<p>In community mobility, walking is commonly completed with other concurrent tasks, described as locomotor multitasks. Many locomotor multitasks rely on vision for both gait and concurrent tasks. When each of the individual tasks uses the same perceptual modality (e.g. vision), structural interference occurs. Structural interference is different from capacity interference, which refers to tasks competing for limited cognitive resources. While locomotor multitask studies have demonstrated that completing the locomotor multitask typically leads to performance impairment in gait and/or the concurrent task, the wide range of tasks has confounded the ability to fully understand how structural and capacity interference affect multitask performance. Thus, the purpose of this dissertation was to delineate how structural interference (Study 1) and capacity interference (Study 2) affect gait multitask performance. To facilitate comparison across studies, the two studies (Study 1 and Study 2) in this dissertation used the same gait task – obstacle crossing – and the same cognitive task – a visual discrete reaction time (RT) task. A discrete RT task was completed while approaching to an obstacle, where visual information regarding obstacle is being gathered to plan for the successful obstacle crossing. In Study 1, to determine if structural interference affects performance impairment in young and older adults, gaze diversion was manipulated by the RT task location (gaze diverted to the obstacle, and gaze diverted away from the obstacle). The RT task was also completed while standing to strengthen the interpretation that any performance impairments were due to structural interference. Study 1 results indicated that structural interference affects both gait and cognitive task performance. Structural interference demonstrated performance impairments in both young and older adults, but the strategies were different. Young adults were more likely adopt gait behavior that increased the risk of tripping when gaze was diverted away from the obstacle (high structural interference), but older adults demonstrated a strategy that decreased the risk of trip when gaze was diverted to the obstacle (low structural interference). This finding highlights the critical role of vision in adaptive gait. In study 2, to determine if capacity interference affects performance impairment in young adults, both gait and cognitive task were manipulated while structural interference was held constant; gait task was manipulated by obstacle height (level walking, 15% leg length height, and 30% leg length height obstacle), and cognitive tasks were three RT tasks (Simple RT, Choice RT, Simon RT). The baseline for each gait task (without RT task) and cognitive task (while seating) was also measured. Capacity interference demonstrated that task prioritization strategy was different for gait challenge versus cognitive challenge in young adults. As gait task difficulty increased, gait task was prioritized. Conversely, as cognitive task difficulty increased, cognitive task was prioritized. This finding highlights that young adults have the ability to flexibly allocate the resources to accomplish the multitask. Lastly, an interesting finding from two studies (Study 1 and Study 2) was when interference is applied during the planning phase – during the approach to the obstacle – structural interference has a greater effect on obstacle crossing performance than capacity interference.</p>

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During the last decades, newly developed medical devices often came along with unappropriate designs, increasing the likelihood of misuse through the operator. Part of the root cause was that no sufficient measures were applied to assimilate user needs. Consequently, usability engineering approaches are now stronger emphasized to ensure that new devices are not only safe to use but are also designed for users’ needs. Besides, testing processes in clinical microbiology laboratories are currently reshaped due to new generations of rapid testing methods. Hence, it is particularly important to apply usability engineering frameworks during the development phase to make sure devices address users’ needs and also fit into the new work- and communication flows. Based on that, this research project applies a usability engineering approach to the design process of a new rapid antibiotic susceptibility testing system of Astrego Diagnostic AB that is supposed to be used in clinical microbiology laboratories in the near future. The research questions focus on how this device can be designed to enable integration into clinical laboratories. -       How can a rapid AST testing system be integrated into the workflow of clinical microbiology laboratories? -       What are the remaining uncertainties for integrating a rapid AST system into the workflow of a clinical microbiology laboratory on the example of Astrego’s AST system? Several methods were used to address these questions, which include literature research, a competitive audit, subject matter interviews and semi-structured interviews, and observations of targeted users. The findings show that a rapid antibiotic susceptibility testing system may be used in several different ways, which also impacts its design. Process-wise, it could be used after Gram staining and bacterial identification has been conducted and, more realistically, simultaneously bacterial identification to pave the way for additional time savings further. However, uncertainties remain regarding the design of the new testing system. Depending on the number of devices that targeted laboratories need to implement to accommodate their testing volume, it makes sense to design a built-in user interface or an external one that can be accessed through a tablet or desktop. Thus, it is uncertain to what extent manual input of bacteria ID is relevant as the dRAST system fully enables manual input of Gram type and bacteria IDs while it might also be possible to avoid manual interaction by receiving this information through software interfaces.

No / Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting. / European Research Council grant (INTERRUPTB; no. 311725), European Research Council grant (TB-ACCELERATE; no. 638553), Foundation for Innovative New Diagnostics, German Center for Infection Research (DZIF), Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018), FWO Odysseus G0F8316N, US National Institutes of Health BD2K K01 (MRF ES026835), Agence Nationale de la Recherche (ANR-16-CD35-0009)

Enteric fever remains the most common febrile illness in urban Nepal. Some individuals may have recurrent infection and some may even progress to become long term chronic carriers. The aim of this thesis was to investigate the rate and factors leading to relapse with typhoid fever in patients who were enrolled in clinical treatment trials for acute enteric fever. The results show that relapses in enteric fever is a common complication and is more likely to be associated with the treatment antimicrobial, cefixime. Gallbladder carriage of invasive Salmonella is considered fundamental in sustaining enteric fever transmission as humans are the only known natural host. This thesis, therefore, also aimed to investigate the prevalence, characteristics, immunological responses, and mechanism of carriage of invasive Salmonella in the gallbladder by examining bile and tissue obtained from individuals who underwent cholecystectomy in Kathmandu. Data presented here demonstrate that S. Paratyphi A is almost as prevalent as S. Typhi in the gallbladder and that carriage may not be driven by antimicrobial resistance. Gallbladders that contained Salmonella were more likely to show evidence of acute inflammation with extensive neutrophil infiltrate. Chronic carriers were found to have dramatically elevated levels of IgG to O:2 and Vi antigens with high bactericidal activity yet low pro-inflammatory cytokine levels suggesting that Salmonella are stimulating a constant immunological response, in the form of antibody. S. Typhi may be controlling the inflammatory process through the expression of the Vi capsule in the gallbladder. Genome sequencing of S. Typhi isolated from chronic carriers were different from those S. Typhi causing acute disease. These data question the current dogmas surrounding the carriage of S. Typhi in gallbladder and predict a pivotal role of Vi capsule and gallstones in maintaining carriage. Therefore, prospectively identifying these individuals is paramount for rapid local and regional elimination. Furthermore, combining cytokine profiles and antibody levels may be a method of prospectively detecting carriers in the general population.

Clostridium difficile is a leading healthcare-associated infection, which causes diarrhoea, and is almost exclusively precipitated by antibiotic exposure. Traditionally C. difficile infection (CDI) has been considered predominantly transmitted within hospitals. However, endemic spread hampers identification of the source of infections, and therefore control and prevention of disease. A cohort of consecutive hospital and community CDI cases in Oxfordshire from September 2007 to March 2011 was investigated. For each case hospital admission, ward movement and demographic data were available allowing contact events between cases to be reconstructed. Initially 944 cases to March 2010 underwent multilocus sequence typing (MLST), subdividing the endemic cases into 69 distinct lineages and demonstrating unexpectedly that ward-based contact with known symptomatic CDI cases only accounts for <25% of disease. To better determine the extent of transmission arising from symptomatic patients, irrespective of the route transmission, isolates from 1223 cases to March 2011 underwent whole genome sequencing. Serially sampled patients with recurrent or on-going disease were used to estimate rates of C. difficile evolution and within-host diversity and to show 0-2 single nucleotide variants (SNVs) are expected between transmitted isolates obtained <124 days apart (95% prediction interval). Mixed infection with more than one strain was investigated, but probably plays only a minor role in onward transmission. In the Oxfordshire CDI cohort, 333/957 (35%) CDI from April 2008 – March 2011 were within 2 SNVs of ≥1 previous case since September 2007 (consistent with transmission). 428/957 (45%) were >10SNVs from all previous cases: these distinct subtypes continued to be identified consistently throughout the study, suggesting cases arise from a considerable reservoir of C. difficile. Surprisingly, declines in the incidence of genetically-related CDI were similar to those in genetically distinct CDI suggesting interventions not just targeting symptomatic individuals, e.g. antimicrobial stewardship, have played a significant role in recent CDI declines. Finally, the feasibility of studying asymptomatic inpatients as potential source of the unexplained transmission was investigated. This thesis provides convincing evidence, in a setting with typical CDI incidence and infection control practice, that only the minority of CDI arises from other symptomatic cases. It demonstrates that much CDI arises from genetically diverse reservoirs, with each exposure resulting in relatively few secondary cases. Future control strategies therefore need to focus on identifying these reservoirs, one of which is plausibly asymptomatic inpatients, and also on interventions that prevent the transition from exposure and colonisation to disease, such as antimicrobial stewardship.

Metagenomic sequencing is an increasingly popular way of determining microbial diversity from environmental and clinical samples. By specifically targeting the 16S rRNA gene found in all bacteria, classifications of pathogens can be determined based on the variable and conserved regions found in the gene. Metagenomic sequencing can therefore highlight the vast difference in microbiological diversity between culture-dependent and culture-independent methods. Today, this has expanded into various next-generation sequencing platforms which can provide massively parallel sequencing of the target fragment. One of these platforms is Ion-torrent, which can be utilized for targeting the 16S rRNA gene and with the help of bioinformatics pipelines be able to classify pathogens using the bacteria’s own variable and conserved regions. The overall aim of the present work is to evaluate the clinical use of Ion-torrent 16S ribosomal RNA sequencing for determining pathogenic species from clinical samples, but also to set up a pipeline for clinical practice. Optimal DNA-extraction and quantification methods were determined towards each evaluated sample-type and DNA-eluates were sent for 16S rRNA Sanger and Next-generation sequencing. The result indicated that the next-generation sequencing shows a concordance in results towards the culturing-based method, but also the importance of experimental design and effective quality trimming of the NGS data. The conclusion of the project is that the Ion-torrent pipeline provided by the Public Health Agency of Sweden shows great promise in determining pathogens from clinical samples. However, there is still a lot of validation and standardisations needed for the successful implementation into a clinical setting.

302 samples were evaluated in the present study including 50 standard quality control samples, 62 repeatability samples and two separate batches of 90 and 100 samples of clinical isolates. Standard samples with registered ATCC or CCUG codes taken from international reference lab, used for performance test (quality control) of Vitek2 compact analyzer. The results of performance test showed total 98% accuracy. Detailed performance test results showed 100% accuracy for Gram positive &amp; Gram negative bacteria and 95% accuracy for NH group members.Comparison between results of different culture media showed that use of conventional culture media instead of commercial branded culture media for preparing bacterial suspensions, doesn’t affect the result’s accuracy level in Vitek2 analyzer.Repeatability and reproducibility study of 62 samples including standard &amp; clinical isolates results, showed 96.8% coalition in reproduced results by Vitek2 analyzer.The comparative results of 90 clinical samples via API 20E / API 20NE Microsystems and Vitek2 compact analyzer showed 77.8% “Complete coalition” or coalition in the &quot;genus&quot; and &quot;species&quot; levels of isolated micro organisms, 10.0% “partial coalition” which means coalition in the &quot;genus&quot; level but difference in &quot;species” of isolates, 6.7% “no coalition” or different results in the &quot;genus&quot; and &quot;species&quot; levels of isolated micro organisms and 5.5% “unidentified” micro organisms by one of the applied methods. Comparative results also showed that total acceptable results rose from 80% in API system to 90% in vitek2 analyzer for clinical samples in this study.Survey on a random selection of 100 samples of Vitek2 reports showed an average analyze time of 5.5 hrs (330 Min.), where the minimum and maximum observed time were 2.75 hrs and 10.25 hrs respectively. Findings in this survey also showed 94% excellent, very good and acceptable identification of bacterial strain, 4% low discrimination, 2% non reactive bio-pattern and unidentified organism. The abundance of different bacteria in the random collection was composed of 71% gram negative, 24% gram positive and 5% NH group members. Escherichia coli (23.2% of total) were the popular bacteria in this collection.

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