Bacterial co-infection and antibiotic stewardship in patients with COVID-19: a systematic review and meta-analysis

Antibiotic Treatment in Patients Hospitalized for Nonsevere COVID-19

Importance

Patients hospitalized with nonsevere COVID-19 continue to receive community-acquired pneumonia (CAP) antibiotic treatment despite a low risk of bacterial coinfection. Unnecessary antibiotic prescribing contributes to global antibiotic resistance and also poses a threat to individual patients.

Objective

To examine the association of CAP antibiotic treatment started on admission with clinical outcomes among a large sample of patients hospitalized for nonsevere COVID-19 in hospitals across the US.

Design, Setting, and Participants

This retrospective cohort study used a target trial emulation design. Participants were adult, immunocompetent patients admitted to general care for COVID-19 from April 2020 to December 2023 at 1053 US-based acute-care hospitals that contribute data to the Premier Healthcare Database. Patients with nonpneumonia bacterial infections present on admission were excluded. Data were analyzed from April to October 2024.

Exposure

Receipt of a CAP antibiotic regimen on the day of admission.

Main Outcomes and Measures

The primary outcome was a composite measure of deterioration (vasopressor, high-flow oxygen, noninvasive ventilation, invasive mechanical ventilation, intermediate care, intensive care unit admission) and in-hospital mortality occurring on day 2 or later. The association between receipt of antibiotic therapy and the primary outcome was assessed using propensity methods while adjusting for a broad set of potential confounders, including cotreatments.

Results

The cohort included 520 405 patients with COVID-19 (median [IQR] age, 66 [53-78] years; 266 186 [51.2%] male), including 92 708 Black patients (17.8%), 63 619 Hispanic patients (12.2%), and 304 649 White patients (58.5%); 279 656 patients (53.7%) had Medicare insurance. A total of 160 482 patients (30.8%) were treated with a CAP antibiotic regimen on day 1 of admission. The primary composite outcome was higher in the CAP group (20.8%) compared with the unexposed (no antibiotic) group (18.4%), but the difference did not meet the predefined criteria for clinical significance (ASD, 4.1%). Patients who received CAP antibiotics had higher odds of poor clinical outcomes (propensity matched-odds ratio [OR], 1.03 [95% CI, 1.01-1.05]; P = .003; inverse probability treatment weighted-OR, 1.03 [95% CI, 1.02-1.05]; P < .001; standardized mortality ratio weighted-OR, 1.10 [95% CI, 1.08-1.12]; P < .001).

Conclusions and Relevance

In this large cohort study of patients hospitalized with nonsevere COVID-19, there was no clinically meaningful difference in outcomes with early antibiotic treatment. Given the risks associated with unnecessary antibiotic treatment, these results argue against routine antibiotic use in this population.

Association between nirmatrelvir/ritonavir treatment and antibiotic prescribing in the outpatient setting among patients with COVID-19

Coronavirus disease 2019 (COVID-19) has complicated the management of acute respiratory infections and impacted antibiotic use. We assessed the relationship between nirmatrelvir/ritonavir (NMV/r) receipt and outpatient antibiotic prescribing among patients with COVID-19 in a large national health system. We conducted a retrospective cohort study among outpatients enrolled in the Veterans Affairs Healthcare System who had a positive severe acute respiratory syndrome coronavirus 2 test or COVID-19 diagnosis and were eligible for NMV/r treatment between 1 April 2022 and 31 March 2024. NMV/r-treated patients were compared with those who did not receive NMV/r and were considered unexposed until NMV/r was dispensed. We assessed the relationship between NMV/r receipt and being prescribed an outpatient antibiotic in the 30 days after a COVID-19 diagnosis using adjusted Cox proportional hazards regression. We included 302,600 NMV/r-eligible outpatients with COVID-19, of whom 67,649 received NMV/r and 234,951 did not receive NMV/r. NMV/r-treated patients were less likely to receive outpatient antibiotics compared to those who did not receive NMV/r (7.2% [4,901/67,649] vs 9.2% [21,533/234,951], respectively; adjusted hazard ratio [HR] 0.65, 95% CI: 0.63‒0.68). After excluding patients who received an antibiotic prescription upon COVID-19 diagnosis (i.e., likely empiric therapy), this relationship was attenuated (HR: 0.91, 95% CI: 0.87‒0.95). NMV/r-eligible patients with COVID-19 who received NMV/r were 35% less likely to be prescribed outpatient antibiotics compared to patients who did not receive NMV/r, possibly driven by a diminished perceived need for empiric antibiotic therapy. Treatment with NMV/r may reduce unnecessary outpatient antibiotic use. Antibiotics should be reserved for patients with a high suspicion of bacterial co-infection.IMPORTANCEAntimicrobial resistance, driven by the overuse of antibiotics, is a major global health threat. The coronavirus disease 2019 (COVID-19) pandemic has complicated this issue, with antibiotics often prescribed to patients with COVID-19 despite being ineffective against viruses. These practices, typically aimed at preventing or empirically treating rare bacterial co-infections, have raised concerns about accelerating resistance. The antiviral nirmatrelvir/ritonavir (NMV/r), widely used in high-risk patients with COVID-19 to prevent severe illness, offers an opportunity to reassess antibiotic use in patients with respiratory infections. Our study of over 300,000 patients in a national healthcare system found that those treated with NMV/r for COVID-19 were 35% less likely to receive antibiotics than those who did not receive the antiviral. Lower antibiotic use among patients treated with NMV/r may reflect a reduction in unnecessary outpatient antibiotic use. These findings highlight the potential role of antivirals in supporting antibiotic stewardship and addressing a critical public health challenge.

National Trends in Antibiotic Prescribing for Adults Hospitalized With Coronavirus Disease 2019 and Other Viral Respiratory Infections

Background

Significant concerns have been raised regarding the overuse of antibiotics among patients hospitalized for coronavirus disease 2019 (COVID-19) and the broad impact of the pandemic on antimicrobial stewardship in acute care. We sought to compare potentially unnecessary antibiotic prescribing over time among patients admitted with symptomatic COVID-19 and non-COVID-19 viral acute respiratory tract infections (ARTIs).

Methods

We conducted a repeated cross-sectional analysis of the monthly antibiotic prescribing rate from March 2020 to December 2023 for COVID-19 admissions and from January 2019 to December 2023 for other viral ARTI admissions to 803 acute care hospitals in the United States that contributed data to the Premier Healthcare Database. Our primary outcome was the receipt of ≥1 dose of an antibiotic during the first 5 days of the admission. Secondary outcomes included days and duration of antibiotic therapy.

Results

This study included 513 698 COVID-19 and 106 932 non-COVID-19 viral ARTI admissions from March 2020 to December 2023. At the onset of the pandemic, >80% of patients admitted for COVID-19 received antibiotics, and antibiotic prescribing for other viral ARTIs increased to nearly 70%. Antibiotic prescribing for these viral infections declined over time, with prescribing for COVID-19 stabilizing around 35% in 2022-2023 and prescribing for other viral ARTIs returning to 2019 seasonal patterns in 2023, with average monthly prescribing around 50%.

Conclusions

Despite improvements since the early part of the COVID-19 pandemic, potentially unnecessary antibiotic prescribing for inpatients with COVID-19 and non-COVID-19 viral ARTIs remains an important antibiotic stewardship target.

Global trends in antibiotic consumption during 2016-2023 and future projections through 2030

Antibiotic resistance is a global public health threat. Many factors contribute to this issue, with human antibiotic consumption being significant among them. Analyzing trends and patterns in consumption can aid in developing policies to mitigate the burden of antimicrobial resistance and global disparities in access to antibiotics. Using pharmaceutical sales data licensed from IQVIA, we estimate national-level trends in antibiotic consumption in 67 countries during 2016-2023 and analyze the effects of economic growth and the COVID-19 pandemic. Finally, we estimate global human consumption and project growth through 2030 assuming current trends. We find that estimated antibiotic consumption in reported countries increased 16.3% from 29.5 to 34.3 billion defined daily doses (DDDs) from 2016 to 2023, reflecting a 10.6% increase in the consumption rate from 13.7 to 15.2 DDDs per 1,000 inhabitants per day. Increases were most pronounced in upper-middle- and lower-middle-income countries. While the COVID-19 pandemic significantly reduced consumption globally, this was most pronounced in high-income countries, and in these countries, reductions in antibiotic use in 2020 were sharper, and lasted longer, than in other countries. By 2030, we project that, without reductions in rapidly developing nations, such as investments to improve infrastructure, particularly water and sanitation, along with improved access to vaccination, global antibiotic consumption will increase by 52.3% from an estimated 49.3 billion in 2023 to 75.1 billion DDDs.

The impact of the COVID-19 pandemic on the antimicrobial stewardship workforce in Scottish acute care hospitals-a qualitative study

Background

Antimicrobial stewardship (AMS) programmes seek to reduce the risk of antimicrobial resistance by minimizing inappropriate antimicrobial use. The SARS-CoV-2 coronavirus (COVID-19) pandemic was characterized by initial widespread use of antimicrobials in patients with COVID-19, with potential negative effects on AMS efforts.

Objective

To explore the impact of the pandemic on the AMS workforce in Scottish acute care hospitals.

Method

Individual, semi-structured online interviews were conducted with a purposive sample of clinical staff who had an AMS focused role in Scottish Health Boards. Interviews explored staff experiences of facilitating AMS during the pandemic. Data were analysed using inductive content analysis.

Results

Thirteen staff from seven of 15 Scotland Health Boards participated. The data revealed negative (including staff redeployment and shortages) and positive effects (including improved working relationships and use of technology) on the AMS workforce. Notably, greater appreciation of the work of the AMS team was a positive outcome.

Conclusions

The robust qualitative methods applied in this original study have generated greater understanding of factors that impeded AMS services in Scotland during the pandemic. These findings may resonate internationally. Adaptation to technology and investment in the workforce are recommended to improve the resilience of AMS services in future crises.

Mortality in hospitalized SARS-CoV-2 patients with contemporaneous bacterial and fungal infections

Background

The interplay between SARS-CoV-2 and contemporaneous bacterial or fungal culture growth may have crucial implications for clinical outcomes of hospitalized patients. This study aimed to quantify the effect of microbiological culture positivity on mortality among hospitalized patients with SARS-CoV-2.

Methods

In this retrospective cohort study, we included adult hospitalized patients from OPTUM COVID-19 specific data set, who tested positive for SARS-CoV-2 within 14 days of hospitalization between 01/20/2020 and 01/20/2022. We examined outcomes of individuals with organisms growing on cultures from the bloodstream infections (BSIs), urinary tract, and respiratory tract, and a composite of the three sites. We used propensity score matching on covariates included demographics, comorbidities, and hospitalization clinical parameters. In a sensitivity analysis, we included same covariates but excluded critical care variables such as length of stay, intensive care unit stays, mechanical ventilation, and extracorporeal membrane oxygenation.

Results

The cohort included 104,560 SARS-CoV-2 positive adult hospitalized patients across the United States. The unadjusted mortality odds increased significantly with BSIs (98.7%) and with growth on respiratory cultures (RC) (176.6%), but not with growth on urinary cultures (UC). Adjusted analyses showed that BSIs and positive RC independently contribute to mortality, even after accounting for critical care variables.

Conclusions

In SARS-CoV-2-positive hospitalized patients, positive bacterial and fungal microbiological cultures, especially BSIs and RC, are associated with an increased risk of mortality even after accounting for critical care variables associated with disease severity. These findings underscore the importance of stringent infection control and the effective management of secondary infections to improve patient outcomes.

A scoping review of bacterial resistance among inpatients amidst the COVID-19 pandemic

OBJECTIVES

The COVID-19 pandemic disrupted antimicrobial stewardship and infection prevention operations worldwide, raising concerns for an acceleration of antimicrobial resistance (AMR). Therefore, we aimed to define the scope of peer reviewed research comparing AMR in inpatient bacterial clinical cultures before and after the start of the COVID-19 pandemic.

METHODS

We conducted a scoping review and searched PubMed, Scopus, and Web of Science through 15 June 2023. Our inclusion criteria were: (1) English language, (2) primary evidence, (3) peer-reviewed, (4) clinical culture data from humans, (5) AMR data for at least one bacterial order/species, (6) inpatient setting, (7) use of statistical testing to evaluate AMR data before and during the COVID-19 pandemic. Reviewers extracted country, study design, type of analysis, study period, setting and population, number of positive cultures or isolates, culture type(s), method of AMR analysis, organisms, and AMR results. Study results were organised by organism and antibiotic class or resistance mechanism. AMR results are also summarised by individual study and across all studies.

RESULTS

In total, 4805 articles were identified with 55 papers meeting inclusion criteria. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were the most commonly studied organisms. There were 464 bacterial AMR results across all studies with 82 (18%) increase, 71 (15%) decrease, and 311 (67%) no change results.

CONCLUSIONS

The literature examining the impact of COVID-19 on AMR among inpatients is diverse with most results reflecting no change pre/post pandemic. Ongoing inquiry is needed into evolving patterns in AMR post COVID-19.

Risk factors and multi-pathogen infections in kidney transplant recipients with omicron variant pneumonia: a retrospective analysis

BACKGROUND

Kidney transplant recipients (KTRs) are at an elevated risk of progressing to severe infections upon contracting COVID-19. We conducted a study on risk factors and multi-pathogen infections in KTRs with SARS-CoV-2 Omicron variant.

METHODS

KTRs were subjected to a thorough etiological evaluation. Whenever feasible, they were also provided with bronchoscopy and bronchoalveolar lavage to enable metagenomic next-generation sequencing (mNGS), ideally within a 48-hour window post-admission. We performed a retrospective analysis for pathogens and risk factors of KTRs with the COVID-19 virus variant Omicron.

RESULTS

We included thirty patients in our study, with sixteen exhibiting single infection of COVID-19 and fourteen experiencing co-infections, predominantly with Pneumocystis jirovecii. Notably, patients with severe cases demonstrated significantly elevated levels of C-reactive protein (CRP) and interleukin-6 compared to those with moderate cases (P < 0.05). Furthermore, individuals whose conditions progressed had markedly higher baseline serum creatinine levels than those without such progression (P < 0.05). The presence of heart failure, acute exacerbation of renal dysfunction, and a history of opportunistic infections were significantly associated with a higher likelihood of deterioration and hospital admission due to the SARS-CoV-2 Omicron variant, as compared to the control group (P < 0.05). In subsequent follow-up analysis, the all-cause rehospitalization rate was observed to be 21.4%, with Pneumocystis jirovecii infection accounting for half of these cases.

CONCLUSION

Among KTRs, a significant coinfection rate of 47% was observed, with Pneumocystis jirovecii emerging as the predominant pathogen in these cases. The development of heart failure, acute exacerbation of chronic renal dysfunction, and a prior history of opportunistic infections have been identified as potential risk factors that may contribute to clinical deterioration in KTRs. Additionally, Pneumocystis jirovecii infection has been established as a critical factor influencing the rate of all-cause rehospitalization within this patient population.

COVID-19 in three waves in a tertiary referral hospital in Belgium: a comparison of patient characteristics, management, and outcome

PURPOSE

Few studies have compared patient characteristics, clinical management, and outcome of patients with COVID-19 between the different epidemic waves. In this study, we describe patient characteristics, treatment, and outcome of patients admitted for COVID-19 in the Antwerp University Hospital over the first three epidemic waves of 2020-2021.

METHODS

Retrospective observational study of COVID-19 patients in a Belgian tertiary referral hospital. All adult patients with COVID-19, hospitalized between February 29, 2020, and June 30, 2021, were included. Standardized routine medical data was collected from patient records. Risk factors were assessed with multivariable logistic regression.

RESULTS

We included 722 patients, during the first (n = 179), second (n = 347) and third (n = 194) wave. We observed the lowest disease severity at admission during the first wave, and more elderly and comorbid patients during the second wave. Throughout the subsequent waves we observed an increasing use of corticosteroids and high-flow oxygen therapy. In spite of increasing number of complications throughout the subsequent waves, mortality decreased each wave (16.6%,15.6% 11.9% in 1st, 2nd and 3rd wave respectively). C-reactive protein above 150 mg/L was predictive for the need for intensive care unit admission (odds ratio (OR) 3.77, 95% confidence interval (CI) 2.32-6.15). A Charlson comorbidity index ≥ 5 (OR 5.68, 95% CI 2.54-12.70) and interhospital transfers (OR 3.78, 95% CI 2.05-6.98) were associated with a higher mortality.

CONCLUSIONS

We observed a reduction in mortality each wave, despite increasing comorbidity. Evolutions in patient management such as high-flow oxygen therapy on regular wards and corticosteroid use may explain this favorable evolution.

Physicians' irrational attitudes on the antibiotic prescribing for the treatment of COVID-19 in Turkey: A multicenter survey

BACKGROUND

The inappropriate and excessive use of antibiotics during the coronavirus pandemic has become an important issue.

OBJECTIVE

Our primary aim is to ascertain the attitudes of physicians toward the antibiotics prescribing for the treatment of COVID-19 in Turkey. Our secondary aim was to identify factors affecting to physicians' decisions regarding antibiotic therapy for the treatment of COVID-19 and risk factors associated with antibiotic overprescribing.

METHODS

It was a multicenter cross-sectional survey. Physicians from 63 different cities were invited to survey through social media (Facebook, Instagram, WhatsApp). Data were collected from respondents through an online questionnaires during November-December 2021.

RESULTS

The survey was completed by 571 participants from 63 cities. Pulmonologists comprised the majority (35.20%), followed by internal medical specialists (27.85%) and general practitioners (23.29%). The rates of participants who started empirical antibiotics in the outpatient, ward, and ICU (intensive care unit) were 70.2%, 85.5%, and 74.6%, respectively. When the practice of prescribing antibiotics by physicians for the treatment of COVID-19 in outpatients was compared according to the healthcare setting (primary, secondary, tertiary care hospitals) no significant difference was found. Sputum purulence (68.2%) was recognized as the most important factor for the decision of antibiotic therapy, followed by procalcitonin levels (64.9%) and abnormal radiological findings (50.3%). The most prescribed antibiotics were respiratory quinolones. (48%, 65.9%, 62.7% outpatient, ward, ICU respectively) CONCLUSIONS: In this study, we found that physicians frequently had irrational attitudes toward antibiotic prescription to COVID-19 patients, including those with minor diseases. Our findings underline that the necessity of particular, workable interventions to guarantee the prudent use of antibiotics in COVID-19.

Bacterial infections in patients with COVID-19: the impact of procalcitonin testing on antibiotics prescription in the real world

BACKGROUND

Bacterial infections are not prevalent among patients hospitalized with COVID-19, while unnecessary prescription of antibiotics was commonly observed. This study aimed to determine the impact of procalcitonin testing on antibiotics prescription in the real-world setting.

METHODS

We performed a territory-wide retrospective cohort study involving all laboratory-confirmed patients hospitalized in public hospitals in Hong Kong in 2020 with COVID-19. We determined the prevalence of bacterial co-infections (documented infections within 72 h of admission) and secondary bacterial infections (infections after 72 h of admission) and antibiotics consumption, and the correlation between procalcitonin testing and antibiotics prescription.

RESULTS

The cohort included 8666 patients, with mean age 45.3 ± 19.9 years, 48.5% male, and comorbidities in 26.9%. Among 2688 patients with bacterial cultures performed, 147 (5.5%) had bacterial co-infections, and 222 (8.3%) had secondary bacterial infections. Antibiotics were prescribed for 2773 (32.0%) patients during the hospital admission. Procalcitonin tests were performed for 2543 (29.3%) patients. More patients with procalcitonin testing received antibiotics (65.9% vs. 17.9%, p < 0.001). Procalcitonin testing was associated with 5-fold increased risk of antibiotics prescription after adjusting for confounding variables. At hospital level, procalcitonin testing correlated with antibiotics prescription. Patients with procalcitonin level < 0.5 ng/mL had a lower probability of antibiotics initiation and shorter duration of antibiotics therapy.

CONCLUSIONS

Procalcitonin testing was not associated with lower prescription of antibiotics. Patients with low procalcitonin level had lower antibiotics exposure, supporting the use of procalcitonin to exclude bacterial infections aiding early stopping of antibiotics among patients hospitalized with COVID-19.

The Impact of Antibiotic Prophylaxis on a Retrospective Cohort of Hospitalized Patients with COVID-19 Treated with a Combination of Steroids and Tocilizumab

OBJECTIVES

In the context of COVID-19, patients with a severe or critical illness may be more susceptible to developing secondary bacterial infections. This study aims to investigate the relationship between the use of prophylactic antibiotic therapy and the occurrence of bacterial or fungal isolates following the administration of tocilizumab in hospitalized COVID-19 patients who had previously received steroids during the first and second waves of the pandemic in Spain.

METHODS

This retrospective observational study included 70 patients hospitalized with COVID-19 who received tocilizumab and steroids between January and December 2020. Data on demographics, comorbidities, laboratory tests, microbiologic results, treatment, and outcomes were collected from electronic health records. The patients were divided into two groups based on the use of antibiotic prophylaxis, and the incidence of bacterial and fungal colonizations/infections was analyzed.

RESULTS

Among the included patients, 45 patients received antibiotic prophylaxis. No significant clinical differences were observed between the patients based on prophylaxis use regarding the number of clinically diagnosed infections, ICU admissions, or mortality rates. However, the patients who received antibiotic prophylaxis showed a higher incidence of colonization by multidrug-resistant bacteria compared to that of the subgroup that did not receive prophylaxis. The most commonly isolated microorganisms were Candida albicans, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus epidermidis. Conclusions: In this cohort of hospitalized COVID-19 patients treated with tocilizumab and steroids, the use of antibiotic prophylaxis did not reduce the incidence of secondary bacterial infections. However, it was associated with an increased incidence of colonization by multidrug-resistant bacteria.

ICU-Acquired Colonization and Infection Related to Multidrug-Resistant Bacteria in COVID-19 Patients: A Narrative Review

A large proportion of ICU-acquired infections are related to multidrug-resistant bacteria (MDR). Infections caused by these bacteria are associated with increased mortality, and prolonged duration of mechanical ventilation and ICU stay. The aim of this narrative review is to report on the association between COVID-19 and ICU-acquired colonization or infection related to MDR bacteria. Although a huge amount of literature is available on COVID-19 and MDR bacteria, only a few clinical trials have properly evaluated the association between them using a non-COVID-19 control group and accurate design and statistical methods. The results of these studies suggest that COVID-19 patients are at a similar risk of ICU-acquired MDR colonization compared to non-COVID-19 controls. However, a higher risk of ICU-acquired infection related to MDR bacteria has been reported in several studies, mainly ventilator-associated pneumonia and bloodstream infection. Several potential explanations could be provided for the high incidence of ICU-acquired infections related to MDR. Immunomodulatory treatments, such as corticosteroids, JAK2 inhibitors, and IL-6 receptor antagonist, might play a role in the pathogenesis of these infections. Additionally, a longer stay in the ICU was reported in COVID-19 patients, resulting in higher exposure to well-known risk factors for ICU-acquired MDR infections, such as invasive procedures and antimicrobial treatment. Another possible explanation is the surge during successive COVID-19 waves, with excessive workload and low compliance with preventive measures. Further studies should evaluate the evolution of the incidence of ICU-acquired infections related to MDR bacteria, given the change in COVID-19 patient profiles. A better understanding of the immune status of critically ill COVID-19 patients is required to move to personalized treatment and reduce the risk of ICU-acquired infections. The role of specific preventive measures, such as targeted immunomodulation, should be investigated.

Use of Electronic Clinical Data to Track Incidence and Mortality for SARS-CoV-2-Associated Sepsis

Importance

Efforts to quantify the burden of SARS-CoV-2-associated sepsis have been limited by inconsistent definitions and underrecognition of viral sepsis.

Objective

To describe the incidence and outcomes of SARS-CoV-2-associated sepsis vs presumed bacterial sepsis using objective electronic clinical criteria.

Design, Setting, and Participants

This retrospective cohort study included adults hospitalized at 5 Massachusetts hospitals between March 2020 and November 2022.

Exposures

SARS-CoV-2-associated sepsis was defined as a positive SARS-CoV-2 polymerase chain reaction test and concurrent organ dysfunction (ie, oxygen support above simple nasal cannula, vasopressors, elevated lactate level, rise in creatine or bilirubin level, and/or decline in platelets). Presumed bacterial sepsis was defined by modified US Centers for Disease Control and Prevention adult sepsis event criteria (ie, blood culture order, sustained treatment with antibiotics, and organ dysfunction using identical thresholds as for SARS-CoV-2-associated sepsis).

Main Outcomes and Measures

Trends in the quarterly incidence (ie, proportion of hospitalizations) and in-hospital mortality for SARS-CoV-2-associated and presumed bacterial sepsis were assessed using negative binomial and logistic regression models.

Results

This study included 431 017 hospital encounters from 261 595 individuals (mean [SD] age 57.9 [19.8] years, 241 131 (55.9%) females, 286 397 [66.5%] from academic hospital site). Of these encounters, 23 276 (5.4%) were from SARS-CoV-2, 6558 (1.5%) had SARS-CoV-2-associated sepsis, and 30 604 patients (7.1%) had presumed bacterial sepsis without SARS-CoV-2 infection. Crude in-hospital mortality for SARS-CoV-2-associated sepsis declined from 490 of 1469 (33.4%) in the first quarter to 67 of 450 (14.9%) in the last (adjusted odds ratio [aOR], 0.88 [95% CI, 0.85-0.90] per quarter). Crude mortality for presumed bacterial sepsis was 4451 of 30 604 patients (14.5%) and stable across quarters (aOR, 1.00 [95% CI, 0.99-1.01]). Medical record reviews of 200 SARS-CoV-2-positive hospitalizations confirmed electronic health record (EHR)-based SARS-CoV-2-associated sepsis criteria performed well relative to sepsis-3 criteria (90.6% [95% CI, 80.7%-96.5%] sensitivity; 91.2% [95% CI, 85.1%-95.4%] specificity).

Conclusions and Relevance

In this retrospective cohort study of hospitalized adults, SARS-CoV-2 accounted for approximately 1 in 6 cases of sepsis during the first 33 months of the COVID-19 pandemic. In-hospital mortality rates for SARS-CoV-2-associated sepsis were high but declined over time and ultimately were similar to presumed bacterial sepsis. These findings highlight the high burden of SARS-CoV-2-associated sepsis and demonstrate the utility of EHR-based algorithms to conduct surveillance for viral and bacterial sepsis.

An immune-protein score combining TRAIL, IP-10 and CRP for predicting severe COVID-19 disease

COVID-19 patients are oftentimes over- or under-treated due to a deficit in predictive management tools. This study reports derivation of an algorithm that integrates the host levels of TRAIL, IP-10, and CRP into a single numeric score that is an early indicator of severe outcome for COVID-19 patients and can identify patients at-risk to deteriorate. 394 COVID-19 patients were eligible; 29% meeting a severe outcome (intensive care unit admission/non-invasive or invasive ventilation/death). The score's area under the receiver operating characteristic curve (AUC) was 0.86, superior to IL-6 (AUC 0.77; p = 0.033) and CRP (AUC 0.78; p < 0.001). Likelihood of severe outcome increased significantly (p < 0.001) with higher scores. The score differentiated severe patients who further deteriorated from those who improved (p = 0.004) and projected 14-day survival probabilities (p < 0.001). The score accurately predicted COVID-19 patients at-risk for severe outcome, and therefore has potential to facilitate timely care escalation and de-escalation and appropriate resource allocation.

Genetic support of the causal association between gut microbiome and COVID-19: a bidirectional Mendelian randomization study

Background

The association between gut microbiome and coronavirus disease 2019 (COVID-19) has attracted much attention, but its causality remains unclear and requires more direct evidence.

Methods

In this study, we conducted the bidirectional Mendelian randomization (MR) analysis to assess the causal association between gut microbiome and COVID-19 based on the summary statistics data of genome-wide association studies (GWASs). Over 1.8 million individuals with three COVID-19 phenotypes (severity, hospitalization and infection) were included. And 196 bacterial taxa from phylum to genus were analyzed. The inverse-variance weighted (IVW) analysis was chosen as the primary method. Besides, false discovery rate (FDR) correction of p-value was used. To test the robustness of the causal relationships with p-FDR < 0.05, sensitivity analyses including the secondary MR analyses, horizontal pleiotropy test, outliers test, and "leave-one-out" analysis were conducted.

Results

In the forward MR, we found that 3, 8, and 10 bacterial taxa had suggestive effects on COVID-19 severity, hospitalization and infection, respectively. The genus Alloprevotella [odds ratio (OR) = 1.67; 95% confidence interval (95% CI), 1.32-2.11; p = 1.69×10^-5, p-FDR = 2.01×10^-3] was causally associated with a higher COVID-19 severity risk. In the reverse MR, COVID-19 severity, hospitalization and infection had suggestive effects on the abundance of 4, 8 and 10 bacterial taxa, respectively. COVID-19 hospitalization causally increased the abundance of the phylum Bacteroidetes (OR = 1.13; 95% CI, 1.04-1.22; p = 3.02×10^-3; p-FDR = 2.72×10^-2). However, secondary MR analyses indicated that the result of COVID-19 hospitalization on the phylum Bacteroidetes required careful consideration.

Conclusion

Our study revealed the causal association between gut microbiome and COVID-19 and highlighted the role of "gut-lung axis" in the progression of COVID-19.

Antimicrobial Stewardship in COVID-19 Patients: Those Who Sow Will Reap Even through Hard Times

BACKGROUND

Since the SARS-CoV-2 pandemic emerged, antimicrobial stewardship (AS) activities need to be diverted into COVID-19 management.

METHODS

In order to assess the impact of COVID-19 on AS activities, we analyzed changes in antibiotic consumption in moderate-to-severe COVID-19 patients admitted to four units in a tertiary-care hospital across three COVID-19 waves. The AS program was introduced at the hospital in 2018. During the first wave, COVID-19 forced the complete withdrawal of hospital AS activities. In the second wave, antibiotic guidance calibration for COVID-19 patients was implemented in all units, with enhanced stewardship activities in Units 1, 2, and 3 (intervention units). In a controlled before and after study, antimicrobial usage during the three waves of the COVID-19 pandemic was compared to the 12-month prepandemic unit (Unit 4 acted as the control). Antibiotic consumption data were analyzed as the overall consumption, stratified by the World Health Organization AWaRe classification, and expressed as defined-daily-dose (DDD) and days-of-therapy (DOT) per 1000 patient-day (PD).

RESULTS

In the first wave, the overall normalized DOT in units 2-4 significantly exceeded the 2019 level (2019: 587 DOT/1000 PD ± 42.6; Unit 2: 836 ± 77.1; Unit 3: 684 ± 122.3; Unit 4: 872, ± 162.6; p < 0.05). After the introduction of AS activities, consumption decreased in the intervention units to a significantly lower level when compared to 2019 (Unit 1: 498 DOT/1000 PD ± 49; Unit 2: 232 ± 95.7; Unit 3: 382 ± 96.9; p < 0.05). Antimicrobial stewardship activities resulted in a decreased amount of total antibiotic consumption over time and positively affected the watch class and piperacillin-tazobactam use in the involved units.

CONCLUSIONS

During a pandemic, the implementation of calibrated AS activities represents a sound investment in avoiding inappropriate antibiotic therapy.

Unfavorable Outcome and Long-Term Sequelae in Cases with Severe COVID-19

Emerging evidence shows that individuals with COVID-19 who survive the acute phase of illness may experience lingering symptoms in the following months. There is no clear indication as to whether these symptoms persist for a short time before resolving or if they persist for a long time. In this review, we will describe the symptoms that persist over time and possible predictors in the acute phase that indicate long-term persistence. Based on the literature available to date, fatigue/weakness, dyspnea, arthromyalgia, depression, anxiety, memory loss, slowing down, difficulty concentrating and insomnia are the most commonly reported persistent long-term symptoms. The extent and persistence of these in long-term follow-up is not clear as there are still no quality studies available. The evidence available today indicates that female subjects and those with a more severe initial disease are more likely to suffer permanent sequelae one year after the acute phase. To understand these complications, and to experiment with interventions and treatments for those at greater risk, we must first understand the physio-pathological mechanisms that sustain them.