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 < 0.001) as a result of higher average weaning weights (+19 kg, P < 0.001) and higher growth during the post-weaning year (+12 kg, P < 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 >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 >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.

Prevalence of Sickle Cell Disease among Newborns in St Vincent and the Grenadines: A Retrospective Study

Objective

In the United States of America (USA), sickle cell disease (SCD) occurs in 1:375 African-American births. However, published data from the Caribbean have revealed higher numbers for some Caribbean islands. St Vincent and the Grenadines (SVG) is a multi-island nation in the Caribbean, and there are currently no data on the incidence or prevalence of the disease in this population. The objective of this study was to obtain birth prevalence estimates for SCD in SVG.

Methods

A retrospective review of haemoglobin electrophoresis test results at the laboratory of the main hospital in SVG for the period of October 1, 2005 to December 31, 2013 was done. Test results and demographic data were extracted to determine the estimated birth prevalence of SCD.

Results

The estimated birth prevalence of SCD was found to be 1:172 live births, and 86% of the patients were diagnosed after one year of age.

Conclusion

The birth prevalence of SCD in SVG was higher than those in the USA, but was similar to the numbers in other Caribbean populations.

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.