Detection and Isolation of Campylobacter spp. from Raw Meat

This article presents a rapid yet robust protocol for isolating Campylobacter spp. from raw meats, specifically focusing on Campylobacter jejuni and Campylobacter coli. The protocol builds upon established methods, ensuring compatibility with the prevailing techniques employed by regulatory bodies such as the Food and Drug Administration (FDA) and the U.S. Department of Agriculture (USDA) in the USA, as well as the International Organization for Standardization (ISO) in Europe. Central to this protocol is collecting a rinsate, which is concentrated and resuspended in Bolton Broth media containing horse blood. This medium has been proven to facilitate the recovery of stressed Campylobacter cells and reduce the required enrichment duration by 50%. The enriched samples are then transferred onto nitrocellulose membranes on brucella plates. To improve the sensitivity and specificity of the method, 0.45 µm and 0.65 µm pore-size filter membranes were evaluated. Data revealed a 29-fold increase in cell recovery with the 0.65 µm pore-size filter compared to the 0.45 µm pore-size without impacting specificity. The highly motile characteristics of Campylobacter allow cells to actively move through the membrane filters towards the agar medium, which enables effective isolation of pure Campylobacter colonies. The protocol incorporates multiplex quantitative real-time polymerase chain reaction (mqPCR) assay to identify the isolates at the species level. This molecular technique offers a reliable and efficient means of species identification. Investigations conducted over the past twelve years involving retail meats have demonstrated the ability of this method to enhance recovery of Campylobacter from naturally contaminated meat samples compared to current reference methods. Furthermore, this protocol boasts reduced preparation and processing time. As a result, it presents a promising alternative for the efficient recovery of Campylobacter from meat. Moreover, this procedure can be seamlessly integrated with DNA-based methods, facilitating rapid screening of positive samples alongside comprehensive whole-genome sequencing analysis.

Whole Genome Sequences, De Novo Assembly, and Annotation of Antibiotic Resistant Campylobacter jejuni Strains S27, S33, and S36 Newly Isolated from Chicken Meat

Campylobacter is a leading bacterial cause of gastrointestinal infections in humans and has imposed substantial medical and public health burdens worldwide. Among a total of 39 species in the Campylobacter genus, C. jejuni is the most important species responsible for approx. 90% of human Campylobacter illness. Most cases of the infection were acquired by ingesting undercooked poultry meat due to the high prevalence of Campylobacter in the products. Here, we reported the dataset of raw sequences, de novo assembled and annotated genomes of C. jejuni strains S27, S33, and S36 recently isolated from retail chicken by using PacBio highly accurate long-read sequencing technology combined with bioinformatics tools. Our data revealed several virulence and antibiotic resistance genes in each of the chromosomes, a type IV secretion system in the plasmid (pCjS33) of C. jejuni S33, and a type VI secretion system and a phage in the plasmid (pCjS36) of C. jejuni S36. This study not only provides new sequence data but also extends the knowledge pertaining to the genomic and functional aspects of this important foodborne pathogen, including the genetic determinants of virulence and antibiotic resistance.

Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products

Successful detection of bacterial pathogens in food can be challenging due to the physical and compositional complexity of the matrix. Different mechanical/physical and chemical methods have been developed to separate microorganisms from food matrices to facilitate detection. The present study benchmarked a commercial tissue digestion system that applies both chemical and physical methods to separate microorganisms from tissues against stomaching, a standard process currently utilized by commercial and regulatory food safety laboratories. The impacts of the treatments on the physical properties of the food matrix were characterized along with the compatibility of the methods with downstream microbiological and molecular detection assays. The results indicate the tissue digestion system can significantly reduce the average particle size of the chicken sample relative to processing via a stomacher (P < 0.001) without adversely affecting either real-time PCR (qPCR) or plate counting assays, which are typically used to detect Salmonella. Furthermore, inoculated chicken treated with the GentleMACS resulted in a significant increase (P < 0.003) in the qPCR's detection capabilities relative to stomached controls. Cohen kappa (κ) coefficient and McNemar's test indicate the plating assays and PCR results agree with measurements obtained via the 3 M Molecular Detection System as defined in the MLG standard (κ > 0.62; P > 0.08). Collectively, the results demonstrate that the technique enables detection of pathogens in meat at lower levels of contamination using current industry standard technologies.

A current affair: worker perceptions of noise exposure and occupational hearing loss in Australian coal mines

BACKGROUND

The objective of the online survey was to determine worker attitudes towards, perceptions on hearing loss, and management of workplace noise; and to identify barriers within current strategies that prevent effective management of hearing health in Australian mines.

DESIGN

This cross-sectional study utilized a modified survey design, initially designed for use by Safe Work Australia for a broader study published in 2010.

STUDY SAMPLE

The survey questionnaire was made available online to volunteer participants, recruited with the assistance of State and National Health and Safety, and mining organizations. Volunteer participants were required to be proficient in English, be employed by an Australian underground or open cut mine, including coal processing plants; or work as a contractor on one of the specified mine sites. All mining employees, regardless of occupation, job title, and occupational hearing loss classification or status, were invited to complete the questionnaire.

RESULTS

Almost 60% of respondents indicated that they had high noise exposure for than 10 yr or more, and have some trouble hearing, mostly associated with infrequent tinnitus. Nearly 71% of these workers believe that the noise control strategies in their workplaces are effective, but this mostly refers to the use of hearing protection devices.

CONCLUSION

The results indicate that general knowledge on the cause and effect of noise exposure in the workplace is well understood. However, due to the long latency associated with the development of noise-induced hearing loss (NIHL), there is an issue urgency in terms of risk management. It is surprising that most of the respondents recommended more inspections and administrative controls, especially since most respondents were health, safety, and environment (HSE) professionals. HSE professionals should be advocating for higher order, more permanent solutions, and not purely administrative controls and personal protective equipment. These findings raise the question of whether there is a multifaceted working-culture issue that needs to be addressed, in combination with higher order control implementation.

Complete Genome Sequence of Campylobacter jejuni BSD5, a Multidrug-Resistant Isolate from a Poultry Processing Facility in the United States

Raw poultry can harbor microbial pathogens. Campylobacter jejuni BSD5, isolated from a critical control point within a poultry production plant, was sequenced. Genome annotation revealed several virulence genes including antibiotic resistance genes in agreement with the phenotypic results, indicating a potential risk of this strain to public health.

Identifying occupational health and safety risks among environmental health officers in Australia and New Zealand through an online survey

To identify the occupational health and safety (OHS) risks among environmental health officers (EHOs) in Australia and New Zealand. The objectives were to profile and compare OHS experiences from different countries and regions to gain a regional perspective on OHS hazards that impact EHOs. An online hazard exposure survey was conducted among 339 EHOs (Australia: n = 301, 88.8%; New Zealand: n = 38, 11.2%). The Mann-Whitney U test was used to compare 2 ordinal data groups, the Kruskal-Wallis H test was used for more than 2 ordinal groups, and the independent samples t test was used to compare the means of 2 independent groups where the dependent variables were normally distributed. Multiple regression techniques were used to analyze workplace incidents and age groups. A high degree of similarity in the types of workplace exposures and risk perceptions as well as concerns with organizational OHS management commitment were observed among EHOs from the 2 countries. Workplace violence and physical and psychosocial demands were the most commonly reported OHS hazards. Employer type, sex, and age group were significantly related to workplace exposure and OHS experience among EHOs in both countries. This study provides a profile of workplace exposure in the environmental health profession in the 2 countries and offers recommendations for the implementation of preventive action.

Pathogenic Potential of Respirable Spodumene Cleavage Fragments following Application of Regulatory Counting Criteria for Asbestiform Fibres

Health risks from exposure to lithium-bearing spodumene cleavage fragments are unknown. While asbestiform fibres can lead to fibrosis, mesothelioma and lung cancer, controversy remains whether non-asbestiform cleavage fragments, having equivalent dimensions, elicit similar pathologic responses. The mineralogy of respirable particles from two alpha (α)-spodumene concentrate grades (chemical and technical) were characterised using semi-quantitative X-ray diffraction (XRD). Particles were measured using scanning electron microscopy (SEM) and the dimensions (length [L], diameter [D], aspect ratio [AR]) applied to regulatory counting criteria for asbestiform fibres. Application of the current World Health Organization (WHO) and National Occupational Health and Safety Commission (NOHSC) counting criteria, L ˃ 5 µm, D ˂ 3 µm, AR ˃ 3:1, to 10 SEM images of each grade identified 47 countable particles in the chemical and 37 in the technical concentrate test samples. Of these particles, 17 and 16 in the chemical and technical test samples, respectively, satisfied the more rigorous, previously used Mines Safety and Inspection Regulations 1995 (Western Australia [WA]) criteria, L ˃ 5 µm and D ≤ 1 µm. The majority of the countable particles were consistent with α-spodumene cleavage fragments. These results suggest elongated α-spodumene particles may pose a health risk. It is recommended the precautionary principle be applied to respirable α-spodumene particles and the identification and control of dust hazards in spodumene extraction, handling and processing industries be implemented.

Health system recovery from Covid-19: What policies are health systems using to tackle backlogs and bring down waiting times in the wake of the pandemic?

The pandemic has left even the most well-equipped health systems vulnerable and required difficult trade-offs to balance both Covid-19 and non-Covid-19 health services. Across the globe, planned and routine health services have been scaled down during peaks of the crisis to meet the needs of acute and Covid-19-related care, resulting in growing care backlogs and increase in the number of patients waiting for treatment. To identify potential policy solutions, we have consulted the Covid-19 Health System Response Monitor, interviewed experts and analysed recovery strategies in 16 OECD and EU countries. Many country responses display striking similarities despite very real differences in the organisation of health and care services. These include:

1) increasing the supply of workforce by widening the scope of authority for different roles, investing heavily in recruitment and training for key roles, and improving the terms and conditions of work;

2) boosting productivity by introducing financial incentives and targets, reconfiguring facilities to better separate planned and emergency work”, optimising referrals and waiting list management, and outsourcing more care to the private sector; and

3) investing in out-of-hospital alternatives to care, including expanding primary and community care models and developing digital, home care and rehabilitative capacity

Policymakers will need to balance the immediate pressures of clearing backlogs with long-term measures that place services on a more sustainable footing. International experience shows how these can be at odds, especially if actions taken in the short term exhaust an already depleted workforce, or resolve Covid-19-specific problems but leave services less prepared for tomorrow's challenges.

Meeting the governance challenges of integrated health and social care

Background

Many countries are experimenting with novel ways of organising and delivering more integrated health and social care. Governance is relatively neglected as a focus of attention in this context but addressing governance challenges is key for successful collaboration.

Methods

Cross-country case analysis involving document review and semi-structured interviews with 27 local, regional and national level stakeholders in Italy, the Netherlands and Scotland. We used the Transparency, Accountability, Participation, Integrity and Capability (TAPIC) framework to structure our analytical enquiry to explore factors that influence the governance arrangements in each system.

Results

Governance arrangements ranged from informal agreements in the Netherlands to mandated integration in Scotland. Novel service models were generally participative involving a wide range of stakeholders, including the public, although integration was seen to be driven, largely, from a health perspective. In Italy and Scotland some reversion to ‘command & control’ was reported in response to the imperatives of the Covid-19 pandemic. Policies, budgets, auditing and reporting systems that are clearly aligned at all levels were seen to help with implementing innovations in service organisation. Where alignment was lacking, cooperation and integration was suboptimal, regardless of whether governance arrangements were statutory or not. There was wide recognition of the importance of buy-in. Enablers of greater engagement included visible leadership, time and long-standing working relationships. Lack of suitable indicators and openness to data sharing to measure integration hindered working relationships and thus the successful delivery of integrated services.

Conclusions

Our study provides important insights into how to more effectively and efficiently govern service delivery structures within care systems. We will discuss approaches to governance that help support more resilient integrated care systems.

Key messages

• Different governance arrangements face common challenges to greater integration of care. Enablers include strong leadership, inclusivity and openness to work across traditional boundaries.

• Meeting the governance challenges of integrated health and social care requires clear lines of accountability, aligned policies, budgets and reporting systems.

A cross-country comparison on providing health services effectively during the first wave of COVID-19

At the onset of the COVID-19 pandemic, health care providers had to abruptly change their way of providing care in order to simultaneously plan for and manage a rise of COVID-19 cases while maintaining essential health services. Even the most well-resourced health systems faced pressures from new challenges brought on by COVID-19, and every country had to make difficult choices about how to maintain access to essential care while treating a novel communicable disease. Using the information available on the HSRM platform from the early phases of the pandemic, we analyze how countries planned services for potential surge capacity, designed patient flows ensuring separation between COVID-19 and non-COVID-19 patients, and maintained routine services in both hospital and outpatient settings. Many country responses displayed striking similarities despite very real differences in the organization of health and care services. These include transitioning the management of COVID-19 mild cases from hospitals to outpatient settings, increasing the use of remote consultations, and cancelling or postponing non-urgent services during the height of the first wave. In the immediate future, countries will have to continue balancing care for COVID-19 and non-COVID-19 patients to minimize adverse health outcomes, ideally with supporting guidelines and COVID-19-specific care zones. Many countries expect to operate at lower capacity for routinely provided care, which will impact patient access and waiting times. Looking forward, policymakers will have to consider whether strategies adopted during the COVID-19 pandemic will become permanent features of care provision.

Evaluating the Effectiveness of a Clinical Practice Intervention in Increasing Obesity Data Recording at a Western Australian Country Health Service Hospital: A Quasi-Experimental Controlled Trial

Purpose

Identification and mitigation of obesity-related risks to staff and healthcare organisations can occur using patient obesity data; however, a 2017/18 audit of obesity data accuracy was assessed to be poor. This study investigates the results of an intervention to improve obesity data recording and coding accuracy at an Australian hospital.

Background

Increasing population obesity rates result in increased organisational and financial risks to hospitals. Australian obesity prevalence has steadily increased since 1995, and 42% of the Australian population is predicted to be obese in 2035. To reduce risks to healthcare staff who care for obese patients, complete and accurate obesity recording is required.

Methods

Following a previous audit of obesity recording and coding accuracy of patients admitted to hospital with Type II diabetes, a 12-month intervention was undertaken, comprising staff education, introduction of tape measures and obesity decision-making tools, recording of patient volunteered height, regular reinforcement of obesity recording requirements and enhanced clinical coding of obesity. A re-audit was subsequently conducted to determine if the intervention impacted obesity recording and coding at the previously audited site.

Results

Improved recording of obesity-related measures and obesity data accuracy were observed, including increased patient BMI, impacted by increased patient height measurements and increased patient weight measurements. Obesity recording accuracy increased due to the intervention, including increased sensitivity, increased negative predictive values and reduced false negatives.

Conclusion

The obesity recording intervention was successful; however, as hospitals increasingly use electronic health records, improvement opportunities should be considered such as compulsory recording of patient weight and height, embedded BMI calculators and “check boxes” for recording impacts of obesity conditions on treatment. Immediate improvement of obesity recording in manual patient files can be achieved in the meantime by implementing targets of 100% weight, height and BMI recording, introducing education programs and auditing compliance.

Estimated Financial Impacts of Inaccurate Obese Patient Data Recorded by the Western Australian Country Health Service

Purpose

Pressure on Australia’s healthcare system is increasing annually due to corresponding increases in chronic diseases such as obesity and rapidly ageing population growth across Australia, resulting in requirements for increased funding. This study investigates the financial impact to hospitals due to inaccurate obese patient recording and coding.

Background

Australian healthcare organisations receive Activity-Based Funding (ABF) which provides reimbursement of costs relating to the type of patient care delivered and the resources required for the patient treatment. Accurate healthcare data are essential to ensure accuracy of ABF and appropriate reimbursement of costs incurred by hospitals that manage obese patients. Managing obese patients results in operational funding requirements such as increased staffing and purchasing of equipment such as hoists, bariatric wheelchairs and bariatric beds, and hospitals must ensure that these clinical requirements are documented accurately in order to be reimbursed of these costs by way of ABF.

Methods

This study identifies the financial implications of inaccurate obesity data within the Western Australian Country Health Service (WACHS) and examines factors that may affect obesity data recording accuracy. The study involves 85 cases of identified obesity data recording inaccuracy that were adjusted by entering corrected obesity codes, which then adjusted Diagnosis-related Groups, National Weighted Activity Units and Activity-Based Funding results.

Results

The study demonstrated estimated annual lost funding opportunities of $2.23 million due to obesity coding inaccuracy. An annual average of 616 cases of obesity data inaccuracy was calculated with an average lost funding opportunity of $3625 per case.

Conclusion

Improvements are required in the clinical recording and coding of patient obesity, such as mandatory recording of patient weight and height data and automated BMI calculations within electronic patient records. Enhanced obesity recording and coding accuracy will result in increased funding opportunities and reduced cost burdens that hospitals currently experience when required to fund obesity-related clinical and safety requirements within operational budgets.

Opportunistic Premise Plumbing Pathogens. A Potential Health Risk in Water Mist Systems Used as a Cooling Intervention

Water mist systems (WMS) are used for evaporative cooling in public areas. The health risks associated with their colonization by opportunistic premise plumbing pathogens (OPPPs) is not well understood. To advance the understanding of the potential health risk of OPPPs in WMS, biofilm, water and bioaerosol samples (n = 90) from ten (10) WMS in Australia were collected and analyzed by culture and polymerase chain reaction (PCR) methods to detect the occurrence of five representative OPPPs: Legionella pneumophila, Pseudomonas aeruginosa, Mycobacterium avium, Naegleria fowleri and Acanthamoeba. P. aeruginosa (44%, n = 90) occurred more frequently in samples, followed by L. pneumophila serogroup (Sg) 2–14 (18%, n = 90) and L. pneumophila Sg 1 (6%, n = 90). A negative correlation between OPPP occurrence and residual free chlorine was observed except with Acanthamoeba, rs (30) = 0.067, p > 0.05. All detected OPPPs were positively correlated with total dissolved solids (TDS) except with Acanthamoeba. Biofilms contained higher concentrations of L. pneumophila Sg 2–14 (1000–3000 CFU/mL) than water samples (0–100 CFU/mL). This study suggests that WMS can be colonized by OPPPs and are a potential health risk if OPPP contaminated aerosols get released into ambient atmospheres.

Risks to Healthcare Organizations and Staff Who Manage Obese (Bariatric) Patients and Use of Obesity Data to Mitigate Risks: A Literature Review

This literature review explores obesity risks to healthcare staff and organizations that manage and caring for obese (bariatric) patients. These risks are anticipated to increase due to Australian population obesity rate projections increasing from 31% in 2018 to 42% by the year 2035, which will result in increased hospital admissions of patients with obesity. Literature searches were conducted through the Cumulative Index to Nursing and Allied Health Literature (CINAHL), MEDLINE, Scopus, and Web of Science. Thirty studies met the inclusion criteria and were tabulated and critiqued using appropriate appraisal techniques. High risk of injury to healthcare staff was identified relating to bariatric patient handling tasks. High liability and financial risks of organizations were also identified relating to workers' compensation and common law claims by injured staff and medical negligence claims by patients with obesity. Availability of obesity data was identified within clinically captured information, which could be utilized to inform obesity risk management programs. Future research should focus on improving the use and quality of obesity data to better understand obesity risks to healthcare organizations and staff, including accurate identification of obese patient admissions, enhanced ability to measure bariatric patient handling hazards and related staff injuries and improved assessment of bariatric intervention effectiveness.

Comparative Methylome Analysis of Campylobacter jejuni Strain YH002 Reveals a Putative Novel Motif and Diverse Epigenetic Regulations of Virulence Genes

Campylobacter jejuni is a major cause of foodborne gastroenteritis worldwide inflicting palpable socioeconomic costs. The ability of this pathogen to successfully infect its hosts is determined not only by the presence of specific virulence genes but also by the pathogen’s capacity to appropriately regulate those virulence genes. Therefore, DNA methylation can play a critical role in both aspects of this process because it serves as both a means to protect the integrity of the cellular DNA from invasion and as a mechanism to control transcriptional regulation within the cell. In the present study we report the comparative methylome data of C. jejuni YH002, a multidrug resistant strain isolated from retail beef liver. Investigation into the methylome identified a putative novel motif (CGCGA) of a type II restriction-modification (RM) system. Comparison of methylomes of the strain to well-studied C. jejuni strains highlighted non-uniform methylation patterns among the strains though the existence of the typical type I and type IV RM systems were also observed. Additional investigations into the existence of DNA methylation sites within gene promoters, which may ultimately result in altered levels of transcription, revealed several virulence genes putatively regulated using this mode of action. Of those identified, a flagella gene (flhB), a RNA polymerase sigma factor (rpoN), a capsular polysaccharide export protein (kpsD), and a multidrug efflux pump were highly notable.

Benign adenoidal hypertrophy caused by adenovirus presenting as a nasopharyngeal mass concerning for malignancy

Benign adenoidal hypertrophy is the most common cause of nasopharyngeal obstruction. However, depending on size and location, masses may cause nasopharyngeal obstruction. We present our experiences with a ten-year-old female who presented with what appeared to be a large nasopharyngeal mass that was initially favored to be malignant and was ultimately found to be adenoid hypertrophy related to acute infection with adenovirus.

Assessment of Worker Exposure to Occupational Organic Dust in a Hemp Processing Facility

The cultivation and processing of industrial hemp, Cannabis sativa L., is a developing industry in Australia. Exposure to hemp dust is demonstrated as producing reactive and respiratory health effects, potentially causing permanent lung disease or damage. The aim of this study was to assess the airborne organic dust concentrations generated in an Australian hemp processing facility. Personal sampling, in the breathing zone of exposed workers was undertaken for exposure to respirable dust, along with parallel static sampling for airborne concentrations of inhalable and respirable dust fractions. Both static and personal sampling showed that respirable dust concentrations (mg m-3) exceeded the Australian Institute of Occupational Hygienists (AIOH) recommended maximum exposure limit of 1 mg m-3 (respirable fraction) for dusts not otherwise specified, with mean exposures (mg m-3) of M = 1.33, standard deviation (SD) = 1.09 (range 0.07-3.67 mg m-3) and M = 4.49, SD = 4.49 (range 0.77-11.08 mg m-3). The results of the investigation indicate that workers in the hemp processing industry are at risk of developing permanent and disabling respiratory disease due to high dust exposure. There is no Australian occupational exposure limit specifically for hemp dust. It is recommended further research is needed and industry-specific guidance material or model code of practice developed to effectively control exposures.

Acute and chronic effects of multivitamin/mineral supplementation on objective and subjective energy measures

Background

Vitamins and minerals play an essential role within many cellular processes including energy production and metabolism. Previously, supplementation with a multivitamin/mineral (MVM) for ≥28 days resulted in improvements to cognition and subjective state. We have also demonstrated shifts in metabolism during cognitively demanding tasks following MVM in females, both acutely and following 8-week supplementation. The current study aimed to assess these effects further in males and females using metabolically challenging exercise and cognitive tasks.

Methods

The current randomised, placebo-controlled, parallel groups study investigated the effects of a MVM complex in 82 healthy young (18-35y) exercisers. Subjective ratings and substrate metabolism were assessed during 30 min each of increasingly effortful incremental exercise and demanding cognitive tasks. Assessments took place on acute study days following a single dose (Day 1) of MVM, containing 3 times recommended daily allowance of water-soluble vitamins plus CoQ10, and following 4-week supplementation (Day 28).

Results

Energy expenditure (EE) was increased during cognitive tasks following MVM across Day 1 and Day 28, with greater effects in males. In males, MVM also increased carbohydrate oxidation and energy expenditure during exercise across Day 1 and Day 28. In females, mental tiredness was lower during exercise; increases in physical tiredness following 30 min of exercise were attenuated; and stress ratings following cognitive tasks were reduced following MVM. In males, MVM only lowered mental tiredness following 10 min of exercise. These effects were apparent irrespective of day, but effects on mental tiredness were greater on Day 28. Ferritin levels were also higher on Day 28 in those receiving MVM.

Conclusion

These findings extend on existing knowledge, demonstrating increased carbohydrate oxidation and increased energy expenditure in males following MVM supplementation for the first time. Importantly, they show modulation of energy expenditure and subjective tiredness following a single dose, providing further evidence for acute effects of MVM. Differential effects in men and women suggest that sex may play an important role in the effects of MVM on energy metabolism and should be considered in future research.

Trial registration

ClinicalTrials.gov, NCT03003442. Registered 22nd November 2016 – retrospectively registered

Comparative Genomic Analysis of a Multidrug-Resistant Campylobacter jejuni Strain YH002 Isolated from Retail Beef Liver

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide. In this study, we report the comparative genomic and functional characteristics of C. jejuni YH002 recently isolated from retail beef liver. Whole-genome sequencing and annotation of the strain revealed novel genetic features, including an integrated intact phage element, multiple antimicrobial resistance (AMR) genes, virulence factors, and a Phd-Doc type toxin-antitoxin (TA) system. Phenotypic tests of AMR showed that C. jejuni YH002 was resistant to amoxicillin and tetracycline, which correlates with the AMR genes found in the strain. Comparative analysis of cell motility at genotypic and phenotypic levels identified discernible patterns of amino acid changes, which could explain the variations of motility among C. jejuni strains. Together, these results provide important clues to the genetic mechanisms of AMR and cell motility in C. jejuni. The finding of a Phd-Doc TA system in the genome of C. jejuni YH002 is the first report of this TA system in Campylobacter spp.

Crossbreeding with a tropically adapted Bos taurus breed (Senepol) to improve meat quality and production from Brahman herds in Northern Australia. 1. Steer performance

The performance of four year groups of Brahman and F1 Senepol × Brahman steers was compared grazing buffel pasture at the Douglas-Daly Research Farm, Douglas-Daly, NT, Australia. F1 Senepol × Brahman steers were on average 32 kg heavier at turnoff at ~18 months of age (P &lt; 0.001) as a result of higher average weaning weights (+19 kg, P &lt; 0.001) and higher growth during the post-weaning year (+12 kg, P &lt; 0.001). These results, combined with previous studies that found that F1 Senepol × Brahman steers had more tender meat and performed better than Brahman in an Indonesian feedlot, indicate that crossbreeding with a tropically adapted Bos taurus breed, such as Senepol, could be an effective way for north Australian cattle producers with Brahman herds to produce cattle that perform well under northern conditions, and are suited to both the live export and domestic markets.

Pulsed-Field Gel Electrophoresis Typing of Staphylococcus aureus Strains

Pulsed-field gel electrophoresis (PFGE) is one of the most effective genotyping methods for the study of genetic relatedness of microorganisms as well as for epidemiologic investigation of outbreaks caused by pathogenic bacteria, including Staphylococcus aureus. The technique relies on the size patterns of large DNA fragments generated by the cleavage of intact bacterial chromosomes with a rare cutting restriction enzyme, and subsequently resolved by pulsed-field electrophoresis with periodic changes of the orientation of the electrical field across the gel. The high discriminatory power, improved reproducibility by standardization of experimental protocols and data analysis guidelines, and establishment of a national PFGE database of S. aureus profiles have made it a valuable means for global tracking of S. aureus infection sources and determination of genetic relatedness of the strains.

Occupational health and safety in cannabis production: an Australian perspective

The legal Australian cannabis industry has been rapidly expanding due to increased awareness of the plant's therapeutic potential, as well its diverse range of applications including biofuel, textiles, building materials, food, nutritional supplement, and animal feed. The objective of this paper is to describe the current landscape of the commercial Australian cannabis industry, summarise occupational health and safety (OHS) hazards in cannabis-related working environments, and provide suggestions for safeguarding worker health and well-being in this emerging industry. A comprehensive search of peer-reviewed and grey literature published between 1900 and 2017 was undertaken to identify case studies and original epidemiological research on OHS hazards associated with the cannabis cultivation and the manufacture of cannabis-based products. The review found that the majority of OHS studies were undertaken in the hemp textile industry during the late twentieth century, with a small number of articles published from a variety of occupational environments including forensic laboratories and recreational marijuana farms. Cannabis harvesting and initial processing is labour intensive, and presents a physical hazard Depending on the operation, workers may also be exposed to a variety of biological, chemical, and physical hazards including: organic dusts, bioaerosols, pollen/allergens, volatile organic compounds, psychoactive substances (tetrahydrocannabinol [THC])), noise, and ultraviolet radiation. Little research has been undertaken on the exposure to inhalable organic dust and other bioaerosols during the commercial cultivation and manufacture of cannabis-based products. Furthermore, there is an absence of Australian-based research and OHS guidance materials to help professionals develop risk management strategies in this evolving industry. It is recommended that: Investigation into the toxicological properties of cannabis dusts, specifically in relation to potential occupational exposures during cultivation and manufacture, should be a priority. The interim adoption of the respirable cotton dust exposure standard of 0.2 mg/m3 for workplace exposure in hemp facilities until a cannabis workplace exposure standard is developed, and that exposure to medicinal cannabis containing THC are kept as low as reasonably practicable. An industry partnership be established for the development of an Australian health and safety guideline for the production of medicinal cannabis and hemp. A classification to meet the requirements of the Global Harmonization Scheme should be undertaken to ensure consistency in the use of safety and risk phrases in cannabis-related industries.

Personal exposure of dairy workers to dust, endotoxin, muramic acid, ergosterol, and ammonia on large-scale dairies in the high plains Western United States

Dairy workers experience a high degree of bioaerosol exposure, composed of an array of biological and chemical constituents, which have been tied to adverse health effects. A better understanding of the variation in the magnitude and composition of exposures by task is needed to inform worker protection strategies. To characterize the levels and types of exposures, 115 dairy workers grouped into three task categories on nine farms in the high plains Western United States underwent personal monitoring for inhalable dust, endotoxin, 3-hydroxy fatty acids (3-OHFA), muramic acid, ergosterol, and ammonia through one work shift. Eighty-nine percent of dairy workers were exposed to endotoxin at concentrations exceeding the recommended exposure guidelines (adjusted for a long work shift). The proportion of workers with exposures exceeding recommended guidelines was lower for inhalable dust (12%), and ammonia (1%). Ergosterol exposures were only measurable on 28% of samples, primarily among medical workers and feed handlers. Milking parlor workers were exposed to significantly higher inhalable dust, endotoxin, 3-OHFA, ammonia, and muramic acid concentrations compared to workers performing other tasks. Development of large modern dairies has successfully made progress in reducing worker exposures and lung disease prevalence. However, exposure to endotoxin, dust, and ammonia continues to present a significant risk to worker health on North American dairies, especially for workers in milking parlors. This study was among the first to concurrently evaluate occupational exposure to assayable endotoxin (lipid A), 3-hydroxy fatty acids or 3-OHFA (a chemical measure of cell bound and noncell-bound endotoxins), muramic acid, ergosterol, and ammonia among workers on Western U.S. dairies. There remains a need for cost-effective, culturally acceptable intervention strategies integrated in OHS Risk Management and production systems to further optimize worker health and farm productivity.

Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA

Introduction:

Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.

Methods:

506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx &gt;10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.

Results:

We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx &gt;10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.

Conclusions:

Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.

Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.

Characterization of exosomes from body fluids of dairy cows

Exosomes are a specific subpopulation of extracellular vesicles that are widely released by cells of different origins with divergent functions that make their way into body fluids that can be conveniently sampled. In the current study, we isolated and evaluated exosomes from concurrently collected samples of milk, plasma, saliva, and urine from a group of 6 pregnant Holstein-Friesian dairy cows (aged 7 mo, 174 to 203 d of gestation). The cows had BCS of 3.5 to 5.25 (on a scale of 1 to 10), and the milk production for the season to the time of sampling ranged between 5,118 and 6,959 kg. The low levels of extracellular vesicles in saliva and urine (more than 86% fewer compared to the extracellular vesicles in milk and plasma) precluded further detailed evaluation since utility for diagnostics was deemed unlikely. In exosomes isolated from milk and plasma, size distribution, morphology, and the presence of exosome markers was confirmed by nanoparticle tracking analysis, electron microscopy, and Western blot. In addition, a targeted proteomic approach using the quadrupole ion trap mass spectrometer was also used in the study to screen for the exosome marker (e.g., Tumor susceptibility gene 101). Following confirmation of the presence of exosomes, the proteomic profiles of milk and plasma exosomes were evaluated using information-dependent acquisition-mediated liquid chromatography-tandem mass spectrometry (LC-MS/MS). The milk exosomes contain proteins that differed greatly from the plasma exosomes, with only 8 similar proteins harbored in both the milk and plasma exosomes. The milk and plasma exosomes were found to contain proteins (e.g., immunoglobulin J chain and α2 macroglobulin) associated with specific biological processes and molecular functions. Hence, the fluid of origin required for exosome analysis will be dependent on the specific information needed. In conclusion, isolated exosomes from milk and plasma samples collected at the same time point from the same dairy cows encapsulated different profiles of proteins associated with different biological processes and molecular functions.

Effect of circulating exosomes from transition cows on Madin-Darby bovine kidney cell function

The greatest risk of metabolic and infectious disease in dairy cows is during the transition from pregnancy to lactating (i.e., the transition period). The objective of this experiment was to determine the effects of extracellular vesicles (microvesicles involved in cell-to-cell signaling) isolated from transition cows on target cell function. We previously identified differences in the protein profiles of exosomes isolated from cows divergent in metabolic health status. Therefore, we hypothesized that these exosomes would affect target tissues differently. To investigate this, 2 groups of cows (n = 5/group) were selected based on the concentration of β-hydroxybutyrate and fatty acids in plasma and triacylglycerol concentration in liver at wk 1 and 2 postcalving. Cows with high concentrations of β-hydroxybutyrate, fatty acids, and triacylglycerol were considered at increased risk of clinical disease during the transition period (high-risk group; n = 5) and were compared with cows that had low concentrations of the selected health indicators (low-risk group; n = 5). At 2 time points during the transition period (postcalving at wk 1 and 4), blood was sampled and plasma exosomes were isolated from the high-risk and low-risk cows. The exosomes were applied at concentrations of 10 and 1 µg/mL to 5 × 10³ Madin-Darby bovine kidney cells grown to 50% confluence in 96-well plates. Results indicate a numerical increase in cell proliferation when exosomes from high-risk cows were applied compared with those from low-risk cows. Consistent with an effect on cell proliferation, quantitative reverse transcriptase PCR indicated a trend for upregulation of 3 proinflammatory genes (granulocyte colony-stimulating factor, ciliary neurotrophic factor, and CD27 ligand) with the application of high-risk exosomes, which are involved in cellular growth and survival. Proteomic analysis indicated 2 proteins in the low-risk group that were not identified in the high-risk group (endoplasmin and catalase), which may also be indicative of the metabolic state of origin. It is likely that the metabolic state of the transition cow affects cellular function through exosomal messaging; however, more in-depth research into cross-talk between exosomes and target cells is required to determine whether exosomes influence Madin-Darby bovine kidney cells in this manner.

Plasma exosome profiles from dairy cows with divergent fertility phenotypes

Cell-to-cell communication in physiological and pathological conditions may be influenced by neighboring cells, distant tissues, or local environmental factors. Exosomes are specific subsets of extracellular vesicles that internalize and deliver their content to near and distant sites. Exosomes may play a role in the maternal-embryo crosstalk vital for the recognition and maintenance of a pregnancy; however, their role in dairy cow reproduction has not been established. This study aimed to characterize the exosome profile in the plasma of 2 strains of dairy cow with divergent fertility phenotypes. Plasma was obtained and characterized on the basis of genetic ancestry as fertile (FERT; <23% North American genetics, New Zealand Holstein-Friesian strain, n=8) or subfertile (SUBFERT; >92% North American genetics, North American Holstein-Friesian strain, n=8). Exosomes were isolated by differential and buoyant density centrifugation and characterized by size distribution (nanoparticle tracking analysis, NanoSight NS500, NanoSight Ltd., Amesbury, UK), the presence of CD63 (Western blot), and their morphology (electron microscopy). The total number of exosomes was determined by quantifying the immunoreactive CD63 (ExoELISA kit, System Biosciences), and the protein content established by mass spectrometry. Enriched exosome fractions were identified as cup-shape vesicles with diameters around 100 nm and positive for the CD63 marker. The concentration of exosomes was 50% greater in FERT cows. Mass spectrometry identified 104 and 117 proteins in FERT and SUBFERT cows, of which 23 and 36 were unique, respectively. Gene ontology analysis revealed enrichment for proteins involved in immunomodulatory processes and cell-to-cell communication. Although the role of exosomes in dairy cow reproduction remains to be elucidated, their quantification and content in models with divergent fertility phenotypes could provide novel information to support both physiological and genetic approaches to improving dairy cow fertility.