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The complex process of manual biomarker extraction from body composition analysis (BCA) has far restricted the analysis of SARS-CoV-2 outcomes to small patient cohorts and a limited number of tissue types. We investigate the association of two BCA-based biomarkers with the development of severe SARS-CoV-2 infections for 918 patients (354 female, 564 male) regarding disease severity and mortality (186 deceased). Multiple tissues, such as muscle, bone, or adipose tissue are used and acquired with a deep-learning-based, fully-automated BCA from computed tomography images of the chest. The BCA features and markers were univariately analyzed with a Shapiro–Wilk and two-sided Mann–Whitney-U test. In a multivariate approach, obtained markers were adjusted by a defined set of laboratory parameters promoted by other studies. Subsequently, the relationship between the markers and two endpoints, namely severity and mortality, was investigated with regard to statistical significance. The univariate approach showed that the muscle volume was significant for female ( p severity  ≤ 0.001, p mortality  ≤ 0.0001) and male patients ( p severity  = 0.018, p mortality  ≤ 0.0001) regarding the severity and mortality endpoints. For male patients, the intra- and intermuscular adipose tissue (IMAT) ( p  ≤ 0.0001), epicardial adipose tissue (EAT) ( p  ≤ 0.001) and pericardial adipose tissue (PAT) ( p  ≤ 0.0001) were significant regarding the severity outcome. With the mortality outcome, muscle ( p  ≤ 0.0001), IMAT ( p  ≤ 0.001), EAT ( p  = 0.011) and PAT ( p  = 0.003) remained significant. For female patients, bone ( p  ≤ 0.001), IMAT ( p  = 0.032) and PAT ( p  = 0.047) were significant in univariate analyses regarding the severity and bone ( p  = 0.005) regarding the mortality. Furthermore, the defined sarcopenia marker ( p  ≤ 0.0001, for female and male) was significant for both endpoints. The cardiac marker was significant for severity (p female  = 0.014, p male  ≤ 0.0001) and for mortality (p female  ≤ 0.0001, p male  ≤ 0.0001) endpoint for both genders. The multivariate logistic regression showed that the sarcopenia marker was significant ( p severity  = 0.006, p mortality  = 0.002) for both endpoints (OR severity  = 0.42, 95% CI severity : 0.23–0.78, OR mortality  = 0.34, 95% CI mortality : 0.17–0.67). The cardiac marker showed significance (p = 0.018) only for the severity endpoint (OR = 1.42, 95% CI 1.06–1.90). The association between BCA-based sarcopenia and cardiac biomarkers and disease severity and mortality suggests that these biomarkers can contribute to the risk stratification of SARS-CoV-2 patients. Patients with a higher cardiac marker and a lower sarcopenia marker are at risk for a severe course or death. Whether those biomarkers hold similar importance for other pneumonia-related diseases requires further investigation.

In order to identify biomarkers for earlier prediction of COVID-19 outcome, we collected blood samples from patients with fatal outcomes (non-survivors) and with positive clinical outcomes (survivors) at ICU admission and after seven days. COVID-19 survivors and non-survivors showed significantly different transcript levels for 93 genes in whole blood already at ICU admission as revealed by RNA-Seq. These differences became even more pronounced at day 7, resulting in 290 differentially expressed genes. Many identified genes play a role in the differentiation of hematopoietic cells. For validation, we designed an RT-qPCR assay for C-type lectin domain family 12 member A ( CLEC12A ) and acetylcholinesterase ( ACHE ), two transcripts that showed highest potential to discriminate between survivors and non-survivors at both time points. Using our combined RT-qPCR assay we examined 33 samples to accurately predict patient survival with an AUROC curve of 0.931 (95% CI = 0.814–1.000) already at ICU admission. CLEC12A and ACHE showed improved prediction of patient outcomes compared to standard clinical biomarkers including CRP and PCT in combination (AUROC = 0.403, 95% CI = 0.108–0.697) or SOFA score (AUROC = 0.701 95% CI = 0.451–0.951) at day 0. Therefore, analyzing CLEC12A and ACHE gene expression from blood may provide a promising approach for early risk stratification of severely ill COVID-19 patients.

Extracorporeal membrane oxygenation (ECMO) is widely used to manage acute respiratory distress syndrome (ARDS); however, biofilm formation on cannulas may contribute to infections. This study investigated the prevalence, timing, and microbial profiles of infectious complications following ECMO decannulation. This prospective, single-center cohort study was conducted in the mixed medical-surgical intensive care unit (ICU) at the University Hospital Essen (01/2022–01/2023). Adults who received ECMO for > 48 h were included. Microbiological sampling (blood cultures and wound swabs) was performed before and after decannulation. Cannulas were assessed for biofilms, and plasma samples were analyzed using next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA). Sepsis was defined according to the most recent Sepsis-3 criteria. The study included 18 patients (56% men); 17 received VV-ECMO and one received VA-ECMO. Post-decannulation sepsis occurred in 10 of 18 patients (56%; 95% CI: 31–79%), and overall infectious complications were observed in 72% of patients. A strong negative correlation was evident between pre-ECMO ventilation duration and biofilm-forming bacteria in the blood during ECMO ( r = − 0.7, p  = 0.002). Blood cultures obtained within 10 min of decannulation were positive in 6 of 18 (33%) patients. NGS identified pathogens in 9 of 12 patients (75%), with 5 (42%) revealing additional organisms not detected by conventional methods. Viral pathogens were detected in 3 of 12 (25%) patients using NGS. Patients with sepsis demonstrated higher antibiotic consumption ( p  = 0.012) and more frequently met SOFA-based sepsis criteria ( p  = 0.007), whereas other parameters were comparable. Sepsis and infection frequently occur after ECMO decannulation and may be associated with biofilm-related pathogens. NGS has improved pathogen detection beyond standard diagnostics, although the findings require clinical correlation. These prospective findings support the need for further investigation of advanced integrated microbiological surveillance post-ECMO in larger multicenter studies. Trial registration : DRKS, DRKS00024842. Registered 12 Apr 2021, https://drks.de/search/de/trial/DRKS00024842 .

Background Extracorporeal membrane oxygenation (ECMO) cannulas are potential reservoirs for pathogens, yet their role in bacteremia and sepsis following decannulation remains poorly understood. This proof-of-concept study aims to characterize bacterial colonization of ECMO cannulas, identify potential sources of these bacteria, and assess their association with post-decannulation bloodstream infections and sepsis. Methods We conducted a single-center observational study including 10 patients receiving venovenous ECMO support between January 2022 and January 2023. Microbial colonization of cannulas, skin sites, and plasma was analyzed using culture-based methods and 16S rDNA amplicon sequencing. Alpha and beta diversity analyses were performed, and findings were correlated with clinical outcomes, including sepsis and bacteremia. Results A total of 117 samples yielded ~ 11 million sequencing reads. Bacteria colonizing ECMO cannulas matched pathogens causing prior bacteremia during ECMO support in all affected patients. Bacteria detected on cannulas and insertion sites were frequently recovered in plasma following decannulation. Notably, 16S rDNA analysis detected circulating pathogens that conventional cultures missed, often those from prior infections that were thought to be eradicated by antibiotics. Patients who developed sepsis post-decannulation exhibited higher bacterial diversity on cannulas and a higher overall abundance of Pseudomonas , while non-septic patients had greater Enterococcus abundance. Conclusions Our results confirm that ECMO cannulas serve as pathogen reservoirs, with decannulation enabling bacterial translocation into the bloodstream and contributing to post-decannulation sepsis. 16S rDNA sequencing exhibited greater sensitivity than cultures for detecting bloodstream pathogens. These findings support re-assessment of prophylactic measures during ECMO decannulation and lay the groundwork for developing early sepsis risk stratification tools.

Ticks are important vectors for Rickettsia spp. of the spotted fever group all around the world. Rickettsia conorii is the etiological agent of boutonneuse fever in the Mediterranean region and Africa. Tick identification was based on morphological features and further characterized using the 16S rRNA gene. The ticks were individually tested using pan- Rickettsia real-time-PCR for screening, and 23S-5S intergenic spacer region, 16S rDNA, glt A, sca 4, omp B, and ompA genes were used to analyze the Rickettsia positive samples . Rickettsia conorii ssp. caspia was detected in tick collected in Zambia for the first time, thus demonstrating the possibility of the occurrence of human disease, namely Astrakhan fever, due to this Rickettsia ssp. in this region of Africa. The prevalence of R. conorii ssp. caspia was 0.06% (one positive tick out of 1465 tested ticks) and 0.07% (one positive tick out of 1254 tested Rh. sanguineus ).

Background: It is widely accepted that SARS-CoV-2 causes a dysregulation of immune and coagulation processes. In severely affected patients, viral sepsis may result in life endangering multiple organ dysfunction. Furthermore, most therapies for COVID-19 patients target either the immune system or coagulation processes. As the exact mechanism causing SARS-CoV-2-induced morbidity and mortality was unknown, we started an in-depth analysis of immunologic and coagulation processes. Methods: 127 COVID-19 patients were treated at the University Hospital Essen, Germany, between May 2020 and February 2022. Patients were divided according to their maximum COVID-19 WHO ordinal severity score (WHO 0–10) into hospitalized patients with a non-severe course of disease (WHO 4–5, n = 52) and those with a severe course of disease (WHO 6–10, n = 75). Non-infected individuals served as healthy controls (WHO 0, n = 42). Blood was analyzed with respect to cell numbers, clotting factors, as well as pro- and anti-inflammatory mediators in plasma. As functional parameters, phagocytosis and inflammatory responses to LPS and antigen-specific stimulation were determined in monocytes, granulocytes, and T cells using flow cytometry. Findings: In the present study, immune and coagulation systems were analyzed simultaneously. Interestingly, many severe COVID-19 patients showed an upregulation of pro-inflammatory mediators and at the same time clear signs of immunosuppression. Furthermore, severe COVID-19 patients not only exhibited a disturbed immune system, but in addition showed a pronounced pro-coagulation phenotype with impaired fibrinolysis. Therefore, our study adds another puzzle piece to the already complex picture of COVID-19 pathology implying that therapies in COVID-19 must be individualized. Conclusion: Despite years of research, COVID-19 has not been understood completely and still no therapies exist, fitting all requirements and phases of COVID-19 disease. This observation is highly reminiscent to sepsis. Research in sepsis has been going on for decades, while the disease is still not completely understood and therapies fitting all patients are lacking as well. In both septic and COVID-19 patients, immune activation can be accompanied by immune paralysis, complicating therapeutic intervention. Accordingly, therapies that lower immune activation may cause detrimental effects in patients, who are immune paralyzed by viral infections or sepsis. We therefore suggest individualizing therapies and to broaden the spectrum of immunological parameters analyzed before therapy. Only if the immune status of a patient is understood, can a therapeutic intervention be successful.

Ticks are important vectors for Rickettsia spp. belonging to the Spotted Fever Group responsible for causing Rickettsiosis worldwide. Rickettsioses pose an underestimated health risk to tourists and local inhabitants. There is evidence of the presence of Rickettsia spp. in Zambia, however there is limited data. A total of 1465 ticks were collected in 20 different locations from dogs and cattle including one cat. Ticks were identified by morphological features or by sequencing of the 16S mitochondrial rRNA gene. Individual ticks were further tested for rickettsiae using a pan-Rickettsia real-time-PCR. Rickettsia species in PCR-positive ticks were identified by sequencing the 23S-5S intergenic spacer region or partial ompA gene, respectively. Seven tick species belonging to three different tick genera were found, namely: Amblyomma variegatum, Rhipicephalus appendiculatus, Rhipicephalus (Boophilus) microplus, Rhipicephalus simus, Rhipicephalus sanguineus, Rhipicephalus zambesiensis and Haemaphysalis elliptica. Out of the 1465 ticks collected, 67 (4.6%) tested positive in the pan-Rickettsia PCR. This study provides detailed data about the presence of Rickettsia species in South Luangwa Valley, Eastern Province, Zambia for the first time. High prevalence of Rickettsia africae in Amblyomma variegatum was found, which indicates the potential risk of infection in the investigated area. Furthermore, to our best knowledge, this is the first time Rickettsia massiliae, a human pathogen causing spotted fever, has been detected in Zambia.

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-infection is associated with an extremely variable disease course. When interstitial pneumonia (IP) occurs, it can lead to acute respiratory distress syndrome and death. Serum Krebs von den Lungen-6 (KL-6) is an established marker of IP, but its role as a marker of SARS-CoV-2 pneumonia is debated. This bicentric study included 157 patients with SARS-CoV-2 pneumonia. The WHO Ordinal Scale for Clinical Improvement (0–10 points) was used to classify the clinical course. Serum samples were collected at admission, and on days 3 and 7 of hospitalization. KL-6 was measured by using automated chemiluminescence immunoassay. A total of 68 patients developed a severe SARS-CoV-2 pneumonia, 135 of them required oxygen, and 15 died during hospitalization. The patients requiring non-invasive ventilation, invasive ventilation, or extracorporeal membrane oxygenation had significantly higher serum KL-6 levels at admission. The serum KL-6 levels were tendentially higher in patients who died than in those who survived. Logistic regression identified serum KL-6 at a cut-off of 335 U/mL at admission as a significant predictor of severe SARS-CoV-2 pneumonia outcome. Serum KL-6 seems to be a candidate biomarker for the clinical routine to stratify patients with SARS-CoV-2 pneumonia for the risk of a severe disease outcome or death.