Antimicrobial susceptibility and genomic analysis of Histophilus somni isolated from cases of bovine respiratory disease in Autralian feedlot cattle.

Histophilus somni is a prevalent commensal organism of the upper respiratory tract of cattle and a major causative agent of bovine respiratory disease (BRD) and other syndromes including myocarditis and infectious thromboembolic meningoencephalitis. This study investigated the antimicrobial susceptibility and phylogenetic relationships of H. somni isolates obtained from lung, heart, and other tissues at post-mortem as well as nasal mucosa swabs from cases of BRD in Australian feedlots (2004-2019). Broth microdilution Minimal Inhibitory Concentration (MIC) assays were determined for 19 antimicrobials using three different media (CLSI approved Veterinary Fastidious Medium [VFM], Mueller-Hinton fastidious broth medium supplemented with yeast extract [MHF-Y] and Columbia Broth [CB] supplemented with 5% lysed horse blood). For all antimicrobials, MICs obtained using CB medium were identical or within 1 dilution step of the MICs obtained for VFM and MHF-Y media. Therefore, CB may be a suitable medium for H. somni antimicrobial susceptibility testing similar to MHF-Y medium. None of the 70 Australian H. somni isolates exhibited resistance to antimicrobials with CLSI breakpoints including those commonly used in the treatment of BRD in Australia (first-line tetracyclines [chlortetracycline and oxytetracycline], second-line macrolides [tulathromycin], and third-line extended-spectrum cephalosporin [ceftiofur]). Whole-genome sequence analysis of 65 H. somni isolates for genomic single nucleotide polymorphism differences identified four phylogenetic clusters, each containing isolates from different Australian states, feedlots and tissue sources that clustered together. These findings demonstrate limited genetic diversity and the absence of significant antimicrobial resistance among Australian isolates of H. somni isolated from feedlot cattle.

Psychometric evaluation of the Suicide Cognitions Scale-Revised (SCS-R).

The measurement of self-reported suicide risk can be complicated in medical settings due to patient apprehension about the potential consequences of self-disclosure. The Suicide Cognitions Scale (SCS) was designed to assess suicide risk by measuring a range of suicidogenic cognitions (e.g., hopelessness, perceived burdensomeness) collectively referred to as the suicidal belief system. The SCS's concurrent, known groups, and prospective validity for suicidal thoughts and behaviors have previously been supported. The present study examined the factor structure, known-groups, and concurrent validity of a revised, 16-item version of the SCS (SCS-R), which removed two items that explicitly used the word "suicide" and changed item scoring from a 1-5 to 0-4 scale, thereby improving the interpretation of scores. In a sample of 2,690 primary care patients presenting for routine medical care at one of six US military clinics, results of bifactor analysis supported the scale's unidimensionality. The SCS-R significantly differentiated participants with a history of suicide attempts and was significantly correlated with frequency of thoughts about death and self-harm during the previous 2 weeks. Results align with earlier research and provide psychometric support for the SCS-R.

Improving Suicide Risk Screening to Identify the Highest Risk Patients: Results From the PRImary Care Screening Methods (PRISM) Study.

PURPOSE: Over 95% of patients who screen positive on the Patient Health Questionnaire-9 (PHQ-9) suicide risk item do not attempt or die by suicide, which could lead to unnecessary treatment and/or misallocation of limited resources. The present study seeks to determine if suicide risk screening can be meaningfully improved to identify the highest-risk patients. METHODS: Patients eligible to receive medical treatment from the US Department of Defense medical system were recruited from 6 military primary care clinics located at 5 military installations around the United States. Patients completed self-report measures including the PHQ-9 and 16 items from the Suicide Cognitions Scale (SCS) during routine primary care clinic visits. Postbaseline suicidal behaviors (suicide attempts, interrupted attempts, and aborted attempts) were assessed by evaluators who were blind to screening results using the Self-Injurious Thoughts and Behaviors Interview. RESULTS: Among 2,744 patients, 13 (0.5%) engaged in suicidal behavior in the 30 days after screening and 28 (1.0%) displayed suicidal behavior in the 90 days after screening. Multiple SCS items differentiated patients with suicidal behavior less than 30 days after screening positive for suicide risk. Augmenting the PHQ-9 suicide risk item with SCS items improved the identification of patients who were most likely to have suicidal behavior within a month of screening positive without sacrificing sensitivity. CONCLUSION: Among primary care patients who screen positive for suicide risk on the PHQ-9, SCS items improved screening efficiency by identifying those patients who are most likely to engage in suicidal behavior within the next 30 days.

Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression.

Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman's correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake.

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types.

Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant bacterial taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. However, a few differentially abundant shared taxa were observed at family and genus levels. Furthermore, between-kit differences in alpha and beta diversity metrics at the amplicon sequence variant level were statistically indistinguishable. Therefore, both kits perform similarly in terms of 16S rRNA gene-based poultry microbiome analysis for the sample types analyzed in this study.

Effects of land-use change and related pressures on alien and native subsets of island communities.

Island species and habitats are particularly vulnerable to human disturbances, and anthropogenic changes are increasingly overwriting natural island biogeographic patterns. However, quantitative comparisons of how native and alien assemblages respond to human disturbances are scarce. Using data from 6,242 species of vertebrates, invertebrates and plants, from 7,718 sites on 81 islands, we model how land-use change, human population density and distance to the nearest road affect local assemblages of alien and native species on islands. We found that land-use change reduces both richness and abundance of native species, whereas the number and abundance of alien species are high in plantation forests and agricultural or urban sites. In contrast to the long-established pattern for native species (i.e., decline in species number with island isolation), more isolated islands have more alien species across most land uses than do less isolated islands. We show that alien species play a major role in the turnover of island assemblages: our models show that aliens outnumber natives among the species present at disturbed sites but absent from minimally-disturbed primary vegetation. Finally, we found a homogenization pattern for both native and alien assemblages across sites within most land uses. The declines of native species on islands in the face of human pressures, and the particular proneness to invasions of the more remote islands, highlight the need to reduce the intensity of human pressures on islands and to prevent the introduction and establishment of alien species.

Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota.

Although poultry microbiome discoveries are increasing due to the potential impact on poultry performance, studies examining the poultry respiratory microbiome are challenging because of the low microbial biomass and uniqueness of the avian respiratory tract, making it difficult to sample enough material for microbial analysis. Invasive sampling techniques requiring euthanasia are currently used to increase microbial mass for the analysis, thus making it impossible to sample individual birds longitudinally. In this study, we compared invasive (nasal wash, upper tracheal wash, lower tracheal wash, and lower respiratory lavage) and noninvasive (tracheal and choanal swabs) respiratory sampling techniques in two independent experiments by using 4-wk-old chickens. We first established the experimental baseline of respiratory microbiota by using invasive techniques to enable reasonable comparisons between sampling methods and between experiments. Although noninvasive sampling (live-bird swabs) resulted in lower 16S ribosomal RNA gene copy numbers compared with invasive sampling, live swabs were able to detect the dominant microbes captured by invasive techniques. Nevertheless, swabs from euthanatized birds were more reflective of the microbiota captured through invasive methods than live swab. Furthermore, from two separate experiments, we also demonstrated that respiratory microbiota sampling is highly reproducible, especially in the trachea and lower respiratory tract. Our study provides new insights and perspectives on decision making when sampling and studying poultry respiratory microbiota.

Viral Subpopulation Screening Guides in Designing a High Interferon-Inducing Live Attenuated Influenza Vaccine by Targeting Rare Mutations in NS1 and PB2 Proteins.

Influenza A viruses continue to circulate among wild birds and poultry worldwide, posing constant pandemic threats to humans. Effective control of emerging influenza viruses requires new broadly protective vaccines. Live attenuated influenza vaccines with truncations in nonstructural protein 1 (NS1) have shown broad protective efficacies in birds and mammals, which correlate with the ability to induce elevated interferon responses in the vaccinated hosts. Given the extreme diversity of influenza virus populations, we asked if we could improve an NS1-truncated live attenuated influenza vaccine developed for poultry (PC4) by selecting viral subpopulations with enhanced interferon-inducing capacities. Here, we deconstructed a de novo population of PC4 through plaque isolation, created a large library of clones, and assessed their interferon-inducing phenotypes. While most of the clones displayed the parental interferon-inducing phenotype in cell culture, few clones showed enhanced interferon-inducing phenotypes in cell culture and chickens. The enhanced interferon-inducing phenotypes were linked to either a deletion in NS1 (NS1Δ76-86) or a substitution in polymerase basic 2 protein (PB2-D309N). The NS1Δ76-86 deletion disrupted the putative eukaryotic translation initiation factor 4GI-binding domain and promoted the synthesis of biologically active interferons. The PB2-D309N substitution enhanced the early transcription of interferon mRNA, revealing a novel role for the 309D residue in suppression of interferon responses. We combined these mutations to engineer a novel vaccine candidate that induced additive amounts of interferons and stimulated protective immunity in chickens. Therefore, viral subpopulation screening approaches can guide the design of live vaccines with strong immunostimulatory properties.IMPORTANCE Effectiveness of NS1-truncated live attenuated influenza vaccines relies heavily on their ability to induce elevated interferon responses in vaccinated hosts. Influenza viruses contain diverse particle subpopulations with distinct phenotypes. We show that live influenza vaccines can contain underappreciated subpopulations with enhanced interferon-inducing phenotypes. The genomic traits of such virus subpopulations can be used to further improve the efficacy of the current live vaccines.

Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics.

Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.

Specific-pathogen-free Turkey model for reoviral arthritis.

Turkey arthritis reovirus (TARV) infections have been recognized since 2011 to cause disease and significant economic losses to the U.S. turkey industry. Reoviral arthritis has been reproduced in commercial-origin turkeys. However, determination of pathogenesis or vaccine efficacy in these turkeys can be complicated by enteric reovirus strains and other pathogens that ubiquitously exist at subclinical levels among commercial turkey flocks. In this study, turkeys from a specific-pathogen-free (SPF) flock were evaluated for use as a turkey reoviral arthritis model. One-day-old or 1-week-old poults were orally inoculated with TARV (O'Neil strain) and monitored for disease onset and progression. A gut isolate of turkey reovirus (MN1 strain) was also tested for comparison. Disease was observed only in TARV-infected birds. Features of reoviral arthritis in SPF turkeys included swelling of hock joints, tenosynovitis, distal tibiotarsal cartilage erosion, and gait defects (lameness). Moreover, TARV infection resulted in a significant depression of body weights during the early times post-infection. Age-dependent susceptibility to TARV infection was unclear. TARV was transmitted to all sentinel birds, which manifested high levels of tenosynovitis and tibiotarsal cartilage erosion. Simulation of stressful conditions by dexamethasone treatment did not affect the viral load or exacerbate the disease. Collectively, the clinical and pathological features of reoviral arthritis in the SPF turkey model generally resembled those induced in commercial turkeys under field and/or experimental conditions. The SPF turkey reoviral arthritis model will be instrumental in evaluation of TARV pathogenesis and reoviral vaccine efficacy.

Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens.

The digestive and respiratory tracts of chickens are colonized by bacteria that are believed to play important roles in the overall health and performance of the birds. Most of the current research on the commensal bacteria (microbiota) of chickens has focused on broilers and gut microbiota, and less attention has been given to layers and respiratory microbiota. This research bias has left significant gaps in our knowledge of the layer microbiome. This study was conducted to define the core microbiota colonizing the upper respiratory tract (URT) and lower intestinal tract (LIT) in commercial layers under field conditions. One hundred eighty-one chickens were sampled from a flock of >80,000 birds at nine times to collect samples for 16S rRNA gene-based bacterial metabarcoding. Generally, the body site and age/farm stage had very dominant effects on the quantity, taxonomic composition, and dynamics of core bacteria. Remarkably, ileal and URT microbiota were compositionally more related to each other than to that from the cecum. Unique taxa dominated in each body site yet some taxa overlapped between URT and LIT sites, demonstrating a common core. The overlapping bacteria also contained various levels of several genera with well-recognized avian pathogens. Our findings suggest that significant interaction exists between gut and respiratory microbiota, including potential pathogens, in all stages of the farm sequence. The baseline data generated in this study can be useful for the development of effective microbiome-based interventions to enhance production performance and to prevent and control disease in commercial chicken layers.IMPORTANCE The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in healthy, optimally performing chicken layers across all stages of the commercial farm sequence. Consequently, the study has set the groundwork for the development of interventions that seek to enhance production performance and to prevent and control infectious diseases through the modulation of gut and respiratory bacteria.

The Role of Care Management as a Population Health Intervention to Address Disparities and Control Hypertension: A Quasi-Experimental Observational Study.

OBJECTIVE: We studied whether care management is a pragmatic solution for improving population blood pressure (BP) control and addressing BP disparities between Blacks and Whites in routine clinical environments. DESIGN: Quasi-experimental, observational study. SETTING AND PARTICIPANTS: 3,964 uncontrolled hypertensive patients receiving primary care within the last year from one of six Baltimore clinics were identified as eligible. INTERVENTION: Three in-person sessions over three months with registered dietitians and pharmacists who addressed medication titration, patient adherence to healthy behaviors and medication, and disparities-related barriers. MAIN MEASURES: We assessed the population impact of care management using the RE-AIM framework. To evaluate effectiveness in improving BP, we used unadjusted, adjusted, and propensity-score matched differences-in-differences models to compare those who completed all sessions with partial completers and non-participants. RESULTS: Of all eligible patients, 5% participated in care management. Of 629 patients who entered care management, 245 (39%) completed all three sessions. Those completing all sessions on average reached BP control (mean BP 137/78) and experienced 9 mm Hg systolic blood pressure (P<.001) and 4 mm Hg DBP (P=.004) greater improvement than non-participants; findings did not vary in adjusted or propensity-score matched models. Disparities in systolic and diastolic BP between Blacks and Whites were not detectable at completion. CONCLUSIONS: It may be possible to achieve BP control among both Black and White patients who participate in a few sessions of care management. However, the very limited reach and patient challenges with program completion should raise significant caution with relying on care management alone to improve population BP control and eliminate related disparities.

Developing and validating the Communication Function Classification System for individuals with cerebral palsy.

AIM: The purpose of this study was to create and validate the Communication Function Classification System (CFCS) for children with cerebral palsy (CP), for use by a wide variety of individuals who are interested in CP. This paper reports the content validity, interrater reliability, and test-retest reliability of the CFCS for children with CP. METHOD: An 11-member development team created comprehensive descriptions of the CFCS levels, and four nominal groups comprising 27 participants critiqued these levels. Within a Delphi survey, 112 participants commented on the clarity and usefulness of the CFCS. Interrater reliability was completed by 61 professionals and 68 parents/relatives who classified 69 children with CP aged 2 to 18 years. Test-retest reliability was completed by 48 professionals who allowed at least 2 weeks between classifications. The participants who assessed the CFCS were all relevant stakeholders: adults with CP, parents of children with CP, educators, occupational therapists, physical therapists, physicians, and speech-language pathologists. RESULTS: The interrater reliability of the CFCS was 0.66 between two professionals and 0.49 between a parent and a professional. Professional interrater reliability improved to 0.77 for classification of children older than 4 years. The test-retest reliability was 0.82. INTERPRETATION: The CFCS demonstrates content validity and shows very good test-retest reliability, good professional interrater reliability, and moderate parent-professional interrater reliability. Combining the CFCS with the Gross Motor Function Classification System and the Manual Ability Classification System contributes to a functional performance view of daily life for individuals with CP, in accordance with the World Health Organization's International Classification of Functioning, Disability and Health.

Phylogenetic and cophylogenetic relationships of entomopathogenic nematodes (Heterorhabditis: Rhabditida) and their symbiotic bacteria (Photorhabdus: Enterobacteriaceae).

Mutualistic association between entomopathogenic Photorhabdus bacteria and Heterorhabditis nematodes represents one of the emerging model systems in symbiosis studies, yet little is known about this partnership from a coevolutionary perspective. Herein, we investigated phylogenetic and cophylogenetic relationships of Heterorhabditis and Photorhabdus strains using molecular markers Internal Transcribed Spacer and gyrase B gene sequences, respectively. The phylogenies presented consistent, well supported, monophyletic groups in the parsimonious and likelihood analyses for both the nematode and bacterial strains and supported the placement of currently recognized taxa, from which a potentially new Heterorhabditis species represented by a Thailand strain MP68 was identified. While the nematode strains with distant geographic distributions showed no detectable phylogenetic divergence within H. bacteriophora or H. georgiana monophyletic groups, their respective symbiotic bacteria speciated into two Photorhabdus species: P. luminescens and P. temperata, indicating the occurrence of duplication. Although such evolutionary process reduces the phylogenetic congruence between Heterorhabditis nematodes and Photorhabdus bacteria, global cophylogenetic tests using ParaFit detected a highly significant correlation between the two phylogenies (ParaFitGlobal = 0.001). Further, the associations between H. zealandica, H. indica and H. megidis strains and their symbiotic bacteria exhibited significant contribution to the overall cophylogenetic structure. Overall, this study reveals evidence of coevolution between Photorhabdus bacteria and Heterorhabditis nematodes and provides a framework for further examination of the evolution of these associations.

Medical dominance and neoliberalisation in maternal care provision: the evidence from Canada and Australia.

Since the 1970s, governments in many high-income countries have implemented a series of reforms in their health care systems to improve efficiency and effectiveness. Many of these reforms have been of a market-oriented character, involving the deregulation of key services, the creation of competitive markets, and the privatization of health and social care. Some scholars have argued that these "neoliberal" reforms have unseated the historical structural embeddedness of medicine, and in some cases even resulted in the proletarianisation of physicians. Other scholars have challenged this view, maintaining that medical hegemony continues to shape health care provision in most high-income countries. In this paper we examine how policy reforms may have altered medical dominance over maternity care in two comparatively similar countries - Canada and Australia. Our findings indicate that neoliberal reforms in these two countries have not substantially changed the historically hegemonic role medicine has played in maternity care provision. We discuss the implications of this outcome for the increased medicalisation of human reproduction.