Clinical factors associated with severe hypophosphataemia after kidney transplant.

BACKGROUND: The mechanism by which hypophosphataemia develops following kidney transplantation remains debated, and limited research is available regarding risk factors. This study aimed to assess the association between recipient and donor variables, and the severity of post-transplantation hypophosphataemia. METHODS: We performed a single-centre retrospective observational study. We assessed the association between demographic, clinical and biochemical variables and the development of hypophosphataemia. We used linear regression analysis to assess association between these variables and phosphate nadir. RESULTS: 87.6% of patients developed hypophosphataemia. Patients developing hypophosphataemia were younger, had a shorter time on renal replacement therapy, were less likely to have had a parathyroidectomy or to experience delayed graft function, were more likely to have received a living donor transplant, from a younger donor. They had higher pre-transplantation calcium levels, and lower alkaline phosphatase levels. Receipt of a living donor transplant, lower donor age, not having had a parathyroidectomy, receiving a transplant during the era of tacrolimus-based immunosuppression, not having delayed graft function, higher pre-transplantation calcium, and higher pre-transplantation phosphate were associated with lower phosphate nadir by multiple linear regression. CONCLUSIONS: This analysis demonstrates an association between variables relating to better graft function and hypophosphataemia. The links with biochemical measures of mineral-bone disease remain less clear.

DIAGNOSING AND CATEGORIZING LEPROSY IN LIVE EURASIAN RED SQUIRRELS (SCIURUS VULGARIS) FOR MANAGEMENT, SURVEILLANCE, AND TRANSLOCATION PURPOSES.

The presence of Mycobacterium lepromatosis and Mycobacterium leprae in Eurasian red squirrel (Sciurus vulgaris, ERS) carcasses throughout the British Isles, and leprosy as a disease, have recently been reported using histological and molecular diagnostic methods. In 2016, the first longitudinal study of ERS affected by leprosy was initiated. One of the main challenges was the reliable diagnosis of leprosy in live ERS, which is important for (a) welfare and case management and (b) surveillance or pretranslocation screening efforts. We explored diagnostic methods ranging from detailed clinical assessment and informative categorization of observed lesions, thermal imaging, serology (antiphenolic glycolipid-I antibody [αPGL-I] detection) to molecular methods (polymerase chain reaction [PCR]). For PCR the ear was established as the optimal sampling site. Based on the experiences from this 2-yr study we propose an objective categorization system for clinical lesions and a diagnostic framework for the combination of the diagnostic tools we found to be effective in live ERS: clinical assessment, αPGL-I serology, and PCR. Thermal imaging did not offer additional information for leprosy diagnostics in ERS. We propose an amended definition of leprosy lesions in ERS as "skin areas of local hair loss, in which a firm-rubbery, glossy swelling develops, that may ulcerate" and standardized terminology for describing ERS leprosy status. The information presented forms the basis of a consistent, reliable diagnostic and reporting system for leprosy cases in ERS.

CLINICAL PROGRESSION OF LEPROSY IN EURASIAN RED SQUIRRELS (SCIURUS VULGARIS) IN A NATURALLY INFECTED WILD POPULATION.

Leprosy has been described in Eurasian red squirrel (Sciurus vulgaris; ERS) carcasses since 2014. Studies of ERS carcasses have not provided information about incubation or disease progression in this host but have provided important insights into pathogen presence and distribution throughout the United Kingdom. Here we present field study data on 31 live ERS from an island population naturally infected with Mycobacterium leprae that were assessed longitudinally over a 2-yr time period. Clinical assessment, serologic (anti-phenolic glycolipid-I antibody [αPGL-I] detection) and molecular methods (polymerase chain reaction) were used to diagnose and categorize ERS at each assessment as a leprosy case, a leprosy suspect, colonized by M. leprae, or a contact ERS. Eight ERS (25.8%) were identified as leprosy cases: four at initial assessment, two at 6 mon and two at 24 mon after initial assessment. One ERS was categorized a leprosy suspect when it developed typical lesions 12 mon after initial assessment, despite negative serologic and molecular test results at this time, though M. leprae DNA had been isolated during the initial assessment. Seven ERS (22.6%) were categorized as colonized and of these, six were reassessed but did not develop clinical signs of leprosy within 6 (n = 2), 12 (n = 3), and 18 (n = 1) mon. Most (48.4%, n = 15) were categorized as contact ERS. Progression of leprosy lesions varied between ERS, but always increased in severity over time and was paralleled with increased antibody response. Based on our dataset, we propose the hypotheses: 1) leprosy in ERS is a chronic, slowly progressing disease in this species, similar to that described for other hosts; 2) lesions can undergo repeated ulceration-healing cycles; and 3) in some instances M. leprae DNA and αPGL-I antibodies are detectable before the onset of clinical signs of disease. Future studies addressing the progression of leprosy in ERS should follow affected animals over a longer time period and include tissue samples to pair molecular diagnostics with serologic results.

Ferumoxytol MR Angiography versus Duplex US for Vascular Mapping before Arteriovenous Fistula Surgery for Hemodialysis.

Background Duplex US is performed routinely for vascular mapping prior to arteriovenous fistula (AVF) creation for hemodialysis but cannot demonstrate the central vasculature. Ferumoxytol, an iron oxide nanoparticle, provides an alternative to gadolinium contrast material for MR angiography for safe use in chronic kidney disease (CKD). Purpose To assess the clinical utility of ferumoxytol-enhanced MR angiography compared with duplex US for vascular mapping before upper limb AVF creation in participants with CKD. Materials and Methods In a prospective comparative study (ClinicalTrials.gov: NCT02997046) from December 2016 to August 2018, participants with CKD underwent ferumoxytol-enhanced MR angiography and duplex US. Two independent readers evaluated vessels for diameter, stenosis or occlusion, arterial disease, and central stenosis. Intraclass correlation coefficients (ICCs) and Bland-Altman plots were used to assess intra- and interreader variability. On the basis of accepted standards for AVF creation, an algorithm was developed to predict AVF outcome based on imaging findings. Multivariable regression models used AVF success as the dependent variable and age, sex, and duplex US or ferumoxytol-enhanced MR angiography findings as independent variables. Results Fifty-nine participants with CKD (mean age, 59 years ± 13 [standard deviation]; 30 women) were evaluated. A total of 51 fistulas were created, of which 24 (47%) were successful. Ferumoxytol-enhanced MR angiography showed excellent inter- and intrareader repeatability (ICC, 0.84-0.99) for all variables assessed. In addition to revealing 15 central vasculature stenoses, ferumoxytol-enhanced MR angiography resulted in characterization of 88 of 236 (37%) of the arterial sections examined as unsuitable for AVF creation compared with 61 of 236 (26%) sections with duplex US (P = .01). Ferumoxytol-enhanced MR angiography independently predicted AVF success in models including (odds ratio, 6.5; 95% confidence interval: 1.7, 25; P = .006) and those excluding (odds ratio, 4.6; 95% confidence interval: 1.3, 17; P = .02) the central vasculature. Conclusion In addition to enabling identification of central vessel pathologic features, ferumoxytol-enhanced MR angiography revealed peripheral arterial disease not recognized with duplex US and was more predictive than duplex US of the outcome of arteriovenous fistula surgery. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Finn in this issue.

The management of lower limb arteriovenous grafts in the perioperative period following renal transplantation.

BACKGROUND: The presence of a lower limb arteriovenous graft (LL-AVG) is indicative of a group of complex hemodialysis patients who have precarious long-term vascular access. The aim of this study is to describe our experience of the clinical decisions and interactions between LL-AVG and renal transplantation. METHODS: The records of 23 patients who received a transplant in the presence of a LL-AVG between 2010 and 2018 were analyzed: firstly, to determine whether patients with a LL-AVG received extended criteria transplants, the implantation procedure, and the management of the LL-AVG in the post-operative period. RESULTS: Seventeen patients (74%) had "end-stage access" and were thus considered for all offer stratified by the kidney donor profile index (KDPI) and donor type (DBD or DCD). In eleven patients (48%), a kidney with a high risk of delayed graft function was transplanted. Same-sided renal transplantation occurred in only 35% of cases, and of these, only one LL-AVG was ligated immediately to improve transplant perfusion. CONCLUSION: A patient-based approach applied in decision-making on management of the LL-AVG post-transplantation should include (a) the likelihood of delayed graft function, (b) the need for post-operative hemodialysis, (c) the side of proposed transplant compared to the LL-AVG, and (d) local complications.

Early Cannulation ePTFE Arteriovenous Access Grafts are Associated with a Low Incidence of Pseudoaneurysm Formation.

BACKGROUND: Pseudoaneurysm formation is common in standard thin-walled polytetrafluoroethylene (sPTFE) grafts, occurring in up to 10% of grafts, and is reported as the most common cause of graft loss for grafts more than 2 years old. The Gore® Acuseal™ graft is an early cannulation graft, needled before incorporation, and thus may be especially prone to pseudoaneurysm formation. In addition, as this is a relatively new product, there are limited data on long-term outcomes such as pseudoaneurysm. We report one center's experience of the incidence and etiological factors associated with pseudoaneurysm formation over 5 years and 265 grafts. METHODS: A total of 265 Acuseal grafts were placed in the last 5 years. All patients had prospective data entered into an electronic searchable patient record. Surveillance was performed with 3 monthly imaging (digital subtraction angiography or ultrasound), clinical examination, and hemodynamic performance. Data examined included the incidence, causative factors, and outcomes of pseudoaneurysm. RESULTS: Eleven grafts (4.15%) developed a pseudoaneurysm, with 2 patients developing significant hemorrhage. The median time to development of a pseudoaneurysm was 25 months interquartile range (IQR, 20-28 months). Several common etiological factors were identified. All but one patient had overuse of needling sites (n = 10; 90.9%). Other factors associated with pseudoaneurysm formation were inadequate surveillance (n = 9; 81.8%), venous outflow stenosis (n = 9; 81.8%), and anticoagulation/dual antiplatelet therapy (n = 7; 63.6%). Management included observation and needle rotation (n = 5; 45.5%), stent grafting (n = 3; 27.3%), or excision (n = 1; 9.1%) of the pseudoaneurysm. Surgical or endovascular augmentation of the venous outflow was required in 9 patients (81.8%). Graft ligation and explantation were required in 5 patients (45.5%) with graft preservation achieved in 6/11 patients (54.5%). CONCLUSIONS: Pseudoaneurysm formation occurs less frequently in Acuseal grafts compared with historical data for standard PTFE grafts. Pseudoaneurysm formation did not occur in any graft within the first 13 months after implantation, suggesting early cannulation before incorporation is not by itself a risk factor for pseudoaneurysm development. Poor needling, venous stenosis, inadequate surveillance, and anticoagulation/dual antiplatelet therapy are remediable factors, and graft preservation is possible. Acuseal is a robust graft with lower rates of pseudoaneurysm formation on long-term follow-up than standard PTFE grafts.

Arteriovenous Access Graft Infection: Standards of Reporting and Implications for Comparative Data Analysis.

There is presently a lack of organization and standardized reporting schema for arteriovenous graft (AVG) infections. The purpose of this article is to evaluate the various types of treatment modalities for access site infections through an analysis of current publications on AVG. Key proposals are made to support standardization in a data-driven manner to make infection reporting more uniform and thereby facilitate more meaningful comparisons between various dialysis modalities and AVG technologies.

The Neglectable Impact of Delayed Graft Function on Long-term Graft Survival in Kidneys Donated After Circulatory Death Associates With Superior Organ Resilience.

OBJECTIVE: To explore putative different impacts of delayed graft function (DGF) on long-term graft survival in kidneys donated after brain death (DBD) and circulatory death (DCD). BACKGROUND: Despite a 3-fold higher incidence of DGF in DCD grafts, large studies show equivalent long-term graft survival for DBD and DCD grafts. This observation implies a differential impact of DGF on DBD and DCD graft survival. The contrasting impact is remarkable and yet unexplained. METHODS: The impact of DGF on DBD and DCD graft survival was evaluated in 6635 kidney transplants performed in The Netherlands. DGF severity and functional recovery dynamics were assessed for 599 kidney transplants performed at the Leiden Transplant Center. Immunohistochemical staining, gene expression profiling, and Ingenuity Pathway Analysis were used to identify differentially activated pathways in DBD and DCD grafts. RESULTS: While DGF severely impacted 10-year graft survival in DBD grafts (HR 1.67; P < 0.001), DGF did not impact graft survival in DCD grafts (HR 1.08; P = 0.63). Shorter dialysis periods and superior posttransplant eGFRs in DBD grafts show that the differential impact was not caused by a more severe DGF phenotype in DBD grafts. Immunohistochemical evaluation indicates that pathways associated with tissue resilience are present in kidney grafts. Molecular evaluation showed selective activation of resilience-associated pathways in DCD grafts. CONCLUSIONS: This study shows an absent impact of DGF on long-term graft survival in DCD kidneys. Molecular evaluation suggests that the differential impact of DGF between DBD and DCD grafts relates to donor-type specific activation of resilience pathways in DCD grafts.

A national study of autogenous arteriovenous access use and patency in a contemporary hemodialysis population.

OBJECTIVE: The predicted outcomes of autogenous arteriovenous (AV) hemodialysis access creation are predominantly based on historical data; however, both the hemodialysis population and clinical practices have changed significantly during the last decade. This study examined contemporary AV access clinical use and patencies. METHODS: A multicenter observational cohort study was performed of all new AV accesses created in Scotland in 2015. The primary end point was efficacy assessed by successful AV access use for a minimum of 30 days and primary, primary assisted, and secondary patency at 1 year. Data obtained included all interventions to maintain or to restore patency. Predictors of patency loss including demographics, comorbid conditions, dialysis status, AV access location, duplex ultrasound surveillance, procedures, prior access, and antiplatelets were assessed. Kaplan-Meier and competing risks analyses were performed to estimate the probability of AV access failure. All patients were followed up for at least 1 year or had a censoring event. RESULTS: A total of 582 AV accesses were created in 537 patients (mean age, 60 [standard deviation, 14] years; 60% men; 42% with diabetes) in nine adult renal centers. Mean follow-up was 11.8 (standard deviation, 7.6) months. By the end of the follow-up, 322 (55.3%) AV accesses were successfully used for dialysis. At 1 year, 48% (95% confidence interval [CI], 44-52) of AV accesses had primary patency, (95% CI, 63-71) had primary assisted patency, and 69% (95% CI, 65-73) had secondary patency. The leading cause of primary patency loss was primary failure (30%). An average of 0.48 intervention per patient-year was required to maintain patency. On multivariable analysis, patency was better for an upper arm than for a forearm AV access (1-year secondary patency of upper arm vs forearm AV accesses, 74% vs 58%). The cumulative hazard and incident functions for AV access failure were 31% (95% CI, 27-35) and 23% (95% CI, 20-27) at 1 year, respectively. CONCLUSIONS: Despite advances in recent years with preoperative vessel assessment and surveillance, patency rates have not improved, with primary failure remaining the major obstacle. Competing events should be taken into consideration; otherwise, biases may occur with overestimation of the probability of AV access failure.

Interaction between socioeconomic deprivation and likelihood of pre-emptive transplantation: influence of competing risks and referral characteristics - a retrospective study.

Socioeconomic deprivation (SED) influences likelihood of pre-emptive kidney transplantation (PET), but the mechanisms behind this are unclear. We explored the relationships between SED and patient characteristics at referral, which might explain this discrepancy. A retrospective cohort study was performed. SED was measured by Scottish Index of Multiple Deprivation (SIMD). Logistic regression evaluated predictors of PET. A competing risks survival analysis evaluated the interaction between SED and progression to end-stage kidney disease (ESKD) and death. Of 7765 patients with follow-up of 5.69 ± 6.52 years, 1298 developed ESKD requiring RRT; 113 received PET, 64 of which were from live donors. Patients receiving PET were "less deprived" with higher SIMD (5 ± 7 vs. 4 ± 5; P = 0.003). This appeared independent of overall comorbidity burden. SED was associated with a higher risk of death but not ESKD. Higher SIMD decile was associated with a higher likelihood of PET (OR 1.14, 95% CI 1.06, 1.23); the presence of diabetes and malignancy also reduced PET. SED was associated with reduced likelihood of PET after adjustment for baseline comorbidity, and this was not explained by risk of death or faster progression to ESKD. Education and outreach into transplantation should be augmented in areas with higher deprivation.

Control of paratuberculosis: who, why and how. A review of 48 countries.

Paratuberculosis, a chronic disease affecting ruminant livestock, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has direct and indirect economic costs, impacts animal welfare and arouses public health concerns. In a survey of 48 countries we found paratuberculosis to be very common in livestock. In about half the countries more than 20% of herds and flocks were infected with MAP. Most countries had large ruminant populations (millions), several types of farmed ruminants, multiple husbandry systems and tens of thousands of individual farms, creating challenges for disease control. In addition, numerous species of free-living wildlife were infected. Paratuberculosis was notifiable in most countries, but formal control programs were present in only 22 countries. Generally, these were the more highly developed countries with advanced veterinary services. Of the countries without a formal control program for paratuberculosis, 76% were in South and Central America, Asia and Africa while 20% were in Europe. Control programs were justified most commonly on animal health grounds, but protecting market access and public health were other factors. Prevalence reduction was the major objective in most countries, but Norway and Sweden aimed to eradicate the disease, so surveillance and response were their major objectives. Government funding was involved in about two thirds of countries, but operations tended to be funded by farmers and their organizations and not by government alone. The majority of countries (60%) had voluntary control programs. Generally, programs were supported by incentives for joining, financial compensation and/or penalties for non-participation. Performance indicators, structure, leadership, practices and tools used in control programs are also presented. Securing funding for long-term control activities was a widespread problem. Control programs were reported to be successful in 16 (73%) of the 22 countries. Recommendations are made for future control programs, including a primary goal of establishing an international code for paratuberculosis, leading to universal acknowledgment of the principles and methods of control in relation to endemic and transboundary disease. An holistic approach across all ruminant livestock industries and long-term commitment is required for control of paratuberculosis.

Maintaining lower limb access with the HeRO device.

Central venous catheters (CVC) remain a mainstay of vascular access particularly for incident patients,but lead to central vein stenosis (CVS) in up to 1 in 6 patents. This often leads to establishing dialysis access in the groin which in turn may result in development of CVS in the lower body, although this is poorly reported. The HeRO device was designed to address CVS by bypassing the stenosed veins with a nitinol-reinforced silicone tube into the right atrium, which acts as an outflow conduit attached to an arterial inflow. The efficacy and safety of the HeRO device in the upper limb is well established, but there is no data on its use in the lower limb. We describe 2 cases of HeRO in the lower limb, one primary and one secondary, which remain in use. Lower limb HeRO is feasible in the lower limb and can work well either as de novo (to achieve vascular access) or as a salvage procedure (to maintain vascular access).

The first 365 days on haemodialysis: variation in the haemodialysis access journey and its associated burden.

Background: The modality by which haemodialysis (HD) is delivered [arteriovenous fistula (AVF), arteriovenous graft (AVG) or central venous catheter (CVC)] varies widely and is influenced by clinical evidence, patient factors and the prevailing service configuration. The aim of this study was to determine the outcome and impact of access strategy on patient outcome by mapping out the HD journey in a cohort of incident patients. Methods: A 2-year cohort of consecutive incident HD patients from the point of referral for first dialysis access to completion of the first 365 days of HD was prospectively reviewed. Data were sought on access type; radiological, surgical and other access-related activity; bacteraemic events; admission rates and cumulative financial cost. Results: A total of 144 patients started RRT for the first time with HD over the 2-year period. All were followed up to 1 year after starting HD, generating a total of 47 753 observed HD days. Activity prior to starting HD for the full cohort was found to average 0.92 arteriovenous (AV) access creation procedures, 0.40 CVC insertions, 0.14 interventional radiology procedures and 0.41 ultrasound examinations per patient. The small number of patients who started on an AVG had a tendency towards higher pre-HD surgical and imaging activity than those who started on an AVF or CVC. Activity after starting HD varied greatly with the access type used at the start of HD, with AVF patients experiencing less hospitalization, procedure and imaging activity and financial costs compared with those who start HD with a CVC. Patients who started on an AVG had a tendency towards lower surgical activity rates and financial costs than those who started on a CVC. Conclusions: Providing, maintaining and dealing with the complications of HD vascular access places a significant burden of activity that is shared across nephrology, surgery and imaging services. A well-functioning AVF is associated with the lowest burden, whereas a failed AVF or CVC access is associated with the highest burden. Patient journeys are shaped by the vascular access that they use and we suggest that the contemporary pursuit of HD access should focus on delivering personalized access solutions.

Uptake, Whole-Body Distribution, and Depuration of Nanoplastics by the Scallop Pecten maximus at Environmentally Realistic Concentrations.

Previous studies of uptake and effects of nanoplastics by marine organisms have been conducted at what may be unrealistically high concentrations. This is a consequence of the analytical challenges in tracking plastic particles in organisms at environmentally relevant concentrations and highlights the need for new approaches. Here, we present pulse exposures of 14C-radiolabeled nanopolystyrene to a commercially important mollusk, Pecten maximus, at what have been predicted to be environmentally relevant concentrations (<15 µg L-1). Uptake was rapid and was greater for 24 nm than for 250 nm particles. After 6 h, autoradiography showed accumulation of 250 nm nanoplastics in the intestine, while 24 nm particles were dispersed throughout the whole-body, possibly indicating some translocation across epithelial membranes. However, depuration was also relatively rapid for both sizes; 24 nm particles were no longer detectable after 14 days, although some 250 nm particles were still detectable after 48 days. Particle size thus apparently influenced the biokinetics and suggests a need for chronic exposure studies. Modeling extrapolations indicated that it could take 300 days of continued environmental exposure for uptake to reach equilibrium in scallop body tissues although the concentrations would still below 2.7 mg g-1. Comparison with previous work in which scallops were exposed to nonplastic (silver) nanomaterials of similar size (20 nm), suggests that nanoparticle composition may also influence the uptake tissue distributions somewhat.

Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

BACKGROUND: Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne's disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods. RESULTS: Single nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species. We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains. WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year. CONCLUSIONS: This study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections.

Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis.

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit-variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates.

A post-mortem study of respiratory disease in small mustelids in south-west England.

BACKGROUND: Stoat (Mustela erminea) and weasel (Mustela nivalis) populations in south-west England are declining whilst polecats (Mustela putorius), absent for over a century, are increasing. Little is known about the health status of these species nationally. This study aimed at investigating respiratory disease in specimens found dead in south-west England. RESULTS: Trauma caused by road traffic, predator attack or being trapped was the predominant cause of death in 42 stoats, 31 weasels and 20 polecats; most were in good physical condition. Skrjabingylus nasicola was present in all species (weasels 37%, polecats 39%, stoats 41%) and infected animals showed no evidence of loss of body condition. Even in carcases stored frozen L1 larvae were frequently alive and highly motile. Angiostrongylus vasorum infection was diagnosed in two stoats and one weasel: in stoats infections were patent and the lung lesions were likely of clinical significance. These are believed to be the first records of A. vasorum in small mustelids. Pleuritis and pyothorax was seen in two polecats, in one case due to a migrating grass awn. Histological examination of lungs showed granulomata in stoats (38%), weasels (52%) and polecats (50%). Spherules consistent with Emmonsia spp. adiaspores were present in the granulomata of stoats (60%), weasels (36%) and polecats (29%). Adiaspore diameter in all three species was similar (means: stoats 39 µm, weasels 30 µm, polecats 36 µm); these are markedly smaller than that normally recorded for E. crescens. Although they lie within the accepted range for spores of Emmonsia parva this arid-zone species is not found in Britain, thus raising a question over the identity of the fungus. Cases showing numerous granulomata but few or no adiaspores were Ziehl-Neelsen-stain negative for acid-fast bacilli and IHC negative for Mycobacterium spp. However, in some cases PCR analyses revealed mycobacteria, including Mycobacterium kumamotonense and Mycobacterium avium Complex. One stoat had numerous unidentified small organisms present centrally within granulomata. CONCLUSIONS: Stoats, weasels and polecats in south-west England share several respiratory diseases, often of high prevalence, but the pathology would appear insufficient to impact on the health status of the populations and other ultimate causes of death should be investigated when examining these species.

Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.

BACKGROUND: Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne's disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. RESULTS: Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including "bison type" isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1-2 to 239-240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. CONCLUSIONS: The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne's disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.

Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review.

Mycobacterium avium subspecies paratuberculosis (Map) is an important pathogen that causes a chronic, progressive granulomatous enteritis known as Johne's disease or paratuberculosis. The disease is endemic in many parts of the world and responsible for considerable losses to the livestock and associated industries. Diagnosis and control are problematic, due mostly to the long incubation period of the disease when infected animals show no clinical signs and are difficult to detect, and the ability of the organism to survive and persist in the environment. The existence of phenotypically distinct strains of Map has been known since the 1930s but the genetic differentiation of Map strain types has been challenging and only recent technologies have proven sufficiently discriminative for strain comparisons, tracing the sources of infection and epidemiological studies. It is important to understand the differences that exist between Map strains and how they influence both development and transmission of disease. This information is required to develop improved diagnostics and effective vaccines for controlling Johne's disease. Here I review the current classification of Map strain types, the sources of the genetic variability within strains, growth characteristics and epidemiological traits associated with strain type and the influence of strain type on infection and pathogenicity.