Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important Pathogenic Phenotypes

Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-?-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen

From customer requirements to technical solutions in the construction industry

Byggindustrin har hamnat på efterkälken i arbetet med att integrera produktutvecklingsprocesser. Ett traditionellt arbetssätt har resulterat i svårigheter att hantera kundkrav i en komplex industrid är många olika aktörer är inblandade. Kundernas krav blir ofta dåligt kommunicerade vilket resulterar i förseningar och ekonomiska förluster i projekt. Studien syftar till att undersöka och utvärdera olika metoder för att identifiera och översätta kundkrav till tekniska lösningar i byggindustrin. Dessutom är syftet att testa och utvärdera en metod från tillverkningsindustrin på byggindustrins produktutvecklingsprocess. För att uppfylla syftet gjordes en kartläggning över vilka metoder organisationer använder för att översätta kundkrav till tekniska lösningar, samt en utvärdering av dessa i ljuset av fördelar och nackdelar. För att testa metoder från tillverkningsindustrin användes metoderna Quality Function Deployment och Pugh’s matris. För att besvara de vetenskapliga frågeställningarna byggdes en teoretisk referensram kring ämnet. Därefter genomfördes semistrukturerade intervjuer på två olika organisationer och en workshop på en av organisationerna. Den teoretiska bakgrunden presenterar olika perspektiv på vem kunden är i byggprocessen och olika vetenskapliga metoder som används för att översätta kundkrav till tekniska lösningar. De sex respondenterna som hördes i intervjuerna och workshopen arbetar inom organisationer som verkar i byggindustrin. Resultatet visade på att organisationerna inte använder någon vetenskapligt förankrad metod utan förlitar sig på traditionellt beprövade metoder. De båda organisationerna arbetar på olika sätt då den ena arbetar kontinuerligt mot en och samma beställare och den andra har olika beställare för varje projekt. Den gemensamma positiva aspekten med deras nuvarande metoder är att arbetet går snabbt. Den gemensamma svårigheten är i kommunikationen för att förhindra möjliga ändringar av krav under projektets gång. De testade metoderna Quality Function Deployment och Pugh’s matris visade sig vara svåra att använda i en av organisationernas arbetsprocess. Studien visar på att det finns ett behov för företagen att arbeta vidare med utvecklingen av deras metoder, där delar av befintliga produktutvecklingsprocesser kan integreras. I ett större perspektiv finns det ett behov i byggindustrin av fler studier inom det här ämnet med tester av andra metoder. The construction industry is limited in its progress to incorporate product development processes in their line of work. Due to a traditional way of working, difficulties in managing customer requirements have increased. The construction industry is complex with many different clients and variables, where customer requirements are often poorly communicated, thus resulting in delays and projects exceeding budget expectations. This degree project aims to investigate and evaluate methods to identify and translate customer requirements into technical solutions in the construction industry. In addition, the purpose is to test and evaluate methods from the manufacturing industry in the construction industry's product development process. To fulfill the purpose, different methods used in organizations to translate customer requirements to technical solutions were mapped and evaluated after their advantages and disadvantages. Quality Function Deployment and Pugh’s matrix were used to test a method from the production industry in one of the organization's processes. To answer the research questions, a theoretical framework was formed and semi-structured interviews were conducted. Also, to test a method from the production industry, a workshop was concluded at one of the organizations. Two organizations and six respondents were included in the study, where all respondents work within organizations that operate in the construction industry. The theoretical framework demonstrates several perspectives of who the customers are in the construction industry as well as different scientifically proven methods to identify and translate customer requirements into technical solutions. Instead of using scientifically established methods, the results exposed that the organizations rely on traditional proven methods. The two organizations work in different ways, as one continuously works with one customer and the other has different clients for every project. The shared positive aspect with the organization's methods is the swiftness, and the negative is the communication between different counterparties that prevent modification of requirements during the project. The tested methods, Quality Function Deployment och Pugh’s matrix proved to be difficult to use in one of the organization's processes. This project reveals a need for the organizations to develop their methods where parts of the existing product development processes can be integrated. Further on, there is a demand for more studies and tests of methods within the construction industry

Genetic Adaptation of Achromobacter sp. during Persistence in the Lungs of Cystic Fibrosis Patients.

Achromobacter species are increasingly isolated from the respiratory tract of cystic fibrosis patients and often a chronic infection is established. How Achromobacter sp. adapts to the human host remains uncharacterised. By comparing longitudinally collected isolates of Achromobacter sp. isolated from five CF patients, we have investigated the within-host evolution of clonal lineages. The majority of identified mutations were isolate-specific suggesting co-evolution of several subpopulations from the original infecting isolate. The largest proportion of mutated genes were involved in the general metabolism of the bacterium, but genes involved in virulence and antimicrobial resistance were also affected. A number of virulence genes required for initiation of acute infection were selected against, e.g. genes of the type I and type III secretion systems and genes related to pilus and flagellum formation or function. Six antimicrobial resistance genes or their regulatory genes were mutated, including large deletions affecting the repressor genes of an RND-family efflux pump and a beta-lactamase. Convergent evolution was observed for five genes that were all implicated in bacterial virulence. Characterisation of genes involved in adaptation of Achromobacter to the human host is required for understanding the pathogen-host interaction and facilitate design of future therapeutic interventions

Number of detected mutations.

<p>¹b, Mutations only found in isolate b compared to isolate a; c, mutations only found in isolate c compared to isolate a; b+c, mutations found in both isolates b and c compared to isolate a.</p><p>²number of mutations in non-coding sequences.</p><p>Number of detected mutations.</p

Overview of patients and isolates.

<p>Overview of patients and isolates.</p

General features of draft genomes of incipient isolates.

<p>*Number of coding sequences as determined by RAST.</p><p>General features of draft genomes of incipient isolates.</p