Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA.We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens

Association between illness severity and timing of initial enteral feeding in critically ill patients: a retrospective observational study

<p>Abstract</p> <p>Background</p> <p>Early enteral nutrition is recommended in cases of critical illness. It is unclear whether this recommendation is of most benefit to extremely ill patients. We aim to determine the association between illness severity and commencement of enteral feeding.</p> <p>Methods</p> <p>One hundred and eight critically ill patients were grouped as “less severe” and “more severe” for this cross-sectional, retrospective observational study. The cut off value was based on Acute Physiology and Chronic Health Evaluation II score 20. Patients who received enteral feeding within 48 h of medical intensive care unit (ICU) admission were considered early feeding cases otherwise they were assessed as late feeding cases. Feeding complications (gastric retention/vomiting/diarrhea/gastrointestinal bleeding), length of ICU stay, length of hospital stay, ventilator-associated pneumonia, hospital mortality, nutritional intake, serum albumin, serum prealbumin, nitrogen balance (NB), and 24-h urinary urea nitrogen data were collected over 21 days.</p> <p>Results</p> <p>There were no differences in measured outcomes between early and late feedings for less severely ill patients. Among more severely ill patients, however, the early feeding group showed improved serum albumin (p = 0.036) and prealbumin (p = 0.014) but worsened NB (p = 0.01), more feeding complications (p = 0.005), and prolonged ICU stays (p = 0.005) compared to their late feeding counterparts.</p> <p>Conclusions</p> <p>There is a significant association between severity of illness and timing of enteral feeding initiation. In more severe illness, early feeding was associated with improved nutritional outcomes, while late feeding was associated with reduced feeding complications and length of ICU stay. However, the feeding complications of more severely ill early feeders can be handled without significantly affecting nutritional intake and there is no eventual difference in length of hospital stay or mortality between groups. Consequently, early feeding shows to be a more beneficial nutritional intervention option than late feeding in patients with more severe illness.</p