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Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.

ABSTRACT: Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.

SUBMITTER: Huang X

PROVIDER: S-EPMC8386442 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ImportanceStaff absences and departures at nursing homes may put residents at risk and present operational challenges.ObjectiveTo quantify changes in nursing home facility staffing during and after a severe COVID-19 outbreak.Design setting and participantsIn this cohort study, daily staffing payroll data were used to construct weekly measures of facility staffing, absences, departures, and use of overtime and contract staff among US nursing homes experiencing a severe COVID-19 outbreak that started between June 14, 2020, and January 1, 2021. Facility outbreaks were identified using COVID-19 case data. An event-study design with facility and week fixed effects was used to investigate the association of severe outbreaks with staffing measures.ExposuresWeeks since the beginning of a severe COVID-19 outbreak (4 weeks prior to 16 weeks after).Main outcomes and measuresTotal weekly staffing hours, staff counts, staff absences, departures, new hires, overtime and contract staff hours measured for all nursing staff and separately by staff type (registered nurses, licensed practical nurses, certified nursing assistants), facility self-reported staff shortages, and resident deaths.ResultsOf the included 2967 nursing homes experiencing severe COVID-19 outbreaks, severe outbreaks were associated with a statistically significant drop in nursing staffing levels owing to elevated absences and departures. Four weeks after an outbreak's start, around when average new cases peaked, staffing hours were 2.6% (95% CI, 2.1%-3.2%) of the mean below preoutbreak levels, despite facilities taking substantial measures to bolster staffing through increased hiring and the use of contract staff and overtime. Because these measures were mostly temporary, staffing declined further in later weeks; 16 weeks after an outbreak's start, staffing hours were 5.5% (95% CI, 4.5%-6.5%) of the mean below preoutbreak levels. Staffing declines were greatest among certified nursing assistants, primarily owing to smaller increases in new hires of this staff type compared with licensed practical nurses and registered nurses.Conclusions and relevanceIn this cohort study of nursing homes experiencing severe COVID-19 outbreaks, facilities experienced considerable staffing challenges during and after outbreaks. These results suggest the need for policy action to ensure facilities' abilities to maintain adequate staffing levels during and after infectious disease outbreaks.

Project description:Background and objectivesThe study aimed to: (i) describe whether culture change (CC) practice implementation related to physical environment, resident-centered care, and staff empowerment increased within the same nursing homes (NHs) over time; and (ii) identify factors associated with observed increases.Research design and methodsThis was a nationally representative panel study of 1,584 U.S. NHs surveyed in 2009/2010 and 2016/2017. Survey data were merged with administrative, NH, and market-level data. Physical environment, staff empowerment, and resident-centered care domain scores were calculated at both time points. Multivariate logistic regression models examined factors associated with domain score increases.ResultsOverall, 22% of NHs increased their physical environment scores over time, 32% their staff empowerment scores, and 44% their resident-centered care scores. However, 32%-68% of NHs with below median baseline scores improved their domain scores over time compared with only 11%-21% of NHs with baseline scores at or above the median. Overall, NHs in states with Medicaid pay-for-performance (with CC components), in community care retirement communities, with special care units and higher occupancy had significantly higher odds of increases in physical environment scores. Only baseline domain scores were associated with increases in staff empowerment and resident-centered care scores.Discussion and implicationsThis is the first nationally representative panel study to assess NH CC adoption. Many NHs increased their CC practices, though numerous others did not. While financial incentives and indicators of financial resources were associated with increase in physical environment scores, factors associated with staff empowerment and resident-centered care improvements remain unclear. Studies are needed to assess whether the observed increases in CC adoption are associated with greater quality of life and care gains for residents and whether there is a threshold effect beyond which the efficacy of additional practice implementation may be less impactful.

Project description:Abstract Background Nursing home residents account for 45% SARS-CoV-2 related deaths in the U.S. but only 0.6% of the population. Our research group conducted a large pragmatic cluster randomized influenza vaccine trial in 965 nursing homes (NCT03965195). Due to the pandemic and its impact after the influenza season, we prospectively collected reports of SARS-CoV-2 outbreaks and performed a prospective study on the association between contract staffing and reported outbreaks of SARS-CoV-2. We hypothesized those using more contract nursing care would have higher risk of an outbreak. Methods From February through April, we collected monthly facility-level, self-reported data on SARS-CoV-2 outbreaks. Facility characteristics were taken from public data from Centers for Medicaid and Medicare services. Predictors of SARS-CoV-2 outbreaks were identified using a LASSO variable selection procedure, with a generalized linear, Poisson family model. Facility characteristics evaluated include demographics (e.g. number of residents), influenza vaccination rates, quality measures (e.g. % with UTI), and functional status (e.g. % with tube feedings). Facilities with contract staffing hours in the upper 25% quantile of direct care (RN, LPN, CNA) were considered ‘heavy use’. Results Of 965 randomized NHs, 663/965 (69%) reported data on SARS-CoV-2 outbreaks. On average, 13% of facilities had at least one outbreak, with 5/842 (0.5%) outbreaks in February, 91/835 (10.8%) in March and 217/686 (30%) in April. SARS-CoV-2 (+) facilities were larger (average total beds, 151 vs. 117), but were mostly similar by functional and cognitive status. Occupancy rate, total residents, Influenza vaccination rate, % with UTI, receiving respiratory treatments, tube feedings, and Medicaid payers were adjusted for in the analysis. The ‘heavy use’ of contract staffing included those with >223 hours per quarter. A multivariable regression found the relative risk SARS-CoV-2 outbreak was 1.56 (95% Confidence Interval: 1.22, 1.99) with heavy use of contract staffing. Conclusion The participating nursing homes in our vaccine trial with SARS-CoV-2 outbreaks were larger. Our study highlights that heavy use of contract staffing was associated with 56% increased risk of an outbreak. Disclosures Kevin McConeghy, Pharm.D., Pfizer (Grant/Research Support)Sanofi-Pasteur (Grant/Research Support)Seqirus Pharmaceuticals (Grant/Research Support) H. Edward Davidson, PharmD, MPH, Sanofi pasteur (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support)Seqirus (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support) Lisa Han, MPH, Sanofi Pasteur (Grant/Research Support)Seqirus (Grant/Research Support) David Canaday, M.D., Pfizer (Research Grant or Support)Sanofi Pasteur (Research Grant or Support)Seqirus (Advisor or Review Panel member, Research Grant or Support) Vincent Mor, Ph.D., naviHealth (Consultant)

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Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.

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