High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds.

Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.

TeamMate: A Longitudinal Study of New Zealand Working Farm Dogs. III. Factors Affecting the Risk of Dogs Being Lost from the Workforce.

Working farm dogs are essential to many livestock farmers. Little is known about factors that influence dogs' risk of being lost from work. This paper explores risk factors for farm dogs being lost through death, euthanasia and retirement. All enrolled dogs were working and a minimum of 18 months old. Five data collection rounds were performed over four years. Data about dogs were collected from owners and dogs were given physical examinations by veterinarians. Dogs that were lost from work were counted and owner-reported reasons for loss were recorded. Multivariable logistic regression modelling was used to investigate risk factors for loss. Of 589 dogs, 81 were lost from work. Of these, 59 dogs died or were euthanized and 22 were retired. Farm dogs tended to reach advanced ages, with 38% being 10 years or older when last examined. Acute injury or illness was the most commonly owner-reported reason for loss. Age group (p < 0.0001) and lameness (p = 0.04, OR = 1.8) significantly affected dogs' risk of being lost. These results expand our knowledge about factors that affect health, welfare and work in farm dogs. Further investigation into reasons for lameness may help improve health and welfare in working farm dogs.

Caprine PRNP polymorphisms N146S and Q222K are associated with proteolytic cleavage of PrPC.

Expression of the cellular prion protein (PrPC) is crucial for the development of prion diseases. Amino acid changes in PrPC or a reduced amount of PrPC may modulate disease resistance. The relative abundance of C1, a natural α-cleavage fragment of PrPC, was previously found to be associated with a resistant PRNP genotype in sheep. Goats are another small ruminant where classical scrapie susceptibility is under strong genetic control. In this study, we assessed PrPC in goats for the existence of similar associations between PrPC fragments and genotype. Brain tissue homogenates from scrapie-free goats with wild type PRNP or polymorphisms (I142M, H143R, N146S, or Q222K) were deglycosylated prior to immunoblot for assessment of the relative abundance of the C1 fragment of PrPC. The presence of K222 or S146 alleles demonstrated significantly different relative levels of C1 compared to that observed in wild type goats, which suggests that the genotype association with C1 is neither unique to sheep nor exclusive to the ovine Q171R dimorphism.

Prevalence and Epidemiology of Non-O157 Escherichia coli Serogroups O26, O103, O111, and O145 and Shiga Toxin Gene Carriage in Scottish Cattle, 2014-2015.

Cattle are a reservoir for Shiga toxin-producing Escherichia coli (STEC), zoonotic pathogens that cause serious clinical disease. Scotland has a higher incidence of STEC infection in the human population than the European average. The aim of this study was to investigate the prevalence and epidemiology of non-O157 serogroups O26, O103, O111, and O145 and Shiga toxin gene carriage in Scottish cattle. Fecal samples (n = 2783) were collected from 110 herds in 2014 and 2015 and screened by real-time PCR. Herd-level prevalence (95% confidence interval [CI]) for O103, O26, and O145 was estimated as 0.71 (0.62, 0.79), 0.43 (0.34, 0.52), and 0.23 (0.16, 0.32), respectively. Only two herds were positive for O111. Shiga toxin prevalence was high in both herds and pats, particularly for stx2 (herd level: 0.99; 95% CI: 0.94, 1.0). O26 bacterial strains were isolated from 36 herds on culture. Fifteen herds yielded O26 stx-positive isolates that additionally harbored the intimin gene; six of these herds shed highly pathogenic stx2-positive strains. Multiple serogroups were detected in herds and pats, with only 25 herds negative for all serogroups. Despite overlap in detection, regional and seasonal effects were observed. Higher herd prevalence for O26, O103, and stx1 occurred in the South West, and this region was significant for stx2 at the pat level (P = 0.015). Significant seasonal variation was observed for O145 prevalence, with the highest prevalence in autumn (P = 0.032). Negative herds were associated with Central Scotland and winter. Herds positive for all serogroups were associated with autumn and larger herd size and were not housed at sampling.IMPORTANCE Cattle are reservoirs for Shiga toxin-producing Escherichia coli (STEC), bacteria shed in animal feces. Humans are infected through consumption of contaminated food or water and by direct contact, resulting in serious disease and kidney failure in the most vulnerable. The contribution of non-O157 serogroups to STEC illness was underestimated for many years due to the lack of specific tests. Recently, non-O157 human cases have increased, with O26 STEC of particular note. It is therefore vital to investigate the level and composition of non-O157 in the cattle reservoir and to compare them historically and by the clinical situation. In this study, we found cattle prevalence high for toxin, as well as for O103 and O26 serogroups. Pathogenic O26 STEC were isolated from 14% of study herds, with toxin subtypes similar to those seen in Scottish clinical cases. This study highlights the current risk to public health from non-O157 STEC in Scottish cattle.

TeamMate: A Longitudinal Study of New Zealand Working Farm Dogs. II. Occurrence of Musculoskeletal Abnormalities.

Musculoskeletal injury and disease are common in dogs, and a major cause of retirement in working dogs. Many livestock farmers rely on dogs for the effective running of their farms. However, the incidence of musculoskeletal disease has not been explored in working farm dogs. Here we explore the occurrence of musculoskeletal abnormalities in 323 working farm dogs that were enrolled in TeamMate, a longitudinal study of working farm dogs in New Zealand. All dogs were free of musculoskeletal abnormalities on enrolment to the study and were present for at least one follow-up examination. During the follow-up period, 184 dogs (57%, 95% confidence interval (CI) = 52%-62%) developed at least one musculoskeletal abnormality during 4,508 dog-months at risk, corresponding to 4.1 dogs (95% CI = 3.5-4.7) with recorded abnormalities per 100 dog-months at risk. The most common abnormalities were reduced range of motion and swelling of the carpus or stifle, while the hip was the most common site of pain. No major differences in incidence rate (IR) between sexes or types of dogs were observed, though Huntaways had a slightly lower rate of carpal abnormalities than Heading dogs (IR ratio = 0.6, 95% CI = 0.3-1.0). Eighty-one of 119 dogs (68%, 95% CI = 60%-76%) that had a first musculoskeletal abormality developed a second abnormality. The most common type of abnormality that was seen in the same dog more than once was reduced range of motion in the carpus (14 of 119 dogs, 12%, 95% CI = 6%-18%). Although we do not provide data on diagnoses, the high incidence rate of recorded musculoskeletal abnormalities and dogs' high activity mean it is likely that working farm dogs are at a high risk of conditions that could impair their welfare and reduce the lengths of their working careers. Preventing and managing musculoskeletal injury and illness should be a priority for owners and veterinarians caring for working farm dogs.

TeamMate: a longitudinal study of New Zealand working farm dogs. I. Methods, population characteristics and health on enrolment.

BACKGROUND: Working farm dogs are invaluable on New Zealand sheep and beef farms. To date no study describing farm dog population and health has included information about incidence of illness and injury, or risk factors affecting health and career duration. This paper describes the methodology and initial results from TeamMate, a longitudinal study that was designed to address this gap. We describe the study population, husbandry practices, and prevalence of clinical abnormalities on enrolment. METHODS: Data about the farms, owners, husbandry practices and dogs were collected on farm at approximately 6-month intervals. All dogs over 18 months old and in full work were enrolled. Dogs were given physical examinations by veterinarians. On examination all abnormalities were noted, regardless of clinical significance. RESULTS: Six hundred forty-one working farm dogs and 126 owners were enrolled from the South Island of New Zealand. Forty-nine percent of dogs were Heading dogs (314 of 641) and 48% Huntaways (308 of 641). Median age of dogs was 4 years (range 1.5-14) and median body condition score (BCS) was four on a 9-point scale (interquartile range (IQR) 3-5). Fifty-four percent of dogs were male (345 of 641), and 6% (41 of 641) were neutered. Eighty-one percent of owners (102 of 126) fed dogs commercial biscuits and meat sourced on farm. Forty-four percent of dogs (279 of 641) had bedding in their kennel, 14% (55 of 393) had insulated kennels, 69% (442 of 641) had been vaccinated and 33% (213 of 641) were insured. Clinical abnormalities were found in 74% of dogs (475 of 641). Common abnormalities involved the musculoskeletal system (43%, 273 of 641), skin (including scars and callouses; 42%, 272 of 641), and oral cavity (including worn and broken teeth; 35%, 227 of 641). CONCLUSIONS: Our results expand on those from previous surveys and indicate that musculoskeletal illness and injury, and skin trauma are the most commonly seen clinical abnormalities in working farm dogs. These results will provide a baseline for investigation of incidence and risk factors for illness, injury, retirement and death in New Zealand working farm dogs.

Variation in the prion protein gene (PRNP) sequence of wild deer in Great Britain and mainland Europe.

Susceptibility to prion diseases is largely determined by the sequence of the prion protein gene (PRNP), which encodes the prion protein (PrP). The recent emergence of chronic wasting disease (CWD) in Europe has highlighted the need to investigate PRNP gene diversity in European deer species, to better predict their susceptibility to CWD. Here we report a large genetic survey of six British deer species, including red (Cervus elaphus), sika (Cervus nippon), roe (Capreolus capreolus), fallow (Dama dama), muntjac (Muntiacus reevesii), and Chinese water deer (Hydropotes inermis), which establishes PRNP haplotype and genotype frequencies. Two smaller data sets from red deer in Norway and the Czech Republic are also included for comparison. Overall red deer show the most PRNP variation, with non-synonymous/coding polymorphisms at codons 98, 168, 226 and 247, which vary markedly in frequency between different regions. Polymorphisms P168S and I247L were only found in Scottish and Czech populations, respectively. T98A was found in all populations except Norway and the south of England. Significant regional differences in genotype frequencies were observed within both British and European red deer populations. Other deer species showed less variation, particularly roe and fallow deer, in which identical PRNP gene sequences were found in all individuals analysed. Based on comparison with PRNP sequences of North American cervids affected by CWD and limited experimental challenge data, these results suggest that a high proportion of wild deer in Great Britain may be susceptible to CWD.

Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD.

Multisystem failure due to three coexisting autoimmune diseases.

Systemic lupus erythematosis (SLE) is a potentially fatal, autoimmune disease, which can affect different organs and can present with protean clinical manifestations. It may be associated with many other autoimmune conditions and two rare such conditions are myelofibrosis and acquired haemophilia. Autoimmune myelofibrosis is a bone marrow disorder characterized by pancytopenia, which can occur in conjunction with the presenting features, or an exacerbation of previously established SLE. Acquired haemophilia is another rare disorder of haemostasis, which can be life threatening without prompt and appropriate treatment. The management of these different conditions in itself poses a difficult problem but when the three conditions present simultaneously in the same individual, the accurate diagnosis and indeed the appropriate management becomes extremely challenging. This report describes a young woman who presented with pancytopenia secondary to myelofibrosis and panserositis with no identifiable precipitating factors. Her condition deteriorated rapidly and she required intensive care support for respiratory failure and renal impairment. A presumed diagnosis of SLE was considered and treatment was initiated which improved and stabilised her condition. However, she developed bleeding complications from acquired haemophilia which required further specialist intervention. Multidisciplinary management of the patient helped in the resolution of the complications and stabilisation of her autoimmune conditions. This report should make physicians aware of the rare presentations of SLE and its complex management.

Topographical characterization of cone photoreceptors and the area centralis of the canine retina.

PURPOSE: The canine is an important large animal model of human retinal genetic disorders. Studies of ganglion cell distribution in the canine retina have identified a visual streak of high density superior to the optic disc with a temporal area of peak density known as the area centralis. The topography of cone photoreceptors in the canine retina has not been characterized in detail, and in contrast to the macula in humans, the position of the area centralis in dogs is not apparent on clinical funduscopic examination. The purpose of this study was to define the location of the area centralis in the dog and to characterize in detail the topography of rod and cone photoreceptors within the area centralis. This will facilitate the investigation and treatment of retinal disease in the canine. METHODS: We used peanut agglutinin, which labels cone matrix sheaths and antibodies against long/medium wavelength (L/M)- and short wavelength (S)-cone opsins, to stain retinal cryosections and flatmounts from beagle dogs. Retinas were imaged using differential interference contrast imaging, fluorescence, and confocal microscopy. Within the area centralis, rod and cone size and density were quantified, and the proportion of cones expressing each cone opsin subtype was calculated. Using a grid pattern of sampling in 9 retinal flatmounts, we investigated the distribution of cones throughout the retina to predict the location of the area centralis. RESULTS: We identified the area centralis as the site of maximal density of rod and cone photoreceptor cells, which have a smaller inner segment cross-sectional area in this region. L/M opsin was expressed by the majority of cones in the retina, both within the area centralis and in the peripheral retina. Using the mean of cone density distribution from 9 retinas, we calculated that the area centralis is likely to be centered at a point 1.5 mm temporal and 0.6 mm superior to the optic disc. For clinical funduscopic examination, this represents 1.2 disc diameters temporal and 0.4 disc diameters superior to the optic disc. CONCLUSIONS: We have described the distribution of rods and cone subtypes within the canine retina and calculated a predictable location for the area centralis. These findings will facilitate the characterization and treatment of cone photoreceptor dystrophies in the dog.

A truncated H-NS-like protein from enteropathogenic Escherichia coli acts as an H-NS antagonist.

The H-NS nucleoid-associated protein of Escherichia coli is the founder member of a widespread family of gene regulatory proteins which have a bipartite structure, consisting of an N-terminal coiled-coil oligomerization domain and a C-terminal DNA-binding domain. Here we characterize a family of naturally occurring truncated H-NS derivatives lacking the DNA-binding domain, which we term the H-NST family. H-NST proteins are found in large genomic islands in pathogenic E. coli strains, which are absent from the corresponding positions in the E. coli K-12 genome. Detailed analysis of the H-NST proteins from enteropathogenic E. coli (EPEC) and uropathogenic E. coli (UPEC) shows that the EPEC protein (H-NST(EPEC)) has a potent anti-H-NS function at the classical H-NS-repressed operon proU. This correlates with the ability of H-NST(EPEC) to co-purify with H-NS in vitro, and can be abolished by a mutation of leucine 30 to proline which is predicted to prevent the N-terminal region from forming a coiled-coil structure. In contrast, despite being 90% identical to H-NST(EPEC) at the protein level, the UPEC homologue (H-NST(UPEC)) has only a weak anti-H-NS activity, correlating with a much-reduced ability to interact with H-NS during column chromatography. A single amino acid difference at residue 16 appears to account for these different properties. The hnsT(EPEC) gene is transcribed monocistronically and expressed throughout the exponential growth phase in DMEM medium. Our data suggest that a truncated derivative of H-NS encoded by an ancestral mobile DNA element can interact with the endogenous H-NS regulatory network of a bacterial pathogen.