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2.
Open forum infectious diseases ; 8(Suppl 1):S280-S280, 2021.
Article in English | EuropePMC | ID: covidwho-1563896

ABSTRACT

Background Antibiotic use among patients with COVID-19 is common, exceeds the prevalence of probable bacterial co-infection, and promotes development of resistant organisms. Lack of diagnostic microbiological data may prolong empiric broad-spectrum therapy. Here we evaluate the use of the BioFire FilmArray pneumonia panel (PP), a novel rapid diagnostic test, and antibiotic decisions among intensive care unit (ICU) patients with COVID-19. Methods We conducted a retrospective review of adult ICU patients admitted with COVID-19 between January 2020 and May 2021 at an academic medical center. ICU patients who underwent bronchoscopy/bronchoalveolar lavage (BAL) with PP (PP group) were matched by age (< 65 or ≥65), BMI (< 30 or ≥30), and BAL date (within 60 days) to ICU patients who did not undergo BAL (no-BAL group). PP patients were matched by age and BMI to ICU patients who underwent BAL without PP (no-PP group). Antibiotic use was compared between groups. Chi squared analysis, t-test, and ANOVA were used for comparisons as appropriate. Results 65 patients were included;the majority were male (65%), < 65 years (86%), and had BMI ≥30 (54%) (Table 1). Only 17 no-PP matches were identified for PP patients due to infrequent BALs. Similar proportion of patients in PP and no-PP groups had organisms identified from BAL (54% vs. 47%, p=0.65). Among PP patients with a detected organism, all (n=13) had subsequent changes in antibiotic regimen ≤72 hours after BAL;10/13 (77%) had a change targeted to detected organism and 5/13 (39%) had antibiotic narrowing. Among PP patients with no detected organism, only 4/11 (36%) had antibiotic narrowing or maintenance off antibiotics. In all groups, average antibiotic use exceeded 70% of admission duration. Table 1. Patient characteristics and antibiotic management. Abbreviations: BAL - bronchoalveolar lavage Conclusion Rapid, highly sensitive diagnostic tests have potential to guide clinical decisions and promote antibiotic stewardship among patients with severe viral pneumonia and suspected bacterial co-infection. In this descriptive analysis, antibiotic management did not differ significantly with use of PP. While most patients with detected organism on PP had targeted antibiotic changes, a negative PP did not appear to influence antibiotic narrowing. Larger studies and provider education are needed to evaluate potential of the PP for antibiotic stewardship. Disclosures Jason Zucker, MD, MS, Nothing to disclose Daniel A. Green, M.D., BioFire (Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member) Deborah Theodore, MD, BioFire Diagnostics (Other Financial or Material Support, Donation of testing materials to support investigator-initiated research)

3.
Nat Med ; 27(4): 601-615, 2021 04.
Article in English | MEDLINE | ID: covidwho-1517636

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic, which has resulted in global healthcare crises and strained health resources. As the population of patients recovering from COVID-19 grows, it is paramount to establish an understanding of the healthcare issues surrounding them. COVID-19 is now recognized as a multi-organ disease with a broad spectrum of manifestations. Similarly to post-acute viral syndromes described in survivors of other virulent coronavirus epidemics, there are increasing reports of persistent and prolonged effects after acute COVID-19. Patient advocacy groups, many members of which identify themselves as long haulers, have helped contribute to the recognition of post-acute COVID-19, a syndrome characterized by persistent symptoms and/or delayed or long-term complications beyond 4 weeks from the onset of symptoms. Here, we provide a comprehensive review of the current literature on post-acute COVID-19, its pathophysiology and its organ-specific sequelae. Finally, we discuss relevant considerations for the multidisciplinary care of COVID-19 survivors and propose a framework for the identification of those at high risk for post-acute COVID-19 and their coordinated management through dedicated COVID-19 clinics.


Subject(s)
COVID-19/complications , SARS-CoV-2 , Acute Disease , COVID-19/epidemiology , COVID-19/ethnology , COVID-19/therapy , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/therapy , Humans , Patient Advocacy , Syndrome , Systemic Inflammatory Response Syndrome/epidemiology , Systemic Inflammatory Response Syndrome/therapy , Venous Thromboembolism/epidemiology , Venous Thromboembolism/prevention & control
4.
Open Forum Infect Dis ; 8(6): ofab201, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1261052

ABSTRACT

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.

5.
PLoS One ; 16(4): e0249349, 2021.
Article in English | MEDLINE | ID: covidwho-1172877

ABSTRACT

BACKGROUND: Tocilizumab, an interleukin-6 receptor blocker, has been used in the inflammatory phase of COVID-19, but its impact independent of corticosteroids remains unclear in patients with severe disease. METHODS: In this retrospective analysis of patients with COVID-19 admitted between March 2 and April 14, 2020 to a large academic medical center in New York City, we describe outcomes associated with tocilizumab 400 mg (without methylprednisolone) compared to a propensity-matched control. The primary endpoints were change in a 7-point ordinal scale of oxygenation and ventilator free survival, both at days 14 and 28. Secondary endpoints include incidence of bacterial superinfections and gastrointestinal perforation. Primary outcomes were evaluated using t-test. RESULTS: We identified 33 patients who received tocilizumab and matched 74 controls based on demographics and health measures upon admission. After adjusting for illness severity and baseline ordinal scale, we failed to find evidence of an improvement in hypoxemia based on an ordinal scale at hospital day 14 in the tocilizumab group (OR 2.2; 95% CI, 0.7-6.5; p = 0.157) or day 28 (OR 1.1; 95% CI, 0.4-3.6; p = 0.82). There also was no evidence of an improvement in ventilator-free survival at day 14 (OR 0.8; 95% CI, 0.18-3.5; p = 0.75) or day 28 (OR 1.1; 95% CI, 0.1-1.8; p = 0.23). There was no increase in secondary bacterial infection rates in the tocilizumab group compared to controls (OR 0.37; 95% CI, 0.09-1.53; p = 0.168). CONCLUSIONS: There was no evidence to support an improvement in hypoxemia or ventilator-free survival with use of tocilizumab 400 mg in the absence of corticosteroids. No increase in secondary bacterial infections was observed in the group receiving tocilizumab.


Subject(s)
Antibodies, Monoclonal, Humanized/administration & dosage , Bacterial Infections , COVID-19 , Disease Outbreaks , Hospitals, Teaching , SARS-CoV-2 , Antibodies, Monoclonal, Humanized/adverse effects , Bacterial Infections/etiology , Bacterial Infections/mortality , COVID-19/drug therapy , COVID-19/mortality , Disease-Free Survival , Female , Humans , Male , Middle Aged , New York City/epidemiology , Respiration, Artificial , Retrospective Studies , Survival Rate
6.
Nat Med ; 27(4): 601-615, 2021 04.
Article in English | MEDLINE | ID: covidwho-1147038

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic, which has resulted in global healthcare crises and strained health resources. As the population of patients recovering from COVID-19 grows, it is paramount to establish an understanding of the healthcare issues surrounding them. COVID-19 is now recognized as a multi-organ disease with a broad spectrum of manifestations. Similarly to post-acute viral syndromes described in survivors of other virulent coronavirus epidemics, there are increasing reports of persistent and prolonged effects after acute COVID-19. Patient advocacy groups, many members of which identify themselves as long haulers, have helped contribute to the recognition of post-acute COVID-19, a syndrome characterized by persistent symptoms and/or delayed or long-term complications beyond 4 weeks from the onset of symptoms. Here, we provide a comprehensive review of the current literature on post-acute COVID-19, its pathophysiology and its organ-specific sequelae. Finally, we discuss relevant considerations for the multidisciplinary care of COVID-19 survivors and propose a framework for the identification of those at high risk for post-acute COVID-19 and their coordinated management through dedicated COVID-19 clinics.


Subject(s)
COVID-19/complications , SARS-CoV-2 , Acute Disease , COVID-19/epidemiology , COVID-19/ethnology , COVID-19/therapy , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/therapy , Humans , Patient Advocacy , Syndrome , Systemic Inflammatory Response Syndrome/epidemiology , Systemic Inflammatory Response Syndrome/therapy , Venous Thromboembolism/epidemiology , Venous Thromboembolism/prevention & control
7.
Antimicrob Agents Chemother ; 65(4)2021 03 18.
Article in English | MEDLINE | ID: covidwho-1048648

ABSTRACT

The role of procalcitonin in identifying community-associated bacterial infections among patients with coronavirus disease 2019 is not yet established. In 2,443 patients of whom 148 had bacterial coinfections, mean procalcitonin levels were significantly higher with any bacterial infection (13.16 ± 51.19 ng/ml; P = 0.0091) and with bacteremia (34.25 ± 85.01 ng/ml; P = 0.0125) than without infection (2.00 ± 15.26 ng/ml). Procalcitonin (cutoff, 0.25 or 0.50 ng/ml) did not reliably identify bacterial coinfections but may be useful in excluding bacterial infection.


Subject(s)
Bacterial Infections/drug therapy , COVID-19/microbiology , Community-Acquired Infections/drug therapy , Procalcitonin/therapeutic use , Aged , Bacteremia/drug therapy , Bacteremia/microbiology , Bacterial Infections/microbiology , Bacterial Infections/virology , Coinfection/drug therapy , Coinfection/microbiology , Coinfection/virology , Community-Acquired Infections/microbiology , Female , Humans , Male , Middle Aged
9.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-999199

ABSTRACT

A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase in blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We sought to evaluate the utilization and diagnostic yield of blood cultures during the COVID-19 pandemic to determine prevalence and common etiologies of bacteremia and to inform a diagnostic approach to relieve blood culture overutilization. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Ordering volume increased by 34.8% in the second half of March 2020 compared to the level in the first half of the month. The rate of bacteremia was significantly lower among COVID-19 patients (3.8%) than among COVID-19-negative patients (8.0%) and those not tested (7.1%) (P < 0.001). COVID-19 patients had a high proportion of organisms reflective of commensal skin microbiota, which, when excluded, reduced the bacteremia rate to 1.6%. More than 98% of all positive cultures were detected within 4 days of incubation. Bloodstream infections are very rare for COVID-19 patients, which supports the judicious use of blood cultures in the absence of compelling evidence for bacterial coinfection. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity.


Subject(s)
Bacteremia/diagnosis , Bacteremia/epidemiology , Blood Culture/statistics & numerical data , Coinfection/diagnosis , Coinfection/epidemiology , Coronavirus Infections/complications , Coronavirus Infections/epidemiology , Pneumonia, Viral/complications , Pneumonia, Viral/epidemiology , Betacoronavirus/isolation & purification , COVID-19 , Hospitals , Humans , New York City/epidemiology , Pandemics , Prevalence , Retrospective Studies , SARS-CoV-2
10.
J Antimicrob Chemother ; 76(2): 380-384, 2021 01 19.
Article in English | MEDLINE | ID: covidwho-929995

ABSTRACT

BACKGROUND: Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE). OBJECTIVES: We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19. METHODS: We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis. RESULTS: We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data. CONCLUSIONS: While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.


Subject(s)
COVID-19/microbiology , Carbapenem-Resistant Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/microbiology , Aged , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/therapeutic use , Antiviral Agents/administration & dosage , Antiviral Agents/therapeutic use , Bacterial Proteins/genetics , COVID-19/complications , COVID-19/drug therapy , COVID-19/epidemiology , Carbapenem-Resistant Enterobacteriaceae/enzymology , Carbapenem-Resistant Enterobacteriaceae/genetics , Cohort Studies , Comorbidity , Enterobacteriaceae Infections/complications , Enterobacteriaceae Infections/drug therapy , Enterobacteriaceae Infections/epidemiology , Female , Hospitals , Humans , Male , Middle Aged , Nanopore Sequencing , New York City/epidemiology , Phylogeny , Retrospective Studies , SARS-CoV-2 , beta-Lactamases/genetics
11.
Clin Infect Dis ; 72(9): e367-e372, 2021 05 04.
Article in English | MEDLINE | ID: covidwho-696354

ABSTRACT

BACKGROUND: The efficacy and safety of methylprednisolone in mechanically ventilated patients with acute respiratory distress syndrome resulting from coronavirus disease 2019 (COVID-19) are unclear. In this study, we evaluated the association between use of methylprednisolone and key clinical outcomes. METHODS: Clinical outcomes associated with the use of methylprednisolone were assessed in an unmatched, case-control study; a subset of patients also underwent propensity-score matching. Patients were admitted between 1 March and 12 April, 2020. The primary outcome was ventilator-free days by 28 days after admission. Secondary outcomes included extubation, mortality, discharge, positive cultures, and hyperglycemia. RESULTS: A total of 117 patients met inclusion criteria. Propensity matching yielded a cohort of 42 well-matched pairs. Groups were similar except for hydroxychloroquine and azithromycin use, which were more common in patients who did not receive methylprednisolone. Mean ventilator-free days were significantly higher in patients treated with methylprednisolone (6.21 ±â€…7.45 vs 3.14 ±â€…6.22; P = .044). The probability of extubation was also increased in patients receiving methylprednisolone (45% vs 21%; P = .021), and there were no significant differences in mortality (19% vs 36%; P = .087). In a multivariable linear regression analysis, only methylprednisolone use was associated with a higher number of ventilator-free days (P = .045). The incidence of positive cultures and hyperglycemia were similar between groups. CONCLUSIONS: Methylprednisolone was associated with increased ventilator-free days and higher probability of extubation in a propensity-score matched cohort. Randomized, controlled studies are needed to further define methylprednisolone use in patients with COVID-19.


Subject(s)
COVID-19 , Methylprednisolone , Case-Control Studies , Humans , Methylprednisolone/therapeutic use , Respiration, Artificial , SARS-CoV-2 , Treatment Outcome
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