Novel approaches for managing and controlling antimicrobial resistance in pigs

Antimicrobial resistance (AMR) continues to threaten One Health with a projected 10 million deaths per year by 2050 if left uncontrolled. While the human medical field has historically demonstrated poor control in the use of antimicrobials, usage in livestock, both historic and current, is also of concern. Resistance to critically important antimicrobials (CIA’s), those reserved for use in life-threatening human infections, has been detected in swine globally. This resistance has the potential to transfer between animals and into humans, and with the accelerated growth of AMR, investigation into novel control strategies for AMR and bacterial infections is now equally as important as surveillance. This thesis determined the diversity of AMR in commensal Escherichia coli (E. coli) within and between pigs and farms, hypothesising that this diversity results in underrepresentation of the true prevalence of AMR by current national AMR surveillance approaches. Secondly, this thesis investigated novel approaches for the control of AMR E. coli and a ubiquitous pathogen, enterotoxigenic E. coli (ETEC), in swine. Postbiotics in the form of Lactobacillus acidophilus fermentation products (LFP) and Saccharomyces cerevisiae fermentation products (SFP) have demonstrated potential effects in alleviating symptoms induced by ETEC infection and in reducing AMR. The thesis evaluated LFP and SFP, as well as their combined effects, on weaner pigs challenged with F4-ETEC, and in a second experimental trial, on weaner pigs challenged with extended-spectrum cephalosporin (ESC) resistant E. coli. Following these trials, a large-scale field-based trial was completed analysing the effects of these postbiotics on AMR E. coli. Finally, the combination of bacteriophages and competitive exclusion clones (CECs) were evaluated in vitro as a novel and targeted approach for the control of ESC-resistant E. coli. The high throughput robotics platform, Robotic Antimicrobial Susceptibility Platform (RASP), was used throughout the project to determine its future application in AMR surveillance and evaluation of control strategies. High levels of phenotypic and genotypic diversity were detected in commensal E coli at both the host and farm level. This was evident in 89% of pigs harbouring more than a single AMR index in the eight E. coli colonies subjected to antimicrobial susceptibility testing (AST). Furthermore, 58 different multi-locus sequence types (MSLTs) were identified from the 151 isolates subjected to whole genome sequencing. This diversity highlights the low reliability of current national surveillance methods that use 1 isolate per farm and less than 200 isolates per animal species. Supplementation with LFP and SFP demonstrated indirect benefits in ETEC-challenged weaner pigs. This was detected as increased growth performance and modulation of the faecal microbiome through increased alpha diversity and abundance in the beneficial bacterial family Lactobacillaceae. However, the postbiotics demonstrated no direct impact on ETEC infection measured through bacterial quantification and faecal consistency scores. Furthermore, the effect of these postbiotics on growth performance and faecal shedding of resistant E. coli were also studied in healthy weaner pigs. The postbiotics demonstrated no impact on growth performance of healthy weaner pigs. Although the postbiotics demonstrated a reduction in ESC-resistant E. coli in pigs challenged with ESC-resistant E. coli, no effects on ciprofloxacin, tetracycline and ESC-resistant E. coli were detected in the farm-based trial. These conflicting results highlight the importance of evaluating strategies in field trials, however, both studies provided a detailed examination of the natural reduction in AMR-carriage over time, whether in experimental models or on farm. Finally, a targeted approach for controlling ESC-resistant E. coli was analysed. The combination of bacteriophages and CECs demonstrated a complimentary relationship, significantly reducing and possibly eliminating ESC-resistant E. coli in vitro. Overall, the high-through put robotics platform, RASP, provided cost-effective bacterial quantification and testing of selected bacterial strains across the project. The sample number in experiments is often restricted due to labour constraints especially during these already labour-intensive trials, however implementation of RASP allowed a high number of samples to be processed and tested, demonstrating future use in AMR research. In conclusion, a more in-depth sampling model for AMR surveillance is necessary to account for the heterogeneity of AMR. Application of robotic platforms, such as the RASP, in AMR surveillance offers a highly economic and low laborious approach for processing this increased sample size. The RASP additionally demonstrated use in investigation of AMR and ETEC control methods, demonstrated by its high resolution into the dynamics of AMR E. coli and ETEC in faecal contents of pigs. Lastly, an in vitro combination approach, using both targeted and preventative therapies, demonstrated superiority in reduction of ESC-resistant E. coli. This novel combined approach requires future analysis to determine if these results are replicated on farm

Contributions and perspectives of Indigenous Peoples to the study of mercury in the Arctic

Arctic Indigenous Peoples are among themost exposed humanswhen it comes to foodbornemercury (Hg). In response, Hgmonitoring and research have been on-going in the circumpolar Arctic since about 1991; this work has beenmainly possible through the involvement of Arctic Indigenous Peoples. The present overview was initially conducted in the context of a broader assessment of Hg research organized by the Arctic Monitoring and Assessment Programme. This article provides examples of Indigenous Peoples' contributions to Hg monitoring and research in the Arctic, and discusses approaches that could be used, and improved upon, when carrying out future activities. Over 40 mercury projects conducted with/by Indigenous Peoples are identified for different circumpolar regions including the U.S., Canada, Greenland, Sweden, Finland, and Russia as well as instances where Indigenous Knowledge contributed to the understanding of Hg contamination in the Arctic. Perspectives and visions of future Hg research as well as recommendations are presented. The establishment of collaborative processes and partnership/co-production approaches with scientists and Indigenous Peoples, using good communication practices and transparency in research activities, are key to the success of research and monitoring activities in the Arctic. Sustainable funding for community-driven monitoring and research programs in Arctic countries would be beneficial and assist in developing more research/monitoring capacity and would promote a more holistic approach to understanding Hg in the Arctic. These activities should be well connected to circumpolar/international initiatives to ensure broader availability of the information and uptake in policy development

Dissemination and persistence of extended-spectrum cephalosporin- resistance encoding IncI1-blaCTXM-1 plasmid among Escherichia coli in pigs

This study investigated the ecology, epidemiology and plasmid characteristics of extended-spectrum cephalosporin (ESC)-resistant E. coli in healthy pigs over a period of 4 years (2013–2016) following the withdrawal of ESCs. High carriage rates of ESC-resistant E. coli were demonstrated in 2013 (86.6%) and 2014 (83.3%), compared to 2015 (22%) and 2016 (8.5%). ESC resistance identified among E. coli isolates was attributed to the carriage of an IncI1 ST-3 plasmid (pCTXM1-MU2) encoding blaCTXM-1. Genomic characterisation of selected E. coli isolates (n = 61) identified plasmid movement into multiple commensal E. coli (n = 22 STs). Major STs included ST10, ST5440, ST453, ST2514 and ST23. A subset of the isolates belong to the atypical enteropathogenic E. coli (aEPEC) pathotype that harboured multiple LEE pathogenic islands. pCTXM1-MU2 was similar (99% nt identity) to IncI1-ST3 plasmids reported from Europe, encoded resistance to aminoglycosides, sulphonamides and trimethoprim, and carried colicin Ib. pCTXM1-MU2 appears to be highly stable and readily transferable. This study demonstrates that ESC resistance may persist for a protracted period following removal of direct selection pressure, resulting in the emergence of ESC-resistance in both commensal E. coli and aEPEC isolates of potential significance to human and animal health.This study was funded by the DVM clinical research programme, University of Adelaide and Small Grant Scheme of School of Veterinary Life Sciences, Murdoch University

Contributions and perspectives of Indigenous Peoples to the study of mercury in the Arctic

Arctic Indigenous Peoples are among the most exposed humans when it comes to foodborne mercury (Hg). In response, Hg monitoring and research have been on-going in the circumpolar Arctic since about 1991; this work has been mainly possible through the involvement of Arctic Indigenous Peoples. The present overview was initially conducted in the context of a broader assessment of Hg research organized by the Arctic Monitoring and Assessment Programme. This article provides examples of Indigenous Peoples' contributions to Hg monitoring and research in the Arctic, and discusses approaches that could be used, and improved upon, when carrying out future activities. Over 40 mercury projects conducted with/by Indigenous Peoples are identified for different circumpolar regions including the U.S., Canada, Greenland, Sweden, Finland, and Russia as well as instances where Indigenous Knowledge contributed to the understanding of Hg contamination in the Arctic. Perspectives and visions of future Hg research as well as recommendations are presented. The establishment of collaborative processes and partnership/co-production approaches with scientists and Indigenous Peoples, using good communication practices and transparency in research activities, are key to the success of research and monitoring activities in the Arctic. Sustainable funding for community-driven monitoring and research programs in Arctic countries would be beneficial and assist in developing more research/ monitoring capacity and would promote a more holistic approach to understanding Hg in the Arctic. These activities should be well connected to circumpolar/international initiatives to ensure broader availability of the information and uptake in policy development

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Isolation and genomic characterization of bacteriophages targeting extended-spectrum cephalosporin resistant E. coli

Overuse of antibiotics has resulted in the emergence of antibiotic resistant bacteria resulting in bacterial infections in livestock and humans, that can no longer be controlled by these drugs [2]. Third generation cephalosporins are an antibiotic class used in critical situations as the last line of defence, however bacteria have now developed resistance to these drugs [3]. Bacteriophages are viruses which can infect and destroy bacteria, and are being developed as a new therapeutic method for the control and management of bacterial infections in swine. This method offers a highly specific therapy with minimal side effects on the gut microflora [4]. Administration of phages in animal feed has resulted in a reduction of the severity of bacterial infections in addition to a reduction in the shedding of bacteria in faecal matter [2, 5]. This shedding is a major human health concern as it has the potential to transfer antibiotic resistant bacteria and plasmids carrying resistant genes to humans through the faecal to oral route. This project isolated 21 bacteriophages, from three separate sources, that are capable of lysing extended-spectrum cephalosporin (ESC) resistant E. coli. Characterisation of these phages, through electron microscopy and genome sequencing, identified phages belonging to the three different families within the order Caudovirales; Siphoviridae, Myoviridae and Podoviridae. Analysis of the phage genomes resulted in the identification of two clusters within the phages belonging to the Siphoviridae family, named Cluster 1 and 2. Comparison of the specificity of phages sourced from pig farms with (South Australia) and without (Murdoch University) ESC resistant bacteria suggests that highly specific phages can be sourced from locations infected and uninfected by the target bacterial isolate. Three of the phages isolated from Murdoch University have a broad host range of the target ESC resistant E. coli isolates, highlighting these phages for further studies and potential development into therapeutic products

Patients' experiences of in-hospital care when nursing staff were engaged in a practice development programme to promote person-centredness: A narrative analysis study

Background: The drive towards person-centred approaches to care delivery has been increasingly promoted. This is in response to the significant challenges within health and social care organisations, which impact on the care experience for patients and their families. Objective: The aim of this paper is to illuminate the experiences of patients of care received in hospital wards during the intervention phase of a programme to develop person-centred practice. Design: A narrative enquiry study was conducted which is a particular way of exploring complex cultural or social patterns. Structural narrative analysis was used to generate explanation and interpretation of in-hospital patients' care experience. Setting: Recruitment was from four different hospital sites in one health care organisation, focussing on patients who were admitted to the nine wards/units where the nursing teams were participating in a practice development programme that had the intention of promoting person-centredness. Participants: Participants were people aged over 18 and receiving care and treatment in the identified wards/units. Twenty-six patients were recruited. Methods: Narrative interviews were audio-recorded at four month intervals and transcribed. The records were subjected to a process of structural analysis. Results: The findings offer insight into patients' experiences of care in a range of clinical settings in which an explicit intervention to promote person-centred practice was underway. There was one overriding theme formulated: Vulnerability at the junctures of systems, care processes and nurses' responses. From this main theme, we derived four sub-themes: (1) confronting vulnerability, (2) experiencing exemplary care, (3) experiencing misalignments in systems, care processes and nurses' responses, and (4) sharing in a sense of belonging with ward nurses. Conclusions: In-hospital patients are exposed to vulnerability in the care experience. They placed value on exemplary care. Experiences of misalignments in systems, care processes and nurses' responses disempower patients and heighten a sense of vulnerability. The ward nursing teams were generating a family like atmosphere. Patients responded by sharing a sense of belonging with ward nurses. These findings confirm components that have influenced the development of person-centred practice, such as the importance of the context and culture of care. They also offer new insights that may contribute to on-going practice development work. 2015 Elsevier Ltd.sch_nur52pub4006pub