Genome Characterization and Annotation of a Cluster S Bacteriophage

Bacteriophages (phages) are viruses that infect their host and cannot reproduce independently outside of them. The application of bacteriophages in the biotechnology and medical sectors has recently increased, including uses as a potential antibacterial agent and CRISPR technology. In this project, the 48,667 to 58,636 base pair region (genes 87-98) of the Corazon phage genome was annotated by five student researchers at Purdue University. Corazon, a cluster S phage was isolated at Lafayette College in Easton, PA. Corazon belongs to the Siphoviridae morphotype and its genome consists of 109 genes. In this study, gene locations were called using evidence consisting of alignment results, coding potential, and comparison to other phage genomes using DNAMaster, NCBI Blast, Phamerator, HHPred, Starterator. The annotation of a genome consists of confidently assigning start sites and functions to genes based on evidence obtained from auto-annotation of the genome and additional evidence collected based on the genome cluster and similar calls in other phages. Notable functions include minor tail proteins, which are found in the tail fiber or sheath of the phage, and HNH endonuclease, which is a component of the phage packaging machinery. Many of the genes annotated have no known function based on the collected evidence but additional research may yield alternative results and additional uses. Further research of bacteriophage genetics allows deeper investigation and heightened understanding of their possible uses

Long-Term Outcomes in Patients with Intestinal Failure Due to Short Bowel Syndrome and Intestinal Fistula

Short bowel syndrome (SBS) and enterocutaneous or enteroatmospheric fistulas are common indications for home parenteral nutrition (HPN). However, there are few data describing factors influencing surgical decision-making or outcomes particularly following fistula development. We aimed to compare outcomes between patients with SBS and fistulas and explore surgical decision-making. HPN-dependent adults from 2001–2018 at a national reference centre were included in this study. HPN cessation was analysed using death as competing risk. In total, 465 patients (SBS (62%), fistula (38%)) were included, with median HPN dependency of 2.6 years. In total, 203 patients underwent reconstructive surgery; while frailty was the commonest reason for not undergoing surgery (49.2%), 22.7% declined surgery. Overall, 170 ceased HPN, with a probability of 13.8%, 34.1% and 38.3% at 1, 5 and 10 years, respectively. Patients undergoing surgery had higher nutritional autonomy rates (109.8 incidences/1000 patient years) compared to those not undergoing surgery (18.1 incidences/1000 patient years; p < 0.001). A total of 295 patients (63.4%) were predicted to cease HPN based on gastrointestinal anatomy but only 162/295 (54.9%) achieved this; those unable to do so were older with a higher comorbidity index. There were no differences in long-term nutritional and survival outcomes or surgical decisions between patients with SBS and fistulas, or between enterocutaneous and enteroatmospheric fistulas. This study represents one of the largest datasets describing the ability of HPN-dependent patients with SBS or fistulas to achieve nutritional autonomy. While reconstructive surgery facilitates HPN cessation, approximately one-fifth of patients declined surgery despite HPN dependency. These data will better inform patient expectation and help plan alternative therapies