Solving genomic puzzles: computational methods for metagenomic binning.

Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.

S. aureus biofilm properties correlate with immune B cell subset frequencies and severity of chronic rhinosinusitis.

Staphylococcus aureus mucosal biofilms are associated with recalcitrant chronic rhinosinusitis (CRS). However, S. aureus colonisation of sinus mucosa is frequent in the absence of mucosal inflammation. This questions the relevance of S. aureus biofilms in CRS etiopathogenesis. This study aimed to investigate whether strain-level variation in in vitro-grown S. aureus biofilm properties relates to CRS disease severity, in vitro toxicity, and immune B cell responses in sinonasal tissue from CRS patients and non-CRS controls. S. aureus clinical isolates, tissue samples, and matched clinical datasets were collected from CRS patients with nasal polyps (CRSwNP), CRS without nasal polyps (CRSsNP), and controls. B cell responses in tissue samples were characterised by FACS. S. aureus biofilms were established in vitro, followed by measuring their properties of metabolic activity, biomass, colony-forming units, and exoprotein production. S. aureus virulence was evaluated using whole-genome sequencing, mass spectrometry and application of S. aureus biofilm exoproteins to air-liquid interface cultures of primary human nasal epithelial cells (HNEC-ALI). In vitro S. aureus biofilm properties were correlated with increased CRS severity scores, infiltration of antibody-secreting cells and loss of regulatory B cells in tissue samples. Biofilm exoproteins from S. aureus with high biofilm metabolic activity had enriched virulence genes and proteins, and negatively affected the barrier function of HNEC-ALI cultures. These findings support the notion of strain-level variation in S. aureus biofilms to be critical in the pathophysiology of CRS.

Plassembler: an automated bacterial plasmid assembly tool.

SUMMARY: With recent advances in sequencing technologies, it is now possible to obtain near-perfect complete bacterial chromosome assemblies cheaply and efficiently by combining a long-read-first assembly approach with short-read polishing. However, existing methods for assembling bacterial plasmids from long-read-first assemblies often misassemble or even miss bacterial plasmids entirely and accordingly require manual curation. Plassembler was developed to provide a tool that automatically assembles and outputs bacterial plasmids using a hybrid assembly approach. It achieves increased accuracy and computational efficiency compared to the existing gold standard tool Unicycler by removing chromosomal reads from the input read sets using a mapping approach. AVAILABILITY AND IMPLEMENTATION: Plassembler is implemented in Python and is installable as a bioconda package using 'conda install -c bioconda plassembler'. The source code is available on GitHub at https://github.com/gbouras13/plassembler. The full benchmarking pipeline can be found at https://github.com/gbouras13/plassembler_simulation_benchmarking, while the benchmarking input FASTQ and output files can be found at https://doi.org/10.5281/zenodo.7996690.

Pharokka: a fast scalable bacteriophage annotation tool.

SUMMARY: In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email-based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5 min to run for an average 50-kb bacteriophage genome. AVAILABILITY AND IMPLEMENTATION: Pharokka is implemented in Python and is available as a bioconda package using 'conda install -c bioconda pharokka'. The source code is available on GitHub (https://github.com/gbouras13/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine.

Phables: from fragmented assemblies to high-quality bacteriophage genomes.

MOTIVATION: Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery. RESULTS: We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. AVAILABILITY AND IMPLEMENTATION: Phables is available on GitHub at https://github.com/Vini2/phables.

A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.

Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.

Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli.

Phage therapy has recently been revitalized in the West with many successful applications against multi-drug-resistant bacterial infections. However, the lack of geographically diverse bacteriophage (phage) genomes has constrained our understanding of phage diversity and its genetics underpinning host specificity, lytic capability, and phage-bacteria co-evolution. This study aims to locally isolate virulent phages against uropathogenic Escherichia coli (E. coli) and study its phenotypic and genomic features. Three obligately virulent Escherichia phages (øEc_Makalu_001, øEc_Makalu_002, and øEc_Makalu_003) that could infect uropathogenic E. coli were isolated and characterized. All three phages belonged to Krischvirus genus. One-step growth curve showed that the latent period of the phages ranged from 15 to 20 min, the outbreak period ~ 50 min, and the burst size ranged between 74 and 127 PFU/bacterium. Moreover, the phages could tolerate a pH range of 6 to 9 and a temperature range of 25-37 °C for up to 180 min without significant loss of phage viability. All phages showed a broad host spectrum and could lyse up to 30% of the 35 tested E. coli isolates. Genomes of all phages were approximately ~ 163 kb with a gene density of 1.73 gene/kbp and an average gene length of ~ 951 bp. The coding density in all phages was approximately 95%. Putative lysin, holin, endolysin, and spanin genes were found in the genomes of all three phages. All phages were strictly virulent with functional lysis modules and lacked any known virulence or toxin genes and antimicrobial resistance genes. Pre-clinical experimental and genomic analysis suggest these phages may be suitable candidates for therapeutic applications.

Quality of life after emergency laparotomy: a systematic review.

BACKGROUND: Emergency laparotomy is a commonly performed surgical procedure that has higher post-operative morbidity and mortality than elective surgery. Previous research has identified that patients valued postoperative quality of life (QoL) more than the risk of mortality when deciding to undergo emergency surgery. Current pre-operative scoring and risk stratification systems for emergency laparotomy do not account for or provide prediction tools for post-operative QoL. This study aims to systematically review previous literature to determine post-operative QoL in patients who undergo emergency laparotomy. METHODS: A literature search was undertaken in Medline, EMBASE and the Cochrane Library to identify studies measuring post-operative QoL in patients who have had emergency laparotomy up to 29th April 2023. Mean QoL scores from the studies included were combined to calculate the average effect of emergency laparotomy on QoL. The primary outcome of the review was postoperative QoL after emergency laparotomy when compared with a comparator group. Secondary outcomes included the quality of included studies. RESULTS: Ten studies in the literature assessing the QoL of patients after emergency laparotomy were identified. Three studies showed that patients had improved QoL and seven showed worse QoL following emergency laparotomy. Length of time for QoL to return to baseline varied ranged from 3 to 12 months post-operatively. Length of hospital stay was identified as an independent risk factor for poorer QoL post-surgery. CONCLUSIONS: Outcome reporting for patients who undergo emergency laparotomy should be expanded further to include QoL. Further work is required to investigate this and elicit factors that can improve QoL post-operatively.

Staphylococcus aureus Biofilm-Secreted Factors Cause Mucosal Damage, Mast Cell Infiltration, and Goblet Cell Hyperplasia in a Rat Rhinosinusitis Model.

Chronic rhinosinusitis (CRS) is an inflammatory condition of the sinonasal mucosa. Despite being a common health issue, the exact cause of CRS is yet to be understood. However, research suggests that Staphylococcus aureus, particularly in its biofilm form, is associated with the disease. This study aimed to investigate the impact of long-term exposure to secreted factors of Staphylococcus aureus biofilm (SABSFs), harvested from clinical isolates of non-CRS carrier and CRS patients, on the nasal mucosa in a rat model. Animals were randomised (n = 5/group) to receive daily intranasal instillations of 40 µL (200 µg/µL) SABSFs for 28 days or vehicle control. The sinonasal samples were analysed through histopathology and transcriptome profiling. The results showed that all three intervention groups displayed significant lymphocytic infiltration (p ≤ 0.05). However, only the SABSFs collected from the CRSwNP patient caused significant mucosal damage, mast cell infiltration, and goblet cell hyperplasia compared to the control. The transcriptomics results indicated that SABSFs significantly enriched multiple inflammatory pathways and showed distinct transcriptional expression differences between the control group and the SABSFs collected from CRS patients (p ≤ 0.05). Additionally, the SABSF challenges induced the expression of IgA and IgG but not IgE. This in vivo study indicates that long-term exposure to SABSFs leads to an inflammatory response in the nasal mucosa with increased severity for S. aureus isolated from a CRSwNP patient. Moreover, exposure to SABSFs does not induce local production of IgE.

A Novel Model of Staphylococcus aureus-Induced Lymphoplasmacytic Rhinosinusitis in Rats.

Chronic rhinosinusitis (CRS) is characterized by sinonasal mucosal inflammation. Staphylococcus aureus (S. aureus) is associated with severe CRS phenotypes. Different animal models have been proposed to study the association of CRS and S. aureus. However, current animal models are expensive due to the use of large animals, have high barriers to ethics approval, or require invasive surgical intervention, necessitating a need for a model that can overcome these limitations. This study aimed at establishing a reliable and efficient rat lymphoplasmacytic inflammatory model for rhinosinusitis. Sprague Dawley rats received a daily intranasal application of 20 µL of saline, S. aureus CI-182 exoprotein (250 µg/mL), or exoprotein CI-182 in combination with S. aureus clinical isolate (CI-908 or CI-913) 108 colony-forming unit (CFU)/mL. The rats' sinuses were harvested at 1 and 2 weeks post-intervention. The CFU and histopathologic examination of inflammation were evaluated. S. aureus clinical isolates CI-908 or CI-913 in combination with the exoprotein (CI-182) had higher CFUs and caused persistently higher inflammation at both the 1 and 2-week post-intervention compared to the exoprotein and saline group. The observed inflammatory cell type was lymphoplasmacytic. This study provided evidence that the combination of a S. aureus exoprotein with S. aureus induces inflammation that persists for a minimum of two weeks post-intervention. This model is the first known animal model to create the lymphoplasmacytic inflammation subtype seen in CRS patients. This offers a cost-effective, accessible, non-invasive, and easy-to-replicate model to study the causes and treatment of such inflammation.

Staphylococcus aureus biofilm properties and chronic rhinosinusitis severity scores correlate positively with total CD4+ T-cell frequencies and inversely with its Th1, Th17 and regulatory cell frequencies.

Chronic rhinosinusitis (CRS) represents chronic inflammation of the sinus mucosa characterised by dysfunction of the sinuses' natural defence mechanisms and induction of different inflammatory pathways ranging from a Th1 to a Th2 predominant polarisation. Recalcitrant CRS is associated with Staphylococcus aureus dominant mucosal biofilms; however, S. aureus colonisation of the sinonasal mucosa has also been observed in healthy individuals challenging the significance of S. aureus in CRS pathogenesis. We aimed to investigate the relationship between CRS key inflammatory markers, S. aureus biofilm properties/virulence genes and the severity of the disease. Tissue samples were collected during endoscopic sinus surgery from the ethmoid sinuses of CRS patients with (CRSwNP) and without (CRSsNP) nasal polyps and controls (n = 59). CD3+ T-cell subset frequencies and key inflammatory markers of CD4+ helper T cells were determined using FACS analysis. Sinonasal S. aureus clinical isolates were isolated (n = 26), sequenced and grown into biofilm in vitro, followed by determining their properties, including metabolic activity, biomass, colony-forming units and exoprotein production. Disease severity was assessed using Lund-Mackay radiologic scores, Lund-Kennedy endoscopic scores and SNOT22 quality of life scores. Our results showed that S. aureus biofilm properties and CRS severity scores correlated positively with total CD4+ T-cell frequencies but looking into CD4+ T-cell subsets showed an inverse correlation with Th1 and Th17 cell frequencies. CD4+ T-cell frequencies were higher in patients harbouring lukF.PV-positive S. aureus while its regulatory and Th17 cell subset frequencies were lower in patients carrying sea- and sarT/U-positive S. aureus. Recalcitrant CRS is characterised by increased S. aureus biofilm properties in relation to increased total CD4+ helper T-cell frequencies and reduced frequencies of its Th1, Th17 and regulatory T-cell subsets. These findings offer insights into the pathophysiology of CRS and could lead to the development of more targeted therapies.

APTC-C-SA01: A Novel Bacteriophage Cocktail Targeting Staphylococcus aureus and MRSA Biofilms.

The high infection and mortality rate of methicillin-resistant Staphylococcus aureus (MRSA) necessitates the urgent development of new treatment strategies. Bacteriophages (phages) have several advantages compared to antibiotics for the treatment of multi-drug-resistant bacterial infections, and thus provide a promising alternative to antibiotics. Here, S. aureus phages were isolated from patients and environmental sources. Phages were characterized for stability, morphology and genomic sequence and their bactericidal activity against the biofilm form of methicillin-susceptible Staphylococcus aureus (MSSA) and MRSA was investigated. Four S. aureus phages were isolated and tested against 51 MSSA and MRSA clinical isolates and reference strains. The phages had a broad host range of 82−94% individually and of >98% when combined and could significantly reduce the viability of S. aureus biofilms. The phages had a latent period of ≤20 min and burst size of >11 plaque forming units (PFU)/infected cell. Transmission electron microscopy (TEM) identified phages belonging to the family of Myoviridae. Genomic sequencing indicated the lytic nature of all four phages, with no identified resistance or virulence genes. The 4 phages showed a high complementarity with 49/51 strains (96%) sensitive to at least 2/4 phages tested. Furthermore, the frequency of bacteriophage insensitive mutant (BIM) generation was lower when the phages were combined into the phage cocktail APTC-C-SA01 than for bacteria exposed to each of the phages alone. In conclusion, APTC-C-SA01, containing four lytic S. aureus phages has the potential for further development as a treatment against MSSA and MRSA infections.

Linked Hospital and Primary Care Database Analysis of the Incidence and Impact of Psychiatric Morbidity Following Gastrointestinal Cancer Surgery in England.

OBJECTIVE: To evaluate risk of psychiatric morbidity and its impact on survival in gastrointestinal surgery. BACKGROUND: Psychiatric morbidity related to surgery is poorly understood, and may be evaluated using linked hospital and primary care data. METHODS: Patients undergoing gastrointestinal surgery from 2000 to 2011 with linkage of Clinical Practice Research Datalink (CPRD), Hospital Episodes Statistics (HES), Office of National Statistics (ONS), and National Cancer Intelligence Network (NCIN) databases were studied. Psychiatric morbidity was defined as a diagnosis code in CPRD or HES, or a prescription code for psychiatric medication in the 36 months before (preoperative) or 12 months after (postoperative) surgery. Newly diagnosed psychiatric morbidity was measured in patients without preoperative psychiatric morbidity. RESULTS: In our study, 14,797 (23.8%) and 47,279 (76.2%) patients had surgery for cancer and benign disease, respectively. Postoperative psychiatric morbidity was observed in 10.1% (1500/14797) of patients undergoing cancer surgery. Logistic regression revealed that when adjusted for other factors, cancer diagnosis [odds ratio (OR) = 1.19] independently predicted postoperative psychiatric morbidity (P < 0.05). Hepatopancreaticobiliary resection (OR = 2.40) and esophagogastrectomy (OR = 2.55) carried the highest risks of postoperative psychiatric morbidity (P < 0.05). Preoperative psychiatric morbidity (OR = 1.16) and newly diagnosed psychiatric morbidity (OR = 1.87) were associated with increased 1-year mortality in cancer patients only (P < 0.05). CONCLUSIONS: Postoperative psychiatric morbidity affected a tenth of patients who underwent gastrointestinal cancer surgery and was associated with increased mortality. Strategies to identify patients at risk preoperatively and to reduce the observed adverse impact of postoperative psychiatric morbidity should be part of perioperative care in complex cancer patients.

Systematic review of the impact of surgical harm on quality of life after general and gastrointestinal surgery.

OBJECTIVE: To assess the impact of surgical harm on quality of life (QoL) in general and gastrointestinal surgery. BACKGROUND: Surgical adverse events (SAEs) are associated with poor outcome. Although SAEs are likely to affect QoL, this has not been demonstrated in surgery. METHODS: Studies in general and gastrointestinal surgery measuring postoperative QoL in patients who suffered SAEs were identified. The overall impact of SAEs on QoL scores was determined by combining results from different studies. Component scores, adjustment for confounders, and time trends were evaluated. RESULTS: Data from 57,058 patients in 31 studies were analyzed. Most studies assessed the combined effect of different SAEs. High-quality studies adjusted for preoperative QoL. When different QoL instruments were scaled down to a common 0 to 1 score, the mean difference in QoL between SAE and no-SAE patients was 0.140 in esophagectomy, 0.110 in the Crohn resection, 0.089 in colorectal resection, 0.085 in gastric bypass, 0.072 in cholecystectomy, and 0.060 in inguinal hernia repair. Studies evaluating ileal pouch formation and antireflux surgery showed conflicting results. SAEs did not significantly affect QoL in emergency laparotomy and pancreatectomy. The frequency of SAEs was 5% to 48%. Physical QoL was affected more than emotional QoL. CONCLUSIONS: Significantly negative effects of SAEs on QoL were demonstrated in a range of procedures. Postoperative QoL seems to be a surrogate for the severity of impact of SAEs on patients. QoL may be an important utility to evaluate the economic and societal impact of SAEs thereby defining the threshold for safe practice.

Emergence characteristics comparing endotracheal tube to reinforced laryngeal mask airway during endoscopic sinus surgery - A randomised controlled study.

Background and Aims: During endoscopic sinus surgery, anaesthetic conditions significantly impact the intraoperative surgical field and bleeding during emergence. While the endotracheal tube (ETT) has been traditionally used in sinus surgery, a reinforced laryngeal mask airway (RLMA) that produces less upper airway stimulation may result in smoother emergence. Methods: A randomised controlled trial of 72 patients undergoing elective sinus surgery was conducted, with the allocation of airway technique to either ETT with a throat pack or RLMA. The primary outcome measure was emergence time, measured by time to opening eyes on commands at the cessation of anaesthesia, and the secondary outcomes were time to removal of airway device, remifentanil use, procedure times, mean arterial pressure (MAP) and the RLMA grade of blood contamination. The continuous variables were analysed using Student's t-tests and discrete variables, count tables were analysed using Fisher's exact tests. Results: There was no significant difference in the emergence time between the ETT and RLMA groups (P = 0.83). Remifentanil use was significantly higher in the ETT group than in the RLMA group (P = 0.022). The ETT group showed a significantly increased total anaesthetic time (P = 0.01). MAP was not significant during preinduction, maintenance or post-RMLA removal. The highest grade of contamination was grade 2 in RLMA. RLMA had lower rates of postoperative adverse events. Conclusions: RLMA comparable to ETT in terms of emergence time. The RMLA group had lower remifentanil use, anaesthesia duration and fewer postoperative adverse events such as cough and throat pain.

Chitogel improves long-term health economic outcomes following endoscopic sinus surgery in severe chronic rhinosinusitis patients.

Introduction: Chronic rhinosinusitis causes severe symptoms that can affect patient quality of life. Endoscopic sinus surgery can be effective in improving symptoms, although surgical outcomes can be compromised post-operatively, and revision surgery is required in a proportion of patients. This study compares outcomes and healthcare resource use in patients undergoing sinus surgery with or without Chitogel as a post-operative dressing. Methods: A retrospective cohort study was conducted using deidentified audit data from adult patients with severe chronic rhinosinusitis, who underwent endoscopic sinus surgery between January 2016 and December 2021. Patients in the intervention group received Chitogel as a post-operative dressing, and control patients received standard best-practice care. Cox Proportional Hazards survival analysis was used to compare revision surgery rates and time to revision between treatment groups. The rate of revision surgery was used to estimate potential health sector savings associated with use of Chitogel following surgery compared to the control arm, considering initial treatment costs and the cost of revision surgery. Results: Over 18-24 months, patients treated with Chitogel demonstrated significantly lower rates of revision surgery (p = 0.035), and a trend towards decreased use of post-operative steroids, compared to control. Potential health sector savings due to reduced rates of revision surgery following use of Chitogel are estimated as NZ $753,000 per 100 patients. Conclusion: Severe chronic rhinosinusitis patients treated with Chitogel had lower rates of revision surgery within the first 18-24 months post-operative. These findings suggest that use of Chitogel can improve long-term patient outcomes and should improve health system efficiency.

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.

It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default and Polypolish-careful commonly introduce false-positive errors at low read depth; (2) most of the benefit of short-read polishing occurs by 25× depth; (3) Polypolish-careful almost never introduces false-positive errors at any depth; and (4) Pypolca-careful is the single most effective polisher. Overall, we recommend the following polishing strategies: Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolca-careful when depth is low (5-25×), and Polypolish-default and Pypolca-careful when depth is sufficient (>25×).

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages.

The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.

Double blind randomized controlled trial measuring the efficacy of nebulized steroid at half dose in comparison to high volume squeeze bottle steroid irrigation in management of patients with chronic rhinosinusitis.

KEY POINTS: Nebulized budesonide is effective at half dose compared to budesonide irrigation in CRS. Nasal nebulizers provide an alternative for delivery of topical steroids to the sinuses.

Chitogel with deferiprone following endoscopic sinus surgery: improved wound healing and microbiome.

Background: Adhesion formation, sinus ostial narrowing, and presence of pathogenic bacteria are associated with poor outcomes following endoscopic sinus surgery (ESS) for chronic rhinosinusitis. Chitogel has been shown to improve wound healing, restore a healthier microbiome, and reduce post-operative infections post ESS. Deferiprone has antibacterial properties and has been shown to reduce adhesion formation. The aim of the study was to assess whether the addition of low concentration deferiprone to Chitogel further improves surgical outcomes following ESS compared with Chitogel alone. Methods: In this double-blinded trial, 45 patients undergoing ESS were prospectively recruited. At the end of the surgery, patients were randomised to receive Chitogel alone, Chitogel with 1 mM of deferiprone, or Chitogel with 5 mM of deferiprone to one side of the sinuses (allowing the other side to serve as control). Patients underwent routine follow-ups with symptom questionnaires and nasoendoscopies performed at 2, 6, and 12 weeks post-operatively. Sinus ostial measurements, microbiology, and microbiome swabs from bilateral middle meatuses were collected intraoperatively and at 12 weeks post-operatively. Results: A significant improvement in the endoscopic appearance of the sinuses and frontal ostial patency was noted at 12 weeks post-operatively (p < 0.05) in all three treatment groups compared with the control. There was no significant difference noted between patients who received Chitogel alone and those who received Chitogel with 1 or 5 mM deferiprone. Conclusion: Chitogel alone, Chitogel with 1 mM deferiprone, and Chitogel with 5 mM deferiprone used following ESS led to a significant improvement in endoscopic appearance of the sinuses and frontal ostial preservation at 12 weeks post-operatively. No significant difference was found with the addition of deferiprone to Chitogel.