Genetic variation in Mycobacterium tuberculosis isolates from a London outbreak associated with isoniazid resistance.

BACKGROUND: The largest outbreak of isoniazid-resistant (INH-R) Mycobacterium tuberculosis in Western Europe is centred in North London, with over 400 cases diagnosed since 1995. In the current study, we evaluated the genetic variation in a subset of clinical samples from the outbreak with the hypothesis that these isolates have unique biological characteristics that have served to prolong the outbreak. METHODS: Fitness assays, mutation rate estimation, and whole-genome sequencing were performed to test for selective advantage and compensatory mutations. RESULTS: This detailed analysis of the genetic variation of these INH-R samples suggests that this outbreak consists of successful, closely related, circulating strains with heterogeneous resistance profiles and little or no associated fitness cost or impact on their mutation rate. CONCLUSIONS: Specific deletions and SNPs could be a peculiar feature of these INH-R M. tuberculosis isolates, and could potentially explain their persistence over the years

Does Comorbidity Index Predict OPAT Readmission?

Objectives – To determine if the Charlson Comorbidity Index (CCI) is an accurate predictor of unplanned readmissions for patients using Outpatient Parenteral Antimicrobial Therapy (OPAT) services. Methods – Retrospective analysis of patients > 16 years of age who had received OPAT at Lancashire Teaching Hospitals between 2019 and 2021. The number of unplanned hospitalisations was measured and categorised as OPAT related or non-OPAT related. The CCI for each patient group was calculated using an online tool and multivariate analysis was used for each group of readmitted patients. Results – The cohort consisted of 741 patients. Unplanned readmission was seen in 112 patients (15.1%). The mean CCI score for patients with OPAT related readmissions was 4.22, 0.92 higher than the mean for patients who were not readmitted (3.30). The mean CCI score for patients with non-OPAT related readmissions was higher still, 4.89. Multivariate analysis showed that increased CCI, age, male gender and home location compared with clinic were associated with increased odds of readmission, although these effects did not meet statistical significance. Conclusions – These results suggest that a higher CCI score is associated with a non-statistically significant increased risk of unplanned hospitalisation. We concluded that the CCI may therefore be used in future decision making regarding the acceptance of patients to OPAT and requires further investigation

Systems medicine and infection

By using a systems based approach, mathematical and computational techniques can be used to develop models that describe the important mechanisms involved in infectious diseases. An iterative approach to model development allows new discoveries to continually improve the model, and ultimately increase the accuracy of predictions. SIR models are used to describe epi demics, predicting the extent and spread of disease. Genome-wide genotyping and sequencing technologies can be used to identify the biological mechanisms behind diseases. These tools help to build strategies for disease prevention and treatment, an example being the recent outbreak of Ebola in West Africa where these techniques were deployed. HIV is a complex disease where much is still to be learnt about the virus and the best effective treatment. With basic mathematical modelling techniques, significant discoveries have been made over the last 20 years. With recent technological advances, the computation al resources now available and interdisciplinary cooperation, further breakthroughs are inevitable. In TB, modelling has traditionally been empirical in nature, with clinical data providing the fuel for this top-down approach. Recently, projects have begun to use data derived from laboratory experiments and clinical trials to create mathematical models that describe the mechanisms responsible for the disease. A systems medicine approach to infection modelling helps identify important biological questions that then direct future experiments , the results of which improve the model in an iterative cycle . This means that data from several model systems can be integrated and synthesised to explore complex biological systems .Postprin

Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples.

The rapid identification of antimicrobial resistance is essential for effective treatment of highly resistant Mycobacterium tuberculosis. Whole-genome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike for conventional molecular tests, this has previously been achievable only from cultures of M. tuberculosis. Here we describe a method utilizing biotinylated RNA baits designed specifically for M. tuberculosis DNA to capture full M. tuberculosis genomes directly from infected sputum samples, allowing whole-genome sequencing without the requirement of culture. This was carried out on 24 smear-positive sputum samples, collected from the United Kingdom and Lithuania where a matched culture sample was available, and 2 samples that had failed to grow in culture. M. tuberculosis sequencing data were obtained directly from all 24 smear-positive culture-positive sputa, of which 20 were of high quality (>20× depth and >90% of the genome covered). Results were compared with those of conventional molecular and culture-based methods, and high levels of concordance between phenotypical resistance and predicted resistance based on genotype were observed. High-quality sequence data were obtained from one smear-positive culture-negative case. This study demonstrated for the first time the successful and accurate sequencing of M. tuberculosis genomes directly from uncultured sputa. Identification of known resistance mutations within a week of sample receipt offers the prospect for personalized rather than empirical treatment of drug-resistant tuberculosis, including the use of antimicrobial-sparing regimens, leading to improved outcomes

International Society of Sports Nutrition Position Stand: Nutritional recommendations for single-stage ultra-marathon; training and racing

Background. In this Position Statement, the International Society of Sports Nutrition (ISSN) provides an objective and critical review of the literature pertinent to nutritional considerations for training and racing in single-stage ultra-marathon. Recommendations for Training. i) Ultra-marathon runners should aim to meet the caloric demands of training by following an individualized and periodized strategy, comprising a varied, food-first approach; ii) Athletes should plan and implement their nutrition strategy with sufficient time to permit adaptations that enhance fat oxidative capacity; iii) The evidence overwhelmingly supports the inclusion of a moderate-to-high carbohydrate diet (i.e., ~60% of energy intake, 5 – 8 g⸱kg−1·d−1) to mitigate the negative effects of chronic, training-induced glycogen depletion; iv) Limiting carbohydrate intake before selected low-intensity sessions, and/or moderating daily carbohydrate intake, may enhance mitochondrial function and fat oxidative capacity. Nevertheless, this approach may compromise performance during high-intensity efforts; v) Protein intakes of ~1.6 g·kg−1·d−1 are necessary to maintain lean mass and support recovery from training, but amounts up to 2.5 g⸱kg−1·d−1 may be warranted during demanding training when calorie requirements are greater; Recommendations for Racing. vi) To attenuate caloric deficits, runners should aim to consume 150 - 400 kcal⸱h−1 (carbohydrate, 30 – 50 g⸱h−1; protein, 5 – 10 g⸱h−1) from a variety of calorie-dense foods. Consideration must be given to food palatability, individual tolerance, and the increased preference for savory foods in longer races; vii) Fluid volumes of 450 – 750 mL⸱h−1 (~150 – 250 mL every 20 min) are recommended during racing. To minimize the likelihood of hyponatraemia, electrolytes (mainly sodium) may be needed in concentrations greater than that provided by most commercial products (i.e., >575 mg·L−1 sodium). Fluid and electrolyte requirements will be elevated when running in hot and/or humid conditions; viii) Evidence supports progressive gut-training and/or low-FODMAP diets (fermentable oligosaccharide, disaccharide, monosaccharide and polyol) to alleviate symptoms of gastrointestinal distress during racing; ix) The evidence in support of ketogenic diets and/or ketone esters to improve ultra-marathon performance is lacking, with further research warranted; x) Evidence supports the strategic use of caffeine to sustain performance in the latter stages of racing, particularly when sleep deprivation may compromise athlete safety

Evaluation of liquid culture for quantitation of Mycobacterium tuberculosis in murine models.

Quantitation of bacterial load in tissues is essential for experimental investigation of Mycobacterium tuberculosis infection and immunity. We have used an automated liquid culture system to determine the number of colony forming units (CFU) in murine tissues and compared the results to those obtained by conventional plating on Middlebrook agar. There is an overall good correlation between results obtained by the two methods. Although less consistency and more contamination was observed in the automated liquid culture, the method is more sensitive, less labour intensive and allows the processing of large numbers of samples

Diagnostics in Ebola virus disease in resource-rich and resource-limited settings

The Ebola virus disease (EVD) outbreak in West Africa was unprecedented in scale and location. Limited access to both diagnostic and supportive pathology assays in both resource-rich and resource-limited settings had a detrimental effect on the identification and isolation of cases as well as individual patient management. Limited access to such assays in resource-rich settings resulted in delays in differentiating EVD from other illnesses in returning travellers, in turn utilising valuable resources until a diagnosis could be made. This had a much greater impact in West Africa, where it contributed to the initial failure to contain the outbreak. This review explores diagnostic assays of use in EVD in both resource-rich and resource-limited settings, including their respective limitations, and some novel assays and approaches that may be of use in future outbreaks