A salicylic acid-associated plant-microbe interaction attracts beneficial Flavobacterium sp. to the Arabidopsis thaliana phyllosphere.

Both above- and below-ground parts of plants are constantly challenged with microbes and interact closely with them. Many plant-growth-promoting rhizobacteria, mostly interacting with the plant's root system, enhance the immunity of plants in a process described as induced systemic resistance (ISR). Here, we characterized local induced resistance (IR) triggered by the model PGPR Pseudomonas simiae WCS417r (WCS417) in Arabidopsis thaliana. Hydroponic application of WCS417 to Arabidopsis roots resulted in propagation of WCS417 in/on leaves and the establishment of local IR. WCS417-triggered local IR was dependent on salicylic acid (SA) biosynthesis and signalling and on functional biosynthesis of pipecolic acid and monoterpenes, which are classically associated with systemic acquired resistance (SAR). WCS417-triggered local IR was further associated with a priming of gene expression changes related to SA signalling and SAR. A metabarcoding approach applied to the leaf microbiome revealed a significant local IR-associated enrichment of Flavobacterium sp.. Co-inoculation experiments using WCS417 and At-LSPHERE Flavobacterium sp. Leaf82 suggest that the proliferation of these bacteria is influenced by both microbial and immunity-related, plant-derived factors. Furthermore, application of Flavobacterium Leaf82 to Arabidopsis leaves induced SAR in an NPR1-dependent manner, suggesting that recruitment of this bacterium to the phyllosphere resulted in propagation of IR. Together, the data highlight the importance of plant-microbe-microbe interactions in the phyllosphere and reveal Flavobacterium sp. Leaf82 as a new beneficial promoter of plant health.

Nutritional management in critically ill patients with COVID-19: a retrospective multicentre study.

INTRODUCTION: Although nutritional treatment is an established pillar of multidisciplinary care provided in critical illness, there are many concerns regarding this issue in severe COVID-19. This observational, retrospective, multicentre study aimed to analyse the approach to nutritional treatment among selected intensive care units (ICUs) in Poland. MATERIAL AND METHODS: The medical records of 129 patients hospitalized in five units due to respiratory failure following COVID-19 were analysed in terms of nutritional management on the eighth day of the ICU stay. The Harris-Benedict equation (HB), Mifflin St. Jeor equation (MsJ) and ESPEN formula (20 kcal kg -1 body weight) were used to estimate the energy target for each patient, and two ESPEN formulas determined the protein target (1 g kg -1 body weight and 1.3 g kg -1 body weight). RESULTS: Evaluation of nutritional therapy was performed in 129 subjects. The fulfilment of caloric requirement considering the HB, MsJ and ESPEN formula was 66%, 66.7% and 62.5%, respectively. Two clinical centres managed to provide 70% or more of daily caloric requirements. According to the ESPEN formula, the implementation of the protein target was 70%; however, one of the investigated units provided a median of 157% of the protein demand. The nutritional management varied in the preferred route of nutrition administration. Neither method nor grade of nutrition supply influenced biochemical parameters on the 8th day of ICU stay. CONCLUSIONS: Significant differences in nutritional treatment of critically ill COVID-19 patients in Polish ICUs were noted, which underlines the importance of setting up clear guidelines regarding this issue.

Addressing the psychosocial aspects of transition to adult care in patients with cystinosis.

Cystinosis is a rare autosomal-recessive lysosomal storage disease that progressively affects multiple organs beginning with the kidneys. Patients require lifelong multidisciplinary care for the management of kidney disease and progressive extra-renal manifestations, and thus, they are especially fragile and vulnerable during transition from pediatric to adult care. Previous documents have provided guidance to help the medical transition of these highly burdened patients. Patients and their families often experience great psychological distress and face significant social challenges; for these reasons, they often need help from psychologists, social workers, and other psychosocial professionals. Due to the rarity of the disease, most psychosocial professionals have no expertise in this disorder and require advice. To this end, a steering committee (SC) composed of six experts, including pediatric nephrologists, psychologists, and social workers with experience in the care for patients with cystinosis, have identified and addressed seven key questions related to psychosocial challenges of the disease and the burden of treatment. Ten additional international experts (the extended faculty, EF) were invited to answer these questions. Since robust evidence is lacking, as in many rare diseases, conclusions were based on collective agreement between members of the SC and the EF, and the consolidated answers were summarized into expert opinion statements. The present document contains information on the concerns and psychosocial burden of patients with cystinosis and of their caregivers, and provides practical advice for timely and appropriate support to facilitate the transition to adult care.

Combined loss of CDH1 and downstream regulatory sequences drive early-onset diffuse gastric cancer and increase penetrance of hereditary diffuse gastric cancer.

BACKGROUND: Germline CDH1 pathogenic or likely pathogenic variants cause hereditary diffuse gastric cancer (HDGC). Once a genetic cause is identified, stomachs' and breasts' surveillance and/or prophylactic surgery is offered to asymptomatic CDH1 carriers, which is life-saving. Herein, we characterized an inherited mechanism responsible for extremely early-onset gastric cancer and atypical HDGC high penetrance. METHODS: Whole-exome sequencing (WES) re-analysis was performed in an unsolved HDGC family. Accessible chromatin and CDH1 promoter interactors were evaluated in normal stomach by ATAC-seq and 4C-seq, and functional analysis was performed using CRISPR-Cas9, RNA-seq and pathway analysis. RESULTS: We identified a germline heterozygous 23 Kb CDH1-TANGO6 deletion in a family with eight diffuse gastric cancers, six before age 30. Atypical HDGC high penetrance and young cancer-onset argued towards a role for the deleted region downstream of CDH1, which we proved to present accessible chromatin, and CDH1 promoter interactors in normal stomach. CRISPR-Cas9 edited cells mimicking the CDH1-TANGO6 deletion display the strongest CDH1 mRNA downregulation, more impacted adhesion-associated, type-I interferon immune-associated and oncogenic signalling pathways, compared to wild-type or CDH1-deleted cells. This finding solved an 18-year family odyssey and engaged carrier family members in a cancer prevention pathway of care. CONCLUSION: In this work, we demonstrated that regulatory elements lying down-stream of CDH1 are part of a chromatin network that control CDH1 expression and influence cell transcriptome and associated signalling pathways, likely explaining high disease penetrance and very young cancer-onset. This study highlights the importance of incorporating scientific-technological updates and clinical guidelines in routine diagnosis, given their impact in timely genetic diagnosis and disease prevention.

Germline mutations in WNK2 could be associated with serrated polyposis syndrome.

BACKGROUND: Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts. METHODS: After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion. RESULTS: We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2. CONCLUSION: After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease.

Solving the genetic aetiology of hereditary gastrointestinal tumour syndromes- a collaborative multicentre endeavour within the project Solve-RD.

BACKGROUND: Patients and families with suspected, but genetically unexplained (unsolved) genetic tumour risk syndromes lack appropriate treatment and prevention, leading to preventable morbidity and mortality. To tackle this problem, patients from the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) are analysed in the European Commission's research project "Solving the unsolved rare diseases" (Solve-RD). The aim is to uncover known and novel cancer predisposing genes by reanalysing available whole-exome sequencing (WES) data of large cohorts in a combined manner, and applying a multidimensional omics approach. APPROACH: Around 500 genetically unsolved cases with suspected hereditary gastrointestinal tumour syndromes (polyposis, early-onset/familial colorectal cancer and gastric cancer) from multiple European centres are aimed to be included. Currently, clinical and germline WES data from 294 cases have been analysed. In addition, an extensive molecular profiling of gastrointestinal tumours from these patients is planned and deep learning techniques will be applied. The ambitious, multidisciplinary project is accompanied by a number of methodical, technical, and logistic challenges, which require the development and implementation of new analysis tools, the standardisation of bioinformatics pipelines, and strategies to exchange data and knowledge. RESULTS: and Outlook. The first re-analysis of 229 known and proposed cancer predisposition genes allowed solving 2-3% of previously unsolved GENTURIS cases. The integration of expert knowledge and new technologies will help to identify the genetic basis of additional unsolved cases within the ongoing project. The ERN GENTURIS approach might serve as a model for other genomic initiatives.

Immunity-associated volatile emissions of ß-ionone and nonanal propagate defence responses in neighbouring barley plants.

Plants activate biochemical responses to combat stress. (Hemi-)biotrophic pathogens are fended off by systemic acquired resistance (SAR), a primed state allowing plants to respond faster and more strongly upon subsequent infection. Here, we show that SAR-like defences in barley (Hordeum vulgare) are propagated between neighbouring plants, which respond with enhanced resistance to the volatile cues from infected senders. The emissions of the sender plants contained 15 volatile organic compounds (VOCs) associated with infection. Two of these, ß-ionone and nonanal, elicited resistance upon plant exposure. Whole-genome transcriptomics analysis confirmed that interplant propagation of defence in barley is established as a form of priming. Although gene expression changes were more pronounced after challenge infection of the receiver plants with Blumeria graminis f. sp. hordei, differential gene expression in response to the volatile cues of the sender plants included an induction of HISTONE DEACETYLASE 2 (HvHDA2) and priming of TETRATRICOPEPTIDE REPEAT-LIKE superfamily protein (HvTPL). Because HvHDA2 and HvTPL transcript accumulation was also enhanced by exposure of barley to ß-ionone and nonanal, our data identify both genes as possible defence/priming markers in barley. Our results suggest that VOCs and plant-plant interactions are relevant for possible crop protection strategies priming defence responses in barley.

Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis.

The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21-42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.

Mutations in the gdpP gene are a clinically relevant mechanism for ß-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants.

In Staphylococcus aureus, resistance to ß-lactamase stable ß-lactam antibiotics is mediated by the penicillinbinding protein 2a, encoded by mecA or by its homologues mecB or mecC. However, a substantial number of meticillin-resistant isolates lack known mec genes and, thus, are called meticillin resistant lacking mec (MRLM). This study aims to identify the genetic mechanisms underlying the MRLM phenotype. A total of 141 MRLM isolates and 142 meticillin-susceptible controls were included in this study. Oxacillin and cefoxitin minimum inhibitory concentrations were determined by broth microdilution and the presence of mec genes was excluded by PCR. Comparative genomics and a genome-wide association study (GWAS) approach were applied to identify genetic polymorphisms associated with the MRLM phenotype. The potential impact of such mutations on the expression of PBP4, as well as on cell morphology and biofilm formation, was investigated. GWAS revealed that mutations in gdpP were significantly associated with the MRLM phenotype. GdpP is a phosphodiesterase enzyme involved in the degradation of the second messenger cyclic-di-AMP in S. aureus. A total of 131 MRLM isolates carried truncations, insertions or deletions as well as amino acid substitutions, mainly located in the functional DHH-domain of GdpP. We experimentally verified the contribution of these gdpP mutations to the MRLM phenotype by heterologous complementation experiments. The mutations in gdpP had no effect on transcription levels of pbp4; however, cell sizes of MRLM strains were reduced. The impact on biofilm formation was highly strain dependent. We report mutations in gdpP as a clinically relevant mechanism for ß-lactam resistance in MRLM isolates. This observation is of particular clinical relevance, since MRLM are easily misclassified as MSSA (meticillin-susceptible S. aureus), which may lead to unnoticed spread of ß-lactam-resistant isolates and subsequent treatment failure.

A mosaic PIK3CA variant in a young adult with diffuse gastric cancer: case report.

Hereditary diffuse gastric cancer (HDGC) is associated with germline deleterious variants in CDH1 and CTNNA1. The majority of HDGC-suspected patients are still genetically unresolved, raising the need for identification of novel HDGC predisposing genes. Under the collaborative environment of the SOLVE-RD consortium, re-analysis of whole-exome sequencing data from unresolved gastric cancer cases (n = 83) identified a mosaic missense variant in PIK3CA in a 25-year-old female with diffuse gastric cancer (DGC) without familial history for cancer. The variant, c.3140A>G p.(His1047Arg), a known cancer-related somatic hotspot, was present at a low variant allele frequency (18%) in leukocyte-derived DNA. Somatic variants in PIK3CA are usually associated with overgrowth, a phenotype that was not observed in this patient. This report highlights mosaicism as a potential, and understudied, mechanism in the etiology of DGC.

Corrigendum: Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus.

[This corrects the article DOI: 10.3389/fmicb.2021.639660.].

Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus.

BACKGROUND: As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. MATERIALS/METHODS: To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. RESULTS: GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. CONCLUSION: We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.

Systemic propagation of immunity in plants.

Systemic immunity triggered by local plant-microbe interactions is studied as systemic acquired resistance (SAR) or induced systemic resistance (ISR) depending on the site of induction and the lifestyle of the inducing microorganism. SAR is induced by pathogens interacting with leaves, whereas ISR is induced by beneficial microbes interacting with roots. Although salicylic acid (SA) is a central component of SAR, additional signals exclusively promote systemic and not local immunity. These signals cooperate in SAR- and possibly also ISR-associated signaling networks that regulate systemic immunity. The non-SA SAR pathway is driven by pipecolic acid or its presumed bioactive derivative N-hydroxy-pipecolic acid. This pathway further regulates inter-plant defense propagation through volatile organic compounds that are emitted by SAR-induced plants and recognized as defense cues by neighboring plants. Both SAR and ISR influence phytohormone crosstalk towards enhanced defense against pathogens, which at the same time affects the composition of the plant microbiome. This potentially leads to further changes in plant defense, plant-microbe, and plant-plant interactions. Therefore, we propose that such inter-organismic interactions could be combined in potentially highly effective plant protection strategies.

Occupational hazards in anaesthesiology during the COVID-19 pandemic.

According to the Occupational Safety and Health Administration of the Department of Labor of the United States, the exposure risk for anaesthesiologists working with COVID-19 patients can be classified as high or very high. This is mostly due to fact that the anaesthesiologists work in close contact with patients' airways, and the aerosol-generating nature of some procedures they perform. Fortunately, despite the occupational hazard, the incidence of COVID-19 among anaesthesiologists and intensivists remains relatively low. Current evidence suggests that the majority of SARS-CoV-2 infections in this group were either contracted outside of the work environment or can be attributed to personal protective equipment (PPE) malfunction. This article focuses on different aspects of anaesthesiologists' safety, risks connected with different clinical scenarios and procedures, issues related to testing and screening, as well as modifiable and non-modifiable risk factors for severe illness or from COVID-19. This analysis is accompanied by a review of guidelines dedicated to mitigating said risks. Educating the personnel, introducing appropriate procedures, and proper utilisation of PPE are essential to the safety of all parties involved in hospital care, particularly those with significant exposure risk.

Dysphagia. Part 1: General issues.

Dysphagia is a common problem among ICU patients. The frequency of dysphagia increases with age and sometimes symptoms can be difficult to recognise. But the consequences of dysphagia can be very serious, including aspiration and subsequently aspiration pneumonia. Therefore, knowing mechanisms and symptoms causing dysphagia is very important and should be well recognised. Proper diagnosis allows one to prevent further complications. However, both the diagnosis and treatment can be very complicated, especially among the patients who do not cooperate. In many cases, the implementation of an appropriate nutrition strategy and proper rehabilitation can alleviate the symptoms of dysphagia and avoid the most severe complications.

Dysphagia. Part 2: Dysphagia in intensive care patients.

Dysphagia is a common problem among ICU patients. The frequency of dysphagia increases with age and sometimes symptoms can be difficult to recognise. But the con-sequences of dysphagia can be very serious, including aspiration and subsequently aspiration pneumonia. Therefore, knowing mechanisms and symptoms causing dysphagia is very important and should be well recognised. Proper diagnosis allows one to prevent further complications. However, both the diagnosis and treatment can be very complicated, especially among the patients who do not cooperate. In many cases, the implementation of an appropriate nutrition strategy and proper rehabilitation can alleviate the symptoms of dysphagia and avoid the most severe complications.

COVID-19 - what should anaethesiologists and intensivists know about it?

Over the past three months, the world has faced an unprecedented health hazard. The World Health Organization has announced a pandemic infection with an unknown species of coronavirus called SARS-CoV-2. Spreading mainly through the droplet route, the virus causes mild symptoms in the majority of cases, the most common being: fever (80%), dry cough (56%), fatigue (22%) and muscle pain (7%); less common symptoms include a sore throat, a runny nose, diarrhea, hemoptysis and chills. A life-threatening complication of SARS-CoV-2 infection is an acute respiratory distress syndrome (ARDS), which occurs more often in older adults, those with immune disorders and co-morbidities. Severe forms of the infection, being an indication for treatment in the intensive care unit, comprise acute lung inflammation, ARDS, sepsis and septic shock. The article presents basic information about etiology, pathogenesis and diagnostics (with particular emphasis on the importance of tomocomputer imaging), clinical picture, treatment and prevention of the infection. It goes on to emphasize the specific risks of providing anesthesiology and intensive care services. Due to the fact that effective causal treatment is not yet available and the number of infections and deaths increases day by day, infection prevention and strict adherence to recommendations of infection control organizations remain the basis for fighting the virus.

Corrigendum: A simple collision model for small bubbles (2017 J. Phys.: Condens. Matter 29 124005).

The original manuscript contains scribal errors in the main equation. This corrigendum contains the correct equations. Results and conclusions in the original manuscript are not affected.

Guidelines of the Association of Polish Surgeons and the Polish Society of Surgical Oncology on the accreditation of healthcare centers providing cytoreductive surgery and HIPEC for primary and secondary peritoneal cancers.

Surgical interventions in patients with peritoneal metastases combined with hyperthermic intraperitoneal chemotherapy (HIPEC) and systemic treatment are becoming more common and, when applied to selected patient groups, they reach 5-year survival rates of 32-52%. Good clinical outcomes require experienced and well-equipped healthcare centers, experienced surgical team and adequate patient qualification process. As a result of the discussion on the need for evaluation of quality of care and treatment outcomes and at the request of the Peritoneal Cancer Section of the Polish Society of Surgical Oncology, accreditation standards have been developed and the Accreditation Committee has been established for healthcare centers providing cytoreductive surgery and HIPEC for the management of primary and secondary peritoneal cancers.