How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.

During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses.

Experimental mummification-In the tracks of the ancient Egyptians.

Understanding natural and artificial postmortem alterations in different tissues of the human body is essential for bioarchaeology, paleogenetics, physical anthropology, forensic medicine, and many related disciplines. With this study, we tried to gain a better understanding of tissue alterations associated with the artificial mummification techniques of ancient Egypt, in particular for mummified visceral organs. We used several entire porcine organs and organ sections (liver, lung, stomach, ileum, and colon), which provided a close approximation to human organs. First, we dehydrated the specimens in artificial natron, before applying natural ointments, according to the ancient literary sources and recent publications. We periodically monitored the temperature, pH value, and weight of the specimens, in addition to radiodensity and volumetric measurements by clinical computed tomography and sampling for histological, bacteriological, and molecular analyses. After seven weeks, mummification was seen completed in all specimens. We observed a considerable loss of weight and volume, as well as similar courses in the decay of tissue architecture but varying levels of DNA degradation. Bacteriologically we did not detect any of the initially identified taxa in the samples by the end of the mummification process, nor any fungi. This feasibility study established an experimental protocol for future experiments modeling ancient Egyptian mummification of visceral organs using human specimens. Understanding desiccation and mummification processes in non-pathological tissues of specific visceral organs may help to identify and interpret disease-specific alterations in mummified tissues in ancient Egyptian canopic jars and organ packages contained in whole mummies.

Ongoing tissue changes in an experimentally mummified human leg.

Artificial mummification has been used since antiquity and is best known from ancient Egypt. Despite ancient Egyptian mummies being studied for several decades, the mummification techniques of that time are not well understood. Modern mummification experiments involving animal and human tissues have contributed additional insights relevant to a broad field of research. In the current study, we present follow-up results of an experiment on artificial mummification, which began in 2009. A human leg was artificially mummified and monitored for almost a year with histological, molecular, and radiological techniques. Since then, it has remained in a dry, natron salt blend for 9 years. The current analyses show further progression of dehydration and tissue alterations, as well as DNA degradation, suggesting an ongoing process. Our results add new insights into the mechanisms of tissue mummification. Taking into account that the process is still ongoing, further research is required, including a re-evaluation of the human leg in the future.

Correction to: Catheter retention as a consequence rather than a cause of unfavorable outcome in candidemia.

In the original publication the members of the FUNGINOS network were provided in such a way that they could not be indexed as collaborators on PubMed.

Fluconazole non-susceptible breakthrough candidemia after prolonged low-dose prophylaxis: a prospective FUNGINOS study.

OBJECTIVES: Breakthrough candidemia (BTC) on fluconazole was associated with non-susceptible Candida spp. and increased mortality. This nationwide FUNGINOS study analyzed clinical and mycological BTC characteristics. METHODS: A 3-year prospective study was conducted in 567 consecutive candidemias. Species identification and antifungal susceptibility testing (CLSI) were performed in the FUNGINOS reference laboratory. Data were analyzed according to STROBE criteria. RESULTS: 43/576 (8%) BTC occurred: 37/43 (86%) on fluconazole (28 prophylaxis, median 200 mg/day). 21% BTC vs. 23% non-BTC presented severe sepsis/septic shock. Overall mortality was 34% vs. 32%. BTC was associated with gastrointestinal mucositis (multivariate OR 5.25, 95%CI 2.23-12.40, p < 0.001) and graft-versus-host-disease (6.25, 1.00-38.87, p = 0.05), immunosuppression (2.42, 1.03-5.68, p = 0.043), and parenteral nutrition (2.87, 1.44-5.71, p = 0.003). Non-albicans Candida were isolated in 58% BTC vs. 35% non-BTC (p = 0.005). 63% of 16 BTC occurring after 10-day fluconazole were non-susceptible (Candida glabrata, Candida krusei, Candida norvegensis) vs. 19% of 21 BTC (C. glabrata) following shorter exposure (7.10, 1.60-31.30, p = 0.007). Median fluconazole MIC was 4 mg/l vs. 0.25 mg/l (p < 0.001). Ten-day fluconazole exposure predicted non-susceptible BTC with 73% accuracy. CONCLUSIONS: Outcomes of BTC and non-BTC were similar. Fluconazole non-susceptible BTC occurred in three out of four cases after prolonged low-dose prophylaxis. This implies reassessment of prophylaxis duration and rapid de-escalation of empirical therapy in BTC after short fluconazole exposure.

Herpes simplex type 1 pneumonitis and acute respiratory distress syndrome in a patient with chronic lymphatic leukemia: a case report.

BACKGROUND: Pulmonary pathogenicity of herpes simplex virus type 1 in patients in intensive care without classic immunosuppression as well as the necessity of antiviral treatment in the case of herpes simplex virus detection in respiratory specimens in these patients is controversial. We present a case of acute respiratory distress syndrome in a patient with stable chronic lymphatic leukemia not requiring treatment, in whom we diagnosed herpes simplex virus type 1 bronchopneumonitis based on herpes simplex virus type 1 detection in bronchoalveolar lavage fluid and clinical response to antiviral treatment. CASE PRESENTATION: A 72-year-old white man presented with symptoms of lower respiratory tract infection. His medical history was significant for chronic lymphatic leukemia, which had been stable without treatment, arterial hypertension, multiple squamous cell carcinomas of the scalp, and alcohol overuse. Community-acquired pneumonia was suspected and appropriate broad-spectrum antibacterial treatment was initiated. Within a few hours, rapid respiratory deterioration led to cardiac arrest. He was successfully resuscitated, but developed acute respiratory distress syndrome. Furthermore, he remained febrile and inflammation markers remained elevated despite antibacterial treatment. Polymerase chain reaction from bronchoalveolar lavage fluid and viral culture from tracheobronchial secretions tested positive for herpes simplex virus type 1. We initiated antiviral treatment with acyclovir. Concomitantly we further escalated the antibacterial treatment, although no bacterial pathogen had been isolated at any point. Defervescence occurred rapidly and his C-reactive protein and leukocyte levels decreased. He was successfully weaned from mechanical ventilation, transferred to the ward, and eventually discharged to home. CONCLUSIONS: Herpes simplex virus should be considered a cause for lower respiratory tract infection in critically ill patients, especially in the setting of an underlying disease.

Post-infection immunocomplex glomerulonephritis and Legionnaires' disease in a patient with adult Still's disease during treatment with interleukin 1 receptor antagonist anakinra: a case report.

INTRODUCTION: Legionellosis is a systemic disease that primarily affects the lungs. However, dysfunction in many organ systems, including the kidneys, has also been described. There are only a few reported cases of renal dysfunction in patients with legionellosis. CASE PRESENTATION: A 27-year-old Caucasian woman with known adult Still's disease was admitted to our hospital for community-acquired pneumonia, due to Legionella infection, with acute renal failure. Although her respiratory symptoms responded well to antibiotic treatment, her renal function worsened, with severe proteinuria and edema. A renal biopsy showed extracapillary and endocapillary proliferative glomerulonephritis with accompanying chronic and acute interstitial nephritis. This was consistent with a post-infection immunocomplex glomerulonephritis. After initiation of steroid therapy, her renal function improved. Additionally, therapy with diuretics and an angiotensin-converting enzyme inhibitor was initiated because of persistent proteinuria. Under this treatment regimen, her severe edema and proteinuria disappeared. CONCLUSION: To the best of our knowledge, there is only a handful of reported cases of post-infection glomerulonephritis with a nephrotic syndrome in a patient with legionellosis. Our findings suggest that, in patients with Legionnaires' disease with renal failure, post-infection immunocomplex glomerulonephritis should be considered and steroid therapy may be an effective modality to treat the renal complication.

Cost-effectiveness of posaconazole compared with standard azole therapy for prevention of invasive fungal infections in patients at high risk in Switzerland.

OBJECTIVE: To evaluate the cost-effectiveness of posaconazole versus standard azoles in the prevention of invasive fungal infection (IFI) in high-risk patients, using a pharmacoeconomic model that was adapted to a Swiss setting. METHODS: Decision tree models based on the results of two registration trials and subsequent Markov models over patient lifetimes were developed for patients with acute myelogenous leukemia (AML) or myelodysplastic syndrome (MDS) with neutropenia and for hematopoietic stem cell transplant recipients with graft-versus-host disease (GVHD). RESULTS: By reducing IFIs in AML/MDS patients with posaconazole prophylaxis, the contained IFI-related treatment costs more than compensated for the incremental cost of posaconazole, resulting in savings of CHF 1,118 per patient. Lifetime posaconazole prophylaxis resulted in a benefit of 0.16 life years saved per patient compared with fluconazole/itraconazole. In patients with GVHD, posaconazole prophylaxis prevented 0.04 IFIs, resulting in incremental costs of CHF 7,040 per patient. Lifetime posaconazole prophylaxis resulted in a benefit of 0.15 life years saved per patient, with an incremental cost-effectiveness rate of CHF 48,324 per life year saved. CONCLUSIONS: Given the conditions of the Swiss setting, posaconazole can be considered a cost-effective early treatment strategy that increases survival in patients at risk for IFI and may have a substantial benefit for the economic burden of IFI.

Rapid colonization with methicillin-resistant coagulase-negative staphylococci after surgery.

BACKGROUND: Antimicrobial resistance may compromise the efficacy of antibiotic prophylaxis before surgery. The aim of this study was to measure susceptibility and clonal distribution of coagulase-negative staphylococci (CoNS) colonizing the skin around the surgery access site before and after the procedure. METHODS: From March to September 2004, a series of 140 patients undergoing elective major abdominal surgery were screened for CoNS colonization at admission and 5 days after surgery. All isolates were tested for antibiotic susceptibility and genotyped by pulsed-field gel electrophoresis (PFGE). RESULTS: Colonization rates with CoNS at admission and after surgery were 85% and 55%, respectively. The methicillin-resistant CoNS rate increased from 20% at admission to 47% after surgery (P = 0.001). The PFGE pattern after surgery revealed more patients colonized with identical clones: 8/140 patients (8/119 strains) and 26/140 patients (26/77 strains), respectively (P < 0.001). CONCLUSIONS: Our results suggest rapid recolonization of disinfected skin by resistant nosocomial CoNS. Larger studies, preferably among orthopedic or cardiovascular patients, are required to clarify whether standard antibiotic prophylaxis with first- or second-generation cephalosporins for CoNS infections may be compromised if the patient requires an additional intervention 5 days or more after the initial surgery.

Impact of a prevention strategy targeting hand hygiene and catheter care on the incidence of catheter-related bloodstream infections.

OBJECTIVES: To study the impact of a teaching intervention on the rate of central venous catheter-related bloodstream infections (CRBSI) in intensive care patients. DESIGN: Prospective before/after interventional cohort study on medical and surgical intensive care units. SETTING: University hospital with five adult intensive care units. PATIENTS: All patients with a central venous catheter on the five ICUs from September to December 2003 (baseline period) and from March to July 2004 (intervention period). INTERVENTIONS: Educational program with teaching of hand hygiene, standards of catheter care, and preparation of intravenous drugs. MEASUREMENTS AND MAIN RESULTS: The primary outcome variable was the rate of CRBSIs per 1000 catheter days during a baseline period of 4 months and an intervention period of 5 months. The secondary outcome variable was compliance with hand hygiene. Of the patients, 499 patients with 6200 catheter days in the baseline period and 500 patients with 7279 catheter days were monitored in the intervention period. The incidence density of CRBSI decreased from 3.9 per 1000 catheter days in the preintervention phase to 1.0 per 1000 catheter days in the intervention phase (p < 0.001). The risk for CRBSI was significantly higher in the baseline period in both univariate and multivariate analysis. Other independent risk factors were hospitalization in the medical ICU and male gender. Time to CRBSI was significantly longer in the intervention period (median 9 days vs. 6.5 days, respectively; p = 0.02). Compliance with hand hygiene improved slightly from 59% in the baseline period to 65% in the intervention period, but the rate of correct performance of the practice increased from 22.5% to 42.6% (p = 0.003). CONCLUSIONS: Evidence-based catheter-care procedures, guided by healthcare workers' perceptions and including bedside teaching, reduce significantly the CRBSI rate and demonstrate that improving catheter care has a major impact on its prevention.

Infectious port complications are more frequent in younger patients with hematologic malignancies than in solid tumor patients.

BACKGROUND: We assessed longevity and complications of totally implantable venous access devices in oncology patients. METHODS: 197 patients received a total of 201 port devices via the subclavian vein for delivery of chemotherapy between January 1, 2005, and December 31, 2006. We reviewed the patient charts for port-related complications and risk factors until July 31, 2007. RESULTS: A total of 47,781 catheter days were analyzed (median, 175 days; range, 1-831). Forty-six different complications occurred (0.96 complications/1,000 catheter days). The only risk factor significantly associated with a higher complication rate was younger age. Older patients had a lower risk for developing complications with a risk reduction of 2.4% for each year. There were no differences regarding underlying tumor, gender, access side, method of placement (subclavian/cephalic vein) or implanting team (thoracic versus visceral surgery). A trend was seen for shorter port longevity in hematologic patients compared to oncologic patients (p = 0.059). The former developed significantly more port-associated infections than solid tumor patients [11/53 cases (21%) versus 2/148 cases (1.4%); p < 0.0001]. CONCLUSIONS: Port-associated infections were mostly observed in younger patients with hematologic neoplasms. Prospective trials should be performed to evaluate the benefit of a prophylactic antimicrobial lock in these selected patients.

Determinants of inter-individual cholesterol level variation in an unbiased young male sample.

QUESTION UNDER STUDY: Affected by individual life style, the total cholesterol serum level is a major morbidity and mortality risk factor for atherosclerotic cardiovascular disease (CVD). We present total cholesterol values and their possible aetiological factors of young Swiss conscripts. Particularly, we study varying impact of these factors depending on different levels of individual cholesterol. METHODS: Male conscripts (n = 19,272) of the 2005 census of the conscripts have been examined, reflecting ca. 59% of a total Swiss male birth cohort. Quantile regression allows us to analyse responses of arbitrary quantiles with respect to variables of interest. RESULTS: Eleven percent of all conscripts show clinically important increased total cholesterol levels. There is a major association of high individual cholesterol level with French regional language. The largest socio-economic subsample--agricultural and construction workers--show significantly higher individual cholesterol levels than employees in the industry sector and students, respectively. CONCLUSIONS: We were able to find that culture, as indicated by the mother tongue, and socioeconomic status as indicated by profession/vocation, influence individual total cholesterol levels while climate as indicated by altitude does not have an influence on cholesterol levels. Such a broad screening programme offers a unique opportunity to target persons at high-risk for CVD morbidity and mortality already early in life.

Heme carrier protein (HCP-1) spatially interacts with the CD163 hemoglobin uptake pathway and is a target of inflammatory macrophage activation.

Macrophages constitute the major cellular compartment for hemoglobin (Hb) degradation and subsequent recycling of heme-iron to erythropoiesis. Dysregulation of macrophage iron and heme metabolism is a major pathophysiologic determinant of anemia of chronic disease. In this study, we show that the heme transporter heme carrier protein 1 (HCP-1) is expressed in human macrophages. Within early endosomes, HCP-1 colocalizes with endocytosed Hb-haptoglobin (Hp) complexes, which are taken up via the CD163 scavenger receptor pathway. Hb-Hp passes the divalent metal transporter 1B/HCP-1-positive endosomal compartment on its route from the cell surface to lysosomes. HCP-1 mRNA and protein expression are down-regulated by stimulation of macrophages with various TLR agonists and IFN-gamma. The profound suppression of HCP-1 expression by inflammatory macrophage activation parallels the regulation of the iron exporter ferroportin. In contrast, dexamethasone enhanced HCP-1 expression significantly. Given the spatial relationship, we propose that the Hb scavenger receptor CD163 and HCP-1 constitute a linked pathway for Hb catabolism and heme-iron recycling in human macrophages.

CD163-expressing monocytes constitute an endotoxin-sensitive Hb clearance compartment within the vascular system.

Hemoglobin (Hb) is released into the circulation during intravascular hemolysis and exerts toxic effects through oxidative damage and NO scavenging. According to the traditional concept of Hb clearance, free Hb is bound to the plasma protein haptoglobin (Hp), and the Hb-Hp complexes are cleared by liver and spleen macrophages via the Hb scavenger receptor CD163. Using a novel whole blood assay, we demonstrate that clearance of Hb-Hp is also mediated by CD14(high)/CD64(high) peripheral blood monocytes, which express CD163. Hb-Hp uptake by these cells is Ca(2+)-dependent and is abrogated by the addition of CD163-blocking antibodies. Accordingly, LPS treatment reduces monocyte surface CD163 and impairs Hb-Hp uptake. Monocytes likely mediate Hp-Hb uptake in vivo, as a high expression of the heme breakdown enzyme heme oxygenase-1 was observed in CD163(+) monocytes but not in other leukocyte populations obtained from healthy blood donors. We propose that CD163-mediated Hb-Hp uptake by peripheral blood monocytes constitutes an Hb-Hp clearance pathway, which acts at the site of intravascular hemolysis to reduce Hb-Hp circulation time and toxicity. Disruption of monocyte Hb-Hp clearance may increase Hb-Hp toxicity and contribute to the pathogenesis of systemic inflammatory diseases associated with reduced monocyte CD163 expression.

Neurological adverse events to voriconazole: evidence for therapeutic drug monitoring.

BACKGROUND: Voriconazole shows a considerable interpatient variation of serum concentrations. METHODS AND RESULT: In an analysis of 28 treatment courses, 6 patients presented with neurological adverse events (hallucination, encephalopathy, and visual disturbance). The hazard ratio per 0.1 mg/mL voriconazole serum level (sVL) increase was 2.27 (95% CI: 1.45-3.56, p <0.001). There was no correlation between sVL and creatinine (r = 0.12, p = 0.114), ALT (r = -0.14, p = 0.072), AST (r = 0.003, p = 0.964), alkaline phosphatase (r = 0.03, p = 0.723). CONCLUSIONS: Our findings demonstrate that elevated sVL is associated with neurological adverse events, and measurement of its serum concentration could improve voriconazole treatment and safety.

Hemophagocytic macrophages constitute a major compartment of heme oxygenase expression in sepsis.

OBJECTIVES: Uncontrolled macrophage activation with hemophagocytosis is a distinctive feature of hemophagocytic syndromes (HPS). We examined whether lympho-histiocytic infiltration of the bone marrow and liver, as well as hemo-/erythrophagocytosis also occurs during sepsis and whether this process could account for the increased production of anti-inflammatory heme-oxygenase (HO-1) products observed during sepsis. METHODS: Hemophagocytosis and expression of CD163, HO-1, ferritin as well as CD8 and granzyme-B were examined in post-mortem bone marrow samples from 28 patients with sepsis and from eight control patients. RESULTS: Comparison of samples from non-septic patients with samples from patients with fatal sepsis revealed that the latter group displayed dense lympho-histiocytic bone marrow infiltration with CD163(+)/HO-1(+)/ferritin(+) macrophages as well as with CD8(+) and granzyme-B(+) T-cells. Hemophagocytosis with prominent phagocytosis of erythroid cells was readily apparent in septic patients, implying that this process is a likely stimulus for the up-regulation of macrophage HO-1 expression. CONCLUSIONS: Lympho-histiocytic activation with hemophagocytosis is a shared pathophysiologic mechanism in HPS and sepsis. Furthermore, the association of hemophagocytosis with an increase in HO-1 expression may indicate a novel role for this apparently futile process as a negative regulator of inflammation.

Constitutive endocytosis of CD163 mediates hemoglobin-heme uptake and determines the noninflammatory and protective transcriptional response of macrophages to hemoglobin.

Heme toxicity contributes to the pathogenesis of chronic inflammatory diseases, atherosclerosis, and hemolysis associated vasculopathy. Macrophage clearance of cell free hemoglobin (Hb) is thus an essential homeostatic function of these cells. We examined the transcriptional response of human PBMC derived macrophages to Hb by gene array analysis. The observed noninflammatory macrophage response was characterized by induction of an antioxidative and antiinflammatory gene expression pattern with most prominent induction of the inducible heme oxygenase (HO-1). The metabolically active Hb-CD163-HO-1 pathway resulted in synthesis of ferritin-1 of the antioxidative and antiinflammatory end products linked to heme breakdown by HO-1. This response was mediated by the Hb scavenger receptor CD163 and heme and was not related to Hb mediated depletion of reduced glutathione. In contrast to other cellular responses induced by CD163, there was no role of protein phosphorylation dependent CD163 signaling in the protective macrophage response to Hb. Instead, CD163 acted as an Hb transporter, which undergoes constitutive and ligand independent internalization and recycling between the cell surface and early endosomes. The expression of CD163 and HO-1 in macrophages of neovascularized atherosclerotic lesions suggests that the pathway described herein is active in vivo. Noninflammatory Hb clearance and intimately linked HO-1 expression may provide the long sought-after explanation for the antiinflammatory activity associated with CD163-positive macrophages.