Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a ...subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST).
The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic–phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging.
For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
We determined the prevalence and types of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli in raw retail beef, chicken, pork, fruit and vegetables in five UK ...regions in 2013–14. Raw meat (n=397), and fruit and vegetable samples (n=400) were purchased from retail stores in London, East Anglia, North West England, Scotland and Wales. Samples were tested for the presence of ESBL-producing E. coli by plating enriched samples on CHROMagar CTX and CHROMagar ESBL, for AmpC-type E. coli by plating on “CHROMagar FOX” (CHROMagar ECC+16mg/L cefoxitin), and for carbapenem-resistant E. coli by plating on CHROMagar KPC. Additionally, pre-enrichment counts were performed on the above agars, and on CHROMagar ECC. Isolates of interest were characterised by MALDI-ToF to confirm identification, by PCR for blaCIT,blaCTX-M,blaOXA, blaSHV and blaTEM genes; ESBL or blaCIT genes were sequenced. Only 1.9% and 2.5% of beef and pork samples, respectively were positive for ESBL-producing E. coli after enrichment compared with 65.4% of chicken samples. 85.6% positive samples from chicken meat carried blaCTX-M-1; blaCTX-M-15 was not detected. None of the fruits or vegetables yielded ESBL-producing E. coli and none of the meat, fruit or vegetable samples yielded carbapenem-resistant E. coli. Retail chicken was more frequently a source of ESBL-producing E. coli than were beef, pork, fruit or vegetables. None of the foodstuffs yielded E. coli with CTX-M-15 ESBL, which dominates in human clinical isolates in the UK, and none yielded carbapenem-resistant E. coli.
•Retail raw meat, fruit and vegetables were tested for antibiotic-resistant E. coli.•Samples were purchased in the UK in 2013 to 2014.•About 2% of beef and pork and 65% of chicken were positive for ESBL-producing E. coli.•None of the fruit and vegetable samples was positive for ESBL-producing E. coli.•Carbapenem-resistant E. coli were not isolated from any of the samples tested.
The epidemiological importance of tracing plasmids conferring drug resistance prompted us to develop a PCR method based on replicons (inc/rep PCR) of the major plasmid incompatibility groups among
...Enterobacteriaceae. Eighteen pairs of primers were designed to perform 5 multiplex- and 3 simplex-PCRs, recognizing FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, and FIIA. The specificity of the method was tested on a collection of 61 reference plasmids and on 20
Salmonella enterica strains of different serotypes isolated in Italy. Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmids in epidemiologically unrelated
Salmonella isolates of different serotypes. These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments.
Hydrodynamic instabilities are a major factor in degradation of inertial confinement fusion (ICF) implosions. In the highest performing implosions on National Ignition Facility, yield amplification ...(YA) due to alpha particle heating approached ∼3, while YA of ∼15-30 is needed for ignition. Understanding and mitigation of the instabilities are critical to achieving ignition. This article reviews several experimental platforms that have been developed to directly measure these instabilities in all phases of ICF implosions. Measurements of ripple-shock propagation at OMEGA laser has provided results on initial seeds for the instabilities in three ablators-plastic (CH), beryllium, and high-density carbon. At the ablation front, instability growth of pre-imposed modulations was measured in the linear regime using the hydrodynamic growth radiography platform. This platform was extended for modulation growth of 'native roughness' modulations and engineering features (fill tubes and capsule support membranes or 'tents'). Several new experimental platforms have or are being developed to measure instability growth at the ablator-ice interface. In the deceleration phase of implosions, complementary 'self-emission' and 'self-backlighting' platforms were developed to measure low-mode asymmetries and high-mode perturbations near peak compression.
Three volcanic arcs have been the source of New Zealand's volcanic activity since the Neogene: Northland arc, Coromandel Volcanic Zone (CVZ) and Taupō Volcanic Zone (TVZ). The eruption chronology for ...the Quaternary, sourced by the TVZ, is well studied and established, whereas the volcanic evolution of the precursor arc systems, like the CVZ (central activity c. 18 to 2 Ma), is poorly known due to limited accessibility to, or identification of, onshore volcanic deposits and their sources. Here, we investigate the marine tephra record of the Neogene, mostly sourced by the CVZ, of cores from IODP Exp. 375 (Sites U1520 and U1526), ODP Leg 181 (Sites 1123, 1124 and 1125), IODP Leg 329 (Site U1371) and DSDP Leg 90 (Site 594) offshore of New Zealand. In total, we identify 306 primary tephra layers in the marine sediments. Multi‐approach age models (e.g. biostratigraphy, zircon ages) are used in combination with geochemical fingerprinting (major and trace element compositions) and the stratigraphic context of each marine tephra layer to establish 168 tie‐lines between marine tephra layers from different holes and sites. Following this approach, we identify 208 explosive volcanic events in the Neogene between c. 17.5 and 2.6 Ma. This is the first comprehensive study of New Zealand's Neogene explosive volcanism established from tephrochronostratigraphic studies, which reveals continuous volcanic activity between c. 12 and 2.6 Ma with an abrupt compositional change at c. 4.5 Ma, potentially associated with the transition from CVZ to TVZ.
Plain Language Summary
Since 18 Ma, volcanic activity in New Zealand is dominantly sourced by the Coromandel Volcanic Zone (CVZ). Most caldera systems of the CVZ identified so far are located on Coromandel Peninsula in the NW of North Island, New Zealand, but studies of the CVZ are rare mainly due to the limited accessibility of its volcanic deposits, as well as missing stratigraphic continuity between different outcrops and the volcanic source. Here, our ocean drilling tephra record—mainly volcanic ash from explosive eruptions, distributed and falling out over the ocean—has a great potential to reveal the eruption history of the CVZ because it is preserved in marine sediments in a nearly undisturbed stratigraphic context. We analyzed ∼400 marine tephra layers from multiple ocean sediment cores off the coast of New Zealand for their geochemical glass compositions and identified 306 as largely undisturbed ash deposits. These primary ash deposits correspond to a total number of 208 Neogene volcanic events. Different dating methods result in a continuous marine tephra record for the last 12 Ma, equivalent to a unique and most complete eruptive history for the CVZ. This enables us to further unravel changes in the composition of the associated magmas with time.
Key Points
New Zealand's Neogene explosive volcanism based on the marine tephra record
Geochemical fingerprinting of marine tephra layers across the study area to establish volcanic events
Insights into geochemical variations with time, repose times and spatiotemporal distribution
Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ...ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking.
To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing.
Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0).
The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days.
Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.
Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic ...Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005-2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A marked increase in the prevalence of S. enterica serovar 4,5,12:i:- with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines (R-type ASSuT) has been noted in food-borne ...infections and in pigs/pig meat in several European countries in the last ten years. One hundred and sixteen strains of S. enterica serovar 4,5,12:i:- from humans, pigs and pig meat isolated in England and Wales, France, Germany, Italy, Poland, Spain and the Netherlands were further subtyped by phage typing, pulsed-field gel electrophoresis and multilocus variable number tandem repeat analysis to investigate the genetic relationship among strains. PCR was performed to identify the fljB flagellar gene and the genes encoding resistance to ampicillin, streptomycin, sulphonamides and tetracyclines. Class 1 and 2 integrase genes were also sought. Results indicate that genetically related serovar 4,5,12:i:- strains of definitive phage types DT193 and DT120 with ampicillin, streptomycin, sulphonamide and tetracycline resistance encoded by blaTEM, strA-strB, sul2 and tet(B) have emerged in several European countries, with pigs the likely reservoir of infection. Control measures are urgently needed to reduce spread of infection to humans via the food chain and thereby prevent the possible pandemic spread of serovar 4,5,12:i:- of R-type ASSuT as occurred with S. Typhimurium DT104 during the 1990s.
The lifetime of methane is controlled to a very large extent by the abundance of the OH radical. The tropics are a key region for methane removal, with oxidation in the lower tropical troposphere ...dominating the global methane removal budget (Bloss et al., 2005). In tropical forested environments where biogenic VOC emissions are high and NOx concentrations are low, OH concentrations are assumed to be low due to rapid reactions with sink species such as isoprene. New, simultaneous measurements of OH concentrations and OH reactivity, k'OH, in a Borneo rainforest are reported and show much higher OH than predicted, with mean peak concentrations of ~2.5×106 molecule cm−3 (10 min average) observed around solar noon. Whilst j(O1D) and humidity were high, low O3 concentrations limited the OH production from O3 photolysis. Measured OH reactivity was very high, peaking at a diurnal average of 29.1±8.5 s−1, corresponding to an OH lifetime of only 34 ms. To maintain the observed OH concentration given the measured OH reactivity requires a rate of OH production approximately 10 times greater than calculated using all measured OH sources. A test of our current understanding of the chemistry within a tropical rainforest was made using a detailed zero-dimensional model to compare with measurements. The model over-predicted the observed HO2 concentrations and significantly under-predicted OH concentrations. Inclusion of an additional OH source formed as a recycled product of OH initiated isoprene oxidation improved the modelled OH agreement but only served to worsen the HO2 model/measurement agreement. To replicate levels of both OH and HO2, a process that recycles HO2 to OH is required; equivalent to the OH recycling effect of 0.74 ppbv of NO. This recycling step increases OH concentrations by 88 % at noon and has wide implications, leading to much higher predicted OH over tropical forests, with a concomitant reduction in the CH4 lifetime and increase in the rate of VOC degradation.
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