Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people.

Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.

The COVID-19 Tracheostomy Experience at a Large Academic Medical Center in New York during the First Year.

Background: New York City was the epicenter of the initial surge of the COVID-19 pandemic in the United States. Tracheostomy is a critical procedure in the care of patients with COVID-19. We hypothesized that early tracheostomy would decrease the length of time on sedation, time on mechanical ventilation, intensive care unit length of stay, and mortality. Methods: A retrospective analysis of outcomes for all patients with COVID-19 who underwent tracheostomy during the first year of the COVID-19 pandemic at the Mount Sinai Hospital in New York City, New York. All adult intensive care units at the Mount Sinai Hospital, New York. Patients/subjects: 888 patients admitted to intensive care with COVID-19. Results: All patients admitted to the intensive care unit with COVID-19 (888) from 1 March 2020 to 1 March 2021 were analyzed and separated further into those intubated (544) and those requiring tracheostomy (177). Of those receiving tracheostomy, outcomes were analyzed for early (≤12 days) or late (>12 days) tracheostomy. Demographics, medical history, laboratory values, type of oxygen and ventilatory support, and clinical outcomes were recorded and analyzed. Conclusions: Early tracheostomy resulted in reduced duration of mechanical ventilation, reduced hospital length of stay, and reduced intensive care unit length of stay in patients admitted to the intensive care unit with COVID-19. There was no effect on overall mortality.

Sociodemographic Factors Associated with Do-Not-Resuscitate Order Utilization in the Surgical Intensive Care Unit: An Observational Study.

The use of a do-not-resuscitate (DNR) order is a powerful tool in outlining end-of-life care. This study explores sociodemographic factors associated with selection of a DNR order and assigning a healthcare proxy in the Surgical Intensive Care Unit (SICU). A retrospective chart review of 312 patients who expired in the SICU over a 7-year period was conducted. We analyzed the association of sociodemographic factors to selection of a DNR order and assignment of a healthcare proxy. Year of admission, age, religion, and proxy were independently associated with selection of DNR. In particular, the relative chance of a DNR selection in 2019 compared to 2012 was 3.538 (95% CL = 2.001-6.255, P < .01). There are significant sociodemographic factors that influence DNR utilization, highlighting the need to consider the social and religious backgrounds when engaging patients and their families in end-of-life care. Future studies will need to be conducted on whether these sociodemographic factors influence surviving patients as this study's findings can only be applied to those who have expired.

Stress Correlates Related to Depressive Symptoms Among Young Black Men in Southern California.

Black men experience higher levels of chronic stress, life stressors, and discrimination due to oppressive social and economic conditions. Black men are at greater risk of depression, but most published research on stress and depression has focused on Black people in general, Black women, or older Black men. We sought to determine whether discrimination, perceived stress, major life stress, daily hassles, and social capital were associated with depressive symptoms in young Black men. Survey data were collected from April 2010 to March 2012 in Southern California from a convenience sample of Black men (N = 201). We used two-sample t tests and one-way analysis of variance (ANOVA) to examine the association of stress correlates with depressive symptoms. Logistic regression was conducted to estimate the likelihood of reporting depressive symptoms for each significant correlate. Over half of the sample reported depressive symptoms. Health status, perceived discrimination, urban hassles, perceived stress, and neighborhood trust and safety were significantly related to depressive symptoms. Those who reported higher perceived stress had higher odds of reporting depressive symptoms, whereas lower everyday discrimination experiences were associated with lower odds of depressive symptoms. Future studies should consider examining the effectiveness of embedding coping mechanisms for stress, including perceived discrimination, in health interventions for young Black men to prevent or reduce depression.

Novel Multidisciplinary Vascular Access Team Helps to Improve ICU Workflow Amidst Covid-19 Pandemic.

OBJECTIVE: The surge in critically ill patients has pressured hospitals to expand their intensive care unit capacities and critical care staff. This was difficult given the country's shortage of intensivists. This paper describes the implementation of a multidisciplinary central line placement team and its impact in reducing the vascular access workload of ICU physicians during the height of the COVID-19 pandemic. METHODS: Vascular surgeons, interventionalists, and anesthesiologists, were redeployed to the ICU Access team to place central and arterial lines. Nurses with expertise in vascular access were recruited to the team to streamline consultation and assist with line placement. RESULTS: While 51 central and arterial lines were placed per 100 ICU patients in 2019, there were 87 central and arterial lines placed per 100 COVID-19 ICU patients in the sole month of April, 2020. The ICU Access Team placed 107 of the 226 vascular access devices in April 2020, reducing the procedure-related workload of ICU treating teams by 46%. CONCLUSIONS: The ICU Access Team was able to complete a large proportion of vascular access insertions without reported complications. Given another mass casualty event, this ICU Access Team could be reassembled to rapidly meet the increased vascular access needs of patients.

Improving Care for Critical Care Patients by Strategic Alignment of Quality Goals With a Physician Financial Incentive Model.

BACKGROUND AND OBJECTIVES: The passage of the Affordable Care Act has ignited a shift from the pay-for-performance model to value-based care with a particular relevance in critical care settings. Provider incentive programs are widely considered as a means to reward providers based on the achievement of preset quality metrics. This article aims to demonstrate the effects of a provider incentive program in the critical care delivery system in a large academic center in the Northeastern United States. METHODS: This article describes the results of a retrospective analysis of a performance-driven quality improvement initiative at a critical care facility of an academic medical center using a quasi-experimental pre-/posttest design. A set of quality measures was selected as outcome metrics. Selection criteria for the process measures are as follows: (i) the metric goals should be influenced by the physician's input to a large degree; (ii) the measure must be transparent and accessible within the hospital-wide data reporting system; (iii) the metric that required group effort and interdisciplinary collaboration to achieve; and (iv) the measure must directly affect patient outcome. The outcome metrics are central line-associated bloodstream infections (CLABSIs) and catheter-associated urinary tract infections (CAUTIs), standardized infection ratio (SIR), Foley catheter and central line utilization standardized utilization ratio (SUR), hand hygiene compliance, and adherence to respiratory recovery pathway goals. These metrics were tracked from for 3 years with success defined as achieving set benchmarks for each metric. RESULTS: The average CLABSI SIR and CAUTI SIR across all intensive care units (ICUs) decreased by 44% (P = .05) and 87% (P = .02) over 3 years as well as the central line and Foley catheter utilization falling by 41% and 30%, respectively. Hand hygiene compliance in the ICUs improved for the same period by 27 percentage points, as did compliance with the respiratory recovery pathway program by 4 percentage points. CONCLUSION: The use of a physician-driven financial incentive model in a critical care setting measured by outcome metrics dependent on physician input is successful with rigorous implementation and careful evaluation.

A comprehensive vascular access service can reduce catheter-associated bloodstream infections and promote the appropriate use of vascular access devices.

This study describes the role of a novel vascular access service in the reduction and prevention of central line-associated bloodstream infections (CLABSIs). We conducted a retrospective analysis of data obtained over a span of 24 months after implementation of our vascular access service. We identified a progressive decline in the CLABSI rate and standardized infection ratio (SIR) in 2017 (rate, 1.75; SIR, 1.25) and in 2018 (rate, 1.037; SIR, 0.91). The reduction in CLABSIs was attributed to appropriate triage, insertion, and maintenance of vascular access devices.

Active surveillance documents rates of clinical care seeking due to respiratory illness.

BACKGROUND: Respiratory viral infections are a leading cause of disease worldwide. However, the overall community prevalence of infections has not been properly assessed, as standard surveillance is typically acquired passively among individuals seeking clinical care. METHODS: We conducted a prospective cohort study in which participants provided daily diaries and weekly nasopharyngeal specimens that were tested for respiratory viruses. These data were used to analyze healthcare seeking behavior, compared with cross-sectional ED data and NYC surveillance reports, and used to evaluate biases of medically attended ILI as signal for population respiratory disease and infection. RESULTS: The likelihood of seeking medical attention was virus-dependent: higher for influenza and metapneumovirus (19%-20%), lower for coronavirus and RSV (4%), and 71% of individuals with self-reported ILI did not seek care and half of medically attended symptomatic manifestations did not meet the criteria for ILI. Only 5% of cohort respiratory virus infections and 21% of influenza infections were medically attended and classifiable as ILI. We estimated 1 ILI event per person/year but multiple respiratory infections per year. CONCLUSION: Standard, healthcare-based respiratory surveillance has multiple limitations. Specifically, ILI is an incomplete metric for quantifying respiratory disease, viral respiratory infection, and influenza infection. The prevalence of respiratory viruses, as reported by standard, healthcare-based surveillance, is skewed toward viruses producing more severe symptoms. Active, longitudinal studies are a helpful supplement to standard surveillance, can improve understanding of the overall circulation and burden of respiratory viruses, and can aid development of more robust measures for controlling the spread of these pathogens.

Longitudinal active sampling for respiratory viral infections across age groups.

BACKGROUND: Respiratory viral infections are a major cause of morbidity and mortality worldwide. However, their characterization is incomplete because prevalence estimates are based on syndromic surveillance data. Here, we address this shortcoming through the analysis of infection rates among individuals tested regularly for respiratory viral infections, irrespective of their symptoms. METHODS: We carried out longitudinal sampling and analysis among 214 individuals enrolled at multiple New York City locations from fall 2016 to spring 2018. We combined personal information with weekly nasal swab collection to investigate the prevalence of 18 respiratory viruses among different age groups and to assess risk factors associated with infection susceptibility. RESULTS: 17.5% of samples were positive for respiratory viruses. Some viruses circulated predominantly during winter, whereas others were found year round. Rhinovirus and coronavirus were most frequently detected. Children registered the highest positivity rates, and adults with daily contacts with children experienced significantly more infections than their counterparts without children. CONCLUSION: Respiratory viral infections are widespread among the general population with the majority of individuals presenting multiple infections per year. The observations identify children as the principal source of respiratory infections. These findings motivate further active surveillance and analysis of differences in pathogenicity among respiratory viruses.

Asymptomatic Shedding of Respiratory Virus among an Ambulatory Population across Seasons.

Most observation of human respiratory virus carriage is derived from medical surveillance; however, the infections documented by this surveillance represent only a symptomatic fraction of the total infected population. As the role of asymptomatic infection in respiratory virus transmission is still largely unknown and rates of asymptomatic shedding are not well constrained, it is important to obtain more-precise estimates through alternative sampling methods. We actively recruited participants from among visitors to a New York City tourist attraction. Nasopharyngeal swabs, demographics, and survey information on symptoms, medical history, and recent travel were obtained from 2,685 adults over two seasonal arms. We used multiplex PCR to test swab specimens for a selection of common respiratory viruses. A total of 6.2% of samples (168 individuals) tested positive for at least one virus, with 5.6% testing positive in the summer arm and 7.0% testing positive in the winter arm. Of these, 85 (50.6%) were positive for human rhinovirus (HRV), 65 (38.7%) for coronavirus (CoV), and 18 (10.2%) for other viruses (including adenovirus, human metapneumovirus, influenza virus, and parainfluenza virus). Depending on the definition of symptomatic infection, 65% to 97% of infections were classified as asymptomatic. The best-fit model for prediction of positivity across all viruses included a symptom severity score, Hispanic ethnicity data, and age category, though there were slight differences across the seasonal arms. Though having symptoms is predictive of virus positivity, there are high levels of asymptomatic respiratory virus shedding among the members of an ambulatory population in New York City.IMPORTANCE Respiratory viruses are common in human populations, causing significant levels of morbidity. Understanding the distribution of these viruses is critical for designing control methods. However, most data available are from medical records and thus predominantly represent symptomatic infections. Estimates for asymptomatic prevalence are sparse and span a broad range. In this study, we aimed to measure more precisely the proportion of infections that are asymptomatic in a general, ambulatory adult population. We recruited participants from a New York City tourist attraction and administered nasal swabs, testing them for adenovirus, coronavirus, human metapneumovirus, rhinovirus, influenza virus, respiratory syncytial virus, and parainfluenza virus. At recruitment, participants completed surveys on demographics and symptomology. Analysis of these data indicated that over 6% of participants tested positive for shedding of respiratory virus. While participants who tested positive were more likely to report symptoms than those who did not, over half of participants who tested positive were asymptomatic.