Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model

A Burkholderia cenocepacia infection usually leads to reduced survival and fatal cepacia syndrome in cystic fibrosis patients. The identification of B. cenocepacia essential genes for in vivo survival is key to designing new anti-infectives therapies. We used the Transposon-Directed Insertion Sequencing (TraDIS) approach to identify genes required for B. cenocepacia survival in the model infection host, Caenorhabditis elegans. A B. cenocepacia J2315 transposon pool of ∼500,000 mutants was used to infect C. elegans. We identified 178 genes as crucial for B. cenocepacia survival in the infected nematode. The majority of these genes code for proteins of unknown function, many of which are encoded by the genomic island BcenGI13, while other gene products are involved in nutrient acquisition, general stress responses and LPS O-antigen biosynthesis. Deletion of the glycosyltransferase gene wbxB and a histone-like nucleoid structuring (H-NS) protein-encoding gene (BCAL0154) reduced bacterial accumulation and attenuated virulence in C. elegans. Further analysis using quantitative RT-PCR indicated that BCAL0154 modulates B. cenocepacia pathogenesis via transcriptional regulation of motility-associated genes including fliC, fliG, flhD, and cheB1. This screen has successfully identified genes required for B. cenocepacia survival within the host-associated environment, many of which are potential targets for developing new antimicrobials.

DemaDb: an integrated dematiaceous fungal genomes database

Many species of dematiaceous fungi are associated with allergic reactions and potentially fatal diseases in human, especially in tropical climates. Over the past 10 years, we have isolated more than 400 dematiaceous fungi from various clinical samples. In this study, DemaDb, an integrated database was designed to support the integration and analysis of dematiaceous fungal genomes. A total of 92 072 putative genes and 6527 pathways that identified in eight dematiaceous fungi (Bipolaris papendorfii UM 226, Daldinia eschscholtzii UM 1400, D. eschscholtzii UM 1020, Pyrenochaeta unguis-hominis UM 256, Ochroconis mirabilis UM 578, Cladosporium sphaerospermum UM 843, Herpotrichiellaceae sp. UM 238 and Pleosporales sp. UM 1110) were deposited in DemaDb. DemaDb includes functional annotations for all predicted gene models in all genomes, such as Gene Ontology, EuKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam and InterProScan. All predicted protein models were further functionally annotated to Carbohydrate-Active enzymes, peptidases, secondary metabolites and virulence factors. DemaDb Genome Browser enables users to browse and visualize entire genomes with annotation data including gene prediction, structure, orientation and custom feature tracks. The Pathway Browser based on the KEGG pathway database allows users to look into molecular interaction and reaction networks for all KEGG annotated genes. The availability of downloadable files containing assembly, nucleic acid, as well as protein data allows the direct retrieval for further downstream works. DemaDb is a useful resource for fungal research community especially those involved in genome-scale analysis, functional genomics, genetics and disease studies of dematiaceous fungi. Database URL: http://fungaldb.um.edu.my.

ClicO FS: an interactive web-based service of Circos

Summary: We present ClicO Free Service, an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots.

Availability and implementation: Online web-service is freely available at http://clicofs.codoncloud.com

Contact: soonjoo.yap@codongenomics.com

Supplementary information:Supplementary data are available at Bioinformatics online.

Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence

Background

Chronic bacterial infections occur as a result of the infecting pathogen’s ability to live within a biofilm, hence escaping the detrimental effects of antibiotics and the immune defense system. Burkholderia pseudomallei, a gram-negative facultative pathogen, is distinctive in its ability to survive within phagocytic and non-phagocytic cells, to persist in vivo for many years and subsequently leading to relapse as well as the development of chronic disease. The capacity to persist has been attributed to the pathogen’s ability to form biofilm. However, the underlying biology of B. pseudomallei biofilm development remains unresolved.

Results

We utilised RNA-Sequencing to identify genes that contribute to B. pseudomallei biofilm phenotype. Transcriptome analysis of a high and low biofilm producer identified 563 differentially regulated genes, implying that expression of ~9.5 % of the total B. pseudomallei gene content was altered during biofilm formation. Genes involved in surface-associated motility, surface composition and cell wall biogenesis were over-expressed and probably play a role in the initial attachment of biofilms. Up-regulation of genes related to two component signal transduction systems and a denitrification enzyme pathway suggest that the B. pseudomallei high biofilm producer is able to sense the surrounding environmental conditions and regulate the production of extracellular polymeric substance matrix, a hallmark of microbial biofilm formation.

Conclusions

The transcriptome profile described here provides the first comprehensive view of genes that contribute to the biofilm phenotype in B. pseudomallei.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1692-0) contains supplementary material, which is available to authorized users.

Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome--which appears to be representative of the genome--is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.

Decreasing lengths of stay: the cost to the community

BACKGROUND

Patients who are discharged earlier from hospital frequently require support from professional and unpaid carers at home after discharge. Hospitals save money per patient by discharging earlier, but it is not known whether the costs to community services and unpaid caters outweigh the savings to the hospital.

METHODS

We prospectively studied the total costs, patient satisfaction, time off work and pain scores of 224 patients who underwent elective herniorrhaphy or laparoscopic cholecystectomy and who lived locally before and after re-engineering the elective surgical service. The components of the re-engineered surgical service were a peri-operative unit, pre-admission anaesthetic assessment based on self-reported questionnaires, day of surgery admissions, enhanced patient education, clinical pathways, and post-acute care.

RESULTS

The patients treated through the re-engineered surgical service had a significantly shorter length of stay (LOS) (mean LOS: 2.2 vs 3.2 days; P < 0.001) but neither they nor their carers required more time off work. Significant determinants of time off work were smoking, heavy lifting at work and a higher pain score at day 7. Patients treated through the re-engineered surgical service recorded significantly higher satisfaction with their treatment. The cost saving to the hospital outweighed the cost of increased services provided in the community, so that the overall cost of providing treatment was over $200 less per patient through the re-engineered service.

CONCLUSIONS

This study demonstrates that changes in care provision that result in shorter LOS and greater cost effectiveness may better meet patients' needs than existing systems.

Re-engineering the elective surgical service of a tertiary hospital: a historical controlled trial

OBJECTIVE

To study the clinical effects of re-engineering the processes associated with elective surgery.

DESIGN

A prospective, historical controlled trial. Control patients were enrolled from March 1995 to January 1996, and postintervention patients from February 1996 to October 1996.

SETTING

A major teaching, tertiary care hospital (Prince of Wales Hospital, Sydney).

PATIENTS

224 patients (123 before and 101 after the intervention) undergoing elective herniorrhaphy of laparoscopic cholecystectomy who lived in the local area.

INTERVENTION

Introduction of a re-engineered surgical service consisting of preadmission assessment and education, admission on day of surgery, and postacute care after discharge. There were no changes to the operative methods or infection control procedures.

MAIN OUTCOME MEASURES

Length of stay, operative complications, pain scores and patient satisfaction.

RESULTS

The risk of a patient suffering one or more complications was reduced in the postintervention group (postintervention v. control patients: 25.7% v. 38.2%; relative risk [RR], 0.66; 95% confidence interval [CI], 0.44-0.98; P = 0.035) because of a reduced risk of wound infections (5.0% v. 16.3%; RR, 0.30; 95% CI, 0.12-0.78; P = 0.0075). Other complications (perioperative or postoperative) and pain scores were unchanged. Patients treated by the re-engineered service had a significantly shorter length of stay, reported a higher level of satisfaction with the preoperative and postdischarge care, and were more likely to say that they would have the same treatment again (92.9% v 82.6%; P = 0.037).

CONCLUSIONS

Re-engineering surgical services, with an associated reduction in length of stay, does not lead to a deterioration in care and may decrease postoperative complications and increase patient satisfaction.

Alterations in endotracheal tube position during general anaesthesia

The effect of head and neck movement and Trendelenburg tilt on endotracheal tube position, relative to the carina, was studied in fifty adult patients requiring intubation for elective surgery. On average, inward movement, that is shortening of the distance between the endotracheal tube tip and the carina, resulted from neck flexion (mean = -5.5 mm), whereas outward movement occurred with neck extension (mean = 6.3 mm). Neck rotation, to right and left, and Trendelenburg tilt did not show any trend towards inward nor outward movement (mean = 0.3 mm/1.7 mm/-0.6 mm, respectively). Whilst these mean positional changes for flexion and extension confirm the findings of earlier investigations, our range of maximum inward and outward displacement for flexion (23 mm in/19 mm out), extension (21 mm in/33 mm out), rotation to right (19 mm in/17 mm out), to left (22 mm in/19 mm out) and Trendelenburg tilt (22 mm in/16 mm out) indicate that for any given postural change in any one patient, the direction and magnitude of endotracheal tube displacement is not readily predictable.