Developing a tool to assess the health-related quality of life in calves with respiratory disease: tool refinement and construct validity testing

Bovine respiratory disease (BRD) is a major source of morbidity and mortality in calves and detection of the disease can be challenging. Diagnostic tools for BRD are typically based on the assessment of clinical signs. As experience of disease is associated with a poor quality of life and this poor emotional experience can be expressed in observable behaviour patterns, a quality-of-life approach might identify new indicators of disease. Health-related quality of life (HRQOL) approaches are widely used in human medicine but are rarely used in livestock. This study aimed to refine and validate an HRQOL tool for calves with BRD that had been created in a previous study. The tool contained 13 items/indicators across two domains (clinical signs and behavioural expression). One hundred preweaned dairy-bred calves were scored daily using the HRQOL tool and also using the industry-recognised Wisconsin health score as a 'gold standard'. The score assigned to each of the 13 items of the HRQOL tool was summed to give an accumulated HRQOL score for each calf/day. To refine the tool, the items within the tool were compared to each other to identify high levels of correlation or redundancy. This resulted in the retention of three items within the clinical signs domain (body and head posture, respiratory effort and ear carriage) and four within the behavioural expression domain (vigour, movement to feed, motivation at feed and volume of feed consumed). To determine whether the refined HRQOL tool could successfully differentiate sick from healthy animals, the Wisconsin score was used to create two matched groups of 28 'sick' and 28 'healthy' calves. There was a significant difference in the HRQOL scores between the two groups (H = 14.09, df = 1, P = 0.000) suggesting that the new tool could differentiate between 'healthy' and 'sick' calves. In terms of the two domains, there was a significant difference (P < 0.001) between the 'healthy' and 'sick' calves for the overall HRQOL tool score for the clinical signs domain, but there was no significant difference (P = 0.154) between 'healthy' and 'sick' calves in the overall HRQOL score for the behavioural expression domain; however, the combined tool was the most accurate. Overall, this study has demonstrated that the new HRQOL tool can differentiate between sick and healthy calves. Some or all of the indicators could be used alongside existing disease-detection tools for preweaned calves. However, future work would be needed to validate this HRQOL tool in other production systems.

Physiotherapists clinical reasoning to prescribe exercise for patients with chronic pain: A qualitative study research protocol

BACKGROUND

Physiotherapists' play a key role in the management of chronic pain, and as part of the National Institute for Health and Care Excellence (NICE) guidelines, prescribe exercise to support patients with chronic pain. However, there is very limited evidence supporting physiotherapists on what type of exercise or dose of exercise should be prescribed. Physiotherapists' therefore have more onus on their ability to clinically reason how to prescribe exercise. At present, there is no research investigating how physiotherapists' working with patients that have chronic pain, clinically reason when prescribing exercise. This study proposes to investigate how physiotherapists experienced in pain management prescribe exercise, to understand what the key influences are on their reasoning, and how these impact on clinical practice.

METHODS

This will be a qualitative study, utilising semi-structured individual interviews. Participants will be Health and Care Professions Council registered physiotherapists, working predominantly with patients that have chronic pain. Recruitment will focus on physiotherapists working within the United Kingdom (UK). Up to twenty participants will be recruited. The study, including the interview guide, will be supported by a steering group consisting of academics and physiotherapists experienced in chronic pain. The data will be analysed using framework analysis.

RESULTS

The study will be reported using the COnsolidated criteria for REporting Qualitative research (COREQ) guidelines. The findings of the study will be disseminated through publication in a peer reviewed journal.

CONCLUSION

This study will provide novel insight into how physiotherapists experienced working with and managing chronic pain patients, prescribe exercise, and will gain new insight into clinical practice to help inform future research and education.

Intrinsic calf factors associated with the behavior of healthy pre-weaned group-housed dairy-bred calves

Technology-derived behaviors are researched for disease detection in artificially-reared calves. Whilst existing studies demonstrate differences in behaviors between healthy and diseased calves, intrinsic calf factors (e.g., sex and birthweight) that may affect these behaviors have received little systematic study. This study aimed to understand the impact of a range of calf factors on milk feeding and activity variables of dairy-bred calves. Calves were group-housed from ~7 days to 39 days of age. Seven liters of milk replacer was available daily from an automatic milk feeder, which recorded feeding behaviors and live-weight. Calves were health scored daily and a tri-axial accelerometer used to record activity variables. Healthy calves were selected by excluding data collected 3 days either side of a poor health score or a treatment event. Thirty-one calves with 10 days each were analyzed. Mixed models were used to identify which of live-weight, age, sex, season of birth, age of inclusion into the group, dam parity, birthweight, and sire breed type (beef or dairy), had a significant influence on milk feeding and activity variables. Heavier calves visited the milk machine more frequently for shorter visits, drank faster and were more likely to drink their daily milk allowance than lighter calves. Older calves had a shorter mean standing bout length and were less active than younger calves. Calves born in summer had a longer daily lying time, performed more lying and standing bouts/day and had shorter mean standing bouts than those born in autumn or winter. Male calves had a longer mean lying bout length, drank more slowly and were less likely to consume their daily milk allowance than their female counterparts. Calves that were born heavier had fewer lying and standing bouts each day, a longer mean standing bout length and drank less milk per visit. Beef-sired calves had a longer mean lying bout length and drank more slowly than their dairy sired counterparts. Intrinsic calf factors influence different healthy calf behaviors in different ways. These factors must be considered in the design of research studies and the field application of behavior-based disease detection tools in artificially reared calves.

Modular Metabolic Engineering and Synthetic Coculture Strategies for the Production of Aromatic Compounds in Yeast

Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. In this study, we used the model yeast Saccharomyces cerevisiae to produce aromatic molecules by exploiting the concept of modularity in synthetic biology. Three different modular approaches were investigated for the production of the valuable fragrance raspberry ketone (RK), found in raspberry fruits and mostly produced from petrochemicals. The first strategy used was modular cloning, which enabled the generation of combinatorial libraries of promoters to optimize the expression level of the genes involved in the synthesis pathway of RK. The second strategy was modular pathway engineering and involved the creation of four modules, one for product formation: RK synthesis module (Mod. RK); and three for precursor synthesis: aromatic amino acid synthesis module (Mod. Aro), p-coumaric acid synthesis module (Mod. p-CA), and malonyl-CoA synthesis module (Mod. M-CoA). The production of RK by combinations of the expression of these modules was studied, and the best engineered strain produced 63.5 mg/L RK from glucose, which is the highest production described in yeast, and 2.1 mg RK/g glucose, which is the highest yield reported in any organism without p-coumaric acid supplementation. The third strategy was the use of modular cocultures to explore the effects of division of labor on RK production. Two two-member communities and one three-member community were created, and their production capacity was highly dependent on the structure of the synthetic community, the inoculation ratio, and the culture media. In certain conditions, the cocultures outperformed their monoculture controls for RK production, although this was not the norm. Interestingly, the cocultures showed up to 7.5-fold increase and 308.4 mg/L of 4-hydroxy benzalacetone, the direct precursor of RK, which can be used for the semi-synthesis of RK. This study illustrates the utility of modularity in synthetic biology tools and their applications to the synthesis of products of industrial interest.

Variability in white blood cell count during uncomplicated malaria and implications for parasite density estimation: a WorldWide Antimalarial Resistance Network individual patient data meta-analysis

BACKGROUND

The World Health Organization (WHO) recommends that when peripheral malarial parasitaemia is quantified by thick film microscopy, an actual white blood cell (WBC) count from a concurrently collected blood sample is used in calculations. However, in resource-limited settings an assumed WBC count is often used instead. The aim of this study was to describe the variability in WBC count during acute uncomplicated malaria, and estimate the impact of using an assumed value of WBC on estimates of parasite density and clearance.

METHODS

Uncomplicated malaria drug efficacy studies that measured WBC count were selected from the WorldWide Antimalarial Resistance Network data repository for an individual patient data meta-analysis of WBC counts. Regression models with random intercepts for study-site were used to assess WBC count variability at presentation and during follow-up. Inflation factors for parasitaemia density, and clearance estimates were calculated for methods using assumed WBC counts (8000 cells/µL and age-stratified values) using estimates derived from the measured WBC value as reference.

RESULTS

Eighty-four studies enrolling 27,656 patients with clinically uncomplicated malaria were included. Geometric mean WBC counts (× 1000 cells/µL) in age groups < 1, 1-4, 5-14 and ≥ 15 years were 10.5, 8.3, 7.1, 5.7 and 7.5, 7.0, 6.5, 6.0 for individuals with falciparum (n = 24,978) and vivax (n = 2678) malaria, respectively. At presentation, higher WBC counts were seen among patients with higher parasitaemia, severe anaemia and, for individuals with vivax malaria, in regions with shorter regional relapse periodicity. Among falciparum malaria patients, using an assumed WBC count of 8000 cells/µL resulted in parasite density underestimation by a median (IQR) of 26% (4-41%) in infants < 1 year old but an overestimation by 50% (16-91%) in adults aged ≥ 15 years. Use of age-stratified assumed WBC values removed systematic bias but did not improve precision of parasitaemia estimation. Imprecision of parasite clearance estimates was only affected by the within-patient WBC variability over time, and remained < 10% for 79% of patients.

CONCLUSIONS

Using an assumed WBC value for parasite density estimation from a thick smear may lead to underdiagnosis of hyperparasitaemia and could adversely affect clinical management; but does not result in clinically consequential inaccuracies in the estimation of the prevalence of prolonged parasite clearance and artemisinin resistance.

Global estimates and determinants of antituberculosis drug pharmacokinetics in children and adolescents: a systematic review and individual patient data meta-analysis

BACKGROUND

Suboptimal exposure to antituberculosis (anti-TB) drugs has been associated with unfavourable treatment outcomes. We aimed to investigate estimates and determinants of first-line anti-TB drug pharmacokinetics in children and adolescents at a global level.

METHODS

We systematically searched MEDLINE, Embase and Web of Science (1990-2021) for pharmacokinetic studies of first-line anti-TB drugs in children and adolescents. Individual patient data were obtained from authors of eligible studies. Summary estimates of total/extrapolated area under the plasma concentration-time curve from 0 to 24 h post-dose (AUC0-24) and peak plasma concentration (C max) were assessed with random-effects models, normalised with current World Health Organization-recommended paediatric doses. Determinants of AUC0-24 and C max were assessed with linear mixed-effects models.

RESULTS

Of 55 eligible studies, individual patient data were available for 39 (71%), including 1628 participants from 12 countries. Geometric means of steady-state AUC0-24 were summarised for isoniazid (18.7 (95% CI 15.5-22.6) h·mg·L-1), rifampicin (34.4 (95% CI 29.4-40.3) h·mg·L-1), pyrazinamide (375.0 (95% CI 339.9-413.7) h·mg·L-1) and ethambutol (8.0 (95% CI 6.4-10.0) h·mg·L-1). Our multivariate models indicated that younger age (especially <2 years) and HIV-positive status were associated with lower AUC0-24 for all first-line anti-TB drugs, while severe malnutrition was associated with lower AUC0-24 for isoniazid and pyrazinamide. N-acetyltransferase 2 rapid acetylators had lower isoniazid AUC0-24 and slow acetylators had higher isoniazid AUC0-24 than intermediate acetylators. Determinants of C max were generally similar to those for AUC0-24.

CONCLUSIONS

This study provides the most comprehensive estimates of plasma exposures to first-line anti-TB drugs in children and adolescents. Key determinants of drug exposures were identified. These may be relevant for population-specific dose adjustment or individualised therapeutic drug monitoring.

Developing a tool to assess the health-related quality of life in calves with respiratory disease: content validation

Bovine respiratory disease (BRD) is a major welfare and productivity issue for calves. Despite the extensive negative impacts on calf welfare and performance, BRD remains challenging to detect and treat effectively. However, the clinical signs of disease are only one aspect of the disease that is experienced by the individual. The assessment of emotional experience in animals is not straightforward, but it is increasingly recognised that the quality of behaviour and demeanour of an individual is a reflection of their internal emotional state. The aim of the present study was to complete the content validation stage of the development process for a health-related quality of life (HRQOL) tool. This was based around indicators from an existing conceptual framework containing twenty-three indicators in two domains (clinical signs and behavioural expression). The content validation stage involves engaging with key stakeholders. For this study, this took the form of a survey and discussions with focus groups, which are standard methods in this field. A survey and stakeholder focus groups were conducted to assess the usefulness of each indicator and its relevance for inclusion within a HRQOL tool. In the survey, participants were asked to rate the usefulness of each of the indicators using a 4-point scale which were then dichotomised into 'useful' and 'less useful'. Based on the 'useful' result, each indicator within the domains was ranked. A similar approach was taken with the responses from the focus groups. Focus group participants were asked to select indicators that they felt were of use and the result of this was used to rank each of the indicators. The ranks of the indicators from both the survey and the focus groups along with the transcripts from the focus groups were used to determine the indicators from each domain to include within the HRQOL tool. Indicators within the clinical signs domain that were included were nasal discharge, cough, respiratory effort, ocular appearance (discharge and vibrancy), body and head posture and ear carriage. For the domain of behavioural expression, the indicators included were movement to feed, responsiveness, spatial proximity, volume of feed intake, motivation at feed and vigour. The next stage will be to validate the construction of the HRQOL tool through its use in practice. The inclusion of indicators that allow the experiential aspects of disease to be recorded in health assessments will likely increase the ability of farmers and others to detect respiratory disease in calves.

Haematological consequences of acute uncomplicated falciparum malaria: a WorldWide Antimalarial Resistance Network pooled analysis of individual patient data

BACKGROUND

Plasmodium falciparum malaria is associated with anaemia-related morbidity, attributable to host, parasite and drug factors. We quantified the haematological response following treatment of uncomplicated P. falciparum malaria to identify the factors associated with malarial anaemia.

METHODS

Individual patient data from eligible antimalarial efficacy studies of uncomplicated P. falciparum malaria, available through the WorldWide Antimalarial Resistance Network data repository prior to August 2015, were pooled using standardised methodology. The haematological response over time was quantified using a multivariable linear mixed effects model with nonlinear terms for time, and the model was then used to estimate the mean haemoglobin at day of nadir and day 7. Multivariable logistic regression quantified risk factors for moderately severe anaemia (haemoglobin < 7 g/dL) at day 0, day 3 and day 7 as well as a fractional fall ≥ 25% at day 3 and day 7.

RESULTS

A total of 70,226 patients, recruited into 200 studies between 1991 and 2013, were included in the analysis: 50,859 (72.4%) enrolled in Africa, 18,451 (26.3%) in Asia and 916 (1.3%) in South America. The median haemoglobin concentration at presentation was 9.9 g/dL (range 5.0-19.7 g/dL) in Africa, 11.6 g/dL (range 5.0-20.0 g/dL) in Asia and 12.3 g/dL (range 6.9-17.9 g/dL) in South America. Moderately severe anaemia (Hb < 7g/dl) was present in 8.4% (4284/50,859) of patients from Africa, 3.3% (606/18,451) from Asia and 0.1% (1/916) from South America. The nadir haemoglobin occurred on day 2 post treatment with a mean fall from baseline of 0.57 g/dL in Africa and 1.13 g/dL in Asia. Independent risk factors for moderately severe anaemia on day 7, in both Africa and Asia, included moderately severe anaemia at baseline (adjusted odds ratio (AOR) = 16.10 and AOR = 23.00, respectively), young age (age < 1 compared to ≥ 12 years AOR = 12.81 and AOR = 6.79, respectively), high parasitaemia (AOR = 1.78 and AOR = 1.58, respectively) and delayed parasite clearance (AOR = 2.44 and AOR = 2.59, respectively). In Asia, patients treated with an artemisinin-based regimen were at significantly greater risk of moderately severe anaemia on day 7 compared to those treated with a non-artemisinin-based regimen (AOR = 2.06 [95%CI 1.39-3.05], p < 0.001).

CONCLUSIONS

In patients with uncomplicated P. falciparum malaria, the nadir haemoglobin occurs 2 days after starting treatment. Although artemisinin-based treatments increase the rate of parasite clearance, in Asia they are associated with a greater risk of anaemia during recovery.

Reconstituting the complete biosynthesis of D-lysergic acid in yeast

The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments, such as Parkinsonism and dementia. Their synthesis via chemical and biological routes are therefore of industrial relevance, but suffer from several challenges. Current chemical synthesis methods involve long, multi-step reactions with harsh conditions and are not enantioselective; biological methods utilizing ergot fungi, produce an assortment of products that complicate product recovery, and are susceptible to strain degradation. Reconstituting the ergot alkaloid pathway in a strain strongly amenable for liquid fermentation, could potentially resolve these issues. In this work, we report the production of the main ergoline therapeutic precursor, D-lysergic acid, to a titre of 1.7 mg L⁻¹ in a 1 L bioreactor. Our work demonstrates the proof-of-concept for the biological production of ergoline-derived compounds from sugar in an engineered yeast chassis.

The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments. Here the authors report on the production of the ergot (fungus)-derived therapeutic precursor, D-lysergic acid (DLA), in baker’s yeast.

Early prediction of respiratory disease in preweaning dairy calves using feeding and activity behaviors

Bovine respiratory disease (BRD) represents one of the major disease challenges affecting preweaning dairy-bred calves. Previous studies have shown that differences in feeding and activity behaviors exist between healthy and diseased calves affected by BRD. The aim of this study was to develop and assess the accuracy of models designed to predict BRD from feeding and activity behaviors. Feeding and activity behaviors were recorded for 100 male preweaning calves between ~8 to 42 d of age. Calves were group housed with ad libitum access to milk via automatic milk feeders, water, starter diet, and straw. Activity was monitored via a leg-mounted accelerometer. Health status of individual calves was monitored daily using an adapted version of the Wisconsin Scoring System to identify BRD. Three models were created to predict disease: (1) deviation from normal lying time based on moving averages (MA); (2) random forest (RF), a machine learning technique based on feeding and activity variables; and (3) a combination of RF and MA output. For the MA model, lying time was predicted based on behavior over previous days (3- and 7-d MA) and the expected value for the current day (based on calf age; measured using accelerometers). Data were not split into training and test data sets. Occasions when the actual lying time increased >9% of predicted lying time were classified as a deviation from normal and a disease alert was provided. Both feeding and activity behaviors were included within the RF model. Data were split into training (70%) and test (30%) data sets based on disease events. Events were classified as 2 d before, the day(s) of the disease event, and 2 d after the event. Accuracy of models was assessed using sensitivity, specificity, balanced accuracy, and Matthews correlation coefficient (MCC). If a positive disease prediction agreed with an actual disease event within a 3-d rolling window, it was classified as a true positive. Stand-alone models (RF; MA) showed high specificity (0.95; 0.97), moderate sensitivity (0.35; 0.43), balanced accuracy (0.65; 0.64), and MCC (0.25; 0.29). Combining outputs increased accuracy (specificity = 0.95, sensitivity = 0.54, balanced accuracy = 0.75, MCC = 0.36). The work presented is the first to demonstrate the use of modeling data derived from precision livestock farming techniques that monitor feeding and activity behaviors for early detection of BRD in preweaning calves, offering a significant advance in health management of youngstock.

Feeding behaviour and activity as early indicators of disease in pre-weaned dairy calves

Across the industry, there is large variation in health status of dairy calves and as a result, disease incidence and antibiotic use is high. This has significant implications for animal welfare, productivity and profitability of dairy and dairy-beef production systems. Technology-based early detection systems could alleviate these issues; however, methods of early detection of disease in dairy calves have not been widely explored. This study aimed to determine whether changes in activity and feeding behaviour can be used as early warning indicators of respiratory disease in calves. In total, 100 pre-weaned male Holstein calves (age: ~8-42 days) were used. Calves were group-housed and provided with starter diet, straw bedding and ad libitum water. Calves were fed milk replacer ad libitum through an automatic calf feeder, and each calf was fitted with a leg-mounted activity monitor. Daily activity and feeding behaviour variables were calculated for each calf. Each calf was assessed daily using a modified version of the Wisconsin Scoring System to assess respiratory disease status. Calves were classed as 'Diseased', 'Intermediate' or 'Healthy' based on their cumulative health score. The peak day of the most extreme illness event was identified for each calf. Data from Diseased and Healthy calves were paired for analysis based on age and BW. Data were compared for the day of peak illness, and for the 3 days previous and post. Compared to healthy calves, diseased calves lay for longer and tended to have longer lying bouts (daily lying: 17.6 ± 0.3 vs 16.7 ± 0.2 h, P < 0.01; bout length: 74.8 ± 10.6 vs 56.0 ± 3.7 min, P = 0.09 for diseased and healthy calves, respectively). Diseased calves fed for a shorter time and had fewer feeder visits (with intake) each day compared to healthy calves (feeding time (min): 19.3 ± 1.4 vs 22.8 ± 1.5; P < 0.05; visits: 2.1 ± 0.2 vs 3.2 ± 0.4; P < 0.05). Importantly, differences between diseased and healthy calves were evident in both activity and feeding behaviour on the days prior to the peak day of disease. Lying bout length was greater in diseased calves for the 2 days prior to the peak day (P < 0.05), lying time was longer on day -1 (P < 0.05) and feeder visits with milk intake were less frequent on day -3 (P < 0.05). Thus, measurement of feeding and activity using precision technology within early detection systems could facilitate early intervention and optimized treatment.

The first case of HIV-2 in Scotland

HIV-1 infects an estimated 37 million people worldwide, while the rarer HIV-2 infects 1–2 million worldwide. HIV-2 is mainly restricted to West African countries. The majority of patients in Scotland are diagnosed with HIV-1, but in 2013 the West of Scotland Specialist Virology Centre (WoSSVC) diagnosed Scotland’s first HIV-2 positive case in a patient from Côte d’Ivoire. HIV-2 differs from HIV-1 in terms of structural viral proteins, viral transmissibility, prolonged period of latency, intrinsic resistance to certain antivirals and how to monitor the effectiveness of treatment. Over the course of 5 years the patient has required several changes in treatment due to both side effects and pill burden. This case highlights the complexity of HIV-2 patient management over time.

Comparison of thermal imaging and rectal temperature in the diagnosis of pyrexia in pre-weaned calves using on farm conditions

Measuring core body temperature is used as part of the diagnostic process in assessing the health of animals. Typically in calves, this is carried out using a rectal thermometer which can be time consuming, stressful to the calf and is invasive by nature. A non-invasive technique that is gaining recognition is thermal imaging. This study investigated the use of thermal imaging as a technique to assess core body temperature in pre-weaned artificially reared calves. A total of 125 male and female calves had rectal temperatures measured daily from day 7 until day 40 of life, and at the same time had a thermal image taken of the area around the medial canthus of the eye. A weak correlation (r = 0.28) was found between calf rectal temperature and thermal image temperature. A multivariable predictive model for core body temperature increased the correlation (r = 0.32) when including the environmental parameters of air temperature (p < .001) and wind speed (p < .001) as well as reconstituted milk replacer consumption (p < .01). The effectiveness of a predictive model including these parameters for the detection of calves with a core body temperature ≥ 39.5 °C was examined and found to have a sensitivity of 0% and a specificity of 100%. The results of this study demonstrate the need to take thermal environmental parameters into consideration when using thermal imaging to assess body temperature. However, the results suggest that accurate measures of core body temperature using thermal imaging cannot be achieved under commercial farm conditions. Further research is needed to determine what other factors could be measured to increase predictive ability.

Yellow fever vaccine-associated neurological disease: it is not just the silver generation at risk

A 35-year-old man presented to his optician with sudden onset diplopia and a 1-week history of headaches. He was noted to have sixth nerve palsy. The following day he was admitted to hospital with confusion and expressive dysphasia. He had been due to travel to Ghana on business and had received yellow fever (YF) vaccination 18 days prior to onset of headaches. His initial cerebrospinal fluid (CSF) revealed elevated protein, increased white cell count but was PCR negative for standard viral pathogens. Herpes simplex virus (HSV)-1 was detected by PCR in CSF at a very low level from a second lumbar puncture performed 6 days later, and the patient was treated for HSV meningoencephalitis. However, retrospective investigation for yellow fever vaccine-associated neurological disease revealed increasing titres of YF IgG in three serial CSF samples, and no evidence of HSV antibodies in CSF or plasma, ruling out HSV encephalitis.

Building a global alliance of biofoundries

Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.

Paradoxical upgrading reaction in extra-pulmonary tuberculosis: association with vitamin D therapy

SETTING:

Glasgow, Scotland, UK.

BACKGROUND:

Paradoxical reactions in tuberculosis (TB) are a notable example of our incomplete understanding of host-pathogen interactions during anti-tuberculosis treatment.

OBJECTIVES:

To determine risk factors for a TB paradoxical reaction, and specifically to assess for an independent association with vitamin D use.

DESIGN:

Consecutive human immunodeficiency virus (HIV) negative adult patients treated for extra-pulmonary TB were identified from an Extended Surveillance of Mycobacterial Infections database. In our setting, vitamin D was variably prescribed for newly diagnosed TB patients. A previously published definition of paradoxical TB reaction was retrospectively applied to, and data on all previously described risk factors were extracted from, centralised electronic patient records. The association with vitamin D use was assessed using multivariate logistic regression.

RESULTS:

Of the 249 patients included, most had TB adenopathy; 222/249 had microbiologically and/or histologically confirmed TB. Vitamin D was prescribed for 57/249 (23%) patients; 37/249 (15%) were classified as having paradoxical reactions. Younger age, acid-fast bacilli-positive invasive samples, multiple disease sites, lower lymphocyte count and vitamin D use were found to be independent risk factors.

CONCLUSION:

We speculate that vitamin D-mediated signalling of pro-inflammatory innate immune cells, along with high antigenic load, may mediate paradoxical reactions in anti-tuberculosis treatment.

A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in P. aeruginosa-Infected Respiratory Samples

Synthetic biology designed cell-free biosensors are a promising new tool for the detection of clinically relevant biomarkers in infectious diseases. Here, we report that a modular DNA-encoded biosensor in cell-free protein expression systems can be used to measure a bacterial biomarker of Pseudomonas aeruginosa infection from human sputum samples. By optimizing the cell-free system and sample extraction, we demonstrate that the quorum sensing molecule 3-oxo-C12-HSL in sputum samples from cystic fibrosis lungs can be quantitatively measured at nanomolar levels using our cell-free biosensor system, and is comparable to LC-MS measurements of the same samples. This study further illustrates the potential of modular cell-free biosensors as rapid, low-cost detection assays that can inform clinical practice.

Prospective Assessment of Virtual Screening Heuristics Derived Using a Novel Fusion Score

High-throughput screening (HTS) is a widespread method in early drug discovery for identifying promising chemical matter that modulates a target or phenotype of interest. Because HTS campaigns involve screening millions of compounds, it is often desirable to initiate screening with a subset of the full collection. Subsequently, virtual screening methods prioritize likely active compounds in the remaining collection in an iterative process. With this approach, orthogonal virtual screening methods are often applied, necessitating the prioritization of hits from different approaches. Here, we introduce a novel method of fusing these prioritizations and benchmark it prospectively on 17 screening campaigns using virtual screening methods in three descriptor spaces. We found that the fusion approach retrieves 15% to 65% more active chemical series than any single machine-learning method and that appropriately weighting contributions of similarity and machine-learning scoring techniques can increase enrichment by 1% to 19%. We also use fusion scoring to evaluate the tradeoff between screening more chemical matter initially in lieu of replicate samples to prevent false-positives and find that the former option leads to the retrieval of more active chemical series. These results represent guidelines that can increase the rate of identification of promising active compounds in future iterative screens.

EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology

Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.

Late Ebola virus relapse causing meningoencephalitis: a case report

BACKGROUND

There are thousands of survivors of the 2014 Ebola outbreak in west Africa. Ebola virus can persist in survivors for months in immune-privileged sites; however, viral relapse causing life-threatening and potentially transmissible disease has not been described. We report a case of late relapse in a patient who had been treated for severe Ebola virus disease with high viral load (peak cycle threshold value 13.2).

METHODS

A 39-year-old female nurse from Scotland, who had assisted the humanitarian effort in Sierra Leone, had received intensive supportive treatment and experimental antiviral therapies, and had been discharged with undetectable Ebola virus RNA in peripheral blood. The patient was readmitted to hospital 9 months after discharge with symptoms of acute meningitis, and was found to have Ebola virus in cerebrospinal fluid (CSF). She was treated with supportive therapy and experimental antiviral drug GS-5734 (Gilead Sciences, San Francisco, Foster City, CA, USA). We monitored Ebola virus RNA in CSF and plasma, and sequenced the viral genome using an unbiased metagenomic approach.

FINDINGS

On admission, reverse transcriptase PCR identified Ebola virus RNA at a higher level in CSF (cycle threshold value 23.7) than plasma (31.3); infectious virus was only recovered from CSF. The patient developed progressive meningoencephalitis with cranial neuropathies and radiculopathy. Clinical recovery was associated with addition of high-dose corticosteroids during GS-5734 treatment. CSF Ebola virus RNA slowly declined and was undetectable following 14 days of treatment with GS-5734. Sequencing of plasma and CSF viral genome revealed only two non-coding changes compared with the original infecting virus.

INTERPRETATION

Our report shows that previously unanticipated, late, severe relapses of Ebola virus can occur, in this case in the CNS. This finding fundamentally redefines what is known about the natural history of Ebola virus infection. Vigilance should be maintained in the thousands of Ebola survivors for cases of relapsed infection. The potential for these cases to initiate new transmission chains is a serious public health concern.

FUNDING

Royal Free London NHS Foundation Trust.

Effects of single- and mixed-sex caging on postweaning development in the rabbit

Postweaning development was monitored in domesticated rabbits reared in single- or mixed-sex groups at a commercial farm. The results suggest that sex composition of cage groups had no significant effect on weight gain, feed intake or mortality rates from weaning (35 days) to marketing (93 days). On sacrifice at 93 days, females from single- and mixed-sex groups showed no significant differences in plasma gonadotropin levels (LH and FSH) or weights of paunched carcase, ovaries, uterus, adrenals, kidneys or kidney fat. Evidence for within-cage dominance hierarchies was found at 63 days of age when 46% of the rabbits inspected showed signs of aggressive attack.

UK malaria treatment guidelines 2016

1.Malaria is the tropical disease most commonly imported into the UK, with 1300-1800 cases reported each year, and 2-11 deaths. 2. Approximately three quarters of reported malaria cases in the UK are caused by Plasmodium falciparum, which is capable of invading a high proportion of red blood cells and rapidly leading to severe or life-threatening multi-organ disease. 3. Most non-falciparum malaria cases are caused by Plasmodium vivax; a few cases are caused by the other species of plasmodium: Plasmodium ovale, Plasmodium malariae or Plasmodium knowlesi. 4. Mixed infections with more than one species of parasite can occur; they commonly involve P. falciparum with the attendant risks of severe malaria. 5. There are no typical clinical features of malaria; even fever is not invariably present. Malaria in children (and sometimes in adults) may present with misleading symptoms such as gastrointestinal features, sore throat or lower respiratory complaints. 6. A diagnosis of malaria must always be sought in a feverish or sick child or adult who has visited malaria-endemic areas. Specific country information on malaria can be found at http://travelhealthpro.org.uk/. P. falciparum infection rarely presents more than six months after exposure but presentation of other species can occur more than a year after exposure. 7. Management of malaria depends on awareness of the diagnosis and on performing the correct diagnostic tests: the diagnosis cannot be excluded until more than one blood specimen has been examined. Other travel related infections, especially viral haemorrhagic fevers, should also be considered. 8. The optimum diagnostic procedure is examination of thick and thin blood films by an expert to detect and speciate the malarial parasites. P. falciparum and P. vivax (depending upon the product) malaria can be diagnosed almost as accurately using rapid diagnostic tests (RDTs) which detect plasmodial antigens. RDTs for other Plasmodium species are not as reliable. 9. Most patients treated for P. falciparum malaria should be admitted to hospital for at least 24 h as patients can deteriorate suddenly, especially early in the course of treatment. In specialised units seeing large numbers of patients, outpatient treatment may be considered if specific protocols for patient selection and follow up are in place. 10. Uncomplicated P. falciparum malaria should be treated with an artemisinin combination therapy (Grade 1A). Artemether-lumefantrine (Riamet(®)) is the drug of choice (Grade 2C) and dihydroartemisinin-piperaquine (Eurartesim(®)) is an alternative. Quinine or atovaquone-proguanil (Malarone(®)) can be used if an ACT is not available. Quinine is highly effective but poorly-tolerated in prolonged treatment and should be used in combination with an additional drug, usually oral doxycycline. 11. Severe falciparum malaria, or infections complicated by a relatively high parasite count (more than 2% of red blood cells parasitized) should be treated with intravenous therapy until the patient is well enough to continue with oral treatment. Severe malaria is a rare complication of P. vivax or P. knowlesi infection and also requires parenteral therapy. 12. The treatment of choice for severe or complicated malaria in adults and children is intravenous artesunate (Grade 1A). Intravenous artesunate is unlicensed in the EU but is available in many centres. The alternative is intravenous quinine, which should be started immediately if artesunate is not available (Grade 1A). Patients treated with intravenous quinine require careful monitoring for hypoglycemia. 13. Patients with severe or complicated malaria should be managed in a high-dependency or intensive care environment. They may require haemodynamic support and management of: acute respiratory distress syndrome, disseminated intravascular coagulation, acute kidney injury, seizures, and severe intercurrent infections including Gram-negative bacteraemia/septicaemia. 14. Children with severe malaria should also be treated with empirical broad spectrum antibiotics until bacterial infection can be excluded (Grade 1B). 15. Haemolysis occurs in approximately 10-15% patients following intravenous artesunate treatment. Haemoglobin concentrations should be checked approximately 14 days following treatment in those treated with IV artemisinins (Grade 2C). 16. Falciparum malaria in pregnancy is more likely to be complicated: the placenta contains high levels of parasites, stillbirth or early delivery may occur and diagnosis can be difficult if parasites are concentrated in the placenta and scanty in the blood. 17. Uncomplicated falciparum malaria in the second and third trimester of pregnancy should be treated with artemether-lumefantrine (Grade 2B). Uncomplicated falciparum malaria in the first trimester of pregnancy should usually be treated with quinine and clindamycin but specialist advice should be sought. Severe malaria in any trimester of pregnancy should be treated as for any other patient with artesunate preferred over quinine (Grade 1C). 18. Children with uncomplicated malaria should be treated with an ACT (artemether-lumefantrine or dihydroartemisinin-piperaquine) as first line treatment (Grade 1A). Quinine with doxycycline or clindamycin, or atovaquone-proguanil at appropriate doses for weight can also be used. Doxycycline should not be given to children under 12 years. 19. Either an oral ACT or chloroquine can be used for the treatment of non-falciparum malaria. An oral ACT is preferred for a mixed infection, if there is uncertainty about the infecting species, or for P. vivax infection from areas where chloroquine resistance is common (Grade 1B). 20. Dormant parasites (hypnozoites) persist in the liver after treatment of P. vivax or P. ovale infection: the only currently effective drug for eradication of hypnozoites is primaquine (1A). Primaquine is more effective at preventing relapse if taken at the same time as chloroquine (Grade 1C). 21. Primaquine should be avoided or given with caution under expert supervision in patients with Glucose-6-phosphate dehydrogenase deficiency (G6PD), in whom it may cause severe haemolysis. 22. Primaquine (for eradication of P. vivax or P. ovale hypnozoites) is contraindicated in pregnancy and when breastfeeding (until the G6PD status of child is known); after initial treatment for these infections a pregnant woman should take weekly chloroquine prophylaxis until after delivery or cessation of breastfeeding when hypnozoite eradication can be considered. 23. An acute attack of malaria does not confer protection from future attacks: individuals who have had malaria should take effective anti-mosquito precautions and chemoprophylaxis during future visits to endemic areas.