Beamline I22 at Diamond Light Source is dedicated to the study of soft‐matter systems from both biological and materials science. The beamline can operate in the range 3.7 keV to 22 keV for ...transmission SAXS and 14 keV to 20 keV for microfocus SAXS with beam sizes of 240 µm × 60 µm full width half‐maximum (FWHM) horizontal (H) × vertical (V) at the sample for the main beamline, and approximately 10 µm × 10 µm for the dedicated microfocusing platform. There is a versatile sample platform for accommodating a range of facilities and user‐developed sample environments. The high brilliance of the insertion device source on I22 allows structural investigation of materials under extreme environments (for example, fluid flow at high pressures and temperatures). I22 provides reliable access to millisecond data acquisition timescales, essential to understanding kinetic processes such as protein folding or structural evolution in polymers and colloids.
Beamline I22, a versatile SAXS/WAXS beamline at Diamond Light Source, is presented, along with an overview of 10 years operation of the beamline.
SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several ...gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbreak detection. Comparisons were made between temporal and spatio-temporal cluster detection models that either defined cases by their SNP address or by phage type, using historical data sets. Clusters of SNP incidents were effectively detected by both methods, but spatio-temporal models consistently detected these clusters earlier than the corresponding temporal models. Unlike phage type, SNP addresses appeared spatially and temporally limited, which facilitated the differentiation of novel, stable, or expanding clusters in spatio-temporal models. Furthermore, these models flagged spatio-temporal clusters containing only two to three cases at first detection, compared with a median of seven cases in phage-type models. The large number of SNP addresses will require automated methods to implement these detection models routinely. Further work is required to explore how temporal changes and different host species may impact the sensitivity and specificity of cluster detection. In conclusion, given validation with more sequencing data, SNP addresses are likely to be a valuable addition to early warning systems in veterinary surveillance.
Three semi-rational approaches, combinatorial site-saturation mutagenesis (CSSM) using a reduced amino acid set and two libraries based on Corbit and CRAM computational design algorithms targeting up ...to 10 active site residues, were used to engineer cytochrome P450 BM3 to demethylate dimethyl ether and hydroxylate propane and ethane. These small libraries (343–1028 variants) were all enriched with respect to the fraction functional and maximal activities compared with a random mutagenesis library and individual site-saturation libraries targeting the same residues. Despite high average amino acid substitution levels of 2.6, 5 and 7.5, the CSSM, Corbit and CRAM libraries had at least 75% of library members properly folded. Propane- and ethane-hydroxylating P450 BM3 variants were identified using all three mutagenesis approaches, with as few as two amino acid substitutions. The library designed using the CRAM algorithm, which sought to reduce the size of the binding pocket, produced both a higher number of active variants and variants supporting the greatest number of catalytic turnovers. The most active variant E32 supports 16 800 propane turnovers at 36% coupling, which rivals the activity of variants obtained after 10–12 rounds of directed evolution using random and site-saturation mutagenesis. None of the variants in this study achieved the complete re-specialization for propane hydroxylation (including 93% coupling) previously obtained via multiple rounds of mutagenesis and screening. However, these semi-rational approaches allowed for large jumps in sequence space to variants with the desired functions.
A longitudinal field trial was carried out on a farm known to harbour cefotaximase (CTX-M)-positive Escherichia coli, in order to assess the impact of feeding waste milk containing antibiotic ...residues (WM+AR) on the prevalence of these bacteria in the faeces of calves. Fifty calves were alternately assigned to one of two groups at birth and fed either milk replacer (control group) or WM+AR (treatment group). Faecal samples were collected from all calves daily for the first week after enrolment, twice weekly until weaning, then weekly for a further six weeks. Environmental samples from the calf housing were collected weekly. WM+AR and powdered milk samples were examined for antibiotic residues and CTX-M-positive E. coli. Total E. coli and CTX-M-positive E. coli in faecal samples were enumerated using selective media. Regression analyses were performed on the bacterial count data using a population-averaged approach based on generalised estimating equations (GEE) to account for repeated measurements on individual calves over time.
Cefquinome, a fourth generation cephalosporin, was detected in 87% of WM+AR samples at a mean concentration of 0.746mg/l. All environmental sampling locations yielded CTX-M-positive E. coli. Significantly more pen floor samples were positive in the treatment group. Calves in the treatment group shed greater numbers of CTX-M-positive E. coli than calves in the control group throughout the study, and shedding decreased at a slower rate in the treatment group. CTX-M-positive E. coli persisted in a larger number of calves fed WM+AR compared with calves fed milk replacer where the prevalence in the treatment group declined significantly slower over time. There was no difference between calves fed WM+AR or calves fed milk replacer in the proportion of E. coli isolates that were CTX-M-positive.
These findings indicate that feeding WM+AR increased the amount of resistant bacteria shed in the faeces. Shedding of CTX-M-positive E. coli persisted for longer in calves fed WM+AR, and persisted after weaning.
The cause for the high prevalence of cefotaximase-producing Escherichia coli reported in dairy calves is unknown but may be partly due to the selective pressure of antimicrobial residues in waste ...milk (milk unfit for human consumption) fed to the calves. Antimicrobial use and waste milk feeding practices were investigated in 557 dairy farms in 2010/2011 that responded to a randomised stratified postal survey. The mean number of cases of mastitis per herd in the previous year was 47, and 93 per cent of respondents used antibiotic intra-mammary tubes to treat mastitis. The most frequently used lactating cow antibiotic tubes contained dihydrostreptomycin, neomycin, novobiocin, and procaine penicillin (37 per cent), and cefquinome (29 per cent). Ninety-six per cent of respondents used antibiotic tubes at the cessation of lactation (‘drying off’). The most frequently used dry cow antibiotic tube (43 per cent) contained cefalonium. Frequently used injectable antibiotics included tylosin (27 per cent), dihydrostreptomycin and procaine penicillin (20 per cent) and ceftiofur (13 per cent). Eighty-three per cent of respondents (413) fed waste milk to calves. Of these 413, 87 per cent fed waste milk from cows with mastitis, and only one-third discarded the first milk after antibiotic treatment. This survey has shown that on more than 90 per cent of the farms that feed waste milk to calves, waste milk can contain milk from cows undergoing antibiotic treatment. On some farms, this includes treatment with third- and fourth-generation cephalosporins. Further work is underway to investigate the presence of these antimicrobials in waste milk.
This study investigated the potential spread of CTX-M-14 Escherichia coli from a known ESBL E. coli positive farm and risk factors for the presence of CTX-M E. coli on dairy farms. Between November ...2009 and March 2010, 65 farms in North West England and North Wales were visited and animals sampled for E. coli producing CTX-M ESBLs. Seventeen of these were known to have received animals from a known ESBL E. coli positive ‘index’ farm since 2005 (linked farms). The prevalence of CTX-M E. coli in the population of linked farms was 58.8% (10/17; CI95% 32.9–81.6%) and in the randomly selected control population was 35.4% (17/48; CI95% 22.2–50.5%). There was no significant (p>0.05) linkage for the detection of any CTX-M E. coli or specifically a CTX-M-14 E. coli to the index farm. Group 1 (CTX-M-15, CTX-M-55, CTX-M-1, CTX-M-32), group 2 (CTX-M-2) and group 9 (CTX-M-14, CTX-M-14B, CTX-M-27) CTX-M E. coli were identified on the study farms. Molecular analysis revealed that three plasmids from linked farms had similar sizes (95kbp), replicon type (IncK) and backbone genes as that from the index farm. Logistic regression analysis revealed that farms that had used a 3rd or 4th generation cephalosporin (ceftiofur, cefoperazone and cefquinome) in livestock in the last 12months were nearly 4times more likely to have ESBL E. coli present (p=0.037; OR=3.93). There was no significant association between presence of CTX-M E. coli and the use of any 1st or 2nd generation cephalosporins. Several other risk factors for the presence of CTX-M E. coli were identified, such as storage of slurry in a pit, operating an open herd policy and infrequent cleaning of calf feeding equipment.
The Far Ultraviolet Spectroscopic Explorer satellite observes light in the far-ultraviolet spectral region, 905-1187 Å, with a high spectral resolution. The instrument consists of four co-aligned ...prime-focus telescopes and Rowland spectrographs with microchannel plate detectors. Two of the telescope channels use Al:LiF coatings for optimum reflectivity between approximately 1000 and 1187 Å, and the other two channels use SiC coatings for optimized throughput between 905 and 1105 Å. The gratings are holographically ruled to correct largely for astigmatism and to minimize scattered light. The microchannel plate detectors have KBr photocathodes and use photon counting to achieve good quantum efficiency with low background signal. The sensitivity is sufficient to examine reddened lines of sight within the Milky Way and also sufficient to use as active galactic nuclei and QSOs for absorption-line studies of both Milky Way and extragalactic gas clouds. This spectral region contains a number of key scientific diagnostics, including O VI, H I, D I, and the strong electronic transitions of H2 and HD.
All European Union (EU) Member States (MSs) were required to conduct a baseline survey from October 2006 to September 2007 to estimate the prevalence of Salmonella infection in finisher pigs at ...slaughter. In the United Kingdom (UK), samples for microbiological culture were collected from the ileo-caecal lymph nodes, from carcass swabs and from caecal contents. Meat juice samples were also collected for testing in an enzyme-linked immunosorbent assay (MJE) to detect a serological response. Salmonella was isolated from 22% (CI95% 19–25%) of ileo-caecal lymph nodes, 15% (CI95% 12–18%) of carcass swabs and 22% (CI95% 19–26%) of caecal contents. A quarter (25%, CI95% 22–29%) of MJE samples were positive for Salmonella antibodies (cut-off, S/P≥0.25). The most frequently identified serovars were Salmonella typhimurium (57%) and Salmonella derby (26%). The results were used to investigate some factors associated with Salmonella infection in slaughter pigs. The weight of the carcass was significant, with a lower probability of obtaining a positive meat juice result from pigs with a weight greater than 75kg (p=0.03). The weight of the lymph node sample was significantly associated with Salmonella status, with a heavier sample of lymph nodes being more likely to be positive (OR=2.16 CI95% 1.07–4.39). ‘Carcass weight’ in two of the classes – 75–79kg and 80–84kg – (OR=0.44 CI95% 0.28–0.70; OR=0.64 CI95% 0.49–0.85) and ‘fewer-than-1500-pigs’ scheduled for slaughter on the day of sampling’ (OR=0.41 CI95% 0.24–0.71) were also associated with a reduced risk of isolating Salmonella from lymph node. The model for carcass swabs showed a positive association with ‘time-elapsed-since-the-start-of-the-line’ indicating a higher risk of contamination as the day progressed (p<0.01). This model also showed positive association between isolation of Salmonella from a carcass swab and the occurrence of Salmonella in caecal contents from the same pig (OR=2.22 CI95% 1.38–3.59) and a negative association with time in singeing units (OR=0.88 CI95% 0.79–0.98).
In 2004/05, all European Union member states were required to carry out standardised prevalence surveys to establish the baseline prevalence of Salmonella in commercial laying flocks. As part of the ...survey in Great Britain, additional data were collected from 380 of the enrolled laying hen holdings to investigate risk factors for Salmonella at farm level. Stratified, simple random sampling was used to select holdings from which dust and boot swab samples were collected and tested for Salmonella using a modification of ISO 6579:2002. Using a multivariable logistic model weighted to account for the survey design, several factors significantly associated with Salmonella and Salmonella Enteritidis status were identified. Larger holdings (≥30,000 birds) were found to be at higher risk of Salmonella (odds ratio OR 4.79, P=0.025), while vaccination (OR 0.28, P=0.013), providing foot dips with brushes (OR 0.27, P=0.042), washing and disinfecting the house at depopulation (OR 0.19, P=0.003), having a clean car park away from house (OR 0.14, P=0.001), using an independent (OR 0.19, P=0.007) or other non-company (OR 0.40, P=0.049) source of feed, being over 1 km from the nearest neighbouring farm (OR 0.45, P=0.021) and the presence of cats and dogs on the farm (OR 0.26, P=0.002) or on contiguous farms (OR 0.44, P=0.030) reduced the risk of any Salmonella serovars being present. Factors found to be associated specifically with an increased risk of S Enteritidis infection included holding size (OR 14.88, P=0.001) and frequent sightings of rats (OR 8.17, P<0.001) or mice (OR 5.78, P=0.006). Non-caged systems (OR 0.14, P=0.002), vaccination (OR 0.08, P=0.001), the use of a non-company feed source (OR 0.11, P=0.003), running the site as all-in/all-out (OR 0.06, P<0.001) and the presence of cats and dogs on the farm (OR 0.14, P=0.002) were associated with a reduced risk.
SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also ...known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals.
To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections.
Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling.
SARS-CoV-2 infection.
PASC and 44 participant-reported symptoms (with severity thresholds).
A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years IQR, 35-60) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% 95% CI, 8.8%-11%) were PASC positive at 6 months.
A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.
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