No abstract

Background Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. Results While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. Conclusions We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition.

Highlights d Triple RNA-seq measures gene expression of co-infected immune cells d Gene correlation networks reveal different hub gene sets under co-infection d Co-infection expression includes synergies and interferences between host and pathogens d Molecular basis of viral/fungal pulmonary infection has potential for the clinic Authors

1In transcriptomics, the study of the total set of RNAs transcribed by the cell, RNA sequencing 2 (RNA-seq) has become the standard tool for analysing gene expression. The primary goal is 3 the detection of genes whose expression changes significantly between two or more conditions, 4 either for a single species or for two or more interacting species at the same time (dual RNA-seq, 5 triple RNA-seq and so forth). The analysis of RNA-seq can be simplified as many steps of the 6 data pre-processing can be standardised in a pipeline. 7 In this publication we present the "GEO2RNAseq" pipeline for complete, quick and concurrent 8 pre-processing of single, dual, and triple RNA-seq data. It covers all pre-processing steps 9 starting from raw sequencing data to the analysis of differentially expressed genes, including 10 various tables and figures to report intermediate and final results. Raw data may be provided 11 in FASTQ format or can be downloaded automatically from the Gene Expression Omnibus 12 repository. GEO2RNAseq strongly incorporates experimental as well as computational metadata. 13 GEO2RNAseq is implemented in R, lightweight, easy to install via Conda and easy to use, but still 14 very flexible through using modular programming and offering many extensions and alternative 15 workflows. 16 GEO2RNAseq is publicly available at https://anaconda.org/xentrics/r-geo2rnaseq 17 and https://bitbucket.org/thomas_wolf/geo2rnaseq/overview, including source 18 code, installation instruction, and comprehensive package documentation. 19 1 Seelbinder et al. GEO2RNAseqthe detection of genes whose expression changes significantly between two or more conditions, and the 25 function relationship of these genes. RNA sequencing (RNA-seq) offers a complete, fast, and cheap way 26 to perform transcriptomics of single organisms using next-generation-sequencing technologies (Mardis, 27 2008). However, species do not exist in isolation. In fact, interspecies interactions are a major part of 28 environmental adaptation. The special variant dual RNA-seq can be applied to analyse the transcriptome 29 of two interacting species at the same time by separating their RNA in silico (Schulze et al., 2016; Wolf 30 et al., 2018). The concept of dual RNA-seq can be further extended: triple RNA-seq allows investigating 31 the interaction of three organisms, e. g. a host and two competing pathogens. 32Both, the number of scientists applying RNA-seq and the number of published datasets have been growing 33 exponentially 1 (Deelen et al., 2014). However, the bottlenecks in transcriptomics are the small number 34 of experts able to pre-process and analyse RNA-seq data, and the small number of easy-to-use tools. A 35 number of pipelines were published in R to handle this issue, but none of them includes the complete set of 36 pre-processing steps and none exploits the available metadata fully. 37Extensive utilisation of metadata is highly important. Wet-lab metadata, e. g. temperature or pH, and 38 dry-lab metadata, e. ...

No abstract

Invasive aspergillosis (IA) is a life-threatening complication among allogeneic hematopoietic stem cell transplant (alloSCT) recipients. Despite well known risk factors and different available assays, diagnosis of invasive aspergillosis remains challenging. 103 clinical variables from patients with hematological malignancies and subsequent alloSCT were collected. Associations between collected variables and patients with (n = 36) and without IA (n = 36) were investigated by applying univariate and multivariable logistic regression. The predictive power of the final model was tested in an independent patient cohort (23 IA cases and 25 control patients). Findings were investigated further by in vitro studies, which analysed the effect of etanercept on A. fumigatus-stimulated macrophages at the gene expression and cytokine secretion. Additionally, the release of C-X-C motif chemokine ligand 10 (CXCL10) in patient sera was studied. Low monocyte concentration (p = 4.8 × 10−06), severe GvHD of the gut (grade 2–4) (p = 1.08 × 10−02) and etanercept treatment of GvHD (p = 3.5 × 10−03) were significantly associated with IA. Our studies showed that etanercept lowers CXCL10 concentrations in vitro and ex vivo and down-regulates genes involved in immune responses and TNF-alpha signaling. Our study offers clinicians new information regarding risk factors for IA including low monocyte counts and administration of etanercept. After necessary validation, such information may be used for decision making regarding antifungal prophylaxis or closely monitoring patients at risk.

No abstract

Despite available diagnostic tests and recent advances, diagnosis of pulmonary invasive aspergillosis (IPA) remains challenging. We performed a longitudinal case-control pilot study to identify host-specific, novel, and immune-relevant molecular candidates indicating IPA in patients post allogeneic stem cell transplantation (alloSCT). Supported by differential gene expression analysis of six relevant in vitro studies, we conducted RNA sequencing of three alloSCT patients categorized as probable IPA cases and their matched controls without Aspergillus infection (66 samples in total). We additionally performed immunoassay analysis for all patient samples to gain a multi-omics perspective. Profiling analysis suggested LGALS2, MMP1, IL-8, and caspase-3 as potential host molecular candidates indicating IPA in investigated alloSCT patients. MMP1, IL-8, and caspase-3 were evaluated further in alloSCT patients for their potential to differentiate possible IPA cases and patients suffering from COVID-19-associated pulmonary aspergillosis (CAPA) and appropriate control patients. Possible IPA cases showed differences in IL-8 and caspase-3 serum levels compared with matched controls. Furthermore, we observed significant differences in IL-8 and caspase-3 levels among CAPA patients compared with control patients. With our conceptual work, we demonstrate the potential value of considering the human immune response during Aspergillus infection to identify immune-relevant molecular candidates indicating IPA in alloSCT patients. These human host candidates together with already established fungal biomarkers might improve the accuracy of IPA diagnostic tools.