ICU-acquired bloodstream infections in critically ill patients with COVID-19. J Hosp Infect. 2021;107:95-97. [PMID: 33217490 PMCID: PMC7671926 DOI: 10.1016/j.jhin.2020.11.009]

Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey

Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p < 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%-25%; p < 0.001) and rectal regions (74.19% - 46.66%; p < 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p < 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p < 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.

Bloodstream infection clusters for critically ill patients: analysis of two-center retrospective cohorts

BACKGROUND

Bloodstream infections (BSI) are highly prevalent in hospitalized patients requiring intensive care. They are among the most serious infections and are highly associated with sepsis or septic shock, which can lead to prolonged hospital stays and high healthcare costs. This study aimed at establishing an easy-to-use nomogram for predicting the prognosis of patients with BSI.

METHODS

In retrospective study, records of patients with BSI admitted to the intensive care unit (ICU) over the period from Jan 1st 2016 to Dec 31st 2021 were included. We used data from two different China hospitals as development cohort and validation cohort respectively. The demographic and clinical data of patients were collected. Based on all baseline data, k-means algorithm was applied to discover the groups of BSI phenotypes with different prognostic outcomes, which was confirmed by Kaplan-Meier analysis and compared using log-rank tests. Univariate Cox regression analyses were used to estimate the risk of clusters. Random forest was used to identified discriminative predictors in clusters, which were utilized to construct nomogram based on multivariable logistic regression in the discovery cohort. For easy clinical applications, we developed a bloodstream infections clustering (BSIC) score according to the nomogram. The results were validated in the validation cohort over a similar period.

RESULTS

A total of 360 patients in the discovery cohort and 310 patients in the validation cohort were included in statistical analyses. Based on baseline variables, two distinct clusters with differing prognostic outcomes were identified in the discovery cohort. Population in cluster 1 was 211 with a ICU mortality of 17.1%, while population in cluster 2 was 149 with an ICU mortality of 41.6% (p < 0.001). The survival analysis also revealed a higher risk of death for cluster 2 when compared with cluster 1 (hazard ratio: 2.31 [95% CI, 1.53 to 3.51], p < 0.001), which was confirmed in validation cohort. Four independent predictors (vasoconstrictor use before BSI, mechanical ventilation (MV) before BSI, Deep vein catheterization (DVC) before BSI, and antibiotic use before BSI) were identified and used to develop a nomogram. The nomogram and BSIC score showed good discrimination with AUC of 0.96.

CONCLUSION

The developed score has potential applications in the identification of high-risk critically ill BSI patients.

Temporal trends in laboratory parameters in survivors and non‑survivors of critical COVID‑19 illness and the effect of dexamethasone treatment

Although coronavirus disease 2019 (COVID-19)-induced changes in laboratory parameters in patients upon admission have been well-documented, information on their temporal changes is limited. The present study describes the laboratory trends and the effect of dexamethasone treatment on these parameters, in patients with COVID-19 in the intensive care unit (ICU). Routine laboratory parameters, namely white blood cell (WBC), neutrophil, lymphocyte and platelet (PLT) counts, fibrinogen, C-reactive protein (CRP), lactate dehydrogenase (LDH) and albumin concentrations, were recorded upon admission to the ICU and, thereafter, on days 3, 5, 10, 15 and 21; these values were compared between survivors and non-survivors, as well as between those who were treated with dexamethasone and those who were not. Among the 733 patients in the ICU, (mean age, 65±13 years; 68% males; ICU mortality rate 45%; 76% of patients treated with dexamethasone), the WBC and neutrophil counts were persistently high in all patients, without significant differences over the first 15 days. Initially, low lymphocyte counts exhibited increasing trends, but remained higher in survivors compared to non-survivors (P=0.01). The neutrophil-to-lymphocyte ratio (NLR) was persistently elevated in all patients, although it was significantly higher in non-survivors compared to survivors (P<0.001). The PLT count was initially increased in all patients, although it was significantly decreased in non-survivors over time. The fibrinogen and LDH values remained similarly elevated in all patients. However, the increased levels of CRP, which did not differ between patients upon admission, further increased in non-survivors compared to survivors after day 10 (P=0.001). Declining trends in albumin levels over time, overall, with a significant decrease in non-survivors compared to survivors, were observed. Dexamethasone treatment significantly affected the temporal progression of fibrinogen and CRP in survivors and that of NLR in non-survivors. On the whole, the present study demonstrates that patients in the ICU with COVID-19 present persistently abnormal laboratory findings and significant differences in laboratory trends of NLR, CRP, PLT and albumin, but not in WBC and neutrophil count, and fibrinogen and LDH levels, between survivors and non-survivors. The temporal progression of fibrinogen, CRP and NLR is affected by dexamethasone treatment.

Pathogenic Potential and Antibiotic Susceptibility: A Comprehensive Study of Enterococci from Different Ecological Settings

The pathway and the lifestyle of known enterococcus species are too complicated. The aim of the present study is to trace the path of pathogenicity of enterococci isolated from seven habitats (Cornu aspersum intestine; Bulgarian yoghurt; goat and cow feta cheese-mature and young, respectively; Arabian street food-doner kebab; cow milk; and human breast milk) by comparing their pathogenic potential. In total, 72 enterococcal strains were isolated and identified by MALDI-TOF, sequencing, and PCR. Hemolytic and gelatinase activity were biochemically determined. PCR was carried out for detection of virulence factors (cylB, esp, gls24, nucl, psaA, agg, gelE, and ace) and antibiotic resistance (erm, ermB, blaZ, vanA, aphA, mefA, gyrA, catpIP501, and aac6'-aph2″). Phenotypic antibiotic resistance was assigned according to EUCAST. Eleven representatives of the genus Enterococcus were identified: E. mundtii, E. casseliflavus, E. gilvus, E. pseudoavium, E. pallens, E. malodoratus, E. devriesei, E. gallinarum, E. durans, E. faecium, and E. faecalis. Twenty-two strains expressed α-hemolysis. Thirteen strains had the cylB gene. Only two strains expressed α-hemolysis and possessed the cylB gene simultaneously. Positive amplification for gelE was found in 35% of the isolates, but phenotypic gelatinase activity was observed only in three strains. All isolates showed varying antibiotic resistance. Only E. faecalis BM15 showed multiple resistance (AMP-HLSR-RP). Correlation between genotypic and phenotypic macrolide resistance was revealed for two E. faecalis strains.

Impact of intensified prevention measures on the rate of hospital-acquired bloodstream infections among mechanically ventilated COVID-19 patients

Background

The COVID-19 pandemic was associated with increased rates of hospital-acquired infections. During the early months of the pandemic, we observed high rates of hospital-acquired bloodstream infections (HA-BSIs) among COVID-19 patients, prompting the implementation of intensified prevention measures.

Objectives

To assess the prevalence of HA-BSI among mechanically ventilated COVID-19 patients, identify risk factors, and evaluate the effect of prevention measures.

Methods

We conducted a retrospective matched case-control study in adult medical step-up units between March 1, 2020, and March 31, 2021. We matched mechanically ventilated COVID-19 patients with ventilated non-COVID-19 patients based on age group and length of stay before ventilation. In response to the high rates of HA-BSI among COVID-19 patients, a comprehensive infection control intervention was implemented.

Results

A total of 136 COVID-19 patients were matched with 136 non-COVID-19 patients. No significant differences were observed in pre-hospitalization characteristics. The central venous catheter utilization ratio was higher in COVID-19 patients (83.6%) versus 35.6% in the control group (p < 0.001). During pre-intervention, 35.2% (32/91) of COVID-19 patients developed HA-BSI, compared to 17.8% (13/73) in the control group (p < 0.001). Following the intervention, no significant difference was observed between the groups (17.8% (8/45) versus 15.9% (10 /63), p = 0.79). In a multivariate analysis, HA-BSI was associated with low body mass index (OR 0.9 (95% CI 0.9-1.0), p = 0.015)) and presence of temporary dialysis catheter (OR 2.7 (95% CI 1.0-7.3), p = 0.05)).

Conclusions

Mechanically ventilated COVID-19 patients were at higher risk for developing HA-BSI compared to non-COVID-19 patients. Intensified prevention measures were associated with decreased rates of HA-BSI.

Healthcare-associated infections in critical COVID-19 patients in Tunis: epidemiology, risk factors, and outcomes

BACKGROUND

Coronavirus disease 2019 (COVID-19) pandemic disrupted adherences to healthcare-associated infection (HAI) prevention protocols. Herein, we studied the characteristics of all HAIs occurring in critically ill COVID-19 patients.

METHODS

A retrospective, single-center cohort of critical COVID-19 patients during 2021. Microbiological samples were collected if HAI was suspected. We analyzed all factors that could potentially induce HAI, using septic shock and mortality as endpoints.

RESULTS

Sixty-four among 161 included patients (39.7%) presented a total of 117 HAIs with an incidence density of 69.2 per 1,000 hospitalization days. Compared to the prior COVID-19 period (2013-2019), the identification of HAI increased in 2021. HAIs were classified into ventilator-associated pneumonia (VAP; n=38), bloodstream infection (n=32), urinary tract infection (n=24), catheter-related infection (n=12), and fungal infection (n=11). All HAIs occurred significantly earlier in the post-COVID-19 period (VAP: 6 vs. 10 days, P=0.045, in 2017 and 2021). Acinetobacter baumannii (39.5%) and Klebsiella pneumoniae (27%) were the most commonly isolated pathogens that exhibited a multidrug-resistant (MDR) profile, observed in 89% and 64.5%, respectively. The HAI factors were laboratory abnormalities (odds ratio [OR], 6.4; 95% confidence interval [CI], 2.3-26.0), cumulative steroid dose (OR, 1.9; 95% CI, 1.3-4.0), and invasive procedures (OR, 20.7; 95% CI, 5.3-64.0). HAI was an independent factor of mortality (OR, 8.5; P=0.004).

CONCLUSIONS

During the COVID-19 era, the incidence of HAIs increased and MDR isolates remained frequent. A severe biological inflammatory syndrome, invasive devices, and elevated cumulative steroid dosages were related to HAIs. HAI was a significant death factor.

Temporal evolution of laboratory characteristics in patients critically ill with COVID‑19 admitted to the intensive care unit (Review)

In the context of coronavirus disease 2019 (COVID-19), laboratory medicine has played a crucial role in both diagnosis and severity assessment. Although the importance of baseline laboratory findings has been extensively reported, data regarding their evolution over the clinical course are limited. The aim of the present narrative review was to provide the dynamic changes of the routine laboratory variables reported in patients with severe COVID-19 over the course of their critical illness. A search was made of the literature for articles providing data on the time-course of routine laboratory tests in patients with severe COVID-19 during their stay in the intensive care unit (ICU). White blood cell, neutrophil and lymphocyte counts, neutrophil to lymphocyte ratio, platelet counts, as well as D-dimer, fibrinogen, C-reactive protein, lactate dehydrogenase and serum albumin levels were selected as disease characteristics and routine laboratory parameters. A total of 25 research articles reporting dynamic trends in the aforementioned laboratory parameters over the clinical course of severe COVID-19 were identified. During the follow-up period provided by each study, the majority of the laboratory values remained persistently abnormal in both survivors and non-survivors. Furthermore, in the majority of studies, the temporal trends of laboratory values distinctly differentiated patients between survivors and non-survivors. In conclusion, there are distinct temporal trends in selected routine laboratory parameters between survivors and non-survivors with severe COVID-19 admitted to the ICU, indicating their importance in the prognosis of clinical outcome.

Predictors of bacteremia and death, including immune status, in a large single-center cohort of unvaccinated ICU patients with COVID-19 pneumonia

BACKGROUND

We investigated the possible role of the immune profile at ICU admission, among other well characterized clinical and laboratory predictors of unfavorable outcome in COVID-19 patients assisted in ICU.

METHODS

Retrospective analysis of clinical and laboratory data collected for all consecutive patients admitted to the ICUs of the General Hospital of Pescara (Abruzzo, Italy), between 1^st March 2020 and 30^th April 2021, with a confirmed diagnosis of COVID-19 respiratory failure. Logistic regressions were used to identify independent predictors of bacteremia and mortality.

RESULTS

Out of 431 patients included in the study, bacteremia was present in N = 191 (44.3%) and death occurred in N = 210 (48.7%). After multivariate analysis, increased risk of bacteremia was found for viral reactivation (OR = 3.28; 95% CI:1.83-6.08), pronation (3.36; 2.12-5.37) and orotracheal intubation (2.51; 1.58-4.02). Increased mortality was found for bacteremia (2.05; 1.31-3.22), viral reactivation (2.29; 1.29-4.19) and lymphocytes < 0.6 × 10³c/µL (2.32; 1.49-3.64).

CONCLUSIONS

We found that viral reactivation, mostly due to Herpesviridae, was associated with increased risk of both bacteremia and mortality. In addition, pronation and intubation are strong predictors of bacteremia, which in turn together with severe lymphocytopenia due to SARS-CoV2 was associated with increased mortality. Most episodes of bacteremia, even due to Acinetobacter spp, were not predicted by microbiological evidence of colonization.

Mortality of Patients With Candidemia and COVID-19: A Systematic Review With Meta-analysis

Mortality of candidemia in coronavirus disease 2019 (COVID-19) patients has not been deeply studied despite evidence suggesting an increased occurrence. We performed a systematic review and meta-analysis to summarize the available evidence about these patients' mortality and length of stay. Data about the in-hospital, all-cause and 30-day mortality, and length of stay were pooled. Subgroup analyses were performed to assess sources of heterogeneity. Twenty-six articles out of the 1915 records retrieved during the search were included in this review. The pooled in-hospital mortality was 62.62% (95% CI, 54.77% to 69.86%), while the mortality in intensive care unit (ICU) was 66.77% (95% CI, 57.70% to 74.75%). The pooled median in-hospital length of stay was 30.41 (95% CI, 12.28 to 48.55) days, while the pooled median length of stay in the ICU was 28.28 (95% CI, 20.84 to 35.73) days. The subgroup analyses did not identify the sources of heterogeneity in any of the analyses. Our results showed high mortality in patients with candidemia and COVID-19, suggesting the need to consider screening measures to prevent this life-threatening condition.

Effect of bloodstream infection on survival in COVID-19 patients admitted to an intensive care unit in Colombia: a matched cohort analysis

Aim

To determine the impact of bloodstream infection (BSI) and other risk factors for mortality in patients with COVID-19 admitted to the intensive care unit (ICU).

Methods

A retrospective cohort was carried out at the Hospital Universitario Nacional (HUN) between March 29 and December 19, 2020. Patients with COVID-19 admitted to the Intensive Care Unit (ICU) were paired 1:4 in two groups, one with BSI and the other without, according to hospital stay and the month of admission. The primary outcome was mortality at 28 days. A Cox proportional hazards model was used to estimate differences in mortality risk.

Results

456 patients were identified and 320 were included in the final cohort, 18% (n = 59) in the BSI group and 82% (n = 261) in the control group. 125 (39%) patients died, 30 (51%) in the BSI group and 95 (36%) in the control group (P = 0.040). BSI was associated with an increased risk of in-hospital mortality at 28 days, [HR] 1.77 (95% CI: 1.03-3.02; P = 0.037). Invasive mechanical ventilation (IMV) and age were associated with increased mortality risk. Some months of the year of the hospital stay were associated with a reduced risk of mortality. There was no difference in mortality between inappropriate and appropriate empirical antimicrobial use.

Conclusion

BSI in patients with COVID-19 in ICU increases in-hospital mortality to 28 days. Other risk factors for mortality were IMV and age.

Comparison of circulating bacterial profiles between mild and severe COVID-19 patients

Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild (n = 15) and severe (n = 13) SARS-CoV-2-infected patients as well as healthy controls (n = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to Sphingomonas, Stenotrophomonas, and Achromobacter, while bacterial genera belonging to Enhydrobacter, Comamonas, and Acinetobacter were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that Stenotrophomonas, Delftia, Achromobacter, and Neisseria were enriched in the mild condition, while Agrobacterium, Comamonas, Pseudomonas, Corynebacterium, Alkaliphilus, and Kocuria were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.

Lesson from the COVID-19 pandemic lockdown: A major change of hospital-diagnosed bacteremia epidemiology

OBJECTIVES

When the COVID-19 pandemic reached France early in 2020, the enforced nationwide lockdown deeply altered lifestyle as well as hospital processes and modalities of care. The aim of the study was to evaluate the impact during the lockdown of the first epidemic wave on the epidemiology of bacteremia in one French University Hospital.

PATIENTS AND METHODS

Retrospective cohort study including adult patients with positive blood culture between 23^rd March to 24^th May 2020. The clinical-microbiological characteristics were compared with those of the period from 25^th March to 26^th May 2019. The data were adjusted to the number of hospitalizations (h).

RESULTS

In 2020, 189 bacteremia were diagnosed from 1939 vials (9658 hospitalizations, 10911 emergency room consultations) compared to 143 from 1976 vials (14797 hospitalizations, 16493 emergency room consultations) recorded in 2019. The incidence of bacteremia increased up to 19.7 per 1000h in 2020 vs 9.7 in 2019 (p<0.001). The main differences (2020 vs 2019) were: Staphylococcus aureus bacteremia (2.4 vs 1.0/1000h, p=0.012), polymicrobial bacteremia (2.2 vs 0.9/1000h p=0.013) and Gram-negative bacteremia (8.9 vs 4.3/1000h, p<0.01). Conversely, Streptococcus pneumoniae incidence decreased (0 vs 0.47/1000h, p=0.047). The standardized incidence ratio calculation confirmed these results.

CONCLUSION

The lockdown and the impact of the first wave of the Covid-19 pandemic on the health system resulted in increased hospital-diagnosed bacteremia and decreased pneumococcal bacteremia. Disruption and overload of ICUs, lockdown with preventive control measures, and decrease in human-to-human interaction may have been the main reasons.

Diagnostic significance of secondary bacteremia in patients with COVID-19

OBJECTIVES

We investigated the occurrence of non-respiratory bacterial and fungal secondary infections, causative organisms, impact on clinical outcomes, and association between the secondary pathogens and mortality in hospitalized patients with coronavirus disease 2019 (COVID-19).

METHODS

This was a retrospective cohort study that included data from inpatients with COVID-19 from multiple centers participating in the Japan COVID-19 Taskforce (April 2020 to May 2021). We obtained demographic, epidemiological, and microbiological data throughout the course of hospitalization and analyzed the cases of COVID-19 complicated by non-respiratory bacterial infections.

RESULTS

Of the 1914 patients included, non-respiratory bacterial infections with COVID-19 were diagnosed in 81 patients (4.2%). Of these, 59 (3.1%) were secondary infections. Bacteremia was the most frequent bacterial infection, occurring in 33 cases (55.9%), followed by urinary tract infections in 16 cases (27.1%). Staphylococcus epidermidis was the most common causative organism of bacteremia. Patients with COVID-19 with non-respiratory secondary bacterial infections had significantly higher mortality, and a multivariate logistic regression analysis demonstrated that those with bacteremia (aOdds Ratio = 15.3 [5.97-39.1]) were at higher risk of death. Multivariate logistic regression analysis showed that age, male sex, use of steroids to treat COVID-19, and intensive care unit admission increased the risk for nosocomial bacteremia.

CONCLUSIONS

Secondary bacteremia is an important complication that may lead to poor prognosis in cases with COVID-19. An appropriate medical management strategy must be established, especially for patients with concomitant predisposing factors.

Healthcare-Associated Bloodstream Infections Due to Multidrug-Resistant Acinetobacter baumannii in COVID-19 Intensive Care Unit: A Single-Center Retrospective Study

Healthcare-associated infections are an emerging cause of morbidity and mortality in COVID-19 intensive care units (ICUs) worldwide, especially those caused by multidrug-resistant (MDR) pathogens. The objectives of this study were to assess the incidence of bloodstream infections (BSIs) among critically ill COVID-19 patients and to analyze the characteristics of healthcare-associated BSIs due to MDR Acinetobacter baumannii in an COVID-19 ICU. A single-center retrospective study was conducted at a tertiary hospital during a 5-month period. The detection of carbapenemase genes was performed by PCR and genetic relatedness by pulsed-field gel electrophoresis (PFGE) and multilocus-sequence typing. A total of 193 episodes were registered in 176 COVID-19 ICU patients, with an incidence of 25/1000 patient-days at risk. A. baumannii was the most common etiological agent (40.3%), with a resistance to carbapenems of 100%. The blaOXA-23 gene was detected in ST2 isolates while the blaOXA-24 was ST636-specific. PFGE revealed a homogeneous genetic background of the isolates. The clonal spread of OXA-23-positive A. baumannii is responsible for the high prevalence of MDR A. baumannii BSIs in our COVID-19 ICU. Further surveillance of resistance trends and mechanisms is needed along with changes in behavior to improve the implementation of infection control and the rational use of antibiotics.

Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus diseases (COVID-19) in late 2019 in China created a devastating economical loss and loss of human lives. To date, 11 variants have been identified with minimum to maximum severity of infection and surges in cases. Bacterial co-infection/secondary infection is identified during viral respiratory infection, which is a vital reason for morbidity and mortality. The occurrence of secondary infections is an additional burden to the healthcare system; therefore, the quick diagnosis of both COVID-19 and secondary infections will reduce work pressure on healthcare workers. Therefore, well-established support from Artificial Intelligence (AI) could reduce the stress in healthcare and even help in creating novel products to defend against the coronavirus. AI is one of the rapidly growing fields with numerous applications for the healthcare sector. The present review aims to access the recent literature on the role of AI and how its subfamily machine learning (ML) and deep learning (DL) are used to curb the pandemic’s effects. We discuss the role of AI in COVID-19 infections, the detection of secondary infections, technology-assisted protection from COVID-19, global laws and regulations on AI, and the impact of the pandemic on public life.

Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19.

METHODS

We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344).

FINDINGS

We included 148 studies of 362  976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%).

INTERPRETATION

Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed.

FUNDING

WHO.

Secondary infections in critically ill patients with viral pneumonia due to COVID-19 and influenza: a historical cohort study

PURPOSE

To compare the incidence and nature of secondary infections (SI) between critically ill patients with viral pneumonia due to COVID-19 and seasonal influenza and explore the association between SI and clinical outcomes.

METHODS

We conducted a historical cohort study of patients admitted to the intensive care unit (ICU) at two tertiary care centers during the first wave of the COVID-19 pandemic and patients admitted with influenza during the 2018-2019 season. The primary outcome was the rate of SI. Secondary outcomes included rates of ICU and in-hospital mortality, organ-support-dependent disease, and length of ICU and hospital stay.

RESULTS

Secondary infections developed in 55% of 95 COVID-19 patients and 51% of 47 influenza patients (unadjusted odds ratio [OR], 1.16; 95% confidence interval [CI], 0.57 to 2.33). After adjusting for baseline differences between cohorts, there were no significant differences between the COVID-19 cohort and the influenza cohort (adjusted OR, 1.00; 95% CI, 0.41 to 2.44). COVID-19 patients with SI had longer ICU and hospital stays and duration of mechanical ventilation. The SI incidence was higher in COVID-19 patients treated with steroids than in those not treated with steroids (15/20, 75% vs 37/75, 49%).

CONCLUSION

Secondary infections were common among critically ill patients with viral pneumonia including COVID-19. We found no difference in the incidence of SI between COVID-19 and influenza in our cohort study, but SI in patients with COVID-19 were associated with worse clinical outcomes and increased healthcare resource use. The small cohort size precludes any causal inferences but may provide a basis for future research.

Clinical outcomes of and risk factors for secondary infection in patients with severe COVID-19: a multicenter cohort study in South Korea

BACKGROUND/AIMS

Secondary infection with influenza virus occurs in critically ill patients and is associated with substantial morbidity and mortality; however, there is limited information about it in patients with severe coronavirus disease 2019 (COVID-19). Thus, we investigated the clinical outcomes of and risk factors for secondary infections in patients with severe COVID-19.

METHODS

This study included patients with severe COVID-19 who were admitted to seven hospitals in South Korea between February 2020 to February 2021. Multivariate logistic regression analyses were performed to assess factors associated with the risk of secondary infections.

RESULTS

Of the 348 included patients, 104 (29.9%) had at least one infection. There was no statistically significant difference in the 28-day mortality (17.3% vs. 12.3%, p = 0.214), but in-hospital mortality was higher (29.8% vs. 15.2%, p = 0.002) in the infected group than in the non-infected group. The risk factors for secondary infection were a high frailty scale (odds ratio [OR], 1.314; 95% confidence interval [CI], 1.123 to 1.538; p = 0.001), steroid use (OR, 3.110; 95% CI, 1.164 to 8.309; p = 0.024), and the application of mechanical ventilation (OR, 4.653; 95% CI, 2.533 to 8.547; p < 0.001).

CONCLUSION

In-hospital mortality was more than doubled in patients with severe COVID-19 and secondary infections. A high frailty scale, the use of steroids and application of mechanical ventilation were risk factors for secondary infection.

Increased rates of secondary bacterial infections, including Enterococcus bacteremia, in patients hospitalized with coronavirus disease 2019 (COVID-19)

OBJECTIVE

We compared the rates of hospital-onset secondary bacterial infections in patients with coronavirus disease 2019 (COVID-19) with rates in patients with influenza and controls, and we investigated reports of increased incidence of Enterococcus infections in patients with COVID-19.

DESIGN

Retrospective cohort study.

SETTING

An academic quaternary-care hospital in San Francisco, California.

PATIENTS

Patients admitted between October 1, 2019, and October 1, 2020, with a positive SARS-CoV-2 PCR (N = 314) or influenza PCR (N = 82) within 2 weeks of admission were compared with inpatients without positive SARS-CoV-2 or influenza tests during the study period (N = 14,332).

METHODS

National Healthcare Safety Network definitions were used to identify infection-related ventilator-associated complications (IVACs), probable ventilator-associated pneumonia (PVAP), bloodstream infections (BSIs), and catheter-associated urinary tract infections (CAUTIs). A multiple logistic regression model was used to control for likely confounders.

RESULTS

COVID-19 patients had significantly higher rates of IVAC and PVAP compared to controls, with adjusted odds ratios of 4.7 (95% confidence interval [CI], 1.7-13.9) and 10.4 (95 % CI, 2.1-52.1), respectively. COVID-19 patients had higher incidence of BSI due to Enterococcus but not BSI generally, and whole-genome sequencing of Enterococcus isolates demonstrated that nosocomial transmission did not explain the increased rate. Subanalyses of patients admitted to the intensive care unit and patients who required mechanical ventilation revealed similar findings.

CONCLUSIONS

COVID-19 is associated with an increased risk of IVAC, PVAP, and Enterococcus BSI compared with hospitalized controls, which is not fully explained by factors such as immunosuppressive treatments and duration of mechanical ventilation. The mechanism underlying increased rates of Enterococcus BSI in COVID-19 patients requires further investigation.

Opportunistic Candida Infections in Critical COVID-19 Patients

The frequency of opportunistic fungal infections in critically ill patients whose intensive care unit stays are prolonged due to coronavirus disease 2019 (COVID-19) is higher than in the period before COVID-19. We planned this study to improve the management of Candida infections by defining the Candida species, the etiology of infections caused by Candida species, and the antifungal susceptibility of the species. This retrospective study included patients older than 18 hospitalized in the intensive care unit (ICU) with a definitive diagnosis of COVID-19 for seven months (from March 2021 to September 2021). All study data that we recorded in a standard study form were analyzed with TURCOSA (Turcosa Analytics Ltd. Co., Turkey, www.turcosa.com.tr) statistical software. The patients were evaluated in four groups as group 1 (candidemia patients, n = 78), group 2 (candiduria patients, n = 189), group 3 (control patients, n = 57), and group 4 (patients with candidemia in urine cultures taken before Candida was detected in blood culture, n = 42). Candida species were identified using both conventional and VITEK® 2 (BioMérieux, France) methods. The antifungal susceptibility of fungi was determined using the E test method. Of the 5,583 COVID-19 patients followed during the study period, 78 developed candidemia, and 189 developed candiduria. The incidence of candidemia (per 1,000 admissions) was determined to be 1.6. As a result of statistical analysis, we found that Candida albicans was the dominant strain in candidemia and candiduria, and there was no antifungal resistance except for naturally resistant strains. Candida strains grown in blood and urine were the same in 40 of 42 patients. Mortality was 69.2% for group 1, 60.4% for group 2, and 57.8% for group 3. Antifungals were used in 34 (43.5%) patients from group 1, and 95 (50.2%) from group 2. In the candidemia group without antifungal use, mortality was quite high (77.2%). Antifungal use reduced mortality in the group 2 (p < 0.05). Length of ICU stays, comorbidity, broad-spectrum antibiotics, and corticosteroids are independent risk factors for candidemia in critically ill COVID-19 patients. Our study contributes to the knowledge of risk factors for developing COVID-19-related candida infections. The effect of candiduria on the development of candidemia in critically ill COVID-19 patients should be supported by new studies.

Complement C3 inhibition in severe COVID-19 using compstatin AMY-101

Complement C3 activation contributes to COVID-19 pathology, and C3 targeting has emerged as a promising therapeutic strategy. We provide interim data from ITHACA, the first randomized trial evaluating a C3 inhibitor, AMY-101, in severe COVID-19 (PaO2/FiO2 ≤ 300 mmHg). Patients received AMY-101 (n = 16) or placebo (n = 15) in addition to standard of care. AMY-101 was safe and well tolerated. Compared to placebo (8 of 15, 53.3%), a higher, albeit nonsignificant, proportion of AMY-101-treated patients (13 of 16, 81.3%) were free of supplemental oxygen at day 14. Three nonresponders and two placebo-treated patients succumbed to disease-related complications. AMY-101 significantly reduced CRP and ferritin and restrained thrombin and NET generation. Complete and sustained C3 inhibition was observed in all responders. Residual C3 activity in the three nonresponders suggested the presence of a convertase-independent C3 activation pathway overriding the drug's inhibitory activity. These findings support the design of larger trials exploring the potential of C3-based inhibition in COVID-19 or other complement-mediated diseases.

Incidence and Risk Factors for Blood Stream Infection in Mechanically Ventilated COVID-19 Patients

It is widely known that blood stream infections (BSIs) in critically ill patients may affect mortality, length of stay, or the duration of mechanical ventilation. There is scarce data regarding blood stream infections in mechanically ventilated COVID-19 patients. Preliminary studies report that the number of secondary infections in COVID-9 patients may be higher. This retrospective analysis was conducted to determine the incidence of BSI. Furthermore, risk factors, mortality, and other outcomes were analyzed. The setting was an Intensive Care Unit (ICU) at a University Hospital. Patients suffering from SARS-CoV-2 infection and requiring mechanical ventilation (MV) for >48 h were eligible. The characteristics of patients who presented BSI were compared with those of patients who did not present BSI. Eighty-four patients were included. The incidence of BSI was 57%. In most cases, multidrug-resistant pathogens were isolated. Dyslipidemia was more frequent in the BSI group (p < 0.05). Moreover, BSI-group patients had a longer ICU stay and a longer duration of both mechanical ventilation and sedation (p < 0.05). Deaths were not statistically different between the two groups (73% for BSI and 56% for the non-BSI group, p > 0.05). Compared with non-survivors, survivors had lower baseline APACHE II and SOFA scores, lower D-dimers levels, a higher baseline compliance of the respiratory system, and less frequent heart failure. They received anakinra less frequently and appropriate therapy more often (p < 0.05). The independent risk factor for mortality was the APACHE II score [1.232 (1.017 to 1.493), p = 0.033].

Fungal colonization and infections in patients with COVID-19 in intensive care units: A real-life experience at a tertiary-care hospital

PURPOSE

To evaluate the management of patients with COVID-19 in the intensive care units (ICUs) with fungal infection/colonization and to highlight diagnostic problems in these patients.

METHODS

We included all patients with a COVID-19 diagnosis who were aged ≥18 years and followed in the ICU for the first 8 months. Patient data were obtained from medical records. We compared the risk factors, laboratory data, and outcomes of patients with fungal infection/colonization.

RESULTS

A total of 118 patients (81 men and 37 women) were included. The mean age was 70.3 ± 14.8 (35-94) years. Of the patients, 79 (66.9%) patients were ≥65 years old. Fungal infection/colonization was detected in 39 (33.1%) patients. Fungi were isolated from 34 (28.8%) patients. Ten fungal species were isolated from 51 samples (the most common being Candida albicans). Three patients (2.5%) had proven candidemia. We observed two (1.7%) possible cases of COVID-19-associated pulmonary aspergillosis (CAPA). Eighteen patients (15.3%) underwent antifungal therapy. The risk of fungal infection/colonization increased as the duration of invasive mechanical ventilation increased. The fatality rate was 61.9% and increased with age and the use of mechanical ventilation. The fatality rate was 4.2-times-higher and the use of mechanical ventilation was 35.9-times-higher in the patients aged ≥65 years than in the patients aged <65 years. No relationship was found between fungal colonization/infection, antifungal treatment, and the fatality rate.

CONCLUSION

During the pandemic, approximately one-third of the patients in ICUs exhibited fungal infection/colonization. Candida albicans was the most common species of fungal infection as in the pre-pandemic area. Because of the cross-contamination risk, we performed diagnostic bronchoscopy and control thorax computed tomography during the ICU stay, and our patients mainly received empirical antifungal therapy.

Occurrence of Candidemia in Patients with COVID-19 Admitted to Five ICUs in France

Whether severe COVID-19 is by itself a significant risk factor for the development of candidemia currently remains an open question as conflicting results have been published. We aim to assess the occurrence of candidemia in patients with severe COVID-19 admitted to the intensive care unit (ICU). We conducted a retrospective study on patients with severe SARS-CoV-2-related pneumonia admitted to 5 ICUs in France who were specifically screened for fungal complications between March 2020 and January 2021. The study population included a total of 264 patients; the median age was 56 years old and most of them were male (n = 186; 70.5%) and immunocompetent (n = 225; 87.5%), and 62.7% (n = 153/244) were on extracorporeal membrane oxygenation support. Microbiological analysis included 4864 blood culture samples and beta-glucan test performed on 975 sera. Candidemia was diagnosed in 13 (4.9%) patients. The species involved were mainly C. albicans (n = 6) and C. parapsilosis (n = 5). Almost all patients (12/13; 92.3%) had a colonization by yeasts. ICU mortality was not significantly impacted by the occurrence of candidemia. Unrelated positive beta-glucan tests were observed in 49 patients (23.4%), including 6 with mold infections and 43 with false positive results. In our series, patients with severe SARS-CoV-2-related pneumonia seemed at low risk of developing invasive candidiasis.

Epidemiology of Candidemia and Fluconazole Resistance in an ICU before and during the COVID-19 Pandemic Era

The objectives of this study were to investigate the incidence of candidemia, as well as the factors associated with Candida species distribution and fluconazole resistance, among patients admitted to the intensive care unit (ICU) during the COVID-19 pandemic, as compared to two pre-pandemic periods. All patients admitted to the ICU due to COVID-19 from March 2020 to October 2021, as well as during two pre-pandemic periods (2005–2008 and 2012–2015), who developed candidemia, were included. During the COVID-19 study period, the incidence of candidemia was 10.2%, significantly higher compared with 3.2% and 4.2% in the two pre-pandemic periods, respectively. The proportion of non-albicans Candida species increased (from 60.6% to 62.3% and 75.8%, respectively), with a predominance of C. parapsilosis. A marked increase in fluconazole resistance (from 31% to 37.7% and 48.4%, respectively) was also observed. Regarding the total patient population with candidemia (n = 205), fluconazole resistance was independently associated with ICU length of stay (LOS) before candidemia (OR 1.03; CI: 1.01–1.06, p = 0.003), whereas the presence of shock at candidemia onset was associated with C. albicans (OR 6.89; CI: 2.2–25, p = 0.001), and with fluconazole-susceptible species (OR 0.23; CI: 0.07–0.64, p = 0.006). In conclusion, substantial increases in the incidence of candidemia, in non-albicansCandida species, and in fluconazole resistance were found in patients admitted to the ICU due to COVID-19, compared to pre-pandemic periods. At candidemia onset, prolonged ICU LOS was associated with fluconazole-resistant and the presence of shock with fluconazole-susceptible species.

A Retrospective, Monocentric Study Comparing Co and Secondary Infections in Critically Ill COVID-19 and Influenza Patients

Few data are available on infectious complications in critically ill patients with different viral infections. We performed a retrospective monocentric study including all of the patients admitted to the intensive care unit (ICU) with confirmed COVID-19 (as of 13 March 2020) or Influenza A and/or B infections (as of 1 January 2015) until 20 April 2020. Coinfection and secondary infections (occurring within and after 48 h from admission, respectively) were recorded. Fifty-seven COVID-19 and 55 Influenza patients were included. Co-infections were documented in 13/57 (23%) COVID-19 patients vs. 40/55 (73%) Influenza patients (p < 0.001), most of them being respiratory (9/13, 69% vs. 35/40, 88%; p = 0.13) and of bacterial origin (12/13, 92% vs. 29/40, 73%; p = 0.25). Invasive aspergillosis infections were observed only in Influenza patients (8/55, 15%). The COVID-19 and Influenza patients presented 1 (0−4) vs. 0 (0−4) secondary infections (p = 0.022), with comparable sites being affected (lungs: 35/61, 57% vs. 13/31, 42%; p = 0.16) and causative pathogens occurring (Gram-negative bacteria: 51/61, 84% vs. 23/31, 74%; p > 0.99). The COVID-19 patients had longer ICU lengths of stay (15 (−65) vs. 5 (1−89) days; p = 0.001), yet the two groups had comparable mortality rates (20/57, 35% vs. 23/55, 41%; p = 0.46). We report fewer co-infections but more secondary infections in the ICU COVID-19 patients compared to the Influenza patients. Most of the infectious complications were respiratory and of bacterial origin.

Comparison of Antibiotic Use between the First Two Waves of COVID-19 in an Intensive Care Unit at a London Tertiary Centre: reducing broad-spectrum antimicrobial use did not adversely affect mortality

BACKGROUND

The COVID-19 pandemic increased the use of broad-spectrum antibiotics due to diagnostic uncertainty, particularly in critical care. Multiprofessional communication became more difficult, weakening stewardship activities.

AIM

To determine changes in bacterial co-/secondary infections and antibiotics used in COVID-19 patients in critical care, and mortality rates, between the first and second waves.

METHODS

Prospective audit comparing bacterial co-/secondary infections and their treatment during the first two waves of the pandemic in a single centre teaching hospital ICU. Data on demographics, daily antibiotic use, clinical outcomes, and culture results in patients diagnosed with COVID-19 infection were collected over 11 months.

FINDINGS

From 9/3/20 to 2/9/20 (Wave 1), there were 156 patients and between 3/9/20 and 1/2/21 (Wave 2) there were 235 patients with COVID-19 infection admitted to intensive care. No significant difference was seen in mortality or positive blood culture rates between the two waves. The proportion of patients receiving antimicrobial therapy (93.0% vs 81.7%; p<0.01), and the duration of meropenem use (median (interquartile range): 5 (2-7) vs 3 (2-5) days; p=0.01) was lower in Wave 2. However, the number of patients with respiratory isolates of Pseudomonas aeruginosa (4/156 vs 21/235; p<0.01) and bacteraemia from a respiratory source (3/156 vs 20/235 p<0.01) increased in Wave 2, associated with an outbreak of infection. There was no significant difference between waves with respect to isolation of other pathogens.

CONCLUSIONS

Reduced broad spectrum antimicrobial use in the second wave of COVID-19 compared with the first wave was not associated with significant change in mortality.

Incidence of Candidemia Is Higher in COVID-19 versus Non-COVID-19 Patients, but Not Driven by Intrahospital Transmission

There is scarce information on the actual incidence of candidemia in COVID-19 patients. In addition, comparative studies of candidemia episodes in COVID-19 and non-COVID-19 patients are heterogeneous. Here, we assessed the real incidence, epidemiology, and etiology of candidemia in COVID-19 patients, and compared them with those without COVID-19 (2020 vs. 2019 and 2020, respectively). We also genotyped all C. albicans, C. parapsilosis, and C. tropicalis isolates (n = 88), causing candidemia in both groups, providing for the first time a genotypic characterization of isolates gathered in patients with either COVID-19 or non-COVID-19. Incidence of candidemia was higher in patients with COVID-19 than non-COVID-19 (4.73 vs. 0.85 per 1000 admissions; 3.22 vs. 1.14 per 10,000 days of stay). No substantial intergroup differences were found, including mortality. Genotyping proved the presence of a low number of patients involved in clusters, allowing us to rule out rampant patient-to-patient Candida transmission. The four patients, involved in two clusters, had catheter-related candidemia diagnosed in the first COVID-19 wave, which demonstrates breaches in catheter management policies occurring in such an overwhelming situation. In conclusion, the incidence of candidemia in patients with COVID-19 is significantly higher than in those without COVID-19. However, genotyping shows that this increase is not due to uncontrolled intrahospital transmission.

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019-June 2021)

Background

Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR).

Objectives

We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings.

Methods

We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences.

Results

Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8–40%; n = 25 studies: I² = 99%) and 0.3% (95% CI 0.1–0.6%; n = 8 studies: I² = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism.

Conclusions

During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01085-z.

Unresolved issues in the epidemiology and diagnosis of bacteremia: an opinion paper

Bacteremia is an important cause of morbidity and mortality worldwide and, despite the diagnostic and therapeutic advances of the last decades, the evidence supporting many diagnostic aspects of bacteremia is scarce. Information on the epidemiological evolution of this entity is limited and many methodological aspects of blood culture collection and analysis are under discussion. Furthermore, the recommendations of the main scientific societies on many of these aspects are variable and, in many cases, have not been updated recently. In this scenario, we have arranged a series of questions on different aspects of bacteremia and reviewed the literature trying to find proper answers for them. We offer our opinion on the topics where the evidence was weak. The topics covered include epidemiological aspects of bacteremia, indications for blood culture extraction, methods for obtaining and incubating samples, or ways of transmitting results from the microbiology laboratory. We do not intend to summarize the current clinical practice guidelines, nor will we deal with the therapeutic management of this entity. The aim of this paper is to review the current perspective on the diagnosis of bacteremia with a critical approach, to point out the gaps in the literature, to offer the opinion of a team dedicated to infectious diseases and clinical microbiology, and to identify some areas of knowledge on which future studies should focus.

Evaluation of prevalance and risk factors for bloodstream infection in severe coronavirus disease 2019 (COVID-19) patients

Objectives:

In this study, we sought to determine the prevalence of bloodstream infection (BSI) in severe coronavirus disease 2019 (COVID-19) patients and to determine the risk factors of BSI in critical COVID-19 patients.

Design:

Retrospective, descriptive study between March 2020 and January 2021.

Setting:

An 1,007-bed university hospital.

Participants:

Patients who were hospitalized due to severe COVID-19 disease and had an aerobic blood culture taken at least once during hospitalization

Methods:

Case definitions were made according to National Institutes of Health clinical definitions. According to the blood culture results, the patients were grouped as with and without BSIs, and compared for BSIs risk factors.

Results:

In total, 195 patients were included in the study. Blood culture positivity was detected in 76 (39.0%) of 196 patients. Excluding blood culture positivity considered as contamination, the prevalence of BSI in all severe COVID-19 cases was 18.5% (n = 36). In intensive care unit patients the prevalence of BSI was 30.6% (n = 26). In multivariate analyses, central venous catheter (odds ratio [OR], 8.17; 95% confidence interval [CI], 2.46–27.1; P < .01) and hospitalization in the multibed intensive care unit (OR, 4.28; 95% CI, 1.28–14.3; P < .01) were risk factors associated with the acquisition of BSI.

Conclusion:

The prevalence of BSI in COVID-19 patients is particularly high in critically ill patients. The central venous catheter and multibed intensive care follow-up are risk factors for BSI. BSIs can be reduced by increasing compliance to infection control measures and central venous catheter insertion-care procedures. The use of single-bed intensive care units where compliance can be achieved more effectively is important for the prevention of BSIs.

Microbiological characteristics of bacteremias among COVID-19 hospitalized patients in a tertiary referral hospital in Northern Greece during the second epidemic wave

Northern Greece was struck by an intense second COVID-19 (coronavirus disease 2019) epidemic wave during the fall of 2020. Because of the coinciding silent epidemic of multidrug-resistant organisms, the handling of COVID-19 patients became even more challenging. In the present study, the microbiological characteristics of bacteremias in confirmed cases of hospitalized COVID-19 patients were determined. Data from 1165 patients hospitalized between September and December 2020 were reviewed regarding the frequency of bloodstream infections, the epidemiology and the antibiotic susceptibility profiles of the causative bacteria. The hospital's antibiotic susceptibility data for all major nosocomial pathogens isolated from bacteremias of COVID-19 patients between September and December 2020 versus those between September and December 2019 were also compared. Overall, 122 patients developed bacteremia (10.47%). The average of time interval between hospitalization date and development of bacteremia was 13.98 days. Admission to ICU occurred in 98 out of 122 patients with an average stay time of 15.85 days and 90.81% in-hospital mortality. In total, 166 pathogens were recovered including 114 Gram-negative bacteria and 52 Gram-positive cocci. Acinetobacter baumannii was the most frequent (n = 51) followed by Klebsiella pneumoniae (n = 45) and Enterococcus faecium (n = 31). Bacteremias in hospitalized COVID-19 patients were related with prolonged time of hospitalization and higher in-hospital mortality, and the isolated microorganisms represented the bacterial species that were present in our hospital before the COVID-19 pandemic. Worryingly, the antibiotic resistance rates were increased compared with the pre-pandemic era for all major opportunistic bacterial pathogens. The pandemic highlighted the need for continuous surveillance of patients with prolonged hospitalization.

Coronavirus Disease 2019-Associated Invasive Fungal Infection

Coronavirus disease 2019 (COVID-19) can become complicated by secondary invasive fungal infections (IFIs), stemming primarily from severe lung damage and immunologic deficits associated with the virus or immunomodulatory therapy. Other risk factors include poorly controlled diabetes, structural lung disease and/or other comorbidities, and fungal colonization. Opportunistic IFI following severe respiratory viral illness has been increasingly recognized, most notably with severe influenza. There have been many reports of fungal infections associated with COVID-19, initially predominated by pulmonary aspergillosis, but with recent emergence of mucormycosis, candidiasis, and endemic mycoses. These infections can be challenging to diagnose and are associated with poor outcomes. The reported incidence of IFI has varied, often related to heterogeneity in patient populations, surveillance protocols, and definitions used for classification of fungal infections. Herein, we review IFI complicating COVID-19 and address knowledge gaps related to epidemiology, diagnosis, and management of COVID-19-associated fungal infections.

Bloodstream Infections in Hospitalized Patients with COVID-19: A Systematic Review and Meta-Analysis

Background: Little is known about the occurrence of bloodstream infections in hospitalized patients with COVID-19 and the related clinical consequences. The aim of this systematic review and meta-analysis was to estimate the pooled occurrence of BSIs among hospitalized patients with COVID-19 and mortality of this patient population. Methods: A systematic search was performed on PubMed, EMBASE, and Web of Science from inception to 19 April 2021. The primary outcome was the occurrence of BSIs among hospitalized patients with COVID-19. The secondary outcome was mortality at the longest available follow-up. Results: Forty-six studies met the inclusion criteria, with a total of 42,694 patients evaluated. The estimated occurrence of BSIs was 7.3% (95% CI 4.7–1.1%) among hospitalized patients with COVID-19, with a mortality rate of 41% (95% CI 30%–52.8%). The subgroup analysis conducted on patients admitted to ICU provided an estimated occurrence of 29.6% (95% CI 21.7%–38.8%). A higher occurrence of BSI was observed in patients with COVID-19, in comparison with patients without COVID-19 (OR 2.77; 95% CI 1.53–5.02; p < 0.001). Conclusions: Our analysis estimated the occurrence of BSIs among hospitalized patients with COVID-19 at around 7%. A four-times higher occurrence was estimated among patients admitted to ICU.

COVID-19 and Antimicrobial Resistance: Data from the Greek Electronic System for the Surveillance of Antimicrobial Resistance-WHONET-Greece (January 2018-March 2021)

Changes in hospitals' daily practice due to COVID-19 pandemic may have an impact on antimicrobial resistance (AMR). We aimed to assess this possible impact as captured by the Greek Electronic System for the Surveillance of Antimicrobial Resistance (WHONET-Greece). Routine susceptibility data of 17,837 Gram-negative and Gram-positive bacterial isolates from blood and respiratory specimens of hospitalized patients in nine COVID-19 tertiary hospitals were used in order to identify potential differences in AMR trends in the last three years, divided into two periods, January 2018-March 2020 and April 2020-March 2021. Interrupted time-series analysis was used to evaluate differences in the trends of non-susceptibility before and after the changes due to COVID-19. We found significant differences in the slope of non-susceptibility trends of Acinetobacter baumannii blood and respiratory isolates to amikacin, tigecycline and colistin; of Klebsiella pneumoniae blood and respiratory isolates to meropenem and tigecycline; and of Pseudomonas aeruginosa respiratory isolates to imipenem, meropenem and levofloxacin. Additionally, we found significant differences in the slope of non-susceptibility trends of Staphylococcus aureus isolates to oxacillin and of Enterococcus faecium isolates to glycopeptides. Assessing in this early stage, through surveillance of routine laboratory data, the way a new global threat like COVID-19 could affect an already ongoing pandemic like AMR provides useful information for prompt action.

Incidence, Risk Factors and Impact on Clinical Outcomes of Bloodstream Infections in Patients Hospitalised with COVID-19: A Prospective Cohort Study

With the aim of describing the burden and epidemiology of community-acquired/healthcare-associated and hospital-acquired bloodstream infections (CA/HCA-BSIs and HA-BSIs) in patients hospitalised with COVID-19, and evaluating the risk factors for BSIs and their relative impact on mortality, an observational cohort study was performed on patients hospitalised with COVID-19 at San Paolo Hospital in Milan, Italy from 24 February to 30 November 2020. Among 1351 consecutive patients hospitalised with COVID-19, 18 (1.3%) had CA/HCA-BSI and 51 (3.8%) HA-BSI for a total of 82 episodes of BSI. The overall incidence of HA-BSI was 3.3/1000 patient-days (95% CI 2.4-4.2). Patients with HA-BSI had a longer hospital stay compared to CA/HCA-BSI and no-BSI groups (27 (IQR 21-35) vs. 12 (7-29) vs. 9 (5-17) median-days, p < 0.001) but a similar in-hospital mortality (31% vs. 33% vs. 25%, p = 0.421). BSI was not associated with an increased risk of mortality (CA/HCA-BSI vs. non-BSI aOR 1.27 95% CI 0.41-3.90, p = 0.681; HA-BSI vs. non-BSI aOR 1.29 95% CI 0.65-2.54, p = 0.463). Upon multivariate analysis, NIMV/CPAP (aOR 2.09, 95% CI 1.06-4.12, p = 0.034), IMV (aOR 5.13, 95% CI 2.08-12.65, p < 0.001) and corticosteroid treatment (aOR 2.11, 95% CI 1.06-4.19, p = 0.032) were confirmed as independent factors associated with HA-BSI. Development of HA-BSI did not significantly affect mortality. Patients treated with corticosteroid therapy had double the risk of developing BSI.

Bloodstream Infection Risk, Incidence, and Deaths for Hospitalized Patients during Coronavirus Disease Pandemic

Hospital-acquired infections are emerging major concurrent conditions during the coronavirus disease (COVID-19) pandemic. We conducted a retrospective review of hospitalizations during March‒October 2020 of adults tested by reverse transcription PCR for severe acute respiratory syndrome coronavirus 2. We evaluated associations of COVID-19 diagnosis with risk for laboratory-confirmed bloodstream infections (LCBIs, primary outcome), time to LCBI, and risk for death by using logistic and competing risks regression with adjustment for relevant covariates. A total of 10,848 patients were included in the analysis: 918 (8.5%) were given a diagnosis of COVID-19, and 232 (2.1%) had LCBIs during their hospitalization. Of these patients, 58 (25%) were classified as having central line‒associated bloodstream infections. After adjusting for covariates, COVID-19‒positive status was associated with higher risk for LCBI and death. Reinforcement of infection control practices should be implemented in COVID-19 wards, and review of superiority and inferiority ranking methods by National Healthcare Safety Network criteria might be needed.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Hospital-Acquired Blood Stream Infection in an Adult Intensive Care Unit

Background

Hospital-acquired blood stream infections are a common and serious complication in critically ill patients.

Methods

A retrospective case series was undertaken investigating the incidence and causes of bacteraemia in an adult intensive care unit with a high proportion of postoperative cardiothoracic surgical and oncology patients.

Results

405 eligible patients were admitted to the intensive care unit over the course of nine months. 12 of these patients developed a unit-acquired blood stream infection. The average Acute Physiology And Chronic Health Evaluation II (APACHE II) score of patients who developed bacteraemia was greater than that of those who did not (19.8 versus 16.8, respectively). The risk of developing bacteraemia was associated with intubation and higher rates of invasive procedures. The mortality rate amongst the group of patients that developed bacteraemia was 33%; this is in contrast to the mortality rate in our unit as 27.2%. There was a higher proportion of Gram-negative bacteria isolated on blood cultures (9 out of 13 isolates) than in intensive care units reported in other studies.

Conclusion

Critical-care patients are at risk of secondary bloodstream infection. This study highlights the importance of measures to reduce the risk of infection in the intensive-care setting, particularly in patients who have undergone invasive procedures.

The Complexity of Co-Infections in the Era of COVID-19

The current frequency of COVID-19 in a pandemic era ensures that co-infections with a variety of co-pathogens will occur. Generally, there is a low rate of bonafide co-infections in early COVID-19 pulmonary infection as currently appreciated. Reports of high co-infection rates must be tempered by limitations in current diagnostic methods since amplification technologies do not necessarily confirm live pathogen and may be subject to considerable laboratory variation. Some laboratory methods may not exclude commensal microbes. Concurrent serodiagnoses have long been of concern for accuracy in these contexts. Presumed virus co-infections are not specific to COVID-19. The association of influenza viruses and SARS-CoV-2 in co-infection has been considerably variable during influenza season. Other respiratory virus co-infections have generally occurred in less than 10% of COVID-19 patients. Early COVID-19 disease is more commonly associated with bacterial co-pathogens that typically represent usual respiratory micro-organisms. Late infections, especially among severe clinical presentations, are more likely to be associated with nosocomial or opportunistic pathogens given the influence of treatments that can include antibiotics, antivirals, immunomodulating agents, blood products, immunotherapy, steroids, and invasive procedures. As anticipated, hospital care carries risk for multi-resistant bacteria. Overall, co-pathogen identification is linked with longer hospital stay, greater patient complexity, and adverse outcomes. As for other viral infections, a general reduction in the use of empiric antibiotic treatment is warranted. Further insight into co-infections with COVID-19 will contribute overall to effective antimicrobial therapies and disease control.

Co-Infections in Critically Ill Patients with or without COVID-19: A Comparison of Clinical Microbial Culture Findings

Co-infections in critically ill patients hospitalized for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have an important impact on the outcome of coronavirus disease 2019 (COVID-19). We compared the microbial isolations found in COVID-19 patients hospitalized in an intensive care unit (ICU) with those in a non-COVID-19 ICU from 22 February to 30 April 2020 and in the same period of 2019. We considered blood, urine or respiratory specimens obtained with bronchoalveolar lavage (BAL) or bronchial aspirate (BASP), collected from all patients admitted in ICUs with or without COVID-19 infection. We found a higher frequency of infections due to methicillin-resistant (MR) staphylococci, vancomycin-resistant Enterococcus faecium, carbapenem-resistant Acinetobacter baumannii and Candida parapsilosis in COVID-19-positive patients admitted in ICUs compared to those who were COVID-19 negative. Carbapenem-resistant Pseudomonas aeruginosa was more frequently isolated from patients admitted in non-COVID-19 ICUs. Several conditions favor the increased frequency of these infections by antibiotic-resistant microorganisms. Among all, the severity of the respiratory tracts was definitely decisive, which required assisted ventilation with invasive procedures. The turnover in the ICU of a large number of patients in a very short time requiring urgent invasive interventions has favored the not always suitable execution of assistance procedures. No less important is the increased exposure to infectious risk from bacteria and fungi in patients with severe impairment due to ventilation. The highest costs for antifungal drugs were shown in the ICU-COVID group.

Clinical efficacy of ceftazidime combined with levofloxacin on heart failure complicated with pulmonary infection and its influence on cardiopulmonary function

OBJECTIVE

This study was designed to analyze the clinical efficacy of ceftazidime combined with levofloxacin on heart failure complicated with pulmonary infection and its influence on cardiopulmonary function.

METHODS

A total of 124 patients with heart failure and pulmonary infection admitted to our hospital from June 2018 to October 2019 were divided into groups according to different treatment schemes. Thereinto, 60 patients who were given ceftazidime intravenous drip on the basis of routine treatment were included in group A, and 64 who were given levofloxacin hydrochloride injection based on intravenous drip in group A were included in group B. The clinical efficacy, cardiac and lung function, pathogenic bacteria, infection, immune indexes and adverse reactions before and after treatment were compared.

RESULTS

After treatment, the adjusted levels of LVEF, LVEDD and LA in group B after treatment were greater than those in group A (P<0.05); the levels of MMV, TLC and FEV1 in group B were increased more than those in group A (P<0.05). After treatment, the levels of BNP, PCT and CRP in groups A and B decreased compared with those before treatment (P<0.05). Furthermore, the down-regulated levels of BNP, PCT and CRP in group B were higher than those in group A after treatment (P<0.05). After treatment, the levels of serum CD3⁺, CD4⁺, CD4⁺/CD8⁺ in group B increased more and CD8⁺ decreased more. The clinical efficacy of group B after 7 days was higher than that of group A (P<0.01). Patients were followed up for one month, and there was no marked difference in their adverse drug reaction rates (P>0.05).

CONCLUSION

To sum up, ceftazidime combined with levofloxacin on patients with heart failure and pulmonary infection can improve the immune function while optimizing the clinical efficacy and cardiopulmonary function.

Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, the microbial composition of the respiratory tract and other infected tissues as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Between 27 January and 26 February 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients in Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. We identified distinct signatures of microbial dysbiosis among severely ill COVID-19 patients on broad spectrum antimicrobial therapy. Co-detection of other human respiratory viruses (including human alphaherpesvirus 1, rhinovirus B, and human orthopneumovirus) was demonstrated in 30.8% (4/13) of the severely ill patients, but not in any of the mildly affected patients. Notably, the predominant respiratory microbial taxa of severely ill patients were Burkholderia cepacia complex (BCC), Staphylococcus epidermidis, or Mycoplasma spp. (including M. hominis and M. orale). The presence of the former two bacterial taxa was also confirmed by clinical cultures of respiratory specimens (expectorated sputum or nasal secretions) in 23.1% (3/13) of the severe cases. Finally, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes was demonstrated in one severely ill patient, which might accelerate his disease deterioration and death occurring one month after ICU admission. Our findings point to SARS-CoV-2-related microbial dysbiosis and various antibiotic-resistant respiratory microbes/pathogens in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking strategies are needed to prevent the spread of antimicrobial resistance, improve the treatment regimen and clinical outcomes of hospitalized, severely ill COVID-19 patients.