Unbiased screen for pathogens in human paraffin-embedded tissue samples by whole genome sequencing and metagenomics

Identification of bacterial pathogens in formalin fixed, paraffin embedded (FFPE) tissue samples is limited to targeted and resource-intensive methods such as sequential PCR analyses. To enable unbiased screening for pathogens in FFPE tissue samples, we established a whole genome sequencing (WGS) method that combines shotgun sequencing and metagenomics for taxonomic identification of bacterial pathogens after subtraction of human genomic reads. To validate the assay, we analyzed more than 100 samples of known composition as well as FFPE lung autopsy tissues with and without histological signs of infections. Metagenomics analysis confirmed the pathogenic species that were previously identified by species-specific PCR in 62% of samples, showing that metagenomics is less sensitive than species-specific PCR. On the other hand, metagenomics analysis identified pathogens in samples, which had been tested negative for multiple common microorganisms and showed histological signs of infection. This highlights the ability of this assay to screen for unknown pathogens and detect multi-microbial infections which is not possible by histomorphology and species-specific PCR alone.

COVID-19 Autopsies Reveal Underreporting of SARS-CoV-2 Infection and Scarcity of Co-infections

Coronavirus disease 2019 (COVID-19) mortality can be estimated based on reliable mortality data. Variable testing procedures and heterogeneous disease course suggest that a substantial number of COVID-19 deaths is undetected. To address this question, we screened an unselected autopsy cohort for the presence of SARS-CoV-2 and a panel of common respiratory pathogens. Lung tissues from 62 consecutive autopsies, conducted during the first and second COVID-19 pandemic waves in Switzerland, were analyzed for bacterial, viral and fungal respiratory pathogens including SARS-CoV-2. SARS-CoV-2 was detected in 28 lungs of 62 deceased patients (45%), although only 18 patients (29%) were reported to have COVID-19 at the time of death. In 23 patients (37% of all), the clinical cause of death and/or autopsy findings together with the presence of SARS-CoV-2 suggested death due to COVID-19. Our autopsy results reveal a 16% higher SARS-CoV-2 infection rate and an 8% higher SARS-CoV-2 related mortality rate than reported by clinicians before death. The majority of SARS-CoV-2 infected patients (75%) did not suffer from respiratory co-infections, as long as they were treated with antibiotics. In the lungs of 5 patients (8% of all), SARS-CoV-2 was found, yet without typical clinical and/or autopsy findings. Our findings suggest that underreporting of COVID-19 contributes substantially to excess mortality. The small percentage of co-infections in SARS-CoV-2 positive patients who died with typical COVID-19 symptoms strongly suggests that the majority of SARS-CoV-2 infected patients died from and not with the virus.

High throughput sequencing reveals high specificity of TNFAIP3 mutations in ocular adnexal marginal zone B-cell lymphomas

The majority of ocular adnexal (OA) lymphomas (OAL) are extranodal marginal zone lymphomas (MZL). First high throughput sequencing (HTS) studies on OA-MZL showed inconsistent results and the distribution of mutations in reactive lymphoid lesions of this anatomic region has not yet been sufficiently addressed. We characterized OAL and lymphoid lesions of the OA by targeted HTS. The study included 34 OA-MZL, 11 chronic conjunctivitis, five mature small cell B-cell lymphomas spreading to the OA, five diseases with increase of IgG4+ plasma cells, three Burkitt lymphomas (BL), three diffuse large B-cell lymphomas (DLBCL), three mantle cell lymphomas, three idiopathic orbital inflammations/orbital pseudo tumors (PT), and three OA lymphoid hyperplasia. All cases were negative for Chlamydia. The mutational number was highest in BL and lowest in PT. The most commonly (and exclusively) mutated gene in OA-MZL was TNFAIP3 (10 of 34 cases). Altogether, 20 out of 34 patients harbored mutually exclusive mutations of either TNFAIP3, BCL10, MYD88, ATM, BRAF, or NFKBIE, or nonexclusive mutations of IRF8, TNFRSF14, KLHL6, and TBL1XR1, all encoding for NK-κB pathway compounds or regulators. Thirteen patients (38%) had, to a great part, mutually exclusive mutations of chromatin modifier-encoding genes: KMT2D, CREBBP, BCL7A, DNMT3A, EP300, or HIST1H1E. Only four patients harbored co-occurring mutations of genes encoding for NK-κB compounds and chromatin modifiers. Finally, PTEN, KMT2D, PRDM1, and HIST1H2BK mutations were observable in reactive lymphoid lesions too, while such instances were devoid of NF-κB compound mutations and/or mutations of acetyltransferase-encoding genes. In conclusion, 80% of OA-MZL display mutations of either NK-κB compounds or chromatin modifiers. Lymphoid lesions of the OA bearing NF-κB compound mutations and/or mutations of acetyltransferase-encoding genes highly likely represent lymphomas.

[Pathology of infectious diseases]

Pathology of infectious diseases Abstract. The pathology of infectious diseases is an exciting interdisciplinary field, despite its niche existence that is somewhat overshadowed by tumor diagnostics. However, the strength of pathology lies in the correlation of the inflammatory patterns and pathogen detection. Moreover, corresponding tissue investigations often allow a rapid diagnosis of the disease, and additional investigations, such as immunohistochemistry or molecular pathology, enable a rapid pathogen characterization with a high sensitivity and specificity. In addition, the molecular analysis allows the detection of pathogens that are difficult, dangerous or not at all to breed. It can be assumed that complex infectious diseases will increase due to iatrogenic interventions, migration, antibiotic resistance and climate change, and that pathology, in close cooperation with its treating colleagues, will increasingly play an important role in the care of patients.

Brain abscess caused by Cladophialophora bantiana: Total remission after full resection and short-course Voriconazole treatment

We report on a brain abscess in an immunocompetent man caused by Cladophialophora bantiana, a black mold known to prefer the brain for abscess-formations with a mortality rate up to 65%. The published cases so far show different therapeutical approaches and outcomes, whereby a standardized treatment could not yet be established. We report on a case of Cladophialophora bantiana brain abscess with total remission of the abscess after full resection and a short antifungal treatment.

Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors

Cleavage factor II (CF II) is a poorly characterized component of the multiprotein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.

MBE Growth of (In)GaN for LED Applications

We report on essential aspects of the growth of InGaN / GaN p-n junctions by gas-source molecular beam epitaxy (MBE) and present the first blue and green electroluminescence from such structures grown entirely by MBE.

A study of the growth conditions for a GaN nucleation layer on sapphire and for the subsequent growth of undoped GaN points out the necessity for Ga-stabilized growth. Unintentionally doped GaN grown at 1 μm/h shows background doping levels below 1017 cm-3 and mobilities up to 320 cm2/Vsec (at 300K). Narrow photoluminescence with very low intensity in the yellow spectral range is observed. N- and p-type doping of GaN with Si and Mg yields layers with high mobilities (220 and 10 cm2/Vsec, respectively at 300K) at carrier densities typical for devices.

Although incorporation of Indium is strongly temperature-dependent, InGaN-layers with In-contents of over 40% are obtained routinely. The optical properties of our InGaN layers typically exhibit the commonly observed, broad deep level luminescence. Finally, we present electroluminescence in the visible spectral range up to 540 nm from InGaN / GaN double-heterojunctions.

In-vitro study to compare the efficacy of N-monochloro-D,L-2-aminobutyrate (NMAB, GK-101E) and water in caries removal

The present in-vitro study was designed to investigate the chemical efficacy of N-monochloro-D,L,-2-aminobutyrate (NMAB, GK 101E) in removing carious material under clinically relevant conditions, using objective methods of measurement. Assuming that the chemical effectiveness of water in caries removal is minimal, a comparison of the efficacy of GK-101E with that of water was made. The force required to achieve complete caries removal from symmetrically separated carious lesions was determined with the Caridex system, modified by a force gauge. One lesion half was treated with GK-101E, while the corresponding half was treated with water. Thus a difference in the chemical potential of the fluids in softening carious material should lead to a difference in the force required to remove equal quantities of caries. Statistical analysis of the findings of the present study revealed no significant difference between GK-101E and water, with regard to both the force and the number of excavation strokes and the time needed for caries removal. It is concluded that, under the given test conditions, the removal of carious dentine is not significantly enhanced by the chemical action of GK-101E.

Isolation ofBacillus schlegelii, a thermophilic, hydrogen oxidizing, aerobic autotroph, from geothermal and nongeothermal environments

Thermophilic hydrogen-oxidizing strains forming round, terminal endospores were isolated from geothermal areas. They were neutrophilic and facultatively autotrophic. They resembledBacillus schlegelii, a thermophilic hydrogen bacterium found so far only in cold environments. Phenotypic similarities, as well as DNA G+C content and DNA:DNA homologies, clearly revealed that the isolated strains belonged to the taxospeciesB. schlegelii. Hence, the strains ofB. schlegelii found in cold environments are probably allochthonous, their origin being geothermal and volcanic areas.

The use of plastic face mask and silicone gloves and boots as alternative to compression suits for treating hypertrophic scars

Prevention and treatment of hypertrophic scars and contractures is usually obtained by the use of compression suits. The compression hood for the burned face is unaesthetical and often refused by the child. A better compression can be obtained by the use of a clear transparent plastic mask. It offers a better view and looks better, thus increasing the cooperation of the patient. Compression gloves and stockings are difficult to adapt to. It is easier to make mittens and boots out of silicone. These two techniques meet the criteria of efficiency: early application of compression, good tolerance, splint support, individually moulded splints for optimum pressure and cooperation.