Search

Fouad MF Elshaghabee,1 Darab Ghadimi,1 Diana Habermann,1 Michael de Vrese,1 Wilhelm Bockelmann,1 Hans-Jürgen Kaatsch,2 Knut J Heller,1 Jürgen Schrezenmeir3,4 1Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Department of Microbiology and Biotechnology, Kiel, Germany; 2Institute of Legal Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany; 3Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Karlsruhe, Germany; 4Clinical Research Center, Kiel Innovation and Technology Center, Kiel, GermanyCorrespondence: Darab Ghadimi Tel +49 4316092512Fax +49 4316092472Email darab.ghadimi@mri.bund.deBackground and Purpose: In previous investigations, Weissella confusa was shown to lack the metabolic pathway from fructose to mannitol and to produce ethanol when cultivated in the presence of fructose. Hence, we assessed the effect of oral administration of W. confusa (strain NRRL-B-14171) on blood and fecal ethanol concentrations, glucose and lipid metabolism and traits of the metabolic syndrome in Wistar rats (n=27) fed diets with two different fat and fructose levels and with or without the addition of W. confusa during a total intervention time of 15 weeks (105 days).Materials and Methods: From week 1 to 6, rats were given a medium fructose and fat (MFru-MF) diet containing 28% fructose and 10% fat without the addition of W. confusa (control group, n=13) or mixed with 30 g per kg diet of lyophilized W. confusa (10.56 ± 0.20 log CFU/g; W. confusa group, n=14). From week 7 to 15, the percentage of dietary fructose and fat in the control and W. confusa group was increased to 56% and 16%, respectively (high fructose-high fat (HFru-HF) diet).Results: In HFru-HF-fed rats, W. confusa was detected in feces, regardless of whether W. confusa was added to the diet or not, but not in rats receiving the MFru-MF diet without added W. confusa or in an additional control group (n=10) fed standard rat food without fructose, increased fat content and W. confusa. This indicates that fecal W. confusa may be derived from orally administered W. confusa as well as – in the case of high fructose and fat intake and obesity of rats – from the intestinal microbiota. As shown by multifactorial ANOVA, blood ethanol, the relative liver weight, serum triglycerides, and serum cholesterol as well as fecal ethanol, ADH, acetate, propionate and butyrate, but not lactate, were significantly higher in the W. confusa – compared to the control group.Discussion: This is the first in vivo trial demonstrating that heterofermentative lactic acid bacteria lacking the mannitol pathway (like W. confusa) can increase fecal and blood ethanol concentrations in mammals on a high fructose-high fat diet. This may explain why W. confusa resulted in hyperlipidemia and may promote development of NAFLD in the host.Keywords: high fructose-high fat diet, fecal ethanol, fecal short-chain fatty acids, lipidemia, glycemia, NAFLD

Background & Aims: Immune responses by CD8 T cells are essential for control of HBV replication. Although selection of escape mutations in CD8 T-cell epitopes has been previously described in HBV infection, its overall influence on HBV sequence diversity and correlation with markers of HBV replication remain unclear., Methods: Whole-genome sequencing was applied to HBV isolates from 532 patients with chronic HBV infection and high-resolution HLA class I genotyping. Using a Bayesian model (HAMdetector) for identification of HLA-associated mutational states (HAMs), the frequency and location of residues under CD8 T-cell selection pressure were determined and the levels of adaptation of individual isolates were quantified., Results: Using previously published thresholds for the identification of HAMs, a total of 295 residues showed evidence of CD8 T-cell escape, the majority of which were located in previously unidentified epitopes. Interestingly, HAMs were highly enriched in the HBV core protein compared to all other proteins. When individual HBV isolates were compared, different levels of adaptation to HLA class I immune pressure were noted. The level of adaptation increased with patient age and correlated with markers of replication, with low levels of adaptation in HBeAg-positive infection. Furthermore, the levels of adaptation negatively correlated with HBV viral load and HBsAg levels, consistent with high levels of HLA class I-associated selection pressure in patients with low replication levels., Conclusions: HBV sequence diversity is shaped by HLA class I-associated selection pressure with the HBV core protein being a predominant target of selection. Importantly, different levels of adaptation to immune pressure were observed between HBV infection stages, which need to be considered in the context of T-cell-based therapies., Impact and Implications: The immune response mediated by CD8 T cells plays a critical role in controlling HBV infection and shows promise for therapeutic strategies aimed at achieving a functional cure. This study demonstrates that mutational escape within CD8 T-cell epitopes is common in HBV and represents a key factor in the failure of immune control. Notably, the HBV core protein emerges as the primary target of CD8 T-cell selection pressure. Additionally, the observed correlation between HBV adaptation levels and viral replication markers indicates that CD8 T-cell immunity may influence transitions between phases of chronic HBV infection., Competing Interests: Conflict of interest TS, JP, MD, SG, DH, FMH, JLM, TL, CM, AK, ESA, CNH, DH, MM, RT, PH declare no conflict of interest. JT reports honoraria for lectures from AbbVie and GSK. AW has received grants for HCV genomic surveillance from Gilead Sciences. HB reports honoraria for lectures or presentations from AbbVie and Gilead Sciences, travel support from AbbVie and Gilead Sciences, and participates on advisory boards for AbbVie, Gilead Sciences, and Ipsen. MKM reports funding from Gilead Sciences for HBV immunology research and received consulting fees from Astrivax and Moderna. MC reports consulting fees from Gilead Sciences, AbbVie, MSD Sharp & Dohme, Falk Foundation, and is the medical CEO of the German Liver Foundation. JN reports grants from the German Research Council, the German Center for Infection Research, the Hector Foundation, and the German Cancer Aid. JSzW reports grants from EU Horizon 20/20, DZIF, DFG CRC1328. HW reports grants from Abbott, Biotest, consulting fees from Abbott, Bristol-Myers-Squibb, F. Hoffmann-La Roche Ltd., Gilead Science, GlaxoSmithKline, Janssen, Roche Diagnostics International Ltd., Vir Biotechnology Inc. and honoraria from Biotest Ag and Gilead Science. HK reports grants from the German Center for Infection Research, EU Horizon Health, German Research Foundation, and internal Funds from Hannover Medical School and support for attending the International DeltaCure Meeting and EASL/AASLD Masterclass. GL reports funding from NIH. Please refer to the accompanying ICMJE disclosure forms for further details., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system., Importance: This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria., Competing Interests: The authors declare no conflict of interest.

Several years of research into the small circular DNA molecules called SPHINX and BMMF (SPHINX/BMMF) have provided information on several areas of research, medicine, microbiology and nutritional science. But there are still open questions that have not yet been addressed. Due to the unclear classification, evolution and sources of SPHINX/BMMF, a risk assessment is currently not possible. However, risk assessment is necessary as SPHINX/BMMF are suspected to be involved in the development of cancer and neurodegenerative diseases. In order to obtain an overview of the current state of research and to identify research gaps, a review of all the publications on this topic to date was carried out. The focus was primarily on the SPHINX/BMMF group 1 and 2 members, which is the topic of most of the research. It was discovered that the SPHINX/BMMF molecules could be integral components of mammalian cells, and are also inherited. However, their involvement in neurodegenerative and carcinogenic diseases is still unclear. Furthermore, they are probably ubiquitous in food and they resemble bacterial plasmids in parts of their DNA and protein (Rep) sequence. In addition, a connection with bacterial viruses is also suspected. Ultimately, it is still unclear whether SPHINX/BMMF have an infectious capacity and what their host or target is.

Sixteen novel circular rep-encoding DNA sequences with high sequence homologies to previously described SPHINX and BMMF sequences were isolated for the first time from non-bovine foods (pork, wild boar, chicken meat, Alaska pollock, pangasius, black tiger shrimp, apple, carrot, and sprouts from alfalfa, radish, and broccoli). The phylogenetic analysis of the full-length circular genomes grouped these together with previously described representatives of SPHINX/BMMF group 1 and 2 sequences (eight in each group). The characterization of genome lengths, genes present, and conserved structures confirmed their relationship to the known SPHINX/BMMF sequences. Further analysis of iteron-like tandem repeats of SPHINX/BMMF group 1-related genomes revealed a correlation with both full-length sequence tree branches as well as Rep protein sequence tree branches and was able to differentiate subtypes of SPHINX/BMMF group 1 members. For the SPHINX/BMMF group 2 members, a distinct grouping of sequences into two clades (A and B) with subgroups could be detected. A deeper investigation of potential functional regions upstream of the rep gene of the new SPHINX/BMMF group 2 sequences revealed homologies to the dso and sso regions of known plasmid groups that replicate via the rolling circle mechanism. Phylogenetic analyses were accomplished by a Rep protein sequence analysis of different ssDNA viruses, pCRESS, and plasmids with the known replication mechanism, as this yielded deeper insights into the relationship of SPHINX/BMMF group 1 and 2 Rep proteins. A clear relation of these proteins to the Rep proteins of plasmids could be confirmed. Interestingly, for SPHINX/BMMF group 2 members, the relationship to rolling circle replication plasmids could also be verified. Furthermore, a relationship of SPHINX/BMMF group 1 Rep proteins to theta-replicating plasmid Reps is discussed.

Introduction: The Hepatitis Delta Virus (HDV) is a defective, single-stranded RNA virusoid encoding for a single protein, the Hepatitis Delta Antigen (HDAg), which requires the hepatitis B virus (HBV) envelope protein (HBsAg) for its transmission. Currently, hepatitis D is the most aggressive form of viral hepatitis and treatment options are limited. Worldwide 12 million people are chronically infected with HDV being at high risk for progression to cirrhosis and development of liver cancer., Objectives: Although it is well established that Mongolia is the country with the highest prevalence of HDV infections, the information on the molecular epidemiology and factors contributing to HDV sequence diversity are largely unclear. The aim of the study was to characterize the sequence diversity of HDV in rural areas from Mongolia and to determine the extent of HLA class I-associated selection pressure., Patients and Methods: From the HepMongolia cohort from rural areas in Mongolia, 451 HBsAg-positive individuals were selected and anti-HDV, HDV-RNA and the sequence of the large HDAg was determined. For all individuals the HLA class I locus was genotyped. Residues under selection pressure in the presence of individual HLA class I types were identified with the recently published analysis tool HAMdetector., Results: Of 431 HBsAg positive patients, 281 were anti-HDV positive (65%), and HDV-RNA could be detected in 207 of 281 (74%) of patients. The complete large HDAg was successfully sequenced from 131 samples. Phylogenetic analysis revealed that all Mongolian HDV isolates belong to genotype 1, however, they separate into several different clusters without clear regional association. In turn, from phylogeny there is strong evidence for recent local transmission events. Importantly, we found multiple residues with strong support for HLA class I-associated selection pressure consistent with a functional CD8 + T cell response directed against HDV., Conclusion: HDV isolates from Mongolia are highly diverse. The molecular epidemiology suggests circulation of multiple subtypes and provides evidence for ongoing recent transmissions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Magvan, Kloeble, Ptok, Hoffmann, Habermann, Gantumur, Paluschinski, Enebish, Balz, Fischer, Chimeddorj, Walker and Timm.)

Background: Immune activation is a significant contributor to HIV pathogenesis and disease progression. In virally-suppressed individuals on ART, low-level immune activation has been linked to several non-infectious comorbid diseases. However, studies have not been systematically performed in sub-Saharan Africa and thus the impact of demographics, ART and regional endemic co-infections on immune activation is not known. We therefore comprehensively evaluated in a large multinational African cohort markers for immune activation and its distribution in various settings., Methods: 2747 specimens from 2240 people living with HIV (PLWH) and 477 without HIV from the observational African Cohort Study (AFRICOS) were analyzed for 13 immune parameters. Samples were collected along with medical history, sociodemographic and comorbidity data at 12 HIV clinics across 5 programs in Uganda, Kenya, Tanzania and Nigeria. Data were analyzed with univariate and multivariate methods such as random forests and principal component analysis., Findings: Immune activation was markedly different between PLWH with detectable viral loads, and individuals without HIV across sites. Among viremic PLWH, we found that all immune parameters were significantly correlated with viral load except for IFN-α. The overall inflammatory profile was distinct between men and women living with HIV, in individuals off ART and with HIV viremia. We observed stronger differences in the immune activation profile with increasing viremia. Using machine learning methods, we found that geographic differences contributed to unique inflammatory profiles. We also found that among PLWH, age and the presence of infectious and/or noninfectious comorbidities showed distinct inflammatory patterns, and biomarkers may be used to predict the presence of some comorbidities., Interpretation: Our findings show that chronic immune activation in HIV-1 infection is influenced by HIV viral load, sex, age, region and ART use. These predictors, as well as associations among some biomarkers and coinfections, influence biomarkers associated with noncommunicable diseases., Funding: This work was supported by the President's Emergency Plan for AIDS Relief via a cooperative agreement between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense [W81XWH-11-2-0174, W81XWH-18-2-0040]. The investigators have adhered to the policies for protection of human subjects as prescribed in AR 70-25. This article was prepared while Michael A. Eller was employed at Henry M. Jackson Foundation for the Advancement of Military Medicine for the U.S. Military HIV Research Program. The views expressed are those of the authors and should not be construed to represent the positions of the US Army or the Department of Defense. The opinions expressed in this article are the author's own, and do not reflect the view of the National Institutes of Health, the U.S. Department of Health and Human Services, or the U.S. government., Competing Interests: Declaration of interests All authors declare no conflicts of interest., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)

Motivation: A key process in anti-viral adaptive immunity is that the human leukocyte antigen (HLA) system presents epitopes as major histocompatibility complex I (MHC I) protein-peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the hosts MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature, HAMs are amenable to detection by statistical methods in paired sequence/HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this., Results: We present a new Bayesian regression model for the detection of HAMs that integrates a sparsity-inducing prior, epitope predictions and phylogenetic bias assessment, and that yields easily interpretable quantitative information on HAM candidates. The model predicts experimentally confirmed HAMs as having high posterior probabilities, and it performs well in comparison to state-of-the-art models for several datasets from individuals infected with HBV, HDV and HIV., Availability and Implementation: The source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license. The data underlying this article were provided by permission. Data will be shared on request to the corresponding author with permission of the respective co-authors., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Based on its viral-associated or UV-associated carcinogenesis, Merkel cell carcinoma (MCC) is a highly immunogenic skin cancer. Thus, clinically evident MCC occurs either in immuno-compromised patients or based on tumor-intrinsic immune escape mechanisms. This notion may explain that although advanced MCC can be effectively restrained by treatment with PD-1/PD-L1 immune checkpoint inhibitors (ICIs), a considerable percentage of patients does not benefit from ICI therapy. Biomarkers predicting ICI treatment response are currently not available., Methods: The present multicenter retrospective study investigated clinical and molecular characteristics in 114 patients with unresectable MCC at baseline before treatment with ICI for their association with therapy response (best overall response, BOR). In a subset of 21 patients, pretreatment tumor tissue was analyzed for activation, differentiation and spatial distribution of tumor infiltrating lymphocytes (TIL)., Results: Of the 114 patients, n=74 (65%) achieved disease control (BOR=complete response/partial response/stable disease) on ICI. A Bayesian cumulative ordinal regression model revealed absence of immunosuppression and a limited number of tumor-involved organ systems was highly associated with a favorable therapy response. Unimpaired overall performance status, high age, normal serum lactate dehydrogenase and normal serum C reactive protein were moderately associated with disease control. While neither tumor Merkel cell polyomavirus nor tumor PD-L1 status showed a correlation with therapy response, treatment with anti-PD-1 antibodies was associated with a higher probability of disease control than treatment with anti-PD-L1 antibodies. Multiplexed immunohistochemistry demonstrated the predominance of CD8 + effector and central memory T cells (T CM ) in close proximity to tumor cells in patients with a favorable therapy response., Conclusions: Our findings indicate the absence of immunosuppression, a limited number of tumor-affected organs, and a predominance of CD8 + T CM among TIL, as baseline parameters associated with a favorable response to PD-1/PD-L1 ICI therapy of advanced MCC. These factors should be considered when making treatment decisions in MCC patients., Competing Interests: Competing interests: SU declares research support from Bristol Myers Squibb and Merck Serono; speakers and advisory board honoraria from Bristol Myers Squibb, Merck Sharp & Dohme, Merck Serono, Novartis and Roche, and travel support from Bristol Myers Squibb, and Merck Sharp & Dohme. LZ served as consultant and/or has received honoraria from Roche, Bristol-Myers Squibb, Merck Sharp & Dohme, Novartis, Pierre-Fabre, and Sanofi; Research funding to institution: Novartis; travel support from Merck Sharp & Dohme, Bristol-Myers Squibb, Amgen, Pierre-Fabre, and Novartis, outside the submitted work. PT declares invited speaker's honoraria from Bristol-Myers Squibb, Novartis, MSD, Pierre-Fabre, CureVac, Roche, Kyowa Kirin, Biofrontera, advisory board honoraria from Bristol-Myers Squibb, Novartis, Pierre-Fabre, Merck Serono, Sanofi, Roche, Kyowa Kirin, and travel support from Bristol-Myers Squibb, and Pierre-Fabre. UL declares advisory board honoraria from MSD, Roche, Sanofi, Novartis, Sun Pharma, Almirall Hermal. TE declares consulting fees from BMS, Novartis, Roche, Pierre Fabre, Sanofi; board membership and payment for lectures in speakers bureau from Pierre Fabre, MSD, Roche, BMS, Novartis and Sanofi. CL reports advisory board honoraria from MSD, BMS, Roche, Pierre Fabre, Novartis, Sun Pharma, Sanofi, Kyowa Kirin, Almiral Hermal, Biontech, Merc; speakers fee from MSD, BMS, Roche, Pierre Fabre, Novartis, Sun Pharma, Sanofi, Merck; travel reimbusment from MSD, BMS, Roche, Pierre Fabre, Novartis, Sun Pharma, Sanofi, Kyowa Kirin, Almiral Hermal, Biontech and Merck. JCH declares research support from Bristol Myers Squibb; advisory board honoraria from Pierre Fabre, Sanofi, Sun Pharma and Merck Sharp & Dome; speakers honoraria from Bristol Myers Squibb, Merck Sharp & Dohme, Novartis, Roche, Sanofi and Almirall and travel support from Pierre Fabre. TG reports receiving speakers and/or advisory board honoraria from BMS, Sanofi-Grenzyme, MSD, Novartis Pharma, Roche, Abbvie, Almirall, Janssen Lilly, Pfizer, Pierre Fabre; speakers and/or advisory board honoraria from BMS, Sanofi-Grenzyme, MSD, Novartis, Pharma, Roche, Abbvie, Almirall, Janssen Lillly, Pfizer, Pierre Fabre. SH declares advisory boards honoraria from Pierre Fabre, MSD, BMS, Novartis, Sanofi. PM reports board membership and payment for lectures in speakers bureau from Pierre Fabre, GSK, MSD, Merck Germany, Roche, BMS, Novartis, Sanofi. P. Mohr reports research support (to institution): Bristol-MyersSquibb, Novartis, MSD. Honoraria for lectures (personally): Pierre Fabre, GSK, MSD, Merck Germany, Roche, BMS, Novartis, Sanofi, Amgen, SUN-Pharma, Roche Pharma, Bristol-MyersSquibb, Novartis, MSD, Almirall-Hermal, Amgen, Merck-Serono, Bayer, Pierre-Fabre, Sanofi. Honoraria for advisory boards: Pierre Fabre, GSK, MSD, Merck Germany, Roche, BMS, Novartis, Sanofi, Beiersdorf, Almiral-Hermal, AmgenBayersdorf, Roche Pharma, Bristol-MyersSquibb, Novartis, MSD, Almirall-Hermal, Amgen, Pierre-Fabre, Merck-Serono, SUN-Pharma, SUN, Merck-Serono, Sanofi. CP received honoraria (speaker honoraria or honoraria as a consultant) and travel support from Novartis, BMS, Roche, Merck Serono, MSD, Celgene, AbbVie, AMGEN, SUNPHARMA, Allergy Therapeutics and LEO. LMH served as consultant and/or has received honoraria from Amgen, BMS, Curevac, MSD, Novartis, Pierre-Fabre, Roche, Sanofi and Sun Pharma, outside the submitted work. Research funding to institution: Novartis. R. Gutzmer reports research support from Pfizer, Johnson & Johnson, Novartis, Amgen, MerckSerono, SUN Pharma; honoraria for lectures from Roche Pharma, Bristol-MyersSquibb, Novartis, MSD, Almirall-Hermal, Amgen, Merck-Serono, SUN, Pierre-Fabre, Sanofi, SUN Pharma, Bayer; honoraria for advice from Roche Pharma, Bristol-MyersSquibb, Novartis, MSD, Almirall-Hermal, Amgen, Pierre-Fabre, Merck-Serono, 4SC, Incyte, SUN Pharma, Sanofi, Pfizer. JSU is on the advisory board or has received honoraria and travel support from Amgen, Bristol Myers Squibb, GSK, LeoPharma, Merck Sharp and Dohme, Novartis, Pierre Fabre, Roche, Sanofi outside the submitted work. H-US is an employee of Targos Molecular Pathology Inc. and reports research support from Novartis Oncology and received honoraria from MSD, BMS, Roche Pharma, Novartis Oncology, AstraZeneca, Eisai, Takeda, Molecular Health, outside of the submitted work. DS reports personal fees from Amgen, GSK, BMS, Novartis, Roche, Merck, Astra Zeneca, Merck-Serono, Pfizer, Incyte, Array Pierre Fabre, Sanofi Genzyme, Regeneron, 4Sc, InFlaRx, Neracare, Ultimovacs, SunPharma, Philogen, Immunocore, Sandoz-Hexal outside the submitted work. JCB is receiving speaker's bureau honoraria from Amgen, Pfizer, MerckSerono, Recordati and Sanofi; is a paid consultant/advisory board member/DSMB member for Almirall, Boehringer Ingelheim, InProTher, ICON, MerckSerono, Pfizer, 4SC, and Sanofi/Regeneron. His group receives research grants from Bristol-Myers Squibb, Merck Serono, HTG, IQVIA, and Alcedis., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Purpose: Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer, which can be effectively controlled by immunotherapy with PD-1/PD-L1 checkpoint inhibitors. However, a significant proportion of patients are characterized by primary therapy resistance. Predictive biomarkers for response to immunotherapy are lacking., Experimental Design: We applied Bayesian inference analyses on 41 patients with MCC testing various clinical and biomolecular characteristics to predict treatment response. Further, we performed a comprehensive analysis of tumor tissue-based immunologic parameters including multiplexed immunofluorescence for T-cell activation and differentiation markers, expression of immune-related genes and T-cell receptor (TCR) repertoire analyses in 18 patients, seven objective responders, and 11 nonresponders., Results: Bayesian inference analyses demonstrated that among currently discussed biomarkers only unimpaired overall performance status and absence of immunosuppression were associated with response to therapy. However, in responders, a predominance of central memory T cells and expression of genes associated with lymphocyte attraction and activation was evident. In addition, TCR repertoire usage of tumor-infiltrating lymphocytes (TILs) demonstrated low T-cell clonality, but high TCR diversity in responding patients. In nonresponders, terminally differentiated effector T cells with a constrained TCR repertoire prevailed. Sequential analyses of tumor tissue obtained during immunotherapy revealed a more pronounced and diverse clonal expansion of TILs in responders indicating an impaired proliferative capacity among TILs of nonresponders upon checkpoint blockade., Conclusions: Our explorative study identified new tumor tissue-based molecular characteristics associated with response to anti-PD-1/PD-L1 therapy in MCC. These observations warrant further investigations in larger patient cohorts to confirm their potential value as predictive markers., (©2020 American Association for Cancer Research.)

Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.

The effect of iodine present in 1.0% table salt in combination with the use of starter cultures in sauerkraut fermentations were investigated in order to determine whether iodine interferes with lactic acid bacteria responsible for the fermentation. The effect of iodine was tested in fermentations performed using selected starter cultures or without starters (spontaneous fermentation). Lactobacillus plantarum and Leuconostoc mesenteroides used as starters at levels of ca. 1 × 10 7  cfu ml -1 led to a quick establishment of lactic acid bacteria (LAB) as predominant microorganisms, reaching 1 × 10 9  cfu ml -1 after 24 h decreasing the pH to below 4.0. In contrast, LAB counts in control fermentations without starters increased slower from 1 × 10 5  cfu ml -1 to 1 × 10 9  cfu ml -1 and a pH reduction below 4.0 was achieved only after 3 days fermentation. A metagenomic investigation showed a more diverse bacterial community in fermentations without starters, consisting of enterobacteria and pseudomonads in the first days of fermentation, and of LAB such as lactococci in the later stages. In fermentations with starters, lactobacilli predominated. Leuconostocs also occurred, but at much lower sequence abundance than lactobacilli, and thus were not able to predominate. Determination of iodine in the fermentation with starter bacteria and with iodized salt showed that the fermentation did not affect iodine concentration. The use of iodized salt did not statistically significantly influence microbial populations in the fermentation. Thus, there is no basis for the popular held belief that the use of iodized salt inhibits the growth of the bacteria important for the sauerkraut fermentation. A statistically near significant effect (p = 0.06), however, was noted for the effect of iodine on yeasts and mould populations in the fermentations performed without starter cultures. As sauerkraut is usually produced without starters, this should be further investigated., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

In this work, we report the draft whole-genome sequence of the multiply antibiotic-resistant Citrobacter portucalensis strain MBTC-1222 isolated from the uziza leafy vegetable in Nigeria. Sequence analysis showed the assembled genome size to be 4,881,935 bp, containing 4,603 protein-coding genes, 131 pseudogenes, 7 rRNAs, 74 tRNAs, and 9 noncoding RNAs (ncRNAs)., (Copyright © 2018 Igbinosa et al.)

A short review is given of concepts which are used to evaluate effects from combined-acting agents. To explore those effects exactly a high multiplicity of experiments must be performed, as an algebraic derivation from the effects of the single-acting agents is not usually possible. For practical purposes (as, for instance, to establish threshold limit values with respect to occupational health standards) a more pragmatic concept is proposed. Accordingly, an experimental setup has been developed which enables us to expose four groups of rodents simultaneously to two different single-acting chemical and/or physical stress parameters, both separately and in combination, and to control conditions.