{'fraction_non_alphanumeric': 0.04847725520431766, 'fraction_numerical': 0.03296067848882035, 'mean_word_length': 5.281476997578692, 'pattern_counts': {'":': 0, '<': 1, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Secondary Bacterial Pneumonias and Bloodstream Infections in Patients Hospitalized with COVID-19

Group Name: The Emory COVID-19 Quality and Clinical Research Collaborative Background: Patients hospitalized with COVID-19 are at risk of secondary infections—10%–33% develop bacterial pneumonia and 2%–6% develop bloodstream infection (BSI). We conducted a retrospective cohort study to identify the prevalence, microbiology, and outcomes of secondary pneumonias and BSIs in patients hospitalized with COVID-19. Methods: Patients aged ≥18 years with a positive SARS-CoV-2 real-time polymerase chain reaction assay admitted to 4 academic hospitals in Atlanta, Georgia, between February 15 and May 16, 2020, were included. We extracted electronic medical record data through June 16, 2020. Microbiology tests were performed according to standard protocols. Possible ventilator-associated pneumonia (PVAP) was defined according to Centers for Disease Control and Prevention (CDC) criteria. We assessed in-hospital mortality, comparing patients with and without infections using the χ2 test. SAS University Edition software was used for data analyses. Results: In total, 774 patients were included (median age, 62 years; 49.7% female; 66.6% black). In total, 335 patients (43.3%) required intensive care unit (ICU) admission, 238 (30.7%) required mechanical ventilation, and 120 (15.5%) died. Among 238 intubated patients, 65 (27.3%) had a positive respiratory culture, including 15 with multiple potential pathogens, for a total of 84 potential pathogens. The most common organisms were Staphylococcus aureus (29 of 84; 34.5%), Pseudomonas aeruginosa (16 of 84; 19.0%), and Klebsiella spp (14 of 84; 16.7%). Mortality did not differ between intubated patients with and without a positive respiratory culture (41.5% vs 35.3%; P = .37). Also, 5 patients (2.1%) had a CDC-defined PVAP (1.7 PVAPs per 1,000 ventilator days); none of them died. Among 536 (69.3%) nonintubated patients, 2 (0.4%) had a positive Legionella urine antigen and 1 had a positive respiratory culture (for S. aureus). Of 774 patients, 36 (4.7%) had BSI, including 5 with polymicrobial BSI (42 isolates total). Most BSIs (24 of 36; 66.7%) had ICU onset. The most common organisms were S. aureus (7 of 42; 16.7%), Candida spp (7 of 42; 16.7%), and coagulase-negative staphylococci (5 of 42; 11.9%); 12 (28.6%) were gram-negative. The most common source was central-line–associated BSI (17 of 36; 47.2%), followed by skin (6 of 36; 16.7%), lungs (5 of 36; 13.9%), and urine (4 of 36; 11.1%). Mortality was 50% in patients with BSI versus 13.8% without (p < 0.0001). Conclusions: In a large cohort of patients hospitalized with COVID-19, secondary infections were rare: 2% bacterial pneumonia and 5% BSI. The risk factors for these infections (intubation and central lines, respectively) and causative pathogens reflect healthcare delivery and not a COVID-19–specific effect. Clinicians should adhere to standard best practices for preventing and empirically treating secondary infections in patients hospitalized with COVID-19. Funding: No Disclosures: None


Secondary Bacterial Pneumonias and Bloodstream Infections in Patients Hospitalized with COVID-19
To the Editor: Hospitalized patients, particularly those who are critically ill, are at risk for "secondary" infections (1,2). Initial reports of patients hospitalized with coronavirus disease (COVID-19) indicate that 10-33% develop bacterial pneumonia (3,4) and 2-6% develop bloodstream infection (BSI) (5,6). Few studies have reported patient characteristics or the impact of intensive care unit (ICU) admission on secondary infections (3,(6)(7)(8). We conducted a descriptive study to identify the prevalence, microbiology, and outcomes of secondary pneumonias and BSIs in patients hospitalized with COVID-19.

Methods
The Emory University Institutional Review Board approved this study. Patients :18 years old with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time polymerase chain reaction assay admitted to four academic hospitals in Atlanta, Georgia, from February 15 to May 16, 2020, were included. Data were extracted from the electronic medical record (Cerner Millennium) through June 16, 2020, including comorbidities (identified by International Classification of Diseases, 10th revision codes).
Blood cultures were considered contaminated if one of two sets grew a typically nonpathogenic organism (e.g., coagulase-negative staphylococci) or if the clinical team determined the organism a contaminant. Two of three infectious diseases physicians (M.W.A., D.R.B., and A.B.) reviewed BSIs to determine clinical source and a third (J.T.J.) arbitrated disagreements. Infections were attributed to skin if there was a clinically infected wound or peripheral intravenous line but no central line.
We assessed in-hospital mortality, comparing patients with and without infections using the x 2 test. SAS University Edition (SAS Institute) was used for data analysis.

Discussion
In this cohort of 774 patients hospitalized with COVID-19, nearly onethird required mechanical ventilation, of whom 27% had positive respiratory cultures and 2% had ventilator-associated pneumonia. Thirty-six patients (5%) developed BSI, of whom 50% died. Secondary infections were associated with traditional risk factors for healthcareassociated infections, including indwelling medical devices, and predominantly in the ICU.
Secondary bacterial pneumonia, commonly due to S. pneumoniae and S. aureus, complicates 20-30% of influenza (10), and methicillin-resistant S. aureus pneumonia has been reported with severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) (11). In our cohort of patients with COVID-19, the risk of secondary bacterial pneumonia was much lower: only three nonintubated patients had microbiologic evidence of bacterial pneumonia. In contrast, intubated patients had a high proportion of cultures positive for S. aureus, P. aeruginosa, and Klebsiella spp., which concurs with a UK multicenter study of patients with    COVID-19 with suspected ventilator-associated pneumonia (7). Importantly, respiratory bacterial pathogens isolated from patients with COVID-19 are similar to pathogens that cause hospitalacquired pneumonia in patients without COVID-19 (2,12), with no change from pre-COVID-19 ICU-level resistance rates. These results suggest that hospitalization and intubation are more important than are COVID-19-specific effects in conferring susceptibility to specific pathogens. We did not observe a mortality difference in intubated patients with or without positive respiratory cultures. This may be due to significant empiric antibiotic use and warrants future investigation. BSIs in our cohort were also largely related to risk factors and pathogens associated with hospitalization. The majority (66.7%) were ICU-onset and nearly half (47.2%) were CLABSIs, which may be related to an increase above the pre-COVID-19 baseline in central line-days among ICU patients (J. Jacob, unpublished results). As with respiratory pathogens, the BSI pathogens (S. aureus, Candida spp., and coagulase-negative staphylococci) were typical for healthcareassociated BSI in patients without COVID-19 (12). The observed high proportion of contaminants-severalfold higher than the baseline contamination rate of 0.4-1.8% in study hospitals during January and February 2020-may be due to obtaining blood cultures through central lines to minimize exposure for phlebotomists. Importantly, there was no change in observed daily bathing and central line maintenance practices observed by infection prevention teams. Maintaining central access in critically ill patients with COVID-19 can minimize emergent central line placement and potential healthcare worker SARS-CoV-2 exposure. Clinicians should continue to balance the need for central venous access with risk of CLABSI.
Our study has several limitations. First, these results are from academic hospitals in the southeastern United States and may not be generalizable to other settings. Second, we used International Classification of Diseases, 10th revision codes to determine comorbidities, which may be less accurate than reviewer adjudication. Third, we defined ventilator-associated pneumonia using CDC surveillance definitions (9), which may not represent clinical practice and have not been validated for use in patients with COVID-19. To mitigate this limitation, we presented data on all respiratory pathogens to inform empiric antimicrobials for patients with COVID-19 with suspected ventilator-associated pneumonia. Fourth, our study period was before publication of the RECOVERY (Randomised Evaluation of COVID-19 Therapy) dexamethasone trial (13), and corticosteroids were not routinely administered; only 7% of this cohort received any dexamethasone. Future studies should assess the risk of corticosteroids on secondary infections in patients with COVID-19. Finally, results from this descriptive study are not risk-adjusted and therefore should not be used to infer risk associated with different interventions (e.g., risk of BSI in patients with COVID-19 with vs. without central lines).
Overall, few of the 744 patients hospitalized with COVID-19 developed secondary bacterial pneumonia (2%) or BSI (5%). This is consistent with findings from a living meta-analysis reporting a 7% prevalence of bacterial secondary infections in patients with COVID-19 (14). Our analysis adds to this previous literature by demonstrating that the risk factors for these infections (intubation and central lines, respectively) and causative pathogens reflect healthcare delivery and not a COVID-19-specific effect. Our results suggest that clinicians, especially ICU clinicians, should adhere to standard best practices for preventing and empirically treating secondary infections in patients hospitalized with COVID-19.
Author disclosures are available with the text of this letter at www.atsjournals.org.

Acknowledgment:
The authors thank their colleagues in Emory Healthcare and the Emory Critical Care Center who have worked so hard to provide excellent clinical care during this global pandemic. They also thank the Emory Medical Laboratory personnel, who continued their usual excellence despite a significant increase in specimens from patients with COVID-19.