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Molecular epidemiology of penicillin-susceptible Staphylococcus aureus bacteremia in Australia and reliability of diagnostic phenotypic susceptibility methods to detect penicillin susceptibility
Full text linkBackground: Defined by the emergence of antibiotic resistant strains, Staphylococcus aureus is a priority bacterial species with high antibiotic resistance. However, a rise in the prevalence of penicillin-susceptible S. aureus (PSSA) bloodstream infections has recently been observed worldwide, including in Australia, where the proportion of methicillin-susceptible S. aureus causing bacteremia identified phenotypically as penicillin-susceptible has increased by over 35%, from 17.5% in 2013 to 23.7% in 2020. Objectives: To determine the population structure of PSSA causing community- and hospital-onset bacteremia in Australia and to evaluate routine phenotypic antimicrobial susceptibility methods to reliably confirm penicillin resistance on blaZ-positive S. aureus initially classified as penicillin-susceptible by the Vitek® 2 automated microbiology system. Results: Whole genome sequencing on 470 PSSA collected in the 2020 Australian Group on Antimicrobial Resistance Australian Staphylococcus aureus Sepsis Outcome Programme identified 84 multilocus sequence types (STs), of which 79 (463 isolates) were grouped into 22 clonal complexes (CCs). The dominant CCs included CC5 (31.9%), CC97 (10.2%), CC45 (10.0%), CC15 (8.7%), and CC188 (4.9%). Many of the CCs had multiple STs and spa types and, based on the immune evasion cluster type, isolates within a CC could be classified into different strains harboring a range of virulence and resistance genes. Phylogenetic analyses of the isolates showed most CCs were represented by one clade. The blaZ gene was identified in 45 (9.6%) PSSA. Although multiclonal, approximately 50% of blaZ-positive PSSA were from CC15 and were found to be genetically distant from the blaZ-negative CC15 PSSA. The broth microdilution, Etest® and cefinase, performed poorly; however, when the appearance of the zone edge was considered; as per the EUCAST and CLSI criteria, disc diffusion detected 100% of blaZ-positive PSSA. Conclusions: In Australia, PSSA bacteremia is not caused by the expansion of a single clone. Approximately 10% of S. aureus classified as penicillin-susceptible by the Vitek® 2 harbored blaZ. Consequently, we recommend that confirmation of Vitek® 2 PSSA be performed using an alternative method, such as disc diffusion with careful interpretation of the zone edge
Genetic solutions through breeding counteract climate change and secure barley production in Australia
Full text linkClimate changes threaten global sustainable food supply by reducing crop yield. Estimates of future crop production under climate change have rarely considered the capacity of genetic improvement in breeding high-yielding and stress-tolerant crop varieties. We believe that technological advancements and developing climate-resilient crop varieties may offset the adverse effects of climate change. In this study, we examined the historical record of barley breeding and yield, and the trends of climate changes over the past 70 years in Australia. We related the selection of fast development varieties to yield improvement, and revealed the genetic connections of fast development and yield potential through genome-wide association studies. Historical records show that Australia's barley yield has experienced a steady growth despite that the seasonal production window has been shortened due to increased risk of frost damage at flowering stage and terminal heat during maturity since the 1970s. The increase in yield is largely the result of higher yield capacity of the more recently developed varieties that develop faster to counteract the impact of increased terminal heat. We also show that the changing temperature may soon reach a critical point that dramatically changes the barley flowering behaviour to impact yield by pushing its growth beyond the seasonal production window to face increasing frost damage. For the first time, we provide evidence that the effects of climate change on crop production might be less severe than what is currently believed because the advancement of technologies and development of climate-resilient crop varieties may mitigate the adverse effect of climate change to some extent. The greater use of genetic techniques in crop breeding will play a vital role in sustainable global food production in the era of climate change
High-Strength formed coke from torrefied biomass and its blend with noncaking coal
No full textIn continuation of our previous study on production of high-strength metallurgical coke from torrefied softwood (cedar), we studied coke production from a mixture of torrefied cedar (TC) and noncaking coal by pulverization to sizes <100 μm, mixing, binderless hot briquetting, and carbonization. These sequential processes produced coke with a tensile strength of 5–17 MPa, which was equivalent to or greater than that of conventional coke (5–6 MPa), from TC-coal mixtures over the entire ranges of TC mass fraction in briquette of 0–100%, torrefaction temperature of 250–300 °C, and choice of coal (sub-bituminous or medium-volatile bituminous coal). The mixing of TC and coal hindered densification of coke due to hindrance of shrinkage of more-shrinkable TC-derived particles during the carbonization under many of the conditions. Nevertheless, positive synergy occurred in the coke strength at TC mass fractions of over 50%, where coal-derived particles were dispersed in the matrix of TC-derived particles, bonded to them during the carbonization, and behaved as a reinforcement of the matrix. The bonding between TC-derived and coal-derived primary particles was revealed by scanning electron microscopy. Copulverization of mixed TC and coal to sizes <40 μm before the briquetting gave cokes having strengths as high as 23–28 MPa. The fine pulverization increased the frequencies of mutual bonding of TC-derived particles and coal-derived particles and bonding between TC-derived and coal-derived particles per coke volume. The strength of coke from the TC-coal mixture generally followed volume-based additivity of strengths of cokes from TC and coal. This was realized by mixing primary particles of TC and coal within ≈10 μm scale or even smaller
Defining employability in the veterinary context, and the capabilities enhancing veterinary success
Full text linkThis thesis explores employability in the veterinary context and presents stakeholder-led evidence for the capabilities contributing to a veterinarian’s success, thus validating the application of this concept in veterinary education. Employability had been widely applied to other professional contexts, but seldom discussed in veterinary or medical education, where the dominant paradigm is competency.
The first paper of this thesis argues to refocus the goal of veterinary education beyond competence to the broader aim of success, from the perspective of multiple stakeholders including the veterinarian. The rest of the thesis presents multi-stakeholder evidence via mixed-methods research (case study interviews, a large-scale semi-quantitative survey and a modified Delphi process) to highlight those capabilities most important for a successful and satisfying career as a veterinarian.
This thesis presents a considerable body of evidence contributing to the outcomes of the VetSet2Go project (www.vetset2go.edu.au), which culminated in the Framework for Veterinary Employability. This multinational collaborative project defined employability in the veterinary context as “a set of adaptive personal and professional capabilities that enable a veterinarian to gain employment, contribute meaningfully to the profession, and develop a career pathway that achieves satisfaction and success”, emphasising the ‘self’ as core to this process and stretching the focus beyond the initial ‘getting a job’ towards a fulfilling and long career as a veterinarian.
In this thesis, success is defined around veterinarians experiencing enjoyment and personal satisfaction with their work, developing proficiency, and maintaining passion for the profession. The capabilities found to be most important for employability, and therefore success as a veterinarian were: effective communication (with clients and colleagues), teamwork, enthusiasm, diligence, reliability, willingness to learn, honesty and ethical behaviour, resilience, life balance, technical knowledge and skills, emotional intelligence, workflow management and empathy and compassion. There was acknowledgement of changing emphasis of capabilities over different career stages (initial employment, transition to practice and longevity in the profession), with work-life balance, continual learning, goal setting and business skills most important for long term success. The relationship between the veterinarian (self) and their work, enabled by engagement, meaning and purpose, and respect for their profession was a key finding of the survey, and illustrative of how to achieve personal satisfaction and well-being within the profession.
There was striking convergence of the stakeholder views throughout the different studies in this thesis. Participants included recent graduate and employee veterinarians, employer veterinarians, non-veterinary employers, veterinary nurses and technical staff, academics, and policy makers, with multiple international regions, clinical and non-clinical contexts, genders and ages represented. With some minor exceptions, all stakeholders rated and ranked capabilities very similarly. The most notable exception was veterinary academics who ranked communicating with clients and work-life balance lower than other stakeholder groups, sounding a note of caution for those responsible for curriculum development.
This work has highlighted many of the important capabilities which are under-emphasised in current competency frameworks and has offered a hierarchical importance of capabilities which competency frameworks lack. The outcomes of this thesis provide a complement to the dominant paradigm of competency, bring needed focus to mental health and healthy working lives, and offer a complementary approach for veterinary educators to consider when preparing veterinary students for a successful and satisfying career
Dietary characteristics of the ecologically-important fish species Centroberyx gerrardi, including discussion of resource partitioning among species of Berycidae in Australia
No full textData for the Berycidae, collected during extensive past scientific surveys, were used to quantify the depth distributions of the four species of Centroberyx and two of Beryx found in Australian coastal waters and thus elucidate the extent to which these species are partitioned by region and depth. The dietary, jaw and dentitional characteristics of the ecologically and fishery-important Centroberyx gerrardi were then determined, providing the first such account for any Centroberyx species. While Centroberyx gerrardi, Centroberyx lineatus, Beryx splendens and Beryx decadactylus are found throughout southern Australia, the last two species extend further up the west and east coasts. Centroberyx australis occurs on the lower half of the west coast eastwards to the central south coast and Centroberyx affinis on the lower half of the east coast. The four Centroberyx species typically occur at depths 350 m. On the south coast of Western Australia, depth distributions undergo an overlapping progressive gradation, from C. lineatus in inshore and nearshore shallow waters, to C. gerrardi and C. australis in nearshore deep waters, and then B. splendens and B. decadactylus in offshore deep waters. The main dietary categories of C. gerrardi change with increasing body size from crabs and isopods in small fish to teleosts in the largest fish, in which volumetrically they constituted >60% of the stomach contents. The wide range of teleost prey (at least 39 species from 33 families) ingested by C. gerrardi would be valuable to this species if continuing climate change or other anthropogenic effects lead to alterations in the composition of potential prey. Differences between depth distributions account for the fish prey of C. gerrardi comprising nearshore species, such as those of clupeids, congrids, pomacentrids and platycephalids, whereas those of B. splendens (from studies elsewhere) are dominated by myctophids, which are abundant in deeper waters. The combination of a large mouth and numerous, exclusively small teeth (edentulate morphotype) strongly suggest that C. gerrardi is a suction feeder adapted to engulfing larger prey. While the co-occurring and likewise commercially-fished Oplegnathus woodwardi also ingests substantial volumes of crabs and teleosts, its diet is distinguished from C. gerrardi by large volumes of poriferans and appreciable volumes of echinoderms, likewise reflecting feeding specialisations. Although differing in depth distributions and dietary compositions, berycid species in general are close to the apex of the food web
Prevalence and molecular characterisation of Trypanosoma spp. in two wild koala populations; Moreton Bay, Queensland and Mount Lofty, South Australia
Full text linkThe koala (Phascolarctos cinereus) is an iconic Australian marsupial that is under threat of extinction across two thirds of its range, with populations recently listed as ‘endangered’ in Queensland (QLD), New South Wales (NSW) and the Australian Capital Territory (ACT). Many risk factors have been implicated in the koala population decline, including habitat loss, vehicle collisions, dog attack and infectious diseases such as chlamydiosis and koala immune deficiency syndrome caused by koala retrovirus (KoRV).
Trypanosomes are blood-borne protozoan parasites that can infect all classes of mammals and are known to cause serious disease in humans and domestic livestock worldwide. Recent studies have identified numerous Trypanosoma species in a range of Australian marsupials, including the koala which is known to harbour up to six species in either single or mixed infections: Trypanosoma irwini, Trypanosoma gilletti, Trypanosoma copemani, Trypanosoma vegrandis, Trypanosoma noyesi and Trypanosoma sp. AB-2017. Importantly, preliminary data from analyses of hospitalised koalas in QLD suggest that trypanosome infections (alone or with concurrent diseases) may adversely affect koala health and survival.
Whilst a large number of studies have been conducted on chlamydia and KoRV, there is still a paucity of research investigating the prevalence, diversity and clinical impact of trypanosomes in koalas. In particular, there is a dearth of research comprising random, representative samples from various wild koala populations across Australia, including more stable populations from South Australia (SA).
This descriptive cross-sectional study utilised nested PCR, targeting partial fragments of the nuclear 18S ribosomal RNA (18S rRNA) gene, to screen blood samples from wild-caught koalas for the presence of trypanosomes. Samples were randomly collected from koalas belonging to two distinct wild populations; Moreton Bay, Queensland (QLD) (n= 72) and Mount Lofty, South Australia (SA) (n= 89). The overall prevalence of Trypanosoma in both populations was 47.2% (76/161; 95% CI: 39.3-55.2%). The prevalence of trypanosomes in koalas from Moreton Bay was 80.6% (58/72; 95% CI: 69.5-88.9%), whereas the prevalence in koalas from Mount Lofty was significantly lower: 20.2% (18/89; 95% CI: 12.4-30.1%). Sanger sequencing of PCR positive products was performed and phylogenetic analysis conducted on the partial 18S rDNA fragments obtained. A total of 35 Trypanosoma isolates from Moreton Bay koalas were identified as Trypanosoma irwini (n= 36), with intra-specific genetic variations ranging from 0% - 2.99%. Remaining QLD isolates (n=16) were identified as Trypanosoma gilletti, with genetic distances ranging from 0% - 1.20%. These results are similar to findings from previous studies of hospitalised koalas from QLD and NSW.
All Trypanosoma isolates from the Mount Lofty population (n = 18) formed a unique, highly diverse clade within the Trypanosoma cruzi clade of trypanosomes. These novel sequences displayed a high genetic variation amongst each other (genetic distances = 0% - 7.04%) and from their most closely related species (T. sp 1EA-2008) (genetic distances = 1.90% - 7.73%). To the best of the author’s knowledge, this is the first report of trypanosomes in koalas from SA. The unique phylogenetic position of the isolates identified, associated with a relatively high genetic distance from their most closely related known Trypanosoma sp., suggests that they may potentially represent novel Trypanosoma spp.. Further analyses of full-length 18S sequences and additional loci are required to confirm this finding and reliably delimit the species.
Sanger sequencing of seven PCR positive isolates from Moreton Bay koalas revealed mixed chromatograms and were excluded from phylogenetic analyses. Further analyses using next-generation metabarcoding are required to identify and characterise mixed trypanosome infections in all positive samples detected in the present study, particularly those that produced mixed Sanger sequencing chromatograms.
This study provides valuable novel baseline data which will contribute to the growing knowledge base of Australian trypanosomes, and future studies on the potential impact of Trypanosoma spp. (with and without concurrent infectious diseases) on the health and conservation of koalas
Impact of folic acid in modulating antioxidant activity, osmoprotectants, anatomical responses, and photosynthetic efficiency of Plectranthus amboinicus under salinity conditions
Full text linkSalinity is a major threat to the sustainability of agricultural production systems. Salt stress has unfavorable implications on various plant physio-morphological and biochemical reactions, causing osmotic and ionic stress. Exogenously applied folic acid (FA) may at least provide one mechanism to evade the injurious stress effects of saline irrigation water on Plectranthus amboinicus. In this regard, two pot trials were performed during the 2018–2019 and 2019–2020 seasons in an open greenhouse of an experimental farm (29°17'N; 30°53'E) in Fayoum, Egypt. We tested four levels of saline irrigation water (SW): 34, 68, and 102 mM NaCl, plus tap water as the control = 0), combined with FA at three concentrations (25 and 50 μM, plus spray with distilled water as the control = 0). The growth parameters, biochemistry, physiology, elemental leaf status, essential oil content, and anatomical responses were assessed. Salt markedly reduced photosynthetic productivity [Fv/Fm and performance index (PI)], total chlorophyll [soil plant analysis development (SPAD)], and leaf osmoprotectant compounds, i.e., total soluble sugars (TSS), free amino acids, proline, and total phenolics, thus hampering P. amboinicus growth and essential oil yield. However, the addition of FA as a foliar spray to P. amboinicus irrigated with saline water induced increases in Fv/Fm, SPAD, and PI. These were linked with enriched stem anatomical structures, leaf osmoprotectant compounds, and enhanced leaf enzymatic activity, e.g., superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, glutathione, ascorbic acid, and antioxidant content. Under salt stress, supplementation of 25 and 50 μM FA increased the growth and production of essential oil by 27.8 and 55.6%, respectively, compared with no applied FA. The highest growth characteristics and elemental leaf contents were obtained when P. amboinicus was irrigated with 0 mM saline water and treated foliarly with 50 μM of FA compared with non-treated plants. Overall, these data showed that foliar spraying with FA reduces the impact of salt stress on P. amboinicus irrigated with saline water
Identification of a novel heterozygous DYSF variant in a large family with a dominantly‐inherited dysferlinopathy
No full textAims
Dysferlinopathy is an autosomal recessive muscular dystrophy, caused by bi-allelic variants in the gene encoding dysferlin (DYSF). Onset typically occurs in the second to third decade and is characterised by slowly progressive skeletal muscle weakness and atrophy of the proximal and/or distal muscles of the four limbs. There are rare cases of symptomatic DYSF variant carriers. Here, we report a large family with a dominantly inherited hyperCKaemia and late-onset muscular dystrophy.
Methods and Results
Genetic analysis identified a co-segregating novel DYSF variant [NM_003494.4:c.6207del p.(Tyr2070Metfs*4)]. No secondary variants in DYSF or other dystrophy-related genes were identified on whole genome sequencing and analysis of the proband's DNA. Skeletal muscle involvement was milder and later onset than typical dysferlinopathy presentations; these clinical signs manifested in four individuals, all between the fourth and sixth decades of life. All individuals heterozygous for the c.6207del variant had hyperCKaemia. Histological analysis of skeletal muscle biopsies across three generations showed clear dystrophic signs, including inflammatory infiltrates, regenerating myofibres, increased variability in myofibre size and internal nuclei. Muscle magnetic resonance imaging revealed fatty replacement of muscle in two individuals. Western blot and immunohistochemical analysis of muscle biopsy demonstrated consistent reduction of dysferlin staining. Allele-specific quantitative PCR analysis of DYSF mRNA from patient muscle found that the variant, localised to the extreme C-terminus of dysferlin, does not activate post-transcriptional mRNA decay.
Conclusions
We propose that this inheritance pattern may be underappreciated and that other late-onset muscular dystrophy cases with mono-allelic DYSF variants, particularly C-terminal premature truncation variants, may represent dominant forms of disease
Changes in microbial community composition drive the response of ecosystem multifunctionality to elevated ozone
No full textIncreasing tropospheric ozone poses a potential threat to both above- and belowground components of the terrestrial biosphere. Microorganisms are the main drivers of soil ecological processes, however, the link between soil microbial communities and ecological functions under elevated ozone remains poorly understood. In this study, we assessed the responses of three crop seedlings (i.e., soybean, maize, and wheat) growth and soil microbial communities to elevated ozone (40 ppb O3 above ambient air) in a pot experiment in the solardomes. Results showed that elevated ozone adversely affected ecosystem multifunctionality by reducing crop biomass, inhibiting soil extracellular enzyme activities, and altering nutrient availability. Elevated ozone increased bacterial and fungal co-occurrence network complexity, negatively correlated with ecosystem multifunctionality. Changes in the relative abundance of some specific bacteria and fungi were associated with multiple ecosystem functioning. In addition, elevated ozone significantly affected fungal community composition but not bacterial community composition and microbial alpha-diversity. Crop type played a key role in determining bacterial alpha-diversity and microbial community composition. In conclusion, our findings suggest that short-term elevated ozone could lead to a decrease in ecosystem multifunctionality associated with changes in the complexity of microbial networks in soils
Interactive effect of boron application methods and Boron-Tolerant Bacteria (Bacillus sp. MN54) improves nodulation, grain yield, profitability and biofortification of kabuli chickpea grown under irrigated and rainfed conditions
No full textBoron (B) is a vital micronutrient essential for human and plants. This two-year field study was conducted to check the efficacy of B application methods along with BTB (Bacillus sp. MN54) to improve nodulation, grain yield, profitability, and B biofortification of kabuli chickpea under irrigated and rainfed conditions. The B application methods consisted of seed coating (1.5 g B kg−1 seed), foliar application (25 mg B L−1 of water), soil application (1 kg B ha−1) and osmopriming (1 mg B L−1 of water solution) [water spray, hydropriming and untreated seeds being taken as control], with and without BTB inoculation grown under irrigated (Layyah) and rainfed (Chakwal) conditions. Interactive effects among B application, BTB inoculation and experimental location showed that B osmopriming coupled with BTB strain recorded maximum 1000-grains weight (24%), grain yield (41%) and biological yield (50%) compared with untreated seed under rainfed conditions while it was at par with B soil application. With respect to B-grain concentration, foliar application of B observed more B contents (86%) compared with control. Economic analysis showed that osmopriming of B along with BTB had highest economic return ($1994.3 ha−1) and benefit cost ratio (3.8) during 2020–21 under rainfed condition of Chakwal. Osmopriming of chickpea seed with B, combined with BTB (Bacillus sp. MN54) inoculation improved nodulation, grain yield and biofortification, profitability and B biofortification of kabuli chickpea under rainfed and irrigated condition. Moreover, rainfed conditions of Chakwal proved more productive with respect to chickpea cultivation