Fibrotic-Like Pulmonary Radiographic Patterns Are Not Associated With Adverse Outcomes in COVID-19 Chronic Critical Illness.

OBJECTIVES: Pulmonary fibrosis is a feared complication of COVID-19. To characterize the risks and outcomes associated with fibrotic-like radiographic abnormalities in patients with COVID-19-related acute respiratory distress syndrome (ARDS) and chronic critical illness. DESIGN: Single-center prospective cohort study. SETTING: We examined chest CT scans performed between ICU discharge and 30 days after hospital discharge using established methods to quantify nonfibrotic and fibrotic-like patterns. PATIENTS: Adults hospitalized with COVID-19-related ARDS and chronic critical illness (> 21 d of mechanical ventilation, tracheostomy, and survival to ICU discharge) between March 2020 and May 2020. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We tested associations of fibrotic-like patterns with clinical characteristics and biomarkers, and with time to mechanical ventilator liberation and 6-month survival, controlling for demographics, comorbidities, and COVID-19 therapies. A total of 141 of 616 adults (23%) with COVID-19-related ARDS developed chronic critical illness, and 64 of 141 (46%) had a chest CT a median (interquartile range) 66 days (42-82 d) after intubation. Fifty-five percent had fibrotic-like patterns characterized by reticulations and/or traction bronchiectasis. In adjusted analyses, interleukin-6 level on the day of intubation was associated with fibrotic-like patterns (odds ratio, 4.40 per quartile change; 95% CI, 1.90-10.1 per quartile change). Other inflammatory biomarkers, Sequential Organ Failure Assessment score, age, tidal volume, driving pressure, and ventilator days were not. Fibrotic-like patterns were not associated with longer time to mechanical ventilator liberation or worse 6-month survival. CONCLUSIONS: Approximately half of adults with COVID-19-associated chronic critical illness have fibrotic-like patterns that are associated with higher interleukin-6 levels at intubation. Fibrotic-like patterns are not associated with longer time to liberation from mechanical ventilation or worse 6-month survival.

Observational Study of Patients Hospitalized With Neurologic Events After SARS-CoV-2 Vaccination, December 2020-June 2021.

Background and Objectives: The global spread of the COVID-19 pandemic accelerated the vaccine development time line, regulatory approval, and widespread implementation in the population underscoring the importance of postauthorization/postlicensure vaccine safety surveillance. To monitor for vaccine-related adverse events, we prospectively identified patients hospitalized for prespecified neurologic conditions who received mRNA or adenovirus COVID-19 vaccines and assessed cases for potential risk factors and alternative etiologies of the adverse event. Methods: We identified prespecified neurologic conditions in hospitalized individuals within 6 weeks of receipt of a dose of any COVID-19 vaccination between December 11, 2020, and June 22, 2021 (Columbia University Irving Medical Center/New York Presbyterian Hospital, New York City, New York). Clinical data from electronic medical records in these vaccinated patients were reviewed for assessment of contributing risk factors and etiologies for these neurologic conditions by use of a published algorithm. Results: Among 3,830 individuals screened for COVID-19 vaccination status and neurologic conditions, 138 (3.6%) cases were included in this study (126 after mRNA and 6 after Janssen vaccines). The 4 most prevalent neurologic syndromes included ischemic stroke (52, 37.7%), encephalopathy (45, 32.6%), seizure (22, 15.9%), and intracranial hemorrhage (ICH) (13, 9.4%). All 138 cases (100%) had 1 or more risk factors and/or evidence for established causes. Metabolic derangement was the most common etiology for seizures (24, 53.3%) and encephalopathy (5, 22.7%) while hypertension was the most significant risk factor in ischemic stroke (45, 86.5%) and ICH cases (4, 30.8%). Discussion: All cases in this study were determined to have at least 1 risk factor and/or known etiology accounting for their neurologic syndromes. Our comprehensive clinical review of these cases supports the safety of mRNA COVID-19 vaccines.

Elevated cardiac biomarkers and outcomes in children and adolescents with acute COVID-19.

Cardiac involvement associated with multi-system inflammatory syndrome in children has been extensively reported, but the prevalence of cardiac involvement in children with SARS-CoV-2 infection in the absence of inflammatory syndrome has not been well described. In this retrospective, single centre, cohort study, we describe the cardiac involvement found in this population and report on outcomes of patients with and without elevated cardiac biomarkers. Those with multi-system inflammatory syndrome in children, cardiomyopathy, or complex CHD were excluded. Inclusion criteriaz were met by 80 patients during the initial peak of the pandemic at our institution. High-sensitivity troponin T and/or N-terminal pro-brain type natriuretic peptide were measured in 27/80 (34%) patients and abnormalities were present in 5/27 (19%), all of whom had underlying comorbidities. Advanced respiratory support was required in all patients with elevated cardiac biomarkers. Electrocardiographic abnormalities were identified in 14/38 (37%) studies. Echocardiograms were performed on 7/80 patients, and none demonstrated left ventricular dysfunction. Larger studies to determine the true extent of cardiac involvement in children with COVID-19 would be useful to guide recommendations for standard workup and management.

The Role of a Tertiary Level Safety Net Hospital in New York City's 2022 Mpox Outbreak.

Similar to the early phases of the COVID-19 pandemic, New York City was the national epicenter of the ongoing 2022 mpox (formerly monkeypox) outbreak. Cases quickly began to rise in July 2022, primarily in gay, bisexual, or other men who have sex with men. Tools in the form of a reliable diagnostic test, an effective vaccine, and a viable treatment option have been available from the onset, although logistically complex to roll out. The special pathogens program at NYC Health + Hospitals/Bellevue, the flagship facility for the largest public hospital system in the United States, collaborated with multiple departments within Bellevue, the hospital system, and the NYC Department of Health and Mental Hygiene, to swiftly establish ambulatory testing, immunizations, patient-centered inpatient care, and outpatient therapeutics. With the ongoing mpox outbreak, hospitals and local health departments must prepare a systemwide response to identify and isolate patients and provide high-quality care. Findings from our experience can help guide institutions in developing a multipronged, comprehensive response to the ongoing mpox outbreak.

Clinical and Temporal Characterization of COVID-19 Subgroups Using Patient Vector Embeddings of Electronic Health Records.

OBJECTIVE: To identify and characterize clinical subgroups of hospitalized COVID-19 patients. MATERIALS AND METHODS: Electronic health records of hospitalized COVID-19 patients at NewYork-Presbyterian/Columbia University Irving Medical Center were temporally sequenced and transformed into patient vector representations using Paragraph Vector models. K-means clustering was performed to identify subgroups. RESULTS: A diverse cohort of 11,313 patients with COVID-19 and hospitalizations between March 2, 2020 and December 1, 2021 were identified; median [IQR] age: 61.2 [40.3-74.3]; 51.5% female. Twenty subgroups of hospitalized COVID-19 patients, labeled by increasing severity, were characterized by their demographics, conditions, outcomes, and severity (mild-moderate/severe/critical). Subgroup temporal patterns were characterized by the durations in each subgroup, transitions between subgroups, and the complete paths throughout the course of hospitalization. DISCUSSION: Several subgroups had mild-moderate SARS-CoV-2 infections but were hospitalized for underlying conditions (pregnancy, cardiovascular disease (CVD), etc.). Subgroup 7 included solid organ transplant recipients who mostly developed mild-moderate or severe disease. Subgroup 9 had a history of type-2 diabetes, kidney and CVD, and suffered the highest rates of heart failure (45.2%) and end-stage renal disease (80.6%). Subgroup 13 was the oldest (median: 82.7 years) and had mixed severity but high mortality (33.3%). Subgroup 17 had critical disease and the highest mortality (64.6%), with age (median: 68.1 years) being the only notable risk factor. Subgroups 18-20 had critical disease with high complication rates and long hospitalizations (median: 40+ days). All subgroups are detailed in the full text. A chord diagram depicts the most common transitions, and paths with the highest prevalence, longest hospitalizations, lowest and highest mortalities are presented. Understanding these subgroups and their pathways may aid clinicians in their decisions for better management and earlier intervention for patients.

Correlates of psychological distress among undergraduate women engaged in remote learning through a New York City college during the COVID-19 pandemic.

OBJECTIVE: The study's objective is to explore psychological distress (PD) among remote learners during COVID-19. PARTICIPANTS: Female undergraduates matriculated at an NYC college in Winter 2020. METHODS: Using the Kessler-6 scale, we defined PD as no/low (LPD), mild/moderate (MPD), and severe (SPD) and assessed if residing in/near NYC modified associations. RESULTS: PD was common (MPD: 34.1%, SPD: 38.9%). Students identifying as Other/Multiracial had lower MPD odds (aOR = 0.39 [0.17-0.88]). SPD was associated with identifying as White (aOR = 2.02 [1.02-3.99]), unbalanced meals (aOR = 2.59 [1.06-6.30]), violence experience (aOR = 1.77 [1.06-2.94]), no social support (aOR = 3.24 [1.37-7.64]), and loneliness (aOR = 2.52 [1.29-4.95]). Among students in/near NYC, moderate/high drug use (aOR = 2.76 [1.15-6.61]), no social support (aOR = 3.62 [1.10-1.19]), and loneliness (aOR = 2.92 [1.11-7.63]) were SPD correlates. CONCLUSIONS: PD was high and associated with food insecurity, violence experience, no social support, and loneliness. Living in/near NYC modified drug use, loneliness, and social support associations. Mental health initiatives should address modifiable risk factors to ameliorate pandemic-associated PD.

Risk Factors for New Neurologic Diagnoses in Hospitalized Patients With COVID-19: A Case-Control Study in New York City.

Background and Objectives: There have been numerous reports of neurologic manifestations identified in hospitalized patients infected with SARS-CoV-2, the virus that causes COVID-19. Here, we identify the spectrum of associated neurologic symptoms and diagnoses, define the time course of their development, and examine readmission rates and mortality risk posthospitalization in a multiethnic urban cohort. Methods: We identify the occurrence of new neurologic diagnoses among patients with laboratory-confirmed SARS-CoV-2 infection in New York City. A retrospective cohort study was performed on 532 cases (hospitalized patients with new neurologic diagnoses within 6 weeks of positive SARS-CoV-2 laboratory results between March 1, 2020, and August 31, 2020). We compare demographic and clinical features of the 532 cases with 532 controls (hospitalized COVID-19 patients without neurologic diagnoses) in a case-control study with one-to-one matching and examine hospital-related data and outcomes of death and readmission up to 6 months after acute hospitalization in a secondary case-only analysis. Results: Among the 532 cases, the most common new neurologic diagnoses included encephalopathy (478, 89.8%), stroke (66, 12.4%), and seizures (38, 7.1%). In the case-control study, cases were more likely than controls to be male (58.6% vs 52.8%, p = 0.05), had baseline neurologic comorbidities (36.3% vs 13.0%, p < 0.0001), and were to be treated in an intensive care unit (62.0% vs 9.6%, p < 0.0001). Of the 394 (74.1%) cases who survived acute hospitalization, more than half (220 of 394, 55.8%) were readmitted within 6 months, with a mortality rate of 23.2% during readmission. Discussion: Hospitalized patients with SARS-CoV-2 and new neurologic diagnoses have significant morbidity and mortality postdischarge. Further research is needed to define the effect of neurologic diagnoses during acute hospitalization on longitudinal post-COVID-19-related symptoms including neurocognitive impairment.

Reduction in Risk of Death Among Patients Admitted With COVID-19 Between the First and Second Epidemic Waves in New York City.

Background: Many regions have experienced successive epidemic waves of coronavirus disease 2019 (COVID-19) since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with heterogeneous differences in mortality. Elucidating factors differentially associated with mortality between epidemic waves may inform clinical and public health strategies. Methods: We examined clinical and demographic data among patients admitted with COVID-19 during the first (March-August 2020) and second (August 2020-March 2021) epidemic waves at an academic medical center in New York City. Results: Hospitalized patients (n = 4631) had lower overall and 30-day in-hospital mortality, defined as death or discharge to hospice, during the second wave (14% and 11%) than the first (22% and 21%). The wave 2 in-hospital mortality decrease persisted after adjusting for several potential confounders. Adjusting for the volume of COVID-19 admissions, a measure of health system strain, accounted for the mortality difference between waves. Several demographic and clinical patient factors were associated with an increased risk of mortality independent of wave: SARS-CoV-2 cycle threshold, do-not-intubate status, oxygen requirement, and intensive care unit admission. Conclusions: This work suggests that the increased in-hospital mortality rates observed during the first epidemic wave were partly due to strain on hospital resources. Preparations for future epidemics should prioritize evidence-based patient risks, treatment paradigms, and approaches to augment hospital capacity.

Reduction in risk of death among patients admitted with COVID-19 between first and second epidemic waves in New York City

Background Many regions have experienced successive epidemic waves of COVID-19 since the emergence of SARS-CoV-2 with heterogeneous differences in mortality. Elucidating factors differentially associated with mortality between epidemic waves may inform clinical and public health strategies. Methods We examined clinical and demographic data among patients admitted with COVID-19 during the first (March-August 2020) and second (August 2020-March 2021) epidemic waves at an academic medical center in New York City. Results Hospitalized patients (N = 4631) had lower overall and 30-day in-hospital mortality, defined as death or discharge to hospice, during the second wave (14% and 11%) than the first (22% and 21%). The wave 2 in-hospital mortality decrease persisted after adjusting for several potential confounders. Adjusting for the volume of COVID-19 admissions, a measure of health system strain, accounted for the mortality difference between waves. Several demographic and clinical patient factors were associated with an increased risk of mortality independent of wave;SARS-CoV-2 cycle threshold, Do-Not-Intubate status, oxygen requirement, and intensive care unit admission. Conclusions This work suggests that increased in-hospital mortality rates observed during the first epidemic wave were partly due to strain on hospital resources. Preparations for future epidemics should prioritize evidence-based patient risks, treatment paradigms, and approaches to augment hospital capacity.

Bacterial Pneumonia and Respiratory Culture Utilization among Hospitalized Patients with and without COVID-19 in a New York City Hospital.

COVID-19 is associated with prolonged hospitalization and a high risk of intubation, which raises concern for bacterial coinfection and antimicrobial resistance. Previous research has shown a wide range of bacterial pneumonia rates for COVID-19 patients in a variety of clinical and demographic settings, but none have compared hospitalized COVID-19 patients to patients testing negative for severe acute respiratory syndrome coronavirus (SARS-CoV-2) in similar care settings. We performed a retrospective cohort study on hospitalized patients with COVID-19 testing from March 10th, 2020 to December 31st, 2020. A total of 19,219 patients were included, of which 3,796 tested positive for SARS-CoV-2. We found a 2.6-fold increase (P < 0.001) in respiratory culture ordering in COVID-19 patients. On a per-patient basis, COVID-19 patients were 1.5-fold more likely than non-COVID patients to have positive respiratory cultures (46.8% versus 30.9%, P < 0.001), which was primarily driven by patients requiring intubation. Among patients with pneumonia, a significantly higher proportion of COVID-19 patients had ventilator-associated pneumonia (VAP) relative to non-COVID patients (86.3% versus 70.8%, P < 0.001), but a lower proportion had community-acquired (11.2% vs 25.5%, P < 0.01) pneumonia. There was also a significantly higher proportion of respiratory cultures positive for methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae, and antibiotic-resistant organisms in COVID-19 patients. Increased rates of respiratory culture ordering for COVID-19 patients therefore appear to be clinically justified for patients requiring intubation, but further research is needed to understand how SARS-CoV-2 increases the risk of VAP.

Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis.

BACKGROUND: COVID-19 messenger RNA (mRNA) vaccines have demonstrated efficacy and effectiveness in preventing symptomatic COVID-19, while being relatively safe in trial studies. However, vaccine breakthrough infections have been reported. OBJECTIVE: This study aims to identify risk factors associated with COVID-19 breakthrough infections among fully mRNA-vaccinated individuals. METHODS: We conducted a series of observational retrospective analyses using the electronic health records (EHRs) of the Columbia University Irving Medical Center/New York Presbyterian (CUIMC/NYP) up to September 21, 2021. New York City (NYC) adult residences with at least 1 polymerase chain reaction (PCR) record were included in this analysis. Poisson regression was performed to assess the association between the breakthrough infection rate in vaccinated individuals and multiple risk factors-including vaccine brand, demographics, and underlying conditions-while adjusting for calendar month, prior number of visits, and observational days in the EHR. RESULTS: The overall estimated breakthrough infection rate was 0.16 (95% CI 0.14-0.18). Individuals who were vaccinated with Pfizer/BNT162b2 (incidence rate ratio [IRR] against Moderna/mRNA-1273=1.66, 95% CI 1.17-2.35) were male (IRR against female=1.47, 95% CI 1.11-1.94) and had compromised immune systems (IRR=1.48, 95% CI 1.09-2.00) were at the highest risk for breakthrough infections. Among all underlying conditions, those with primary immunodeficiency, a history of organ transplant, an active tumor, use of immunosuppressant medications, or Alzheimer disease were at the highest risk. CONCLUSIONS: Although we found both mRNA vaccines were effective, Moderna/mRNA-1273 had a lower incidence rate of breakthrough infections. Immunocompromised and male individuals were among the highest risk groups experiencing breakthrough infections. Given the rapidly changing nature of the SARS-CoV-2 pandemic, continued monitoring and a generalizable analysis pipeline are warranted to inform quick updates on vaccine effectiveness in real time.

Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City.

Public health interventions such as social distancing and mask wearing decrease the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether they decrease the viral load of infected patients and whether changes in viral load impact mortality from coronavirus disease 2019 (COVID-19). We evaluated 6923 patients with COVID-19 at six New York City hospitals from March 15-May 14, 2020, corresponding with the implementation of public health interventions in March. We assessed changes in cycle threshold (CT) values from reverse transcription-polymerase chain reaction tests and in-hospital mortality and modeled the impact of viral load on mortality. Mean CT values increased between March and May, with the proportion of patients with high viral load decreasing from 47.7% to 7.8%. In-hospital mortality increased from 14.9% in March to 28.4% in early April, and then decreased to 8.7% by May. Patients with high viral loads had increased mortality compared to those with low viral loads (adjusted odds ratio 2.34). If viral load had not declined, an estimated 69 additional deaths would have occurred (5.8% higher mortality). SARS-CoV-2 viral load steadily declined among hospitalized patients in the setting of public health interventions, and this correlated with decreases in mortality.

Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19.

Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV. However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown. Here, we aimed to elucidate the relationship between saliva microbiota and SARS-CoV-2 in a cohort of newly hospitalized COVID-19 patients and controls. We used 16S rRNA sequencing to compare microbiome diversity and taxonomic composition between COVID-19 patients (n = 53) and controls (n = 59) and based on saliva SARS-CoV-2 viral load as measured using reverse transcription PCR (RT-PCR). The saliva microbiome did not differ markedly between COVID-19 patients and controls. However, we identified significant differential abundance of numerous taxa based on saliva SARS-CoV-2 viral load, including multiple species within Streptococcus and Prevotella. IMPORTANCE Alterations to the saliva microbiome based on SARS-CoV-2 viral load indicate potential biologically relevant bacterial-viral relationships which may affect clinical outcomes in COVID-19 disease.

Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York.

SARS-CoV-2 infections have surged across the globe in recent months, concomitant with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten the efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies that are in clinical use and is less susceptible to neutralization by plasma from individuals who had recovered from SARS-CoV-2 infection or serum from vaccinated individuals, posing a modest antigenic challenge. The presence of the B.1.526 lineage has now been reported in all 50 states in the United States and in many other countries. B.1.526 rapidly replaced earlier lineages in New York, with an estimated transmission advantage of 35%. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrently with the rise of B.1.1.7 and ensuing variants.

Supervised Machine Learning Approach to Identify Early Predictors of Poor Outcome in Patients with COVID-19 Presenting to a Large Quaternary Care Hospital in New York City.

BACKGROUND: The progression of clinical manifestations in patients with coronavirus disease 2019 (COVID-19) highlights the need to account for symptom duration at the time of hospital presentation in decision-making algorithms. METHODS: We performed a nested case-control analysis of 4103 adult patients with COVID-19 and at least 28 days of follow-up who presented to a New York City medical center. Multivariable logistic regression and classification and regression tree (CART) analysis were used to identify predictors of poor outcome. RESULTS: Patients presenting to the hospital earlier in their disease course were older, had more comorbidities, and a greater proportion decompensated (<4 days, 41%; 4-8 days, 31%; >8 days, 26%). The first recorded oxygen delivery method was the most important predictor of decompensation overall in CART analysis. In patients with symptoms for <4, 4-8, and >8 days, requiring at least non-rebreather, age ≥ 63 years, and neutrophil/lymphocyte ratio ≥ 5.1; requiring at least non-rebreather, IL-6 ≥ 24.7 pg/mL, and D-dimer ≥ 2.4 µg/mL; and IL-6 ≥ 64.3 pg/mL, requiring non-rebreather, and CRP ≥ 152.5 mg/mL in predictive models were independently associated with poor outcome, respectively. CONCLUSION: Symptom duration in tandem with initial clinical and laboratory markers can be used to identify patients with COVID-19 at increased risk for poor outcomes.

Placental response to maternal SARS-CoV-2 infection.

The coronavirus disease 2019 (COVID-19) pandemic affected people at all ages. Whereas pregnant women seemed to have a worse course of disease than age-matched non-pregnant women, the risk of feto-placental infection is low. Using a cohort of 66 COVID-19-positive women in late pregnancy, we correlated clinical parameters with disease severity, placental histopathology, and the expression of viral entry and Interferon-induced transmembrane (IFITM) antiviral transcripts. All newborns were negative for SARS-CoV-2. None of the demographic parameters or placental histopathological characteristics were associated with disease severity. The fetal-maternal transfer ratio for IgG against the N or S viral proteins was commonly less than one, as recently reported. We found that the expression level of placental ACE2, but not TMPRSS2 or Furin, was higher in women with severe COVID-19. Placental expression of IFITM1 and IFITM3, which have been implicated in antiviral response, was higher in participants with severe disease. We also showed that IFITM3 protein expression, which localized to early and late endosomes, was enhanced in severe COVID-19. Our data suggest an association between disease severity and placental SARS-CoV-2 processing and antiviral pathways, implying a role for these proteins in placental response to SARS-CoV-2.

Cycle Thresholds Among Solid Organ Transplant Recipients Testing Positive for SARS-CoV-2.

BACKGROUND: The optimal duration of transmission-based precautions among immunocompromised patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. METHODS: Retrospective review of patients with solid organ transplant with positive SARS-CoV-2 polymerase chain reaction result from nasopharyngeal specimens admitted to the hospital between March 13, 2020 and May 15, 2020. RESULTS: Twenty-one percent of solid organ transplant recipients with positive SARS-CoV-2 polymerase chain reaction detected ≥20 d after symptom onset (or after first positive test among asymptomatic individuals) had a low cycle threshold (ie, high viral load). The majority of these patients were asymptomatic or symptomatically improved. CONCLUSIONS: Solid organ transplant recipients may have prolonged high viral burden of SARS-CoV-2. Further data are needed to understand whether cycle threshold data can help inform strategies for prevention of healthcare-associated transmission of SARS-CoV-2 and for appropriate discontinuation of transmission-based precautions.

Characterization of Bacterial and Fungal Infections in Hospitalized Patients With Coronavirus Disease 2019 and Factors Associated With Health Care-Associated Infections.

BACKGROUND: Patients hospitalized with coronavirus disease 2019 (COVID-19) are at increased risk of health care-associated infections (HAIs), especially with prolonged hospital stays. We sought to identify incidence, antimicrobial susceptibilities, and outcomes associated with bacterial/fungal secondary infections in a large cohort of patients with COVID-19. METHODS: We evaluated adult patients diagnosed with COVID-19 between 2 March and 31 May 2020 and hospitalized >24 hours. Data extracted from medical records included diagnoses, vital signs, laboratory results, microbiological data, and antibiotic use. Microbiologically confirmed bacterial and fungal pathogens from clinical cultures were evaluated to characterize community- and health care-associated infections, including describing temporal changes in predominant organisms on presentation and throughout hospitalization. Univariable and multivariable logistic regression analyses were performed to investigate risk factors for HAIs. RESULTS: A total of 3028 patients were included and accounted for 899 positive clinical cultures. Overall, 516 (17%) patients with positive cultures met criteria for infection. Community-associated coinfections were identified in 183 (6%) patients, whereas HAIs occurred in 350 (12%) patients. Fifty-seven percent of HAIs were caused by gram-negative bacteria and 19% by fungi. Antibiotic resistance increased with longer hospital stays, with incremental increases in the proportion of vancomycin resistance among enterococci and ceftriaxone and carbapenem resistance among Enterobacterales. Intensive care unit stay, invasive mechanical ventilation, and steroids were associated with HAIs. CONCLUSIONS: HAIs occur in a small proportion of patients hospitalized with COVID-19 and are most often caused by gram-negative and fungal pathogens. Antibiotic resistance is more prevalent with prolonged hospital stays. Antimicrobial stewardship is imperative in this population to minimize unnecessary broad-spectrum antibiotic use.

Characterising the long-term clinical outcomes of 1190 hospitalised patients with COVID-19 in New York City: a retrospective case series.

OBJECTIVE: To characterise the long-term outcomes of patients with COVID-19 admitted to a large New York City medical centre at 3 and 6 months after hospitalisation and describe their healthcare usage, symptoms, morbidity and mortality. DESIGN: Retrospective cohort through manual chart review of the electronic medical record. SETTING: NewYork-Presbyterian/Columbia University Irving Medical Center, a quaternary care academic medical centre in New York City. PARTICIPANTS: The first 1190 consecutive patients with symptoms of COVID-19 who presented to the hospital for care between 1 March and 8 April 2020 and tested positive for SARS-CoV-2 on reverse transcriptase PCR assay. MAIN OUTCOME MEASURES: Type and frequency of follow-up encounters, self-reported symptoms, morbidity and mortality at 3 and 6 months after presentation, respectively; patient disposition information prior to admission, at discharge, and at 3 and 6 months after hospital presentation. RESULTS: Of the 1190 reviewed patients, 929 survived their initial hospitalisation and 261 died. Among survivors, 570 had follow-up encounters (488 at 3 months and 364 at 6 months). An additional 33 patients died in the follow-up period. In the first 3 months after admission, most encounters were telehealth visits (59%). Cardiopulmonary symptoms (35.7% and 28%), especially dyspnoea (22.1% and 15.9%), were the most common reported symptoms at 3-month and 6-month encounters, respectively. Additionally, a large number of patients reported generalised (26.4%) or neuropsychiatric (24.2%) symptoms 6 months after hospitalisation. Patients with severe COVID-19 were more likely to have reduced mobility, reduced independence or a new dialysis requirement in the 6 months after hospitalisation. CONCLUSIONS: Patients hospitalised with SARS-CoV-2 infection reported persistent symptoms up to 6 months after diagnosis. These results highlight the long-term morbidity of COVID-19 and its burden on patients and healthcare resources.