-based serotyping of Pasteurella multocida

2017 ◽  
Vol 30 (1) ◽  
pp. 42-55 ◽  
Author(s):  
Karen J. LeCount ◽  
Linda K. Schlater ◽  
Tod Stuber ◽  
Suelee Robbe Austerman ◽  
Timothy S. Frana ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Restriction Endonuclease ◽  
Genome Sequencing ◽  
Pasteurella Multocida ◽  
Restriction Endonuclease Analysis ◽  
The United States ◽  
Snp Analysis ◽  
Whole Genome ◽  
Gel Diffusion ◽  
Endonuclease Analysis

The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in the serotyping and genotyping of Pasteurella multocida. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis has become the gold standard for other organisms, offering higher resolution than previously available methods. We compared WGS to REA and GDPT on 163 isolates of P. multocida to determine if WGS produced more precise results. The isolates used represented the 16 reference serovars, isolates with REA profiles matching an attenuated fowl cholera vaccine strain, and isolates from 10 different animal species. Isolates originated from across the United States and from Chile. Identical REA profiles clustered together in the phylogenetic tree. REA profiles that differed by only a few bands had fewer SNP differences than REA profiles with more differences, as expected. The GDPT results were diverse but it was common to see a single serovar show up repeatedly within clusters. Several errors were found when examining the REA profiles. WGS was able to confirm these errors and compensate for the subjectivity in analysis of REA. Also, results of WGS and SNP analysis correlated more closely with the epidemiologic data than GDPT. In silico results were also compared to a lipopolysaccharide rapid multiplex PCR test. From the data produced in our study, WGS and SNP analysis was superior to REA and GDPT and highlighted some of the issues with the older tests.

scholarly journals Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

2016 ◽  
Vol 60 (9) ◽  
pp. 5515-5520 ◽  
Author(s):  
Patrick F. McDermott ◽  
Gregory H. Tyson ◽  
Claudine Kabera ◽  
Yuansha Chen ◽  
Cong Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
The United States ◽  
Whole Genome ◽  
Content Type ◽  
Structural Resistance ◽  
Retail Meat

ABSTRACTLaboratory-basedin vitroantimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidalSalmonellaand correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred fortySalmonellaof 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n =59) in the 104 human isolates than in the 536 retail meat isolates (n =36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum β-lactamases (ESBLs) (blaCTX-M1andblaSHV2a) in retail meat isolates ofSalmonellain the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidalSalmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

scholarly journals Improving Healthcare Value: COVID-19 Emergency Regulatory Relief and Implications for Post-Acute Skilled Nursing Facility Care

2020 ◽  
Vol 15 (8) ◽  
pp. 495-497
Author(s):  
Ann M Sheehy ◽  
Charles FS Locke ◽  
Farah A Kaiksow ◽  
W Ryan Powell ◽  
Andrea Gilmore Bykovskyi ◽  
...  
Keyword(s):  
Care Delivery ◽  
Skilled Nursing Facility ◽  
Marked Change ◽  
Hospital Medicine ◽  
The United States ◽  
Medicare Beneficiaries ◽  
Nursing Facility ◽  
Skilled Nursing ◽  
Social Security Act ◽  
The 1960S

Rarely, if ever, does a national healthcare system experience such rapid and marked change as that seen with the COVID-19 pandemic. In March 2020, the president of the United States declared a national health emergency, enabling the Department of Health & Human Services authority to grant temporary regulatory waivers to facilitate efficient care delivery in a variety of healthcare settings. The statutory requirement that Medicare beneficiaries stay three consecutive inpatient midnights to qualify for post-acute skilled nursing facility coverage is one such waiver. This so-called Three Midnight Rule, dating back to the 1960s as part of the Social Security Act, is being scrutinized more than half a century later given the rise in observation hospital stays. Despite the tragic emergency circumstances prompting waivers, the Centers for Medicare & Medicaid Services and Congress now have a unique opportunity to evaluate potential improvements revealed by COVID-19 regulatory relief and should consider permanent reform of the Three Midnight Rule. Journal of Hospital Medicine 2020;15:XXX-XXX. © 2020 Society of Hospital Medicine

scholarly journals Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

2019 ◽  
Vol 116 (18) ◽  
pp. 9014-9019 ◽  
Author(s):  
Lei Zhang ◽  
Xiao Dong ◽  
Moonsook Lee ◽  
Alexander Y. Maslov ◽  
Tao Wang ◽  
...  
Keyword(s):  
B Cell ◽  
Whole Genome Sequencing ◽  
Single Cell ◽  
B Lymphocytes ◽  
Genome Sequencing ◽  
Somatic Mutations ◽  
Whole Genome ◽  
Healthy Individuals ◽  
Human Lifespan ◽  
Increased Risk

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell–specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

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