Co-infection and ICU-acquired infection in COIVD-19 ICU patients: a secondary analysis of the UNITE-COVID data set

BACKGROUND

The COVID-19 pandemic presented major challenges for critical care facilities worldwide. Infections which develop alongside or subsequent to viral pneumonitis are a challenge under sporadic and pandemic conditions; however, data have suggested that patterns of these differ between COVID-19 and other viral pneumonitides. This secondary analysis aimed to explore patterns of co-infection and intensive care unit-acquired infections (ICU-AI) and the relationship to use of corticosteroids in a large, international cohort of critically ill COVID-19 patients.

METHODS

This is a multicenter, international, observational study, including adult patients with PCR-confirmed COVID-19 diagnosis admitted to ICUs at the peak of wave one of COVID-19 (February 15th to May 15th, 2020). Data collected included investigator-assessed co-infection at ICU admission, infection acquired in ICU, infection with multi-drug resistant organisms (MDRO) and antibiotic use. Frequencies were compared by Pearson's Chi-squared and continuous variables by Mann-Whitney U test. Propensity score matching for variables associated with ICU-acquired infection was undertaken using R library MatchIT using the "full" matching method.

RESULTS

Data were available from 4994 patients. Bacterial co-infection at admission was detected in 716 patients (14%), whilst 85% of patients received antibiotics at that stage. ICU-AI developed in 2715 (54%). The most common ICU-AI was bacterial pneumonia (44% of infections), whilst 9% of patients developed fungal pneumonia; 25% of infections involved MDRO. Patients developing infections in ICU had greater antimicrobial exposure than those without such infections. Incident density (ICU-AI per 1000 ICU days) was in considerable excess of reports from pre-pandemic surveillance. Corticosteroid use was heterogenous between ICUs. In univariate analysis, 58% of patients receiving corticosteroids and 43% of those not receiving steroids developed ICU-AI. Adjusting for potential confounders in the propensity-matched cohort, 71% of patients receiving corticosteroids developed ICU-AI vs 52% of those not receiving corticosteroids. Duration of corticosteroid therapy was also associated with development of ICU-AI and infection with an MDRO.

CONCLUSIONS

In patients with severe COVID-19 in the first wave, co-infection at admission to ICU was relatively rare but antibiotic use was in substantial excess to that indication. ICU-AI were common and were significantly associated with use of corticosteroids. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021).

Clinical and organizational factors associated with mortality during the peak of first COVID-19 wave: the global UNITE-COVID study

PURPOSE

To accommodate the unprecedented number of critically ill patients with pneumonia caused by coronavirus disease 2019 (COVID-19) expansion of the capacity of intensive care unit (ICU) to clinical areas not previously used for critical care was necessary. We describe the global burden of COVID-19 admissions and the clinical and organizational characteristics associated with outcomes in critically ill COVID-19 patients.

METHODS

Multicenter, international, point prevalence study, including adult patients with SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) and a diagnosis of COVID-19 admitted to ICU between February 15th and May 15th, 2020.

RESULTS

4994 patients from 280 ICUs in 46 countries were included. Included ICUs increased their total capacity from 4931 to 7630 beds, deploying personnel from other areas. Overall, 1986 (39.8%) patients were admitted to surge capacity beds. Invasive ventilation at admission was present in 2325 (46.5%) patients and was required during ICU stay in 85.8% of patients. 60-day mortality was 33.9% (IQR across units: 20%-50%) and ICU mortality 32.7%. Older age, invasive mechanical ventilation, and acute kidney injury (AKI) were associated with increased mortality. These associations were also confirmed specifically in mechanically ventilated patients. Admission to surge capacity beds was not associated with mortality, even after controlling for other factors.

CONCLUSIONS

ICUs responded to the increase in COVID-19 patients by increasing bed availability and staff, admitting up to 40% of patients in surge capacity beds. Although mortality in this population was high, admission to a surge capacity bed was not associated with increased mortality. Older age, invasive mechanical ventilation, and AKI were identified as the strongest predictors of mortality.

Visualizing Genome Reorganization Using 3D DNA FISH

Understanding how the genome is organized within the cell nucleus is increasingly recognized to be important to understand gene regulation. In 3D DNA fluorescence in situ hybridization (3D DNA FISH) labeled probes complementary to specific loci of interest are hybridized to the genome. The samples are then imaged using fluorescence microscopy, collecting z-stacks through the nuclei, and the relative positions of the hybridized probes are analyzed in the reconstructed 3D images. In this way 3D DNA FISH provides a powerful tool to interrogate how the organization of specific genomic loci changes in response to stimuli. This chapter describes protocols which have allowed us to produce consistent data in cultured cells and paraffin-embedded tissue sections.

Divergent transcriptional activation by glucocorticoids in mouse and human macrophages

BACKGROUND

Innate immune cells are major targets of glucocorticoids as anti-inflammatory therapies. Glucocorticoids are metabolic hormones that provide natural feedback regulation of immune function. They are widely prescribed, but use is restricted by side-effects. Much of our knowledge about how glucocorticoids work comes from studies in mice. However, since mice are imperfect models of human macrophage biology, for example in inflammation, whether this knowledge can be directly translated to man is uncertain. We aimed to address this uncertainty.

METHODS

We performed global expression profiling of primary cultured mouse and human macrophages, sampling at six points during 24 h after treatment with glucocorticoids. To assess the mechanism behind the regulation of transcription we also determined the DNA-binding pattern of the nuclear glucocorticoid receptor (GR) using chromatin immunoprecipitation followed by sequencing (ChIP-seq).

FINDINGS

Glucocorticoids initiated a temporal cascade of predominantly induced gene regulation in both species, but with little overlap in the gene sets. Single nucleotide polymorphisms (SNPs) linked to inflammatory disease were enriched near human (but not mouse) glucocorticoid-regulated genes. Using our genes as candidates, we identified eight SNPs reported as low significance that might be of biological relevance. We found that GR bound at candidate enhancers in the vicinity of induced genes and that this was strongly associated with canonical GR-dimer binding motifs. By contrast, promoters of induced genes, and the smaller set of repressed genes, showed no association with GR binding. Sites bound by GR were also not conserved between human and mouse macrophages, due to loss of the GR binding motif, which reflects the divergence in transcription.

INTERPRETATION

We conclude that the response of innate immune cells to glucocorticoids has diverged significantly between species because of the gain or loss of glucocorticoid-responsive enhancers.

FUNDING

Wellcome Trust.

Zinc presence in invasive ductal carcinoma of the breast and its correlation with oestrogen receptor status

Zinc is known to play an important role in many cellular processes, and the levels of zinc are controlled by specific transporters from the ZIP (SLC39A) influx transporter group and the ZnT (SLC30A) efflux transporter group. The distribution of zinc was measured in 59 samples of invasive ductal carcinoma of breast using synchrotron radiation micro probe x-ray fluorescence facilities. The samples were formalin fixed paraffin embedded tissue micro arrays (TMAs) enabling a high throughput of samples and allowing us to correlate the distribution of trace metals with tumour cell distribution and, for the first time, important biological variables. The samples were divided into two classes, 34 oestrogen receptor positive (ER+ve) and 25 oestrogen receptor negative (ER-ve) based on quantitative immunohistochemistry assessment. The overall levels of zinc (i.e. in tumour and surrounding tissue) in the ER+ve samples were on average 60% higher than those in the ER-ve samples. The zinc levels were higher in the ER+ve tumour areas compared to the ER-ve tumour areas with the mean levels in the ER+ve samples being approximately 80% higher than the mean ER-ve levels. However, the non-tumour tissue regions of the samples contained on average the same levels of zinc in both types of breast cancers. The relative levels of zinc in tumour areas of the tissue were compared with levels in areas of non-tumour surrounding tissue. There was a significant increase in zinc in the tumour regions of the ER+ve samples compared to the surrounding regions (P < 0.001) and a non-significant increase in the ER-ve samples. When comparing the increase in zinc in the tumour regions expressed as a percentage of the surrounding non-tumour tissue zinc level in the same sample, a significant difference between the ER+ve and ER-ve samples was found (P < 0.01).