Establishing proof of concept for utility of Trueprep®-extracted DNA in line-probe assay testing

BACKGROUND AND OBJECTIVES: With an increased demand for rapid, diagnostic tools for TB and drug resistance detection, Truenat® MTB-RIF assay has proven to be a rapid point of care molecular test. The present study aimed to establish a proof of concept of using Trueprep-extracted DNA for line-probe assay (LPA) testing.METHODS: A total of 150 sputum samples (MTB-positive at Truenat sites) were divided into two aliquots. One aliquot was used for DNA extraction using the Trueprep device and MTB testing. The second aliquot of the sample was subjected to GenoLyse® DNA extraction. DNA from both the Trueprep and GenoLyse methods was subjected to first-line (FL) and second-line (SL) LPA testing.RESULTS: Of 139 Trueprep-extracted DNA, respectively 135 (97%) and 105 (75%) had interpretable results by FL and SL-LPA testing. Of 128 GenoLyse-extracted DNA, all 128 (100%) had interpretable FL-LPA results and 114 (89%) had interpretable SL-LPA results.CONCLUSION: The results obtained in this study indicate that Trueprep-extracted DNA can be used in obtaining valid LPA results. However, the study needs to be conducted on a larger sample size before our recommendations can be used for policy-making decisions.

Intratumoral Dose Escalation Using Lattice Radiotherapy for Hepatocellular Carcinoma with Unfavorable Size and Location

PURPOSE/OBJECTIVE(S)

Stereotactic body radiation therapy (SBRT) is a standard of care for unresectable hepatocellular carcinoma (HCC). However, its safe delivery is limited by tumor size and adjacent organs-at-risk (OARs). RTOG 1112 showed a survival benefit with local control in advanced HCC, but median dose was limited to 35 Gy in 5 fractions due to OARs. Here, we demonstrate the dosimetric feasibility of lattice radiation therapy (LRT) for dose escalation in advanced HCC.

MATERIALS/METHODS

Five-fraction volumetric arc-based (VMAT) LRT plans were generated using a customized Python v3.6 script. For each combination of peak/valley doses and sphere size and spacing, a bounding box was generated around the gross tumor volume (GTV) and divided into equal segments in the x, y, and z planes. Individual spheres were constructed for a given parameter set and those fully encompassed within the target contracted by 2 cm were used to create peak dose targets with values of 30, 40, or 50 Gy. Valley dose target volumes over a range of 2 to 45 Gy were generated by subtracting an 8 mm expansion of the peak dose spheres from the overall target volume. Multi-criteria optimization (MCO) was applied to generate a final plan. The planning target volume (PTV) was a 5-mm uniform expansion from the GTV. All plans were generated at maximum inspiration on 4D-CT. OAR parameters were compared against a standard 5-fraction SBRT plan using Wilcoxon signed-rank testing.

RESULTS

GTV and PTV measured 593 (23%) and 804 (32%) cm3, respectively, of a total liver volume of 2525 cm3. The minimum distance of GTV from stomach and duodenum was 6 mm and 2 mm, respectively. Plans were evaluated as per RTOG 1112 with stepwise reduction from a maximum PTV dose of 50 Gy based upon ability to meet mean liver dose (MLD, defined as liver-GTV) constraints; the 30 Gy threshold was the highest achievable. Of 7 eligible LRT plans, 5 with ablative 50 Gy peak doses were analyzed. Associated valley doses were 15 or 20 Gy. Median values of mean GTV and PTV doses for these plans were 36.2 (IQR, 34.6 - 37.8) and 32.9 (IQR, 31.3 - 33.4) Gy, respectively. A median of 12.4% (IQR, 7.4 - 28.4) of the GTV received a dose of 50 Gy. Median doses to 0.5 cc of stomach and duodenum were 16.7 Gy (range, 15.6 - 19.6) and 14.4 Gy (range, 12.3 - 23.9), respectively. The median value for MLD was 13.9 Gy (range, 13.6 to 14.8) and the median volume of normal liver spared 15 Gy was 1114 cm3 (range, 969 to 1154). These hepatic parameters were significantly decreased compared to a standard 30 Gy SBRT plan (18.1 Gy and 611.3 cc spared, p = 0.043 for both) which did not meet constraints.

CONCLUSION

Dose escalation of advanced HCC using LRT is dosimetrically feasible. Though mean target doses remained limited by MLD, LRT allowed delivery of ablative dose to 12.4% of the GTV while meeting critical OAR constraints. Intratumoral dose-escalation may improve local control in advanced HCC patients.

Measurement of the Lifetime and Λ Separation Energy of _{Λ}^{3}H

The most precise measurements to date of the _{Λ}^{3}H lifetime τ and Λ separation energy B_{Λ} are obtained using the data sample of Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV collected by ALICE at the LHC. The _{Λ}^{3}H is reconstructed via its charged two-body mesonic decay channel (_{Λ}^{3}H→^{3}He+π^{-} and the charge-conjugate process). The measured values τ=[253±11(stat)±6(syst)]  ps and B_{Λ}=[102±63(stat)±67(syst)]  keV are compatible with predictions from effective field theories and confirm that the _{Λ}^{3}H structure is consistent with a weakly bound system.

Measurement of the J/ψ Polarization with Respect to the Event Plane in Pb-Pb Collisions at the LHC

We study the polarization of inclusive J/ψ produced in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV at the LHC in the dimuon channel, via the measurement of the angular distribution of its decay products. We perform the study in the rapidity region 2.5 Collapse

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First Measurement of Antideuteron Number Fluctuations at Energies Available at the Large Hadron Collider

The first measurement of event-by-event antideuteron number fluctuations in high energy heavy-ion collisions is presented. The measurements are carried out at midrapidity (|η|<0.8) as a function of collision centrality in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV using the ALICE detector. A significant negative correlation between the produced antiprotons and antideuterons is observed in all collision centralities. The results are compared with a state-of-the-art coalescence calculation. While it describes the ratio of higher order cumulants of the antideuteron multiplicity distribution, it fails to describe quantitatively the magnitude of the correlation between antiproton and antideuteron production. On the other hand, thermal-statistical model calculations describe all the measured observables within uncertainties only for correlation volumes that are different with respect to those describing proton yields and a similar measurement of net-proton number fluctuations.

Enhanced Deuteron Coalescence Probability in Jets

The transverse-momentum (p_{T}) spectra and coalescence parameters B_{2} of (anti)deuterons are measured in p-p collisions at sqrt[s]=13  TeV for the first time in and out of jets. In this measurement, the direction of the leading particle with the highest p_{T} in the event (p_{T}^{lead}>5  GeV/c) is used as an approximation for the jet axis. The event is consequently divided into three azimuthal regions, and the jet signal is obtained as the difference between the toward region, that contains jet fragmentation products in addition to the underlying event (UE), and the transverse region, which is dominated by the UE. The coalescence parameter in the jet is found to be approximately a factor of 10 larger than that in the underlying event. This experimental observation is consistent with the coalescence picture and can be attributed to the smaller average phase-space distance between nucleons in the jet cone as compared with the underlying event. The results presented in this Letter are compared to predictions from a simple nucleon coalescence model, where the phase-space distributions of nucleons are generated using pythia8 with the Monash 2013 tuning, and to predictions from a deuteron production model based on ordinary nuclear reactions with parametrized energy-dependent cross sections tuned on data. The latter model is implemented in pythia8.3. Both models reproduce the observed large difference between in-jet and out-of-jet coalescence parameters, although the almost flat trend of the B_{2}^{Jet} is not reproduced by the models, which instead give a decreasing trend.

Correction to: Genetic Spectrum in F13A1 Detected by Next-Generation Sequencing Among North Indian Patients with FXIII Deficiency

[This corrects the article DOI: 10.1007/s12288-022-01579-1.].

Systems genetics identifies miRNA-mediated regulation of host response in COVID-19

BACKGROUND

Individuals infected with SARS-CoV-2 vary greatly in their disease severity, ranging from asymptomatic infection to severe disease. The regulation of gene expression is an important mechanism in the host immune response and can modulate the outcome of the disease. miRNAs play important roles in post-transcriptional regulation with consequences on downstream molecular and cellular host immune response processes. The nature and magnitude of miRNA perturbations associated with blood phenotypes and intensive care unit (ICU) admission in COVID-19 are poorly understood.

RESULTS

We combined multi-omics profiling-genotyping, miRNA and RNA expression, measured at the time of hospital admission soon after the onset of COVID-19 symptoms-with phenotypes from electronic health records to understand how miRNA expression contributes to variation in disease severity in a diverse cohort of 259 unvaccinated patients in Abu Dhabi, United Arab Emirates. We analyzed 62 clinical variables and expression levels of 632 miRNAs measured at admission and identified 97 miRNAs associated with 8 blood phenotypes significantly associated with later ICU admission. Integrative miRNA-mRNA cross-correlation analysis identified multiple miRNA-mRNA-blood endophenotype associations and revealed the effect of miR-143-3p on neutrophil count mediated by the expression of its target gene BCL2. We report 168 significant cis-miRNA expression quantitative trait loci, 57 of which implicate miRNAs associated with either ICU admission or a blood endophenotype.

CONCLUSIONS

This systems genetics study has given rise to a genomic picture of the architecture of whole blood miRNAs in unvaccinated COVID-19 patients and pinpoints post-transcriptional regulation as a potential mechanism that impacts blood traits underlying COVID-19 severity. The results also highlight the impact of host genetic regulatory control of miRNA expression in early stages of COVID-19 disease.

Morphological and molecular characterization of Haemonchus contortus isolated from the small ruminants of south Gujarat, India

The successful design of strategic control measures against the blood-sucking gastrointestinal nematode, Haemonchus contortus in small ruminants can be facilitated by revealing its general features from morphology to the molecular level. In the south Gujarat region of India, a total of 2408 H. contortus were collected from 84 slaughtered sheep's abomasum, consisting of 347 males and 2061 females (1:6 ratio) (p<0.05). Furthermore, 726 H. contortus were collected from 61 goats, comprising 145 males and 581 females (1:4 ratio) (p<0.05). The male worms were approximately 12±0.06 mm long, while female worms were about 20±0.09 mm long. The vulvar morphotypes of the female worms were found to be 17.7% linguiform, 76.6 % knobbed/button (p<0.05), and 5.7 % smooth type, demonstrating common features of H. contortus. The nucleotide sequences of the Internal Transcribed Spacer 1 (ITS-1) of 165 bp or ITS-2 plus of 256 bp were aligned, and it was found that the genotypes of male and female specimens of either sheep or goat origin were identical, with a 100 % match. The present isolates shared >95 % and >94 % homology with published sequences of ITS-1 and ITS-2 plus of H. contortus, respectively, with more nucleotide transitions than transversions in the aligned sequences. The reconstructed phylogram of either ITS-1 or ITS-2 plus revealed two major clades, one for H. contortus and another for other nematodes, with Haemonchus placei showing its proximity with the clade of H. contortus. The study established the role of morphological and molecular features in identifying and differentiating H. contortus parasite at the local level.

The NIN-LIKE PROTEIN 7 transcription factor modulates auxin pathways to regulate root cap development in Arabidopsis

The root cap is a small tissue located at the tip of the root with critical functions for root growth. Present in nearly all vascular plants, the root cap protects the root meristem, influences soil penetration, and perceives and transmits environmental signals that are critical for root branching patterns. To perform these functions, the root cap must remain relatively stable in size and must integrate endogenous developmental pathways with environmental signals, yet the mechanism is not clear. We previously showed that low pH conditions altered root cap development, and these changes are mediated by the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling. Here we show that in Arabidopsis NLP7 integrates nitrate signaling with auxin pathways to regulate root cap development. We found that low nitrate conditions promote aberrant release of root cap cells. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Mutations in NLP7 abolish the auxin minimum in the last layer of the root cap and alter root cap expression of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7) as well as transcription factors that regulate PIN expression. Together, our data reveal NLP7 as a link between endogenous auxin pathways and nitrate signaling in the root cap.

Ferromagnetism in Defected TMD (MoX2, X = S, Se) Monolayer and Its Sustainability under O2, O3, and H2O Gas Exposure: DFT Study

Spin-polarized density-functional theory (DFT) has been employed to study the effects of atmospheric gases on the electronic and magnetic properties of a defective transition-metal dichalcogenide (TMD) monolayer, MoX₂ with X = S or Se. This study focuses on three single vacancies: (i) molybdenum "V_Mo"; (ii) chalcogenide "V_X"; and (iii) di-chalcogenide "V_X2". Five different samples of sizes ranging from 4 × 4 to 8 × 8 primitive cells (PCs) were considered in order to assess the effect of vacancy-vacancy interaction. The results showed that all defected samples were paramagnetic semiconductors, except in the case of V_Mo in MoSe₂, which yielded a magnetic moment of 3.99 μ_B that was independent of the sample size. Moreover, the samples of MoSe₂ with V_Mo and sizes of 4 × 4 and 5 × 5 PCs exhibited half-metallicity, where the spin-up state becomes conductive and is predominantly composed of dxy and dz2 orbital mixing attributed to Mo atoms located in the neighborhood of V_Mo. The requirement for the establishment of half-metallicity is confirmed to be the provision of ferromagnetic-coupling (FMC) interactions between localized magnetic moments (such as V_Mo). The critical distance for the existence of FMC is estimated to be dc≅ 16 Å, which allows small sample sizes in MoSe₂ to exhibit half-metallicity while the FMC represents the ground state. The adsorption of atmospheric gases (H₂O, O₂, O₃) can drastically change the electronic and magnetic properties, for instance, it can demolish the half-metallicity characteristics. Hence, the maintenance of half-metallicity requires keeping the samples isolated from the atmosphere. We benchmarked our theoretical results with the available data in the literature throughout our study. The conditions that govern the appearance/disappearance of half-metallicity are of great relevance for spintronic device applications.

Ex Vivo Colonic Tissue Susceptibility to HIV-1 in Cisgender Men and Women

The biology of HIV-1 acquisition through unprotected receptive anal intercourse is understudied. Considering that sex hormones are implicated in intestinal physiology, pathology, and HIV acquisition and pathogenesis, we explored links between sex hormones, ex vivo HIV-1BaL infection of colonic mucosa, and candidate biomarkers of susceptibility to HIV-1 (CD4+ T cell frequencies and immune mediators) in cisgender women and men. No consistent significant associations between sex hormone concentrations and ex vivo tissue infection with HIV-1BaL were detected. In men, serum estradiol (E2) concentrations were positively associated with tissue proinflammatory mediators (IL17A, GM-CSF, IFNγ, TNFα, and MIG/CXCL9) and serum testosterone concentrations were negatively associated with frequencies of activated CD4+ T cells (CD4+CCR5+, CD4+HLA-DR+, and CD4+CD38+HLA-DR+). In women, the only significant interactions were positive associations between progesterone (P4)/E2 ratios and tissue ILRA concentrations and between P4/E2 ratios and frequencies of tissue CD4+α4β7high+ T cells. The study did not reveal relationships between biological sex or phase of the menstrual cycle and ex vivo tissue HIV-1BaL infection and tissue immune mediators. A comparison of CD4+ T cell frequencies between study groups revealed a higher frequency of tissue CD4+α4β7high+ T cells in women versus men. In contrast, higher frequencies of tissue CD4+CD103+ T cells were detected in men versus women in the follicular phase of the menstrual cycle. Overall, the study identified associations between systemic sex hormone concentrations, biological sex, and tissue candidate biomarkers of susceptibility to HIV-1. The significance of these results for tissue susceptibility to HIV-1 and early HIV-1 pathogenesis warrants further investigation.

Enhanced photocatalytic activity of cubic ZnSn(OH)6 by in-situ partial phase transformation via rapid thermal annealing

In this study, a mixed phase ZnSn(OH)₆/ZnSnO₃ photocatalyst was synthesized by calcining ZHS nanostructures via rapid thermal annealing (RTA) process. The composition ratio of ZnSn(OH)₆/ZnSnO₃ was controlled by changing the duration of the RTA process. The obtained mixed-phase photocatalyst was characterized by X-ray diffraction, field emission scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis diffuse reflectance spectroscopy, ultraviolet photoelectron spectroscopy, photoluminescence, and physisorption analysis. Results showed that ZnSn(OH)₆/ZnSnO₃ photocatalyst obtained by calcining ZHS at 300 °C for 20 s displayed the best photocatalytic performance under UVC light illumination. Under optimized reaction conditions, ZHS-20 (0.125 g) demonstrated nearly complete removal (>99%) of MO dye in 150 min. Scavenger study revealed the predominant role of OH^• in photocatalysis. The enhanced photocatalytic activity of the ZnSn(OH)₆/ZnSnO₃ composites was mainly ascribed to the photosensitization of ZHS by ZTO and effective electron-hole separation at the ZnSn(OH)₆/ZnSnO₃ heterojunction interface. It is expected that this study will provide new research input for the development of photocatalyst through thermal annealing-induced partial phase transformation.

The activated partial thromboplastin time-clot waveform analysis in hemophilia: Does it help in differentiation?

INTRODUCTION

The clot waveform analysis (CWA) provide valuable information beyond clotting time. The present study was planned to assess whether the activated partial thromboplastin time (aPTT)-CWA can differentiate between hemophilia A (HA), hemophilia B (HB), or hemophilia A with inhibitors (HAWI).

METHODS

The aPTT-CWA was generated by an optical detection system (ACL-TOP™ 500 coagulation analyzer) and the other tests were performed as per instructions from the manufacturer in the kit.

RESULTS

A total of 75 samples (47-HA, 16-HAWI, and 12-HB) with prolonged aPTT were recruited. On analyzing the quantitative aPTT-CWA data of HA (non-inhibitors) and HB samples, the width of acceleration 1 [+] peak was the differentiating finding. Among the significant parameters, the second derivative [+] peak was lower in both mild and moderate HA, equating to HB. The time for the height of 1/2 fibrin formation and width of velocity was significantly higher in mild, moderate and severe HA. The study did not show any significant differentiating finding while comparing HAWI and hemophilia A non-inhibitors (HANI). In the subgroups of HAWI and HANI with aPTT <70 s and 70-100 s, the second derivative [+] peak (2A) was higher and the time for the height of 1/2 fibrin formation (1C) was lesser in HAWI.

CONCLUSION

The aPTT-CWA parameters may be supportive for the differentiation of hemophilia including its severity and the existence of inhibitors.

Genetic Spectrum in F13A1 Detected by Next-Generation Sequencing Among North Indian Patients with FXIII Deficiency

Purpose

The study aimed to explore the molecular defects underlying FXIII deficiency.

Materials and Methods

Sixteen unrelated cases were enrolled based on the indication of the urea clot solubility test and Factor XIII-A antigen levels. Cases were further subjected to targeted next-generation sequencing (custom gene panel: F7, F8, VWF, F9, F13A1, F13B). The pathogenic/likely pathogenic variants were validated by Sanger sequencing in the patients and family members.

Results

Mean age of referral to our center was 27.2 years (8 week-67 years). Consanguinity was found in only one of the 16 cases and 9 cases presented in infancy. The most common symptoms were skin bleeds (69%) and umbilical cord bleed (50%). The clot solubility test was positive in 12, inconclusive in 1, and normal in 3. Mean FXIII-A levels were 15.7 IU/dL (range 0.6 to 49.5 IU/dL). Pathogenic/likely pathogenic variants in F13A1 were found in 11 (69%). Nine cases (82%) were homozygous, and two were compound heterozygous. Total eleven variants were found of which four were missense (c.1226G>A; c.998C>T; c.631G>C; c.2134A>C); three deletion (c.521delG; c.742delA; c.1405_1408delCAAA); two nonsense (c.1112G>A; c.1127G>A) and two splice site (c.1909-1G>C; c.2045G>A). No probably pathogenic variant was found in the F13B.

Conclusion

Inherited FXIII deficiency with bleeding is associated with genetic defects in predominantly the F13A1 gene. A variety of variants were seen in this cohort. A nonsense variant c.1127G>A found in three of our cases seems to be recurrent. This data will contribute to designing functional studies and antenatal testing in affected families.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12288-022-01579-1.

Tobacco use and its impact on survival in young patients with oral cancer

Background

Tobacco is a major risk factor associaetd with developing oral factor. Recent studies have shown that the age of onset, especially in Asia, is reducing. This study was to determine if tobacco exposure correlated with prognosis in oral squamous cell carcinoms (OSCC) based on age at diagnosis.

Methods

Six hundred and forty three patients of OSCC treated in our institution were divided into four groups, younger patients (≤45 years) with or without tobacco exposure and older patients (>45 years) with or without tobacco exposure, and compared with respect to prognostically relevant variables, disease-free survival (DFS) and overall survival (OS). Survival analysis was performed.

Results

The percentage of those with tobacco exposure was comparable in both age groups. Tobacco correlated with known pathological determinants in OSCC; however, perineural invasion, lymphovascular invasion, and extranodal extension were significantly more common in the young. On survival analysis, tobacco exposure impacted OS (P = 0.04) and DFS (P = 0.03) in patients ≤45 years, and not in older patients >45 years. On multivariate analysis, tobacco exposure in the young was significantly associated with recurrence (P = 0.03, hazard ratio (HR) 1.77, 95% confidence interval (CI) 1.07-2.94) but not survival.

Conclusion

Younger patients with a history of tobacco use have a significantly higher risk of recurrence and mortality due to OSCC, but this difference could not be attributed to any of the known prognostic determinants in OSCC. Younger patients also had more adverse pathological features. Whether this occurs because of altered disease biology or pathways of carcinogenesis in the young with tobacco exposure is unknown. Younger tobacco users with oral cancer are more likely to have a poor prognosis.

Impact of ABO blood group antigens on residual factor VIII levels and risk of inhibitor development in hemophilia A

Background

The clinical phenotype of hemophilia A (HA) does not always correlate with severity. Similarly, the presence of inhibitors does not necessarily increase the risk of bleeding. This paradox between clinical and laboratory findings may be partially attributed to non-modifiable factors, such as blood group, which is known to influence FVIII levels in healthy individuals. Our aim was to assess the effect of ABO blood group antigens on FVIII levels across the severity spectrum of HA and risk of inhibitor development.

Methods

Data of consecutive patients with HA who visited the coagulation unit of a northern Indian tertiary care hospital between 2010-2021 were reviewed. Patients with missing blood group data, transfusion histories, or baseline FVIII levels were excluded.

Results

Mild, moderate, and severe HA was present in 41 (6.9%), 72 (12.2%), and 479 (80.9%) patients, respectively. There were no differences in the FVIII levels among the various blood groups across the HA severity spectrum. Inhibitors were administered to 35 patients (5.9%). In the multivariate analysis, blood group A was an independent risk factor for the development of inhibitors (adjusted odds ratio 2.70, P=0.04) after adjusting for age at onset of bleeding, FVIII transfusion, age at first FVIII transfusion, and severity of HA.

Conclusion

Unlike what is observed in healthy individuals, blood group did not influence residual FVIII levels across the severity spectrum of HA. Patients in group A had a higher risk of developing inhibitors.

Identification and Characterization of Aluminium Tolerant Bacteria Isolated from Soil Contaminated by Electroplating and Automobile Waste

Due to anthropogenic activities and the advancement of industries, metal contamination is growing globally. Aluminum toxicity is seriously endangering plants, animals, and humans by rapidly rising in soil and water. Even though some fungi can tolerate aluminum, researchers are interested in finding bacteria that are resistant to aluminum. The current state of knowledge on bacteria resistant to aluminum is extremely limited. In the present study, bacterial isolates from soil near a metal electroplating and automobile industry in Punjab, India, were isolated and then screened for high aluminum metal tolerance. The aluminum tolerant bacterial isolate was identified as Cedecea davisae M1, a member of the Enterobacteriaceae family, using morphological, biochemical, and 16srRNA gene sequence analyses. The spectroscopic results indicate that the strain may tolerate up to 150 ppm of aluminum. Antibiotic resistance of Cedecea davisae M1 was determined using disks on Luria agar plates, and the bacteria were found to be resistant to vancomycin, ampicillin, carbenicillin, and rifampicin. The findings of the study indicated that the strain might be able to remove aluminum toxicity from the environment, which needs to be further explored.

Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017

Serotype 3 pneumococci remains a significant cause of disease despite its inclusion in PCV13. Whilst clonal complex 180 (CC180) represents the major clone, recent studies have refined the population structure into three clades: Iα, Iβ and II, with the last being a recent divergent and more antibiotic-resistant. We present a genomic analysis of serotype 3 isolates from paediatric carriage and all-age invasive disease, collected between 2005 and 2017 in Southampton, UK. Forty-one isolates were available for analysis. Eighteen were isolated during the annual cross-sectional surveillance of paediatric pneumococcal carriage. The remaining 23 were isolated from blood/cerebrospinal fluid specimens at the University Hospital Southampton NHS Foundation Trust laboratory. All carriage isolates were CC180 GPSC12. Greater diversity was seen with invasive pneumococcal disease (IPD) with three GPSC83 (ST1377: n=2, ST260: n=1) and one GPSC3 (ST1716). For both carriage and IPD, Clade Iα was dominant (94.4 and 73.9 % respectively). Two isolates were Clade II with one from carriage (a 34-month-old, October 2017) and one invasive isolate (49-year-old, August 2015). Four IPD isolates were outside the CC180 clade. All isolates were genotypically susceptible to penicillin, erythromycin, tetracycline, co-trimoxazole and chloramphenicol. Two isolates (one each from carriage and IPD; both CC180 GPSC12) were phenotypically resistant to erythromycin and tetracycline; the IPD isolate was also resistant to oxacillin.In the Southampton area, carriage and invasive disease associated with serotype 3 is predominantly caused by Clade Iα CC180 GPSC12.

Molecular spectrum of inherited FVII deficiency in North India revealed a recurrent variant with a founder effect

INTRODUCTION

Inherited Factor VII (FVII) deficiency is commonest among the rare bleeding disorders. A small number of patients present in infancy with severe bleeding, and many may remain asymptomatic but detected before surgery/invasive procedures. Genetic testing may be helpful in predictive testing/prenatal diagnosis in severe cases.

AIM

Characterisation of clinical and genotypic spectrum of patients with inherited FVII deficiency.

METHODS

Retro-prospectively, 35 cases with prolonged prothrombin time and FVII activity (FVII:C) <50 IU/dl were subjected to targeted resequencing. After in-silico analysis, variant/s were validated by Sanger sequencing in index cases and family members. Haplotype analysis was done for F7 polymorphisms.

RESULTS

Severe FVII deficiency was found in 50% of patients (FVII:C ≤1 IU/dl), and 42.9% were asymptomatic. Clinical severity assessment revealed 17% severe, 17% moderate and 22.9% patients with mild bleeds. FVII levels ranged from .3 to 38 IU/dl. Molecular analysis revealed variants in 30/35 cases, of which 17 were homozygous, 10 were compound heterozygous and 3 were heterozygous. Twelve genetic variants were identified, one promoter variant c.-30A>C; seven missense (c.215C>G, c.244T>C, c.253G>C, c.904G>A, c.961C>T, c.1109G>T, c.1211G>A), two deletions (c.21delG, c.868_870delATC), and one each of nonsense c.634C>T and splice-site variant c.316+1G>A. Recurrent variants c.1109G>T and c.215C>G were found in 17 and 8 cases, 12 of the former cases were homozygous. They had the same haplotype, indicating the founder effect in North Indians.

CONCLUSION

This is the largest cohort of FVII genotyping from India, confirming heterogeneity in terms of clinical manifestations, FVII activity and zygosity of the variants with a limited genotypic phenotypic correlation.

Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study

The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.

Cherenkov Radiation in Optical Fibres as a Versatile Machine Protection System in Particle Accelerators

Machine protection systems in high power particle accelerators are crucial. They can detect, prevent, and respond to events which would otherwise cause damage and significant downtime to accelerator infrastructure. Current systems are often resource heavy and operationally expensive, reacting after an event has begun to cause damage; this leads to facilities only covering certain operational modes and setting lower limits on machine performance. Presented here is a new type of machine protection system based upon optical fibres, which would be complementary to existing systems, elevating existing performance. These fibres are laid along an accelerator beam line in lengths of ∼100 m, providing continuous coverage over this distance. When relativistic particles pass through these fibres, they generate Cherenkov radiation in the optical spectrum. This radiation propagates in both directions along the fibre and can be detected at both ends. A calibration based technique allows the location of the Cherenkov radiation source to be pinpointed to within 0.5 m with a resolution of 1 m. This measurement mechanism, from a single device, has multiple applications within an accelerator facility. These include beam loss location monitoring, RF breakdown prediction, and quench prevention. Detailed here are the application processes and results from measurements, which provide proof of concept for this device for both beam loss monitoring and RF breakdown detection. Furthermore, highlighted are the current challenges for future innovation.