1,577 research outputs found
Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites.
CAUL read and publish agreement 2023Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.Publishe
Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.
Three strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were isolated from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome sequences. This information provided the first genomic insights into the nature of G. stearothermophilus strains present in the milk powder manufacturing environment.Published onlin
Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments.
(c) The Author/sAntimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic "One Health" approach to address.Published onlin
Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage
Publishe
Bulk Axions, Brane Back-reaction and Fluxes
Extra-dimensional models can involve bulk pseudo-Goldstone bosons (pGBs)
whose shift symmetry is explicitly broken only by physics localized on branes.
Reliable calculation of their low-energy potential is often difficult because
it requires details of the stabilization of the extra dimensions. In rugby ball
solutions, for which two compact extra dimensions are stabilized in the
presence of only positive-tension brane sources, the effects of brane
back-reaction can be computed explicitly. This allows the calculation of the
shape of the low-energy pGB potential and response of the extra dimensional
geometry as a function of the perturbing brane properties. If the
pGB-dependence is a small part of the total brane tension a very general
analysis is possible, permitting an exploration of how the system responds to
frustration when the two branes disagree on what the proper scalar vacuum
should be. We show how the low-energy potential is given by the sum of brane
tensions (in agreement with common lore) when only the brane tensions couple to
the pGB. We also show how a direct brane coupling to the flux stabilizing the
extra dimensions corrects this result in a way that does not simply amount to
the contribution of the flux to the brane tensions. We calculate the mass of
the would-be zero mode, and briefly describe several potential applications,
including a brane realization of `natural inflation,' and a dynamical mechanism
for suppressing the couplings of the pGB to matter localized on the branes.
Since the scalar can be light enough to be relevant to precision tests of
gravity (in a technically natural way) this mechanism can be relevant to
evading phenomenological bounds.Comment: 36 pages, JHEP styl
Dynein structure and power stroke
Dynein ATPases are microtubule motors that are critical to diverse processes such as vesicle transport and the beating of sperm tails; however, their mechanism of force generation is unknown. Each dynein comprises a head, from which a stalk and a stem emerge. Here we use electron microscopy and image processing to reveal new structural details of dynein c, an isoform from Chlamydomonas reinhardtii flagella, at the start and end of its power stroke. Both stem and stalk are flexible, and the stem connects to the head by means of a linker approximately 10 nm long that we propose lies across the head. With both ADP and vanadate bound, the stem and stalk emerge from the head 10 nm apart. However, without nucleotide they emerge much closer together owing to a change in linker orientation, and the coiled-coil stalk becomes stiffer. The net result is a shortening of the molecule coupled to an approximately 15-nm displacement of the tip of the stalk. These changes indicate a mechanism for the dynein power stroke
Towards strange metallic holography
We initiate a holographic model building approach to `strange metallic'
phenomenology. Our model couples a neutral Lifshitz-invariant quantum critical
theory, dual to a bulk gravitational background, to a finite density of gapped
probe charge carriers, dually described by D-branes. In the physical regime of
temperature much lower than the charge density and gap, we exhibit anomalous
scalings of the temperature and frequency dependent conductivity. Choosing the
dynamical critical exponent appropriately we can match the non-Fermi liquid
scalings, such as linear resistivity, observed in strange metal regimes. As
part of our investigation we outline three distinct string theory realizations
of Lifshitz geometries: from F theory, from polarised branes, and from a
gravitating charged Fermi gas. We also identify general features of
renormalisation group flow in Lifshitz theories, such as the appearance of
relevant charge-charge interactions when . We outline a program to
extend this model building approach to other anomalous observables of interest
such as the Hall conductivity.Comment: 71 pages, 8 figure
Extended spectrum β-lactamase-and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: A case-control study.
(c) The Author/sOBJECTIVES: To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS: An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n=141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL- producing Enterobacterales. Controls (n=525) were recruited from the community. A telephone questionnaire on pet ownership, and other factors was administered, and associations were assessed using logistic regression. RESULTS: Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the previous six months. Among isolates with an ESBL-/ACBL-producing phenotype 126/134 (94%) were Escherichia coli, with sequence type (ST) 131 being the most common (47/126). CONCLUSIONS: Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales related community-acquired UTI in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.Published onlin
Composite Fermion Metals from Dyon Black Holes and S-Duality
We propose that string theory in the background of dyon black holes in
four-dimensional anti-de Sitter spacetime is holographic dual to conformally
invariant composite Dirac fermion metal. By utilizing S-duality map, we show
that thermodynamic and transport properties of the black hole match with those
of composite fermion metal, exhibiting Fermi liquid-like. Built upon
Dirac-Schwinger-Zwanziger quantization condition, we argue that turning on
magnetic charges to electric black hole along the orbit of Gamma(2) subgroup of
SL(2,Z) is equivalent to attaching even unit of statistical flux quanta to
constituent fermions. Being at metallic point, the statistical magnetic flux is
interlocked to the background magnetic field. We find supporting evidences for
proposed holographic duality from study of internal energy of black hole and
probe bulk fermion motion in black hole background. They show good agreement
with ground-state energy of composite fermion metal in Thomas-Fermi
approximation and cyclotron motion of a constituent or composite fermion
excitation near Fermi-point.Comment: 30 pages, v2. 1 figure added, minor typos corrected; v3. revised
version to be published in JHE
Andy's Algorithms: new automated digital image analysis pipelines for FIJI.
Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy's Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3'-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy's Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy's algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy's Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm
- …