A cattle graph genome incorporating global breed diversity.

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.

Phenotypic and genotypic analysis of benzimidazole resistance in reciprocal genetic crosses of Haemonchus contortus.

Haemonchus contortus is arguably one of the most economically important and ubiquitous parasites of livestock globally and commonly involved in cases of anthelmintic resistance. Here, we performed reciprocal genetic crosses using susceptible (MHco3(ISE)) and multiple anthelmintic resistant (MHco18(UGA2004)) H. contortus isolates. Resultant admixed populations were designated MHco3/18 or MHco18/3, where the lead isolate reflects the origin of the females. Three independent filial generations were generated for each cross, which were subjected to bioassays, molecular approaches and population genetic analyses to investigate the phenotypic and genotypic inheritance of benzimidazole (BZ) resistance at each stage. A panel of microsatellite markers confirmed the success of the genetic cross as markers from both parents were seen in the F1 crosses. Egg hatch tests revealed a stark difference between the two F1 crosses with ED50 estimates for MHco18/3 being 9 times greater than those for MHco3/18. Resistance factors based on ED50 estimates ranged from 6 to 57 fold in the filial progeny compared to MHco3(ISE) parents. Molecular analysis of the F167Y and F200Y SNP markers associated with BZ resistance were analysed by pyrosequencing and MiSeq deep amplicon sequencing, which showed that MHco3/18.F1 and MHco18/3.F1 both had similar frequencies of the F200Y resistant allele (45.3% and 44.3%, respectively), whereas for F167Y, MHco18/3.F1 had a two-fold greater frequency of the resistant-allele compared to MHco3/18.F1 (18.2% and 8.8%, respectively). Comparison between pyrosequencing and MiSeq amplicon sequencing revealed that the allele frequencies derived from both methods were concordant at codon 200 (rc = 0.97), but were less comparable for codon 167 (rc = 0.55). The use of controlled reciprocal genetic crosses have revealed a potential difference in BZ resistance phenotype dependent on whether the resistant allele is paternally or maternally inherited. These findings provide new insight and prompt further investigation into the inheritance of BZ resistance in H. contortus.

A 4 year observation of gastrointestinal nematode egg counts, nemabiomes and the benzimidazole resistance genotypes of Teladorsagia circumcincta on a Scottish sheep farm.

Anthelmintic resistance threatens the sustainability of sheep production globally. Advice regarding strategies to reduce the development of anthelmintic resistance incorporates the outcomes of modelling exercises. Further understanding of gastrointestinal nematode species diversity, and population dynamics and genetics (which may vary between species) is required to refine these models; and field studies combining faecal egg outputs, species composition and resistance genetics are needed to calibrate them. In this study, faecal samples were taken from ewes and lambs on a commercial farm in south-eastern Scotland at approximately 3 t-4 week intervals between spring and autumn over a period of 4 years. Faecal egg counts were performed on these samples, and L3 were collected from pooled coprocultures. Deep amplicon sequencing was used to determine both the species composition of these L3 and the proportions of benzimidazole-resistant single nucleotide polymorphisms in the isotype-1 ß-tubulin locus of the predominant species, Teladorsagia circumcincta L3. Despite consistent management throughout the study, the results show variation in gastrointestinal nematode species composition with time and between age groups, that was potentially associated with weather conditions. The F200Y benzimidazole resistance mutation is close to genetic fixation in the T. circumcincta population on this farm. There was no evidence of variation in isotype-1 ß-tubulin single nucleotide polymorphisms frequency between age groups, and no genetic evidence of reversion to benzimidazole susceptibility, despite targeted benzimidazole usage. This study highlights the need to include speciation when investigating gastrointestinal nematode epidemiology and anthelmintic resistance, and serves as an example of how genetic data may be analysed alongside species diversity and faecal egg counts, when markers for other anthelmintic classes are identified.

Investigation of a gamasid mite infestation in a UK textile mill caused by Dermanyssus gallinae (DeGeer, 1778) (Mesostigmata: Dermanyssidae) special lineage L1.

A recurrent mite infestation affecting a room used to inspect fabric in a UK textile mill was investigated to allay concerns of any potential health risks to factory staff, and to inform the unknown risk of downgrading of the product. The approach integrated conventional morphological examination of adult female mites by referring to published identification keys, with molecular speciation based on amplification of a 16S ribosomal DNA fragment. The methods enabled the mites to be unambiguously identified as Dermanyssus gallinae 'special lineage L1'. Subsequent investigations showed the source of infestation to be pigeons nesting in the air ducts, with the gamasid mites moving into the room once the young birds had fledged. This is the first report of D. gallinae 'special lineage L1' in northern Europe. Previous reports of nosocominal gamasoidosis caused by D. gallinae 'special lineage L1' originating from feral pigeon populations have been from southern Europe. Confirmation of the mite identity was important in allowing the mill to take remedial and preventive action. In this clinical communication, we provide images of the key morphological features used to identify D. gallinae and describe a molecular protocol to confirm 'special lineage L1'.

Investigation of a gamasid mite infestation in a UK textile mill caused by dermanyssus gallinae (DeGeer, 1778) (Mesostigmata: Dermanyssidae) special lineage L1

A recurrent mite infestation affecting a room used to inspect fabric in a UK textile mill was investigated to allay concerns of any potential health risks to factory staff, and to inform the unknown risk of downgrading of the product. The approach integrated conventional morphological examination of adult female mites by referring to published identification keys, with molecular speciation based on amplification of a 16S ribosomal DNA fragment. The methods enabled the mites to be unambiguously identified as Dermanyssus gallinae ‘special lineage L1’. Subsequent investigations showed the source of infestation to be pigeons nesting in the air ducts, with the gamasid mites moving into the room once the young birds had fledged. This is the first report of D. gallinae ‘special lineage L1’ in northern Europe. Previous reports of nosocominal gamasoidosis caused by D. gallinae ‘special lineage L1’ originating from feral pigeon populations have been from southern Europe. Confirmation of the mite identity was important in allowing the mill to take remedial and preventive action. In this clinical communication, we provide images of the key morphological features used to identify D. gallinae and describe a molecular protocol to confirm ‘special lineage L1’

Investigation of a gamasid mite infestation in a UK textile mill caused by dermanyssus gallinae (DeGeer, 1778) (Mesostigmata: Dermanyssidae) special lineage L1

A recurrent mite infestation affecting a room used to inspect fabric in a UK textile mill was investigated to allay concerns of any potential health risks to factory staff, and to inform the unknown risk of downgrading of the product. The approach integrated conventional morphological examination of adult female mites by referring to published identification keys, with molecular speciation based on amplification of a 16S ribosomal DNA fragment. The methods enabled the mites to be unambiguously identified as Dermanyssus gallinae ‘special lineage L1’. Subsequent investigations showed the source of infestation to be pigeons nesting in the air ducts, with the gamasid mites moving into the room once the young birds had fledged. This is the first report of D. gallinae ‘special lineage L1’ in northern Europe. Previous reports of nosocominal gamasoidosis caused by D. gallinae ‘special lineage L1’ originating from feral pigeon populations have been from southern Europe. Confirmation of the mite identity was important in allowing the mill to take remedial and preventive action. In this clinical communication, we provide images of the key morphological features used to identify D. gallinae and describe a molecular protocol to confirm ‘special lineage L1’

Idiopathic ventricular fibrillation - Long term prognosis in relation to clinical findings and ECG patterns in a Swedish cohort.

BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare cause of sudden cardiac arrest which may pose therapeutic and prognostic challenges. To date, the only effective treatment for survivors of cardiac arrest is the insertion of an implantable cardioverter-defibrillator (ICD). We sought to review the long-term outcome of a Swedish cohort with IVF. METHODS AND RESULTS: Fifty patients with IVF diagnosis between 1988 and 2016 (mean age at index 34.3, 56% male), were followed for a median 13.8 years in this retrospective multicenter observational study. No cardiac mortality was reported. 32% (n = 16) of patients had recurrence of ventricular fibrillation or sustained ventricular tachycardia, requiring ICD therapy, at a median time of 1.9 years (range 0.1-20.3) from the index event. Annual incidence rate of ventricular tachyarrhythmia was 3.1%. Abnormal ECG at baseline did not predict appropriate ICD therapy (p = 0.56). During the follow-up period, 14% (n = 7) patients received a cardiac diagnosis. Follow-up genetic testing was low (26%), however did confirm pathogenic mutations in three cases. CONCLUSION: Idiopathic VF is a rare diagnosis with a relatively good prognosis provided ICD therapy is initiated. Routine clinical follow-up is recommended due to potential late emerging cardiac pathology. ECG changes are common, but have no prognostic value in determining the risk of ventricular arrhythmias recurrence. Screening for genetic diseases has previously been low, and this calls for improvement, especially since cheaper and more comprehensive genetic panels are now readily available.

Semi-automated QRS score as a predictor of survival in CRT treated patients with strict left bundle branch block.

BACKGROUND: Cardiac Resynchronization Therapy (CRT) is widely used for treating selected heart failure patients, but patients with myocardial scar respond worse to treatment. The Selvester QRS scoring system estimates myocardial scar burden using 12-lead ECG. This study's objective was to investigate the scores correlation to mortality in a CRT population. METHODS AND RESULTS: Data on consecutive CRT patients was collected. 401 patients with LBBB and available ECG data were included in the study. QuAReSS software was used to perform Selvester scoring. Mean Selvester score was 6.4, corresponding to 19% scar burden. The endpoint was death or heart transplant; outcome was analyzed using Cox proportional hazards models. A Selvester score >8 was significantly associated with higher risk of the combined endpoint (HR 1.59, p=.014, CI 1.09-2.3). CONCLUSION: Higher Selvester scores correlate to mortality in CRT patients with strict LBBB and might be of value in prognosticating survival.

Molecular evidence shows that the liver fluke Fasciola gigantica is the predominant Fasciola species in ruminants from Pakistan.

Fascioliasis is an important disease affecting livestock, with great costs to producers worldwide. It has also become a serious issue for human populations in some endemic areas as an emerging zoonotic infection. There are two Fasciola species of liver fluke responsible for this disease, which occur worldwide, Fasciola hepatica and Fasciola gigantica. Identifying these two species on the basis of adult or egg morphology requires specialist knowledge due to the similarity of characters, and may misidentify putative intermediate or hybrid forms. In this study we sequenced the internal transcribed spacer 2 (ITS-2) rDNA of liver flukes collected from multiple species of hosts from seven localities in the Punjab and Baluchistan provinces of Pakistan, to determine the distribution of these two species. All 46 flukes processed in this study, collected from seven sites, showed the rDNA ITS-2 genotype corresponding to F. gigantica, contradicting previous reports, based on adult and egg morphology, that both species are present in Pakistan, with F. hepatica being the more common.

Susceptibility-weighted MR imaging: a better technique in the detection of capillary telangiectasia compared with T2* gradient-echo.

BACKGROUND AND PURPOSE: Enhancing lesions on brain MR imaging can present a diagnostic quandary as both benign lesions such as brain capillary telangiectasia and pathologic lesions such as demyelination may appear similar. Stagnation of blood in low-flow venous channels of brain capillary telangiectasias results in susceptibility effect secondary to the increased local deoxyhemoglobin. Both T2* gradient-echo imaging and SWI were demonstrated as valuable in the diagnosis of brain capillary telangiectasia. Because SWI is more sensitive to susceptibility changes than gradient-echo, we aim to demonstrate increased diagnostic value of SWI compared with gradient-echo in making the diagnosis of brain capillary telangiectasia. MATERIALS AND METHODS: We retrospectively reviewed the MR images of 17 patients with a presumed diagnosis of brain capillary telangiectasia and who were examined from June 2010 to September 2012. All patients underwent MR imaging at 1.5T with T1, T2, FLAIR, gradient-echo, SWI, and gadolinium-enhanced T1 sequences. Lesions were evaluated for the presence or absence of signal abnormality on each particular sequence. RESULTS: All 17 brain capillary telangiectasias demonstrated distinct signal-intensity loss on SWI compared with 7 of 17 (41%) who showed signal-intensity loss on gradient-echo. The increased frequency of detection using SWI versus gradient-echo is statistically significant (z = 2.85, P < .01; χ(2) = 8.10, P < .01). Six of the lesions showed signal-intensity changes on T1 and/or T2 whereas the remaining lesions were isointense to normal brain. CONCLUSIONS: Brain capillary telangiectasias are more conspicuous on SWI than gradient-echo imaging and other precontrast MR imaging. SWI is a valuable tool in diagnosing these benign lesions and should serve to increase diagnostic confidence.

Tuberculosis simulating brain tumour.

The purpose of the study is to highlight the varied presentation of tuberculosis (TB) simulating a brain tumour. Headache and seizures are becoming frequent presenting complaints without any history of tuberculosis. The study comprises 1200 patients of both sexes with ages ranging from ten to sixty years. CT scan and MRI brain control with and without contrast medium were the investigations performed in these cases. In some patients Electroencephalography (EEG), cerebral angiography (DSA) and spectroscopy were also performed. The final diagnosis of tuberculosis was made on the basis of craniotomy, stereotactic and burr hole biopsies with histopathology in most of the cases. Forty per cent of the patients were followed up for eight months. They were put on anti-tuberculosis treatment with symptomatic and anti-epileptic drugs. The incidence was 544 and 757 per 100,000 in Africa and Indo Pakistan respectively. The male to female ratio was 1:1. Tuberculosis, especially with CNS involvement, is not only common in immunosuppressed patients in our setting, but TB has been and remains an important public health problem. TB may involve the CNS either as meningitis or as parenchymal granulomas or abscesses. Patients with brain TB usually present with fever, multiple cranial nerve involvement and occasional behavioural changes. CSF findings remain non specific in most cases. The most common sites are the cerebral hemisphere and basal ganglion in adults and the cerebellum in children. Tuberculosis has unique findings on brain CT and MRI. Cortical and subcortical locations are typical whereas the brain stem is a less common site. Tuberculosis lesions are usually solitary but multiple in 10% to 35% of cases. In spite of all these facts some cases of brain TB still need aggressive neurointervention to reach the final diagnosis of brain TB. Tuberculosis in the CNS may manifest in many different ways. So one should always include tuberculosis in the differential diagnosis in the etiology of delayed onset epilepsy and acute on chronic headache. In case of a discrepancy between clinical manifestations and CT/MRI findings, one can always anticipate tuberculous lesion in the brain.

Paediatric dentistry in outreach settings: an essential part of undergraduate curricula?

INTRODUCTION: Although placements in primary care settings remote from dental schools are becoming a common feature of undergraduate dental curricula, little evidence is available regarding the experience of paediatric dentistry gained in this way. MATERIALS AND METHODS: Treatment logs relating to salaried primary care placements undertaken by the Class of 2007 at Cardiff University School of Dentistry were examined, particular attention being paid to paediatric-specific procedures. RESULTS: Forty-nine logs relating to placements undertaken in South East Wales and 51 relating to those in North Wales were retrieved. In South East Wales, 90% of students gained experience of primary tooth restoration, 61% carrying out primary endodontics. Sixty-three percent of students undertaking placements in South East Wales and 69% of those placed in North Wales gained experience of primary tooth extraction under local anaesthesia. All but three students gained experience of administering inhalation sedation. DISCUSSION: The findings of this study should go some way towards reassuring those who have expressed concern that recruitment difficulties within dental schools inevitably lead to increasing numbers of students qualifying without clinical experience of paediatric dental procedures considered to be within the remit of a newly qualified dental practitioner. However, there remains wide variation in the breadth and depth of experience of individual students and it is still possible for some students to graduate without what might be considered core experience in paediatric dentistry. CONCLUSION: Salaried primary care settings are ideally placed to provide students with experience of paediatric-specific procedures. Clinical education in paediatric dentistry should, therefore, incorporate the strengths of dental school and placement education.

Combined simultaneous endoscopic transsphenoidal and endoscopic transventricular resection of a giant pituitary macroadenoma.

Intrasellar and sellar-suprasellar adenomas are generally removed through a transsphenoidal approach. Giant adenomas with significant suprasellar extension often require a craniotomy or combined "above and below" approach. The use of endoscopes has increased the visualization capacity of the transsphenoidal route and made these surgeries less invasive. In this report, we describe a novel combination of the endoscopic transsphenoidal approach with the endoscopic transventricular approach to remove a giant pituitary macroadenoma extending into the third and lateral ventricles. The tumor was initially removed via an endoscopic transnasal transsphenoidal, transtuberculum, transplanum approach. A second endoscope was then advanced into the lateral ventricle through a pre-coronal burr hole to assist in mobilizing the tumor and assure a complete resection. Multilayer closure and a ventriculo-peritoneal shunt were performed to insure a watertight seal of the skull base. Giant pituitary adenomas have traditionally been removed with staged or combined transsphenoidal and transcranial approaches. We describe the successful implementation of a minimal access endoscopic combined extended transsphenoidal and transventricular approach that avoids craniotomy and brain retraction.

Mutation patterns in gyrA and parC genes of ciprofloxacin resistant isolates of Neisseria gonorrhoeae from India.

AIM: To analyse mutations in the gyrA and parC genes leading to possible increase in ciprofloxacin resistance (high MIC values for ciprofloxacin) in clinical isolates of Neisseria gonorrhoeae in Delhi, India. METHOD: MIC of ciprofloxacin for 63 clinical isolates of N gonorrhoeae were examined by the Etest method. Subsequently, gyrA and parC genes of these isolates were amplified and sequenced for possible mutations. RESULTS: Out of the 63 clinical isolates tested, only five (8%) isolates were found to be susceptible to ciprofloxacin (MIC <0.06 micro g/ml). DNA sequence analysis of the gyrA and the parC genes of all these isolates (n = 63) revealed that all isolates which were not susceptible to ciprofloxacin (n=58) had mutation(s) in gyrA and parC genes. 12 isolates (19%) exhibited high resistance with an MIC for ciprofloxacin of 32 micro g/ml. Two out of these 12 isolates (UD62 and UD63), harboured triple mutations (Ser-91 to Phe, Asp-95 to Asn and Val-120 to Leu) in the gyrA gene. The third mutation of Val-120 to Leu, lies downstream of the quinolone resistance determining region (QRDR) of the gyrA and has not been described before in gonococcus. In addition, both these isolates had a Phe-100 to Tyr substitution in the parC, a hitherto unknown mutation. CONCLUSIONS: Emergence of ciprofloxacin resistance with high levels of MIC values (up to 32 micro g/ml) in India is alarming. Double and triple mutations in gyrA alone or together in gyrA and parC could be responsible for such a high resistance.

Detection ofNeisseria Gonorrhoeae by polymerase chain reaction (PCR).

Three different sets of primers were designed using FASTA homology search and PRIMERSELECT for the specific detection ofNeisseria gonorrhoeae using polymerase chain reaction (PCR). These primers amplified the highly conserved regions of genes for Open Reading Frame (ORF), Outer Membrane Protein (OMP) and 23S rRNA sequences ofN. gonorrhoeae. Each of the PCR primer set was evaluated using the DNA samples isolated from eight different positive isolates ofN. gonorrhoeae cultured from urethral swabs of patients visiting Maulana Azad Medical College and Safdarjung Hospital. Amplification products were analyzed on agarose gel electrophoresis. Two sets of PCR primers, designated as Ngu1/Ngu2 and Ngu5/Ngu6, specific for ORF and OMP gene respectively, amplified four regions of the gene which may help to differentiate the various strains ofN. gonorrhoeae infecting indigenous population. In contrast, a single, specific PCR product of 650 bp was visualized on agarose gel with primers Ngu3/Ngu4, amplifying the 23S rRNA gene. Under optimum conditions, as low as 25ng of DNA isolated from eight different clinical strains ofN. gonorrhoeae could be detected by PCR using Ngu3/Ngu4 set of primers. Our results suggested that Ngu3/Ngu4 could serve as good primers for the specific, reproducible and sensitive diagnosis ofNeisseria gonorrhoeae from clinical samples.

Selection of local therapy after neoadjuvant chemotherapy in patients with stage IIIA,B breast cancer.

BACKGROUND: Stage IIIA,B breast cancer is commonly treated with neoadjuvant chemotherapy because of high objective response rates and improved operability. Criteria for subsequent selection of local therapy--mastectomy, radiotherapy, or both--are not well defined. We adopted a policy of selective local therapy based on rebiopsy of the breast and clinical axillary lymph node status at the time of best response to chemotherapy. METHODS: Between 1980 and 1993, 126 patients with stage IIIA,B breast cancer were treated with neoadjuvant chemotherapy and definitive local therapy. The long-term incidence of locoregional failure (in-breast, chest wall, axilla, supraclavicular, neck), relapse-free survival, and overall survival was determined. RESULTS: The overall clinical objective response rate to chemotherapy was 95.2%. Eighty-three patients underwent mastectomy, with negative margins achieved in 91.6%. Forty-two patients had breast preservation; the overall in-breast recurrence rate was 19.0% (8 of 42 patients). The overall locoregional recurrence rate by site was: chest wall-8.7% (11 of 126 patients), axilla-8.7% (11 of 126 patients), supraclavicular-5.6% (7 of 126 patients), and neck-4.0% (5 of 126 patients). The axillary recurrence rate was 6.6% (5 of 76 patients) for clinically negative axilla treated with radiotherapy only, and 12.0% (6 of 50 patients) for clinically positive axilla treated with surgery only. The overall long-term survival probabilities (6 years) according to stage were: stage IIIA-58.0%, stage IIIB(noninflam)-58.0%, stage IIIB(inflam)-36.0%. CONCLUSIONS: These findings support a selective approach to local therapy in patients with stage IIIA,B breast cancer. This approach provides local control in most patients, and allows for breast preservation and elimination of axillary dissection in selected patients.

siaD PCR ELISA for confirmation and identification of serogroup Y and W135 meningococcal infections.

Non-culture diagnosis and serogroup determination of meningococcal infection is important in contact management where vaccination may be possible. A serogroup B and C PCR ELISA assay for the non-culture diagnosis and serogroup determination has proved invaluable for enhanced epidemiological surveillance and contact management. A polymerase chain reaction assay, based on a restriction fragment length polymorphism in the meningococcal serogroup Y and W135 sialyltransferase (siaD) gene, was developed to enhance the range of non-culture diagnosis of meningococcal infection from clinical samples. The PCR assay was adapted to an ELISA format incorporating hybridisation with serogroup-specific Y and W135 oligonucleotide probes. The serogroup-specific W135 and Y PCR ELISA is a useful addition to currently available serogroup B and C assay for non-culture diagnosis of meningococcal infection and outbreak investigation.