Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data

Introduction. Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen Staphylococcus aureus . The reported prevalence of these resistances varies, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures. Gap Statement. The value and limitations of routinely collected hospital data to gain insight into AMR dynamics at the hospital and individual levels simultaneously are unclear. Methodology. We explored S. aureus AMR diversity in 70 000 isolates from a UK paediatric hospital between 2000–2021, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms and information on hospitalization and antibiotic consumption. Results. At the hospital level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014–2020 from 25–50 %, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible S. aureus . Ciprofloxacin resistance in MRSA decreased from 70–40 % of tested isolates between 2007–2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4 % of patients ever positive for S. aureus simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3 % of patients ever positive for S. aureus . These changes equally represented gain and loss of resistance. Conclusion. Within this routinely collected dataset, we found that 65 % of changes in resistance within a patient’s S. aureus population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single S. aureus clones

Optimal purification of thermal graph states

In this paper, a purification protocol is presented and its performance is proven to be optimal when applied to a particular subset of graph states that are subject to local Z-noise. Such mixed states can be produced by bringing a system into thermal equilibrium, when it is described by a Hamiltonian which has a particular graph state as its unique ground state. From this protocol, we derive the exact value of the critical temperature above which purification is impossible, as well as the related optimal purification rates. A possible simulation of graph Hamiltonians is proposed, which requires only bipartite interactions and local magnetic fields, enabling the tuning of the system temperature.Comment: 5 pages, 4 figures v2: published versio

Validation of the CREST score for predicting circulatory-aetiology death in out-of-hospital cardiac arrest without STEMI

Aims: The CREST tool was recently developed to stratify the risk of circulatory-aetiology death (CED) in out-of-hospital cardiac arrest (OHCA) patients without ST-elevation myocardial infarction (STEMI). We aimed to validate the CREST score using an external cohort and determine whether it could be improved by the addition of serum lactate on admission. Methods: The study involved the retrospective analysis of consecutive patients admitted to a single tertiary centre with OHCA of presumed cardiac origin over a 51-month period. The CREST score was calculated by attributing points to the following variables: Coronary artery disease (CAD), non-shockable Rhythm, Ejection fraction <30%, cardiogenic Shock at presentation and ischaemic Time ≥25 minutes. The primary endpoint was CED vs neurological aetiology death (NED) or survival. Results: Of 500 patients admitted with OHCA, 211 did not meet criteria for STEMI and were included. 115 patients died in hospital (71 NED, 44 CED). When analysed individually, CED was associated with all CREST variables other than a previous diagnosis of CAD. The CREST score accurately predicted CED with excellent discrimination (C-statistic 0.880, 95% CI 0.813-0.946) and calibration (Hosmer and Lemeshow P=0.948). Although an admission lactate ≥7 mmol/L also predicted CED, its addition to the CREST score (the C-AREST score) did not significantly improve the predictive ability (CS 0.885, 0.815-0.954, HS P=0.942, X2 difference in -2 log likelihood =0.326, P=0.850). Conclusion: Our study is the first to independently validate the CREST score for predicting CED in patients presenting with OHCA without STEMI. Addition of lactate on admission did not improve its predictive ability.Publisher PDFPeer reviewe

Monotonicity of Fitness Landscapes and Mutation Rate Control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Intranasal H5N1 vaccines, adjuvanted with chitosan derivatives, protect ferrets against highly pathogenic influenza intranasal and intratracheal challenge

We investigated the protective efficacy of two intranasal chitosan (CSN and TM-CSN) adjuvanted H5N1 Influenza vaccines against highly pathogenic avian Influenza (HPAI) intratracheal and intranasal challenge in a ferret model. Six groups of 6 ferrets were intranasally vaccinated twice, 21 days apart, with either placebo, antigen alone, CSN adjuvanted antigen, or TM-CSN adjuvanted antigen. Homologous and intra-subtypic antibody cross-reacting responses were assessed. Ferrets were inoculated intratracheally (all treatments) or intranasally (CSN adjuvanted and placebo treatments only) with clade 1 HPAI A/Vietnam/1194/2004 (H5N1) virus 28 days after the second vaccination and subsequently monitored for morbidity and mortality outcomes. Clinical signs were assessed and nasal as well as throat swabs were taken daily for virology. Samples of lung tissue, nasal turbinates, brain, and olfactory bulb were analysed for the presence of virus and examined for histolopathological findings. In contrast to animals vaccinated with antigen alone, the CSN and TM-CSN adjuvanted vaccines induced high levels of antibodies, protected ferrets from death, reduced viral replication and abrogated disease after intratracheal challenge, and in the case of CSN after intranasal challenge. In particular, the TM-CSN adjuvanted vaccine was highly effective at eliciting protective immunity from intratrache

Temporal and spatial patterns of bovine Escherichia coli O157 prevalence and comparison of temporal changes in the patterns of phage types associated with bovine shedding and human E. coli O157 cases in Scotland between 1998-2000 and 2002-2004

Background: Escherichia coli O157 is an important cause of acute diarrhoea, haemorrhagic colitis and, especially in children, haemolytic uraemic syndrome (HUS). Incidence rates for human E. coli O157 infection in Scotland are higher than most other United Kingdom, European and North American countries. Cattle are considered the main reservoir for E. coli O157. Significant associations between livestock related exposures and human infection have been identified in a number of studies. Results: Animal Studies: There were no statistically significant differences (P = 0.831) in the mean farm-level prevalence between the two studies (SEERAD: 0.218 (95% CI: 0.141-0.32); IPRAVE: 0.205 (95% CI: 0.135-0.296)). However, the mean pat-level prevalence decreased from 0.089 (95% CI: 0.075-0.105) to 0.040 (95% CI: 0.028-0.053) between the SEERAD and IPRAVE studies respectively (P &lt; 0.001). Highly significant (P &lt; 0.001) reductions in mean pat-level prevalence were also observed in the spring, in the North East and Central Scotland, and in the shedding of phage type (PT) 21/28. Human Cases: Contrasting the same time periods, there was a decline in the overall comparative annual reported incidence of human cases as well as in all the major PT groups except 'Other' PTs. For both cattle and humans, the predominant phage type between 1998 and 2004 was PT21/28 comprising over 50% of the positive cattle isolates and reported human cases respectively. The proportion of PT32, however, was represented by few (&lt;5%) of reported human cases despite comprising over 10% of cattle isolates. Across the two studies there were differences in the proportion of PTs 21/28, 32 and 'Other' PTs in both cattle isolates and reported human cases; however, only differences in the cattle isolates were statistically significant (P = 0.002). Conclusion: There was no significant decrease in the mean farm-level prevalence of E. coli O157 between 1998 and 2004 in Scotland, despite significant declines in mean pat-level prevalence. Although there were declines in the number of human cases between the two study periods, there is no statistically significant evidence that the overall rate (per 100,000 population) of human E. coli O157 infections in Scotland over the last 10 years has altered. Comparable patterns in the distribution of PTs 21/28 and 32 between cattle and humans support a hypothesized link between the bovine reservoir and human infections. This emphasizes the need to apply and improve methods to reduce bovine shedding of E. coli O157 in Scotland where rates appear higher in both cattle and human populations, than in other countrie

Bendable X-ray Optics at the ALS: Design, Tuning, Performance and Applications

We review the development at the Advanced Light Source (ALS) of bendable x-ray optics widely used for focusing of beams of soft and hard x-rays. Typically, the focusing is divided in the tangential and sagittal directions into two elliptically cylindrical reflecting elements, the so-called Kirkpatrick-Baez (KB) pair [1]. Because fabrication of elliptical surfaces is complicated, the cost of directly fabricated tangential elliptical cylinders is often prohibitive. This is in contrast to flat optics, that are simpler to manufacture and easier to measure by conventional interferometry. The figure of a flat substrate can be changed by placing torques (couples) at each end. Equal couples form a tangential cylinder, and unequal couples can approximate a tangential ellipse or parabola. We review the nature of the bending, requirements and approaches to the mechanical design, and describe a technique developed at the ALS Optical Metrology Laboratory (OML) for optimal tuning of bendable mirrors before installation in the beamline [2]. The tuning technique adapts a method previously used to adjust bendable mirrors on synchrotron radiation beamlines [3]. However, in our case, optimal tuning of a bendable mirror is based on surface slope trace data obtained with a slope measuring instrument--in our case, the long trace profiler (LTP). We show that due to the near linearity of the bending problem, the minimal set of data, necessary for tuning of two benders, consists of only three slope traces measured before and after a single adjustment of each bending couple. We provide an algorithm that was used in dedicated software for finding optimal settings for the mirror benders. The algorithm is based on the method of regression analysis with experimentally found characteristic functions of the benders. The resulting approximation to the functional dependence of the desired slope shape provides nearly final settings for the benders. Moreover, the characteristic functions of the benders found in the course of tuning, can be used for retuning of the optics to a new desired shape without removing it from the beamline and re-measuring with the LTP. The result of practical use of the developed technique to precisely tune a KB mirror used at the ALS for micro-focusing is also presented. We also describe a simple ray trace using the profiler data which shows expected performance in the beamline and compare the simulation with experimental data. In summary, we also discuss the next steps in the systematic improvement of optical performance for the application of KB pairs in synchrotron beamlines at the ALS

Regional differences in prostaglandin E₂ metabolism in human colorectal cancer liver metastases

Background: Prostaglandin (PG) E₂ plays a critical role in colorectal cancer (CRC) progression, including epithelial-mesenchymal transition (EMT). Activity of the rate-limiting enzyme for PGE₂ catabolism (15-hydroxyprostaglandin dehydrogenase [15-PGDH]) is dependent on availability of NAD+. We tested the hypothesis that there is intra-tumoral variability in PGE₂ content, as well as in levels and activity of 15-PGDH, in human CRC liver metastases (CRCLM). To understand possible underlying mechanisms, we investigated the relationship between hypoxia, 15-PGDH and PGE₂ in human CRC cells in vitro. Methods: Tissue from the periphery and centre of 20 human CRCLM was analysed for PGE₂ levels, 15-PGDH and cyclooxygenase (COX)-2 expression, 15-PGDH activity, and NAD+/NADH levels. EMT of LIM1863 human CRC cells was induced by transforming growth factor (TGF) β. Results: PGE₂ levels were significantly higher in the centre of CRCLM compared with peripheral tissue (P = 0.04). There were increased levels of 15-PGDH protein in the centre of CRCLM associated with reduced 15-PGDH activity and low NAD+/NADH levels. There was no significant heterogeneity in COX-2 protein expression. NAD+ availability controlled 15-PGDH activity in human CRC cells in vitro. Hypoxia induced 15-PGDH expression in human CRC cells and promoted EMT, in a similar manner to PGE₂. Combined 15-PGDH expression and loss of membranous E-cadherin (EMT biomarker) were present in the centre of human CRCLM in vivo.Conclusions: There is significant intra-tumoral heterogeneity in PGE₂ content, 15-PGDH activity and NAD+ availability in human CRCLM. Tumour micro-environment (including hypoxia)-driven differences in PGE₂ metabolism should be targeted for novel treatment of advanced CRC

Environmental pleiotropy and demographic history direct adaptation under antibiotic selection

Evolutionary rescue following environmental change requires mutations permitting population growth in the new environment. If change is severe enough to prevent most of the population reproducing, rescue becomes reliant on mutations already present. If change is sustained, the fitness effects in both environments, and how they are associated-termed 'environmental pleiotropy'-may determine which alleles are ultimately favoured. A population's demographic history-its size over time-influences the variation present. Although demographic history is known to affect the probability of evolutionary rescue, how it interacts with environmental pleiotropy during severe and sustained environmental change remains unexplored. Here, we demonstrate how these factors interact during antibiotic resistance evolution, a key example of evolutionary rescue fuelled by pre-existing mutations with pleiotropic fitness effects. We combine published data with novel simulations to characterise environmental pleiotropy and its effects on resistance evolution under different demographic histories. Comparisons among resistance alleles typically revealed no correlation for fitness-i.e., neutral pleiotropy-above and below the sensitive strain's minimum inhibitory concentration. Resistance allele frequency following experimental evolution showed opposing correlations with their fitness effects in the presence and absence of antibiotic. Simulations demonstrated that effects of environmental pleiotropy on allele frequencies depended on demographic history. At the population level, the major influence of environmental pleiotropy was on mean fitness, rather than the probability of evolutionary rescue or diversity. Our work suggests that determining both environmental pleiotropy and demographic history is critical for predicting resistance evolution, and we discuss the practicalities of this during in vivo evolution

Opposing effects of final population density and stress on Escherichia coli mutation rate

Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis-SIM) and decrease at high final population density (density-associated mutation-rate plasticity-DAMP). We hypothesised that these two forms of mutation-rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM results in a mutation rate minimum at intermediate nutrient levels (which can support 7 × 10  cells ml ). These findings demonstrate a strikingly close and nuanced relationship of ecological factors-stress and population density-with mutation, the fuel of all evolution