Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.

Introduction: Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples. Methods: This pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing. Results: Non-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads. Discussion: By increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system.

IMPORTANCE: Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.

Impact of wastewater treatment upgrade and nitrogen removal on bacterial communities and their interactions in eutrophic prairie streams.

Eutrophication can impact bacteria by altering fluxes and processing of nutrients and organic matter. However, relatively little is known of how bacterial communities, diversity, and interactions with phytoplankton might respond to nutrient management. We used 16S rRNA amplicon sequencing to compare bacterial assemblages in the water column upstream (control) and downstream (impact) of a wastewater treatment plant (WWTP) located on a eutrophic prairie stream. Sampling occurred before (2012) and after (2018) the 2016 biological nutrient removal (BNR) upgrade that removed >90% of nitrogen (N, mainly NH4+). Multivariate ordination suggested that effluent-impacted bacterial communities were associated mainly with elevated NH4+ concentrations before the upgrade, whereas those after BNR were characteristic of reference systems (low NO3-, diverse regulation). Genera such as Betaproteobacteria and Rhodocyclacea were abundant at impacted sites in 2012, whereas Flavobacterium and a potential pathogen (Legionella) were common at impacted sites in 2018. Nitrifier bacteria (Nitrospira and Nitrosomonas) were present but rare at all sites in 2012, but recorded only downstream of the WWTP in 2018. Generalized additive models showed that BNR reduced bacterial diversity, with ∼70% of the deviance in diversity explained by hydrology, pH, nutrients, and phytoplankton abundance. Overall, NH4+ removal reduced symptoms of cultural eutrophication in microbe assemblages.

The effectiveness of play as an intervention using International Classification of Functioning outcome measures for children with disabilities - a systematic review and meta-synthesis.

PURPOSE: Over 240 million children worldwide experience inequities due to disablement/disability. Play is important for children's global development, to enable participation in life, and has been used in therapeutic settings. The purpose of this systematic review is to determine the effectiveness of play used in therapy for children with disabilities, to explore ways that play is used in therapy, and to classify and map outcome measures used in play-based interventions to the International Classification of Functioning. METHODS: A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. RESULTS: The search yielded 22 articles eligible for inclusion. A meta-analysis found significant heterogeneity for play-based intervention outcomes, precluding estimates of effectiveness. Body function and structure outcomes accounted for 61% of reported outcome measures. CONCLUSION: There is a trend towards a small positive effect of play used in therapy for children with disabilities, but certainty of the effect is poor, and replication difficult due to heterogeneous reports of how play is used. Research aims and outcome measures focusing on meaningful aspects of activity and participation in addition to body function and structure domains of the International Classification of Functioning should be considered for play-based interventions for children with disabilities.

Play-based interventions trend towards a positive effect on ICF outcomes, but the certainty of effect is limited.Play is used in diverse ways making it a versatile method to promote engagement or deliver therapy to a wide variety of children with disabilities.Play-based studies measuring outcomes solely related to body function and structure domains of the ICF may not capture the broader holistic benefits of play.When using play in clinical practice, professionals should consider the child's personal and environmental factors and the influence of play on activity and participation.

Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle.

BACKGROUND: Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD by confirming the presence of causative pathogens and to support antimicrobial selection. However, given that bacterial culture takes up to a week and early intervention is critical for treatment success, culture has limited utility for informing rapid therapeutic decision-making. In contrast, metagenomic sequencing has the potential to quickly resolve all nucleic acid in a sample, including pathogen biomarkers and antimicrobial resistance genes. In particular, third-generation Oxford Nanopore Technology sequencing platforms provide long reads and access to raw sequencing data in real-time as it is produced, thereby reducing the time from sample collection to diagnostic answer. The purpose of this study was to compare the performance of nanopore metagenomic sequencing to traditional culture and sensitivity methods as applied to nasopharyngeal samples from segregated groups of chronically ill feedlot cattle, previously treated with antimicrobials for nonresponsive pneumonia or lameness. RESULTS: BRD pathogens were isolated from most samples and a variety of different resistance profiles were observed across isolates. The sequencing data indicated the samples were dominated by Moraxella bovoculi, Mannheimia haemolytica, Mycoplasma dispar, and Pasteurella multocida, and included a wide range of antimicrobial resistance genes (ARGs), encoding resistance for up to seven classes of antimicrobials. Genes conferring resistance to beta-lactams were the most commonly detected, while the tetH gene was detected in the most samples overall. Metagenomic sequencing detected the BRD pathogens of interest more often than did culture, but there was limited concordance between phenotypic resistance to antimicrobials and the presence of relevant ARGs. CONCLUSIONS: Metagenomic sequencing can reduce the time from sampling to results, detect pathogens missed by bacterial culture, and identify genetically encoded determinants of resistance. Increasing sequencing coverage of target organisms will be an essential component of improving the reliability of this technology, such that it can be better used for the surveillance of pathogens of interest, genetic determinants of resistance, and to inform diagnostic decisions.

Metagenomic and metatranscriptomic analysis reveals enrichment for xenobiotic-degrading bacterial specialists and xenobiotic-degrading genes in a Canadian Prairie two-cell biobed system.

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, the microbiomes in these environments remain largely understudied both taxonomically and functionally. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

Adapting Traditional Healing Values and Beliefs into Therapeutic Cultural Environments for Health and Well-Being.

Although research has long established that interaction with the natural environment is associated with better overall health and well-being outcomes, the Western model mainly focuses on treating symptoms. In Aotearoa/New Zealand, the Indigenous Maori have long demonstrated significantly more negative health outcomes than non-Maori. Little research has examined the causes compared to Western populations or the role of the natural environment in health outcomes for Maori. An exploration of rongoa Maori (traditional healing system) was conducted to ascertain the importance of landscape in the process of healing. Eight rongoa healers or practitioners took part in semi-structured narrative interviews from June to November 2020. Transcribed interviews were analysed using an interpretative phenomenological analysis and Kaupapa Maori techniques. The findings show how rongoa is underpinned by a complex set of cultural values and beliefs, drawing from the connection to wairua (spirit), tinana (body), tikanga and whakaora (customs and healing), rakau (plants), whenua (landscape) and whanau (family). Incorporating such constructs into the landscape can foster our understanding of health and well-being and its implications for conceptualising therapeutic environments and a culturally appropriate model of care for Maori and non-Maori communities.

Uptake and Engagement of Activities to Promote Native Species in Private Gardens.

Activities undertaken by householders in their gardens have huge potential to enhance city-wide biodiversity, but programs aimed at activating householders require an understanding of the factors encouraging or acting as barriers to the uptake of different kinds of activities. We provided 42 householders with two species-enhancing activities, selected from six possibilities, free-of-charge (to remove the barrier of initial cost). We collected socio-demographic data as well as information on knowledge of common urban species, pro-environmental behaviors and nature connectedness. We monitored ongoing engagement at two time points: 1 and 6 months. Characteristics of householders opting for different activities varied in terms of their degree of environmental engagement, their knowledge about common species, and the size of their gardens; e.g., bird feeders and bee planters were popular with people who did not know the names of common species and were not particularly engaged in pro-environmental activities respectively, whereas lizard habitat creation was attractive to people who were already engaged in wildlife gardening activities. Cost to continue with activities was a significant barrier for some people, but most householders were willing to practice relatively inexpensive activities in small spaces. Esthetics was an important factor to be considered when enhancing invertebrate habitat (e.g., bug hotels are more attractive than log piles, and planters for bees contain colorful flowers). A commonly cited barrier was lack of information about wildlife-friendly activities, despite much being available online. Most participants (85%) talked about their activities with others, potentially acting as influencers and shifting social norms.

Metatranscriptomic Insights Into the Response of River Biofilm Communities to Ionic and Nano-Zinc Oxide Exposures.

Manufactured Zn oxide nanoparticle (ZnO-NP) are extensively used world-wide in personal care and industrial products and are important contaminants of aquatic environments. To understand the overall impact of ZnO-NP contamination on aquatic ecosystems, investigation of their toxicity on aquatic biofilms is of particular consequence, given biofilms are known sinks for NP contaminants. In order to assess alterations in the functional activity of river microbial biofilm communities as a result of environmentally-relevant ZnO-NP exposure, biofilms were exposed to ionic zinc salt or ZnOPs that were uncoated (hydrophilic), coated with silane (hydrophobic) or stearic acid (lipophilic), at a total concentration of 188 µg l-1 Zn. ICP-MS analyses of biofilms indicated ZnO-NP concentrated in the biofilms, with hydrophilic, hydrophobic, and lipophilic treatments reaching 0.310, 0.250, and 0.220 µg Zn cm-2 of biofilm, respectively, while scanning transmission X-ray microspectroscopy (STXM) analyses of biofilms confirmed that Zn was extensively- and differentially-sorbed to biofilm material. Microbial community composition, based on taxonomic affiliation of mRNA sequences and enumeration of protozoa and micrometazoa, was not affected by these treatments, and the total transcriptional response of biofilms to all experimental exposures was not indicative of a global toxic-response, as cellular processes involved in general cell maintenance and housekeeping were abundantly transcribed. Transcripts related to major biological processes, including photosynthesis, energy metabolism, nitrogen metabolism, lipid metabolism, membrane transport, antibiotic resistance and xenobiotic degradation, were differentially expressed in Zn-exposures relative to controls. Notably, transcripts involved in nitrogen fixation and photosynthesis were decreased in abundance in response to Zn-exposure, while transcripts related to lipid degradation and motility-chemotaxis were increased, suggesting a potential role of Zn in biofilm dissolution. ZnO-NP and ionic Zn exposures elicited generally overlapping transcriptional responses, however hydrophilic and hydrophobic ZnO-NPs induced a more distinct effect than that of lipophilic ZnO-NPs, which had an effect similar to that of low ionic Zn exposure. While the physical coating of ZnO-NP may not induce specific toxicity observable at a community level, alteration of ecologically important processes of photosynthesis and nitrogen cycling are an important potential consequence of exposure to ionic Zn and Zn oxides.

The impacts of ageing on connection to nature: the varied responses of older adults.

Access to nature is important for wellbeing at all ages with significant benefits for older adults. This paper explores the impacts of older adults' age-related health conditions on nature connection, their responses to the changes and identifies the types of nature connections and greenspaces available to and prioritised by older adults. It is based on the experiences of 72 New Zealand older adults aged 65-99, living in family homes, down-sized homes and rest homes. Data were gathered through interviews, photographs and assessments of the natural features of their home environment. Nearly all participants experienced age-related changes in their ways of connecting with nature as living accommodation and especially health and mobility changed. Reduced mobility was the primary factor limiting nature experiences especially for frailer adults. In contrast, for 'younger' older adults, retirement can provide more time and opportunities to engage with nature. Nature connection opportunities are valued by nearly all adults irrespective of age and health. Accessible nature opportunities in the nearby and home environment should be available to all adults irrespective of health and accommodation type. Dedicated resources need to be provided to ensure these opportunities are present for the frailest whose opportunities to have direct contact with nature are frequently absent.

Transport behaviours among older teenagers from semi-rural New Zealand.

OBJECTIVE: Transport impacts teenagers by affecting their autonomy and independent access to activities. This manuscript reports descriptive findings of transport behaviours among teenagers in Southland, New Zealand, and discusses the implications of these for public health and policy. METHODS: An online survey was implemented to investigate transport among respondents aged 16 years and older from twelve secondary schools. Two methods of survey distribution were used (in-class and at home). Descriptive results were analysed using Stata. RESULTS: Response rate was 71.5% (n=775). The most common forms of transport were as a passenger in a car and walking. Two-thirds of participants had some form of driving licence. Half the sample expressed frustration at being unable to access activities. Significant gender differences existed regarding transport and types of activities accessed. Licence status was associated with physical activity, screen time and transport frustration. CONCLUSIONS: The transport decisions made by teenagers, in aggregate, have implications for policy and infrastructure, and findings provide a foundation for discussions around potential changes to driver education programming, the school uniform policy in New Zealand and further research. Implications for public health: Inquiring about everyday transport habits, outside of the trip to school, and activities accessed provided data about an under-researched group, supporting the ecological approach to transport in the context of public health.

The importance of urban gardens in supporting children's biophilia.

Exposure to and connection with nature is increasingly recognized as providing significant well-being benefits for adults and children. Increasing numbers of children growing up in urban areas need access to nature to experience these benefits and develop a nature connection. Under the biophilia hypothesis, children should innately affiliate to nature. We investigated children's independent selection of spaces in their neighborhoods in relation to the biodiversity values of those spaces, in three New Zealand cities, using resource-selection analysis. Children did not preferentially use the more biodiverse areas in their neighborhoods. Private gardens and yards were the most preferred space, with the quality of these spaces the most important factor defining children's exposure to nature. Children's reliance on gardens and yards for nature experiences raises concerns for their development of a nature connection, given disparities in biodiversity values of private gardens in relation to socioeconomic status, and the decline in sizes of private gardens in newer urban developments.

A more "normal" life: residents', family, staff, and managers' experience of active support at a residential facility for people with physical and intellectual impairments.

BACKGROUND: Active support (AS) has gained popularity as an approach for assisting people with intellectual disability to engage more fully in everyday activities. Although research has identified changes in the extent that residents are engaged in meaningful activities, the experience of stakeholders such as residents, staff, and family in AS is underexplored. METHOD: A general inductive approach was used to analyse focus group and interview transcripts of residents (n = 4), staff (n = 13), and family (n = 2) about their experience of involvement in an AS pilot project at one residential care facility in New Zealand. RESULTS: Three superordinate themes common to all stakeholders' experiences emerged: "living normal lives," "caring means doing with," and "engaging with risk." CONCLUSION: Transitioning to AS had been enriching but at times challenging for all stakeholders. Valuing resident autonomy and preparedness for greater exposure to risk are significant considerations in the implementation of AS.

Through the eyes of young people: favourite places for physical activity.

INTRODUCTION: A decrease in physical activity amongst adolescents has been observed and it is well documented that low levels of activity are associated with poor health. In an attempt to understand factors that influence physical activity (PA) in young people research was undertaken with high school students in New Zealand to identify preferred places for PA and establish factors that they felt influenced levels of PA. METHODS: One hundred males and 73 females in year nine (aged 12-13) in health and physical education classes completed mapping exercises in which they delineated favourite and least favourite places for PA, where they went on a particular Sunday, how they got there and what they did, and chosen after-school activities and how they got there. RESULTS: Open public spaces were the most favoured places for PA with a nearby beach and park most frequently cited. Specific physical activities, having fun, and having friends to do an activity with were the most frequently cited reasons for liking these places. An industrial harbour area, other schools, and cemeteries were the least favoured places. Less than 2% biked somewhere on the Sunday surveyed and only 23% walked somewhere. The majority were driven to activities by car and a similar reliance on cars was observed for after-school activities. CONCLUSIONS: A combination of environmental and social factors is important in both encouraging and discouraging PA and should be taken into account when seeking to enhance PA of young people.

The productive partnerships framework: harnessing health consumer knowledge and autonomy to create and predict successful rehabilitation outcomes.

PURPOSE: This article examines the role of power distribution in partnerships between health consumers and professionals in determining successful desired outcomes, and the contributing role of consumer knowledge and autonomy. Recognition is given to the lack of practical tools, from both consumer and professional perspectives, to assist in the creation of productive partnerships. METHOD: A conceptual analysis of the notions of consumer knowledge and autonomy in the context of outcomes, followed by the development of a prototype framework that aims to facilitate productive health partnerships. RESULTS: The authors present prototype tools, which are shared between health consumer and professional, for identifying the strength of their cumulative power relative to their alignment to a common desired outcome (goal). The tools provide a choice of power contexts for the partnership to operate within, and a simple method for testing alignment to a common goal. CONCLUSION: Increased health consumer knowledge and autonomy is associated with improved outcomes and these can in turn be influenced through productive health partnerships. The P2 framework is one approach to establishing robust working relationships between health professionals and consumers.

Patterns and predictors of uptake and adherence to cardiac rehabilitation.

PURPOSE: Despite the recognized effectiveness of cardiac rehabilitation (CR), these programs are frequently reported to be underutilized. This prospective study sought to describe the uptake of and adherence to phase 3 of a CR service in Glasgow, UK. METHODS: The study recorded psychological, social, and demographic characteristics of patients in an attempt to ascertain variables associated with failure to initiate attendance or poor adherence to the program. Consecutive patients (N = 91) were included in the study before inviting them to participate in a comprehensive CR program. RESULTS: Thirty-one (35%) patients eligible to attend phase 3 CR indicated no intention to attend the program. A further 31 (35%) patients were considered nonadherent to the program. No factors predicting initiation or adherence emerged as significant. More than two-thirds of the patients eligible for CR did not engage in the program either through failure to initiate rehabilitation or poor adherence following initiation. CONCLUSION: Alternative means of service delivery should be considered to broaden access to CR. Psychological interventions aimed at enhancing motivation and adherence should be developed and appropriately evaluated.