INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

BACKGROUND

Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.

RESULTS

The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis.

CONCLUSIONS

The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).

Radiopharmaceutical extravasation in bone scintigraphy: a cross-sectional study

OBJETIVES

Tc-99m Hydroxymethylene diphosphonate (HMDP) bone scintigraphy is commonly used to diagnose bone disorders. We aimed to quantify and characterize the occurrence of radiopharmaceutical extravasation in bone scintigraphy, using Tc-99m HMDP, as well as to compare the visual classification of the events with an independent analysis using image processing software.

METHODS

We conducted a cross-sectional study, using data from a total of 400 (9.1%) exams, randomly selected from all the procedures performed in 2018 in the Portuguese Institute of Oncology of Porto, Portugal. Prevalence estimate and the corresponding 95% confidence interval (CI) was computed for the presence of extravasation. Odds ratios and 95% CI were computed to quantify the association between demographic and clinical characteristics, and the occurrence of extravasation.

RESULTS

The prevalence of Tc-99m HMDP extravasation was 26.5% (95% CI: 22.4-31.0). Those from an inpatient setting had almost seven-fold higher odds of extravasation than those from an outpatient setting. When the wrist was used for administration, there was three times more odds of extravasation when compared to the use of hand. There were statistically significant differences in the median scores of extravasations severity obtained from image processing software according to the different grades attributed by visual appreciation ( P  < 0.001).

CONCLUSION

Tc-99m HMDP extravasation occurred in one out of four patients, being more frequent among those from an inpatient setting and when the wrist was used for administration. Visual appreciation of the extravasation seems to be acceptable to classify its severity.

Myocardial RNA Sequencing Reveals New Potential Therapeutic Targets in Heart Failure with Preserved Ejection Fraction

Heart failure with preserved ejection fraction (HFpEF) represents a global health challenge, with limited therapies proven to enhance patient outcomes. This makes the elucidation of disease mechanisms and the identification of novel potential therapeutic targets a priority. Here, we performed RNA sequencing on ventricular myocardial biopsies from patients with HFpEF, prospecting to discover distinctive transcriptomic signatures. A total of 306 differentially expressed mRNAs (DEG) and 152 differentially expressed microRNAs (DEM) were identified and enriched in several biological processes involved in HF. Moreover, by integrating mRNA and microRNA expression data, we identified five potentially novel miRNA-mRNA relationships in HFpEF: the upregulated hsa-miR-25-3p, hsa-miR-26a-5p, and has-miR4429, targeting HAPLN1; and NPPB mRNA, targeted by hsa-miR-26a-5p and miR-140-3p. Exploring the predicted miRNA-mRNA interactions experimentally, we demonstrated that overexpression of the distinct miRNAs leads to the downregulation of their target genes. Interestingly, we also observed that microRNA signatures display a higher discriminative power to distinguish HFpEF sub-groups over mRNA signatures. Our results offer new mechanistic clues, which can potentially translate into new HFpEF therapies.

AB1173 INCIDENT CASES OF COVID-19 AND VACCINATION ADHERENCE IN A MULTICENTRIC COHORT OF INFLAMMATORY ARTHRITIS IN BRAZIL

Background

The SARS-CoV-2 virus has caused a worldwide health crisis. Patients with inflammatory arthritis are at higher risk of hospitalization and death by COVID-19 due to comorbidities or immunosuppressive treatments. Vaccination is one the most important strategies to control the pandemic.

Objectives

To evaluate the incident cases of SARS-CoV-2 infection in a multicentric cohort of inflammatory arthritis in Brazil.

Methods

BiobadaBrasil is a multicentric registry-based cohort study of Brazilian patients with rheumatic diseases starting their first bDMARD or tsDMARD (1). The present analysis is a retrospective evaluation of adult patients with inflammatory arthritis (rheumatoid arthritis – RA, spondylarthritis -SpA and psoriatic arthritis-PsA) that were alive since the beginning of the COVID-19 pandemics in Brazil in February 2020. We evaluated the incidence and severity of COVID-19 infection and the adherence to anti- SARS-CoV-2 vaccines schedules, up to January 2022.

Results

A total of 300 patients were interviewed and 69 (23.0%) reported confirmed anti-SARS-CoV infection and 5 (1.7%) had a second infection. Among known infected patients, 18.8% need hospitalization and oxygen support, 7.2% were admitted at ICU, and 5.8% died. After COVID-19 infection, 31.8% reported worsening of disease activity but only 6.1% had modification in medication due to disease activity. Distribution of cases followed the pattern of waves observed in Brazil (Figure 1). Regarding vaccination, 285 (95%) reported to have received at least one dose of any anti-SARS-CoV-2 vaccine: 43% received the first with the adenovirus ChAdOx1 nCoV-19 (AstraZeneca) adenovirus vaccine, 32% received the Sinovac-CoronaVac inactivated vaccine, 22% received the BNT162b2 (Pfizer-BioNtech) mRNA vaccine and 3% received the BNT162b2 (Pfizer-BioNtech) adenovirus vaccine. Almost all (98.1%) of these patients had already received the second dose of vaccine and after the first and second vaccine doses, 6% and 4% of patients, respectively, reported worsening of articular disease activity, while, after the third dose, no patient reported disease activity worsening.

Figure 1.

Conclusion

During the pandemics, patients with inflammatory arthritis had a pattern of distribution of cases very similar to general population. Adherence to vaccination is high and well tolerated.

References

[1]Bredemeier et al. J Rheumatol 2021;48:1519-27

Disclosure of Interests

None declared

Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis

PURPOSE

A significant barrier to adoption of de-escalated treatment protocols for human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is that few predictors of poor prognosis exist. We conducted the first large whole-genome sequencing (WGS) study to characterize the genetic variation of the HPV type 16 (HPV16) genome and to evaluate its association with HPV-OPC patient survival.

PATIENTS AND METHODS

A total of 460 OPC tumor specimens from two large United States medical centers (1980-2017) underwent HPV16 whole-genome sequencing. Site-specific variable positions [single nucleotide polymorphisms (SNPs)] across the HPV16 genome were identified. Cox proportional hazards model estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival by HPV16 SNPs. Harrell C-index and time-dependent positive predictive value (PPV) curves and areas under the PPV curves were used to evaluate the predictive accuracy of HPV16 SNPs for overall survival.

RESULTS

A total of 384 OPC tumor specimens (83.48%) passed quality control filters with sufficient depth and coverage of HPV16 genome sequencing to be analyzed. Some 284 HPV16 SNPs with a minor allele frequency ≥1% were identified. Eight HPV16 SNPs were significantly associated with worse survival after false discovery rate correction (individual prevalence: 1.0%-5.5%; combined prevalence: 15.10%); E1 gene position 1053 [HR for overall survival (HRos): 3.75, 95% CI 1.77-7.95; Pfdr = 0.0099]; L2 gene positions 4410 (HRos: 5.32, 95% CI 1.91-14.81; Pfdr = 0.0120), 4539 (HRos: 6.54, 95% CI 2.03-21.08; Pfdr = 0.0117); 5050 (HRos: 6.53, 95% CI 2.34-18.24; Pfdr = 0.0030), and 5254 (HRos: 7.76, 95% CI 2.41-24.98; Pfdr = 0.0030); and L1 gene positions 5962 (HRos: 4.40, 95% CI 1.88-10.31; Pfdr = 0.0110) and 6025 (HRos: 5.71, 95% CI 2.43-13.41; Pfdr = 0.0008) and position 7173 within the upstream regulatory region (HRos: 9.90, 95% CI 3.05-32.12; Pfdr = 0.0007). Median survival time for patients with ≥1 high-risk HPV16 SNPs was 3.96 years compared with 18.67 years for patients without a high-risk SNP; log-rank test P < 0.001. HPV16 SNPs significantly improved the predictive accuracy for overall survival above traditional factors (age, smoking, stage, treatment); increase in C-index was 0.069 (95% CI 0.019-0.119, P < 0.001); increase in area under the PPV curve for predicting 5-year survival was 0.068 (95% CI 0.015-0.111, P = 0.008).

CONCLUSIONS

HPV16 genetic variation is associated with HPV-OPC prognosis and can improve prognostic accuracy.

POS0650 THE IMPACT OF OLD AGE ON THE PERSISTENCE AND SAFETY OF TREATMENT WITH BIOLOGIC AGENTS OR JAK INHIBITORS IN RHEUMATOID ARTHRITIS

Background

The effect of age on persistence and safety of treatment with biologic disease modifying anti-rheumatic drugs (bDMARDs) in rheumatoid arthritis has been a subject to research interest. Two recently published studies did not observe significantly different survival of treatment with bDMARDs among older age (≥ 65 years) individuals (1,2); incidence of serious adverse events was higher in these patients (2).

Objectives

to evaluate association of the age with treatment survival and overall safety among patients receiving one or multiple courses of bDMARDs or targeted synthetic (ts-) DMARDs.

Methods

BiobadaBrasil is a multicentric registry-based cohort study of Brazilian patients with rheumatic diseases starting their first bDMARD or tsDMARD (3). The present analysis includes RA patients recruited from Jan 2009 to Oct 2019, followed-up over one or multiple (up to six) courses of treatment necessarily involving a bDMARD or tsDMARD (latest date, Nov 19, 2019). Treatment course is defined as a period during which the medication scheme does not change, except for dose adjustments. Primary outcome was the incidence treatment interruption for any reason (except for pregnancy or disease remission), while interruption due to adverse events (AEs; including death) and due to inefficacy served as secondary outcomes. Incidence of serious adverse events (SAEs) also served as a secondary outcome. Extended (frailty) multivariate Cox proportional hazards models and negative binomial regression with generalized estimating equations (to calculate incidence rate ratios [IRRs]) were used for statistical analyses (both types of analyses including time-varying covariates over multiple courses of treatment).

Results

In total, 1316 patients (2335 treatment courses, 6508 patient-years [PY]) were enrolled. Of these, 160 patients (643 PY; 237 treatment courses) were ≥ 65 years old, mean age at starting treatment = 71 ± 5 yrs (84% female). Old age was not significantly associated with treatment interruption for any reason, but presented higher risk of interruption due to adverse events (after multivariate adjustment) and lower risk of stopping because of inefficacy (see Table 1). Older patients presented higher incidence of SAEs than younger ones (16.0 vs 8.4/100 PY, respectively; multivariate IRR: 2.06, 95% CI: 1.51 to 2.80, P<0.001). Among old patients, tocilizumab (HR: 2.73, 95% CI: 1.13 to 6.64, P=0.026), etanercept (2.13, 1.12 to 4.07, P=0.022), and infliximab (2.39, 1.19 to 4.79, P=0.014) presented higher risk of treatment termination as compared with adalimumab. In this subgroup (age ≥65 yrs), there was no significant difference in the risk of SAEs between different bDMARDs/tsDMARDs.

Table 1.

Univariate and multivariate hazard ratios (HRs) of interruption of treatment course comparing older (≥65 years) versus younger patients (reference category). Results are HRs, 95% CIs, and P values.

Cause of interruption (n of events)Crude analysisAdjusted covariates*Interruption - any reason (1321)0.96 (0.75 to 1.23), P=0.7601.09 (0.82 to 1.43), P=0.550Interruption - adverse events (368)1.33 (0.75 to 0.89), P=0.1601.59 (1.07 to 2.35), P=0.020Interruption - inefficacy (680)0.56 (0.39 to 0.80), P=0.0020.57 (0.38 to 0.87), P=0.009

* Age, baseline DAS28, disease duration, gender, smoking, RF or anti-CCP, previous malignancy, interstitial lung disease, diabetes, hypertension, hypercholesterolemia, renal failure, ischemic cardiomyopathy, COPD, heart failure, concomitant use of each cs-, b-, and tsDMARDs, corticosteroids, starting year, osteoporosis, hepatitis B,C, treatment sequence.

Conclusion

The overall risk of treatment interruption with biologic or targeted synthetic DMARDs is not higher in older patients. Higher risk of interruption due to AE was balanced by a lower risk of stopping treatment due to inefficacy. Older patients had a higher incidence of SAEs.

References

[1]Mathieu et al. Rheumatol Int 2021;41:879-85.

[2]Freitas et al. Drugs Aging 2020;37:899-907.

[3]Bredemeier et al. J Rheumatol 2021;48:1519-27.

Disclosure of Interests

None declared

POS1285 IMMUNOGENICITY AND SAFETY OF THE CHADOX 1 COVID-19 VACCINE IN PATIENTS WITH AUTOIMMUNE DISEASES AND HEALTHY CONTROLS: DATA FROM SAFER STUDY

Background

Patients with autoimmune inflammatory diseases (AID) have been prioritized for urgent vaccination to mitigate COVID-19 risk. However, few studies in the literature assessed the immunogenicity and safety of the COVID-19 vaccine in patients with AID.

Objectives

In this context, the present study aims to evaluate the immunogenicity and safety of the vaccine against COVID-19 in patients with AID.

Methods

These data are from “Safety and efficacy on COVID-19 Vaccine in Rheumatic Disease” - SAFER study, a Brazilian multicentric prospective phase IV study to evaluate COVID-19 Vaccine in AID, in the real-life, in Brazil. Immunogenicity and adverse events (AE) from a single center were assessed, after 2 doses of ChAdOx1 (Oxford/AstraZeneca), 8 weeks of interval, in patients with AID and healthy controls (HC). Inclusion criteria were age ≥ 18 years and fulfilling criteria according to international classification for AID. Exclusion criteria: pregnancy, previous severe AE to any vaccine, other immunosuppression causes. Stratification of post-vaccination AE was performed using a diary, filled out daily and returned at the end of 28 days for each dose. Participants were followed up through blood collection for measurement of IgG antibodies against SARS-CoV-2 spike receptor-binding domain by chemiluminescence (SARS-CoV-2 IgG II Quant assay, Abbott Laboratories, Abbott Park, IL, USA) at baseline and 28 days after the second dose. The seropositivity was defined for titers ≥50 AU/mL. Quantitative analyses were presented as observed frequency, percentage, central tendency, and variability measurements. The sample’s normal distribution was verified through the Shapiro-Wilk test. The Kruskal-Wallis test and the post-hoc Dwass-Steel-Critchlow-Fligner pairwise comparisons test were used to compare the IgG-S titers between the groups through the evaluation period. Categorical data were addressed using the Fisher´s exact or Chi-squared (χ2) test. An alpha level of 5% significance was used in all analyses.

Results

A total of 377 volunteers with AID and 50 HC were included in the study. Patients with spondyloarthritis (N=64), systemic lupus erythematosus (N=63), rheumatoid arthritis (N=61), primary Sjögren’s syndrome (N=61), vasculitis (N=31), systemic sclerosis (N=14), inflammatory myopathy (N=9), Crohn´s disease (N=49), ulcerative colitis (N=11) and other systemics AID (N=12) were evaluated. Both groups had female predominance (73.5% vs. 74.0%, p=0.937) and were homogeneous for age (43.5 vs. 41.7,p=0.308). The seroconversion among those not reactive (IgG-S negative at baseline) (46 HC and 191 AID), 28 days after second dose was 97.1% for spondyloarthritis (p=0.425), systemic lupus erythematosus 88.2% (0.006), rheumatoid arthritis 93.5% (0.158), primary Sjögren’s syndrome 92.6% (0.133), systemic sclerosis or inflammatory myopathy 47.1% (0.001), inflammatory bowel disease 100% (0.999) and vasculitis 80% (0.006), while in healthy control was 100%. In comparison with HC, there was a statistically significant difference in IgG-S titles only in systemic sclerosis or inflammatory myopathy (1.694 AU/ml vs. 3.719 AU/ml; p=0.006). Both groups only presented mild AE. Pain at the injection (85.7% vs. 78.4%, p=0.239), headache (67.3% vs. 53.8, p=0.074) and fatigue (59.2% Vs. 46.2%, p=0.089) were more common in HC than AID. Overall, reactions like arthralgia (52.6 vs. 22.4%, p<0.001), hematoma (14.1 vs. 4.1%, p=0.05), cutaneous rash (9.5 vs. 0%, p=0.024) were more frequent in AID. Most participants related that they felt safer after receiving a COVID-19 vaccination, and 52.4% did not reported a worse patient global assessment (PGA) index.

Conclusion

In conclusion, our data indicated that ChAdOx1 vaccine is safe and induced high titers and seroconversion rate in AID. More severe AID, such as vasculitis, systemic lupus erythematosous, and systemic sclerosis and myositis showed a lower seroconversion rate. Further analysis will explore the association between immunossupressant and reactivity, and booster dose.

Acknowledgements

Acknowledgements to DECIT/MS and ICEPI/SESA for supporting the study.

Disclosure of Interests

None declared

POS0242 THE EFFECT OF ANTIMALARIALS ON THE OVERALL SAFETY AND PERSISTENCE OF TREATMENT WITH BIOLOGIC AGENTS OR JAK INHIBITORS IN RHEUMATOID ARTHRITIS

Background

Antimalarials (AM) are frequently part of the initial scheme of conventional synthetic DMARDs in the treatment of rheumatoid arthritis (RA), and have been associated with lower incidence of diabetes and better lipid profile in these patients (1). However, the role of AM in schemes involving biologic (b-) or targeted synthetic (ts-) DMARDs has been much less extensively studied. In addition, a recent large scale study (2) and a consensus article (1) casted doubt on the long-term cardiovascular safety of AM.

Objectives

To evaluate the association of concomitant use of AM with the overall safety and survival of

treatment course among patients receiving one or multiple courses of bDMARDs or tsDMARDs

Methods

BiobadaBrasil is a multicentric registry-based cohort study of Brazilian patients with rheumatic diseases starting their first bDMARD or tsDMARD (3). The present analysis includes RA patients recruited from Jan 2009 to Oct 2019, followed-up over one or multiple (up to six) courses of treatment (latest date, Nov 19, 2019). A treatment course is defined as a period during which the medication scheme does not change. The primary outcome was the incidence of serious adverse events (SAEs). Total and system-specific adverse events (AEs), treatment interruption for any reason, interruption due to AEs and due to inefficacy served as secondary outcomes. Negative binomial regression with generalized estimating equations (to calculate the incidence rate ratios [ÌRRs]) and extended (frailty) Cox proportional hazards models were used for statistical analyses (both types of analyses including time-varying covariates over multiple courses of treatment).

Results

In total, 1316 patients (2335 treatment courses, 6711 patient-years [PY]) were enrolled. The overall incidence of serious adverse events was 9.2/100 PY. AM were used over 354 courses (1254.5 PY) of therapy. The IRRs for the primary and secondary outcomes are presented in Table 1. AM were also associated with better treatment course survival (Figure 1), reducing the risk of interruption due to AEs (multivariate hazard ratio: 0.56, 95% CI: 0.39 to 0.81, P=0.002) and inefficacy (0.65, 0.48 to 0.87, P=0.003).

Figure 1.Table 1.

Univariate and multivariate incidence rate ratios (IRRs) of adverse events comparing use versus non-use (reference category) of antimalarials. Results are IRRs, 95% CIs, and P values.

Type of adverse event (n of events)Crude analysisAdjusted covariates*Serious adverse events (617)0.60 (0.41 to 0.87), P=0.0070.51 (0.37 to 0.69), P<0.001Any adverse event (3494)0.65 (0.54 to 0.77), P<0.0010.68 (0.57 to 0.81), P<0.001Cardiovascular‡Serious (52)1.04 (0.49 to 2.20), P=0.9241.06 (0.45 to 2.50), P=0.891Total (163)0.90 (0.59 to 1.38), P=0.6420.93 (0.59 to 1.45), P=0.737InfectionsSerious (277)0.78 (0.44 to 1.39), P=0.4040.53 (0.34 to 0.83), P=0.006Total (1400)0.77 (0.61 to 0.98), P=0.0330.75 (0.60 to 0.94), P=0.014Hepatic‡Total (66)0.20 (0.07 to 0.64), P=0.0070.16 (0.04 to 0.57), P=0.005Glicemic control-relatedTotal (34)0.74 (0.29 to 1.92), P=0.5400.73 (0.26 to 2.00), P=0.535DyslipidemiaTotal (83)0.60 (0.31 to 1.13), P=0.1140.55 (0.28 to 1.06), P=0.074

*Age, baseline DAS28, disease duration, gender, smoking, seropositivity (RF or anti-CCP), previous malignancy, interstitial lung disease, diabetes, hypertension, hypercholesterolemia, renal failure, ischemic cardiomyopathy, COPD, heart failure, concomitant use of each cs-, b-, and tsDMARDs, corticosteroids, starting year, osteoporosis, hepatitis B and C, and treatment sequence. ‡ Excluding infections.

Conclusion

Among RA patients on treatment with bDMARDs or tsDMARDs, concomitant use of antimalarials reduced the incidence of serious and total AEs, including infections and hepatic AEs, and prolonged treatment course survival. No significant increase in the risk of cardiovascular AEs was observed.

References

[1]Desmarais et al. Arthritis Rheumatol 2021;73:2151-60.

[2]Lane et al. Lancet Rheumatol 2020;2:e698–e711

[3]Bredemeier et al. J Rheumatol 2021;48:1519-27.

Disclosure of Interests

None declared

OP0249 CHARACTERISTICS ASSOCIATED WITH POOR COVID-19 OUTCOMES IN PEOPLE WITH PSORIASIS AND SPONDYLOARTHRITIS: DATA FROM THE COVID-19 PsoProtect AND GLOBAL RHEUMATOLOGY ALLIANCE PHYSICIAN-REPORTED REGISTRIES

Background

Some factors associated with severe COVID-19 outcomes have been identified in patients with psoriasis (PsO) and inflammatory/autoimmune rheumatic diseases, namely older age, male sex, comorbidity burden, higher disease activity, and certain medications such as rituximab. However, information about specificities of patients with PsO, psoriatic arthritis (PsA) and axial spondyloarthritis (axSpA), including disease modifying anti-rheumatic drugs (DMARDs) specifically licensed for these conditions, such as IL-17 inhibitors (IL-17i), IL-23/IL-12 + 23 inhibitors (IL-23/IL-12 + 23i), and apremilast, is lacking.

Objectives

To determine characteristics associated with severe COVID-19 outcomes in people with PsO, PsA and axSpA.

Methods

This study was a pooled analysis of data from two physician-reported registries: the Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection (PsoProtect), comprising patients with PsO/PsA, and the COVID-19 Global Rheumatology Alliance (GRA) registry, comprising patients with PsA/axSpA. Data from the beginning of the pandemic up to 25 October, 2021 were included. An ordinal severity outcome was defined as: 1) not hospitalised, 2) hospitalised without death, and 3) death. A multivariable ordinal logistic regression model was constructed to assess the relationship between COVID-19 severity and demographic characteristics (age, sex, time period of infection), comorbidities (hypertension, other cardiovascular disease [CVD], chronic obstructive lung disease [COPD], asthma, other chronic lung disease, chronic kidney disease, cancer, smoking, obesity, diabetes mellitus [DM]), rheumatic/skin disease (PsO, PsA, axSpA), physician-reported disease activity, and medication exposure (methotrexate, leflunomide, sulfasalazine, TNFi, IL17i, IL-23/IL-12 + 23i, Janus kinase inhibitors (JAKi), apremilast, glucocorticoids [GC] and NSAIDs). Age-adjustment was performed employing four-knot restricted cubic splines. Country-adjustment was performed using random effects.

Results

A total of 5008 individuals with PsO (n=921), PsA (n=2263) and axSpA (n=1824) were included. Mean age was 50 years (SD 13.5) and 51.8% were male. Hospitalisation (without death) was observed in 14.6% of cases and 1.8% died. In the multivariable model, the following variables were associated with severe COVID-19 outcomes: older age (Figure 1), male sex (OR 1.53, 95%CI 1.29-1.82), CVD (hypertension alone: 1.26, 1.02-1.56; other CVD alone: 1.89, 1.22-2.94; vs no hypertension and no other CVD), COPD or asthma (1.75, 1.32-2.32), other lung disease (2.56, 1.66-3.97), chronic kidney disease (2.32, 1.50-3.59), obesity and DM (obesity alone: 1.36, 1.07-1.71; DM alone: 1.85, 1.39-2.47; obesity and DM: 1.89, 1.34-2.67; vs no obesity and no DM), higher disease activity and GC intake (remission/low disease activity and GC intake: 1.96, 1.36-2.82; moderate/severe disease activity and no GC intake: 1.35, 1.05-1.72; moderate/severe disease activity and GC intake 2.30, 1.41-3.74; vs remission/low disease activity and no GC intake). Conversely, the following variables were associated with less severe COVID-19 outcomes: time period after 15 June 2020 (16 June 2020-31 December 2020: 0.42, 0.34-0.51; 1 January 2021 onwards: 0.52, 0.41-0.67; vs time period until 15 June 2020), a diagnosis of PsO (without arthritis) (0.49, 0.37-0.65; vs PsA), and exposure to TNFi (0.58, 0.45-0.75; vs no DMARDs), IL17i (0.63, 0.45-0.88; vs no DMARDs), IL-23/IL-12 + 23i (0.68, 0.46-0.997; vs no DMARDs) and NSAIDs (0.77, 0.60-0.98; vs no NSAIDs).

Conclusion

More severe COVID-19 outcomes in PsO, PsA and axSpA are largely driven by demographic factors (age, sex), comorbidities, and active disease. None of the DMARDs typically used in PsO, PsA and axSpA, were associated with severe COVID-19 outcomes, including IL-17i, IL-23/IL-12 + 23i, JAKi and apremilast.

Acknowledgements

We thank all the contributors to the COVID-19 PsoProtect, GRA and EULAR Registries.

Disclosure of Interests

None declared

Evaluation of the genetic risk for COVID-19 outcomes in COPD and differences among worldwide populations

Background

Populations seem to respond differently to the global pandemic of severe acute respiratory syndrome coronavirus 2. Recent studies show individual variability in both susceptibility and clinical response to COVID-19 infection. People with chronic obstructive pulmonary disease (COPD) constitute one of COVID-19 risk groups, being already associated with a poor prognosis upon infection. This study aims contributing to unveil the underlying reasons for such prognosis in people with COPD and the variability in the response observed across worldwide populations, by looking at the genetic background as a possible answer to COVID-19 infection response heterogeneity.

Methods

SNPs already associated with susceptibility to COVID-19 infection (rs286914 and rs12329760) and severe COVID-19 with respiratory failure (rs657152 and rs11385942) were assessed and their allelic frequencies used to calculate the probability of having multiple risk alleles. This was performed on a Portuguese case-control COPD cohort, previously clinically characterized and genotyped from saliva samples, and also on worldwide populations (European, Spanish, Italian, African, American and Asian), using publicly available frequencies data. A polygenic risk analysis was also conducted on the Portuguese COPD cohort for the two mentioned phenotypes, and also for hospitalization and survival to COVID-19 infection.

Findings

No differences in genetic risk for COVID-19 susceptibility, hospitalization, severity or survival were found between people with COPD and the control group (all p-values > 0.01), either considering risk alleles individually, allelic combinations or polygenic risk scores. All populations, even those with European ancestry (Portuguese, Spanish and Italian), showed significant differences from the European population in genetic risk for both COVID-19 susceptibility and severity (all p-values < 0.0001).

Conclusion

Our results indicate a low genetic contribution for COVID-19 infection predisposition or worse outcomes observed in people with COPD. Also, our study unveiled a high genetic heterogeneity across major world populations for the same alleles, even within European sub-populations, demonstrating the need to build a higher resolution European genetic map, so that differences in the distribution of relevant alleles can be easily accessed and used to better manage diseases, ultimately, safeguarding populations with higher genetic predisposition to such diseases.

Neuroendocrine pathways at risk? Simvastatin induces inter and transgenerational disruption in the keystone amphipod Gammarus locusta

The primary focus of environmental toxicological studies is to address the direct effects of chemicals on exposed organisms (parental generation - F0), mostly overlooking effects on subsequent non-exposed generations (F1 and F2 - intergenerational and F3 transgenerational, respectively). Here, we addressed the effects of simvastatin (SIM), one of the most widely prescribed human pharmaceuticals for the primary treatment of hypercholesterolemia, using the keystone crustacean Gammarus locusta. We demonstrate that SIM, at environmentally relevant concentrations, has significant inter and transgenerational (F1 and F3) effects in key signaling pathways involved in crustaceans' neuroendocrine regulation (Ecdysteroids, Catecholamines, NO/cGMP/PKG, GABAergic and Cholinergic signaling pathways), concomitantly with changes in apical endpoints, such as depressed reproduction and growth. These findings are an essential step to improve hazard and risk assessment of biological active compounds, such as SIM, and highlight the importance of studying the transgenerational effects of environmental chemicals in animals' neuroendocrine regulation.

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.

POS0676 SURVIVAL OF THE FIRST COURSE OF BIOLOGIC OR JAK INHIBITOR IN RHEUMATOID ARTHRITIS: ASSOCIATION WITH THE CHOICE OF AGENT AND CONCOMITANT CONVENTIONAL SYNTHETIC DMARDS

Background:

After failure of conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) in the therapy of rheumatoid arthritis (RA), treatment may be escalated to biologic (bDMARDs) or JAK inhibitors (JAKi) (1). Analysis of drug survival can provide useful information on the effectiveness of these therapeutic schemes.

Objectives:

to evaluate the association of the choice of therapeutic agent with the survival of treatment course in RA patients receiving their first bDMARD or JAKi.

Methods:

BiobadaBrasil is a multicentric registry-based cohort study of Brazilian patients starting their first bDMARD/JAKi (2). This analysis includes RA patients recruited from Jan 2009 to Oct 2019, followed-up over the first course of treatment with a bDMARD/JAKi until censoring (latest date, Nov 19, 2019) or occurrence of the outcome of interest. A treatment course is defined as a period during which the medication scheme does not change, except for dose adjustments. The primary outcome was the interruption of treatment course for any reason (except for pregnancy or disease remission); interruption of treatment due to adverse events (AEs) or death and due to inefficacy served as secondary outcomes. Multivariate Cox proportional hazards models were used for analyses.

Results:

In total, 1177 patients (3800 patient-years [PY]) were enrolled. The overall incidence of treatment interruption was 17.5/100 PY. Adalimumab was the most frequently prescribed agent, followed by infliximab (n= 267). The hazards ratios (HR) of the primary and secondary outcomes are presented in Table 1. Figure 1 compares the survival of treatment curves of different bDMARDs/JAKi.

Table 1.

Hazard ratios (HR) of interruption of therapy course of each therapeutic agent (the reference category for bDMARDs/ JAKi is infliximab). Results are HR, 95% CIs, and P values*.

Agent (number of patients)Interruption for any reason (665 events)Interruption due to adverse events or death (196 events)Interruption due to inefficacy (319 events)Adalimumab (354)0.83 (0.68 to 1.01), P= 0.0620.68 (0.48 to 0.96), P=0.0291.08 (0.80 to 1.44), P=0.621Etanercept (257)0.81 (0.66 to 1.01), P=0.0630.56 (0.37 to 0.83), P=0.0040.93 (0.68 to 1.29), P=0.674Certolizumab (80)0.74 (0.47 to 1.16), P=0.1850.33 (0.13 to 0.86), P=0.0241.32 (0.74 to 2.35), P=0.350Golimumab (53)0.86 (0.53 to 1.38), P=0.5300.46 (0.18 to 1.19), P=0.1111.07 (0.53 to 2.15), P=0.849JAKi (tofacitinib) (59)0.54 (0.30 to 0.99), P=0.0470.19 (0.04 to 0.82), P=0.0260.89 (0.41 to 1.96), P=0.779Rituximab (48)0.87 (0.55 to 1.37), P=0.5400.48 (0.20 to 1.18), P=0.1090.58 (0.26 to 1.34), P=0.205Abatacept (30)0.52 (0.25 to 1.07), P=0.0770.46 (0.14 to 1.56), P=0.2150.46 (0.14 to 1.52), P=0.203Tocilizumab (29)0.29 (0.14 to 0.63), P=0.0020.40 (0.12 to 1.30), P=0.1260.28 (0.09 to 0.90), P=0.033Methotrexate (792)0.95 (0.79 to 1.14), P=0.5610.86 (0.62 to 1.19), P=0.3620.98 (0.75 to 1.28), P=0.860Leflunomide (497)1.17 (0.99 to 1.39), P=0.0611.44 (1.06 to 1.96), P=0.0201.02 (0.80 to 1.30), P=0.856Sulfasalazine (48)1.18 (0.80 to 1.75), P=0.4011.94 (1.07 to 3.54), P=0.0300.85 (0.45 to 1.59), P=0.605Antimalarials (230)0.80 (0.65 to 0.98), P=0.0270.67 (0.45 to 0.99), P=0.0430.67 (0.50 to 0.92), P=0.011

* All tests adjusted for other variables presented in the table and for age, baseline DAS28, disease duration, gender, smoking, seropositivity (RF/anti-CCP), previous malignancy, diabetes, hypertension, hypercholesterolemia, renal failure, ischemic cardiomyopathy, COPD, heart failure, use of corticosteroids, starting year, hypercholesterolemia, osteoporosis, hepatitis B and C.

Conclusion:

In our study, infliximab was related to an overall higher hazard of treatment course interruption than tolicizumab and tofacitinib, and higher hazard of interruption due to AEs than most other anti-TNF agents and tofacitinib. Maintaining antimalarials in patients receiving advanced therapies for RA may reduce interruption of treatment due to inefficacy and AEs.

Disclosure of Interests:

None declared

POS0924 PREDICTORS OF 1-YEAR TREATMENT RESPONSE AMONG UPADACITINIB-TREATED PATIENTS WITH ANKYLOSING SPONDYLITIS: A POST HOC ANALYSIS OF SELECT-AXIS 1

Background:

Upadacitinib (UPA) is an oral Janus kinase inhibitor that has demonstrated efficacy and safety among patients with ankylosing spondylitis (AS) in the phase 2/3 SELECT-AXIS 1 study.1 If identified, early predictors of treatment response may inform treat-to-target strategies and optimize patient outcomes in AS.

Objectives:

To determine whether baseline (BL) characteristics or early responses predict clinical response at 1 year in UPA-treated patients with AS.

Methods:

In the double-blind, randomized, placebo (PBO)-controlled SELECT-AXIS 1 study, patients received UPA 15 mg once daily or PBO until Week 14.1 At Week 14, PBO-treated patients switched to UPA 15 mg; patients originally randomized to UPA continued UPA therapy. Data from patients in the PBO and UPA arms were combined based on overall exposure to UPA; in the switch arm, exposure was defined as current visit minus 14 weeks (time of switch). The following outcomes were assessed at 1 year: Ankylosing Spondylitis Disease Activity Score with C-reactive protein (ASDAS[CRP]) inactive disease (ID; <1.3) and low disease activity (LDA; <2.1), Assessment of SpondyloArthritis International Society (ASAS) partial remission (PR), and ≥40% improvement in ASAS criteria (ASAS40) response. The ability of BL characteristics, efficacy at Week 12, and back pain at Week 12 to predict 1-year outcomes was assessed using a univariable logistic regression model generating odds ratios (ORs; 95% confidence intervals). LASSO regression was used to select the best-fitted multivariable model at Week 12 for each outcome measure.

Results:

Among 187 patients who received or switched to UPA 15 mg, 70 (37.4%), 134 (71.7%), 73 (39.0%), and 131 (70.1%) achieved ASDAS(CRP) ID, ASDAS(CRP) LDA, ASAS PR, and ASAS40, respectively, following 1 year of UPA treatment. No meaningful predictors of 1-year efficacy outcomes were identified based on BL demographics (including disease duration, gender, and human leukocyte antigen B27 status) or BL disease characteristics (including ASDAS, Bath Ankylosing Spondylitis Disease Activity Index, and CRP levels). In univariable analyses, Week 12 responses based on several disease activity measures and patient-reported outcomes (PROs), including reductions (much better improvement [MBI], ≥30/≥50/≥70% reduction, or improvement) in back pain score, along with lower scores for back pain at Week 12, were associated with the achievement of ASDAS(CRP) ID, ASDAS(CRP) LDA, ASAS PR, and ASAS40 at 1 year (Figure 1). In a multivariable analysis, improvement from BL to Week 12 in back pain score consistently predicted several efficacy outcomes at 1 year.

Conclusion:

In upadacitinib-treated patients with AS, improvement in PROs and reduction in back pain score at 12 weeks predicted clinical outcomes at 1 year.

References:

[1]van der Heijde D, et al. Lancet 2019;394:2108–17.

Figure 1.

Association between Week 12 response or back pain at Week 12 and achievement of efficacy outcomes at 1 year (univariable analysis)

All ASDAS scores are calculated using C-reactive protein

ASDAS CII: change from BL ≥1.1; ASDAS MI: change from BL ≥2.0; MBI back pain: ≥2-point reduction in absolute score and ≥33% reduction from BL on a 0–10 NRS

ASAS, Assessment of SpondyloArthritis International Society; ASAS40, ≥40% improvement in ASAS criteria; ASDAS, Ankylosing Spondylitis Disease Activity Score; BASDAI50, ≥50% improvement in the Bath Ankylosing Spondylitis Disease Activity Index; BL, baseline; CI, confidence interval; CII, clinically important improvement; ID, inactive disease; LDA, low disease activity; MBI, much better improvement; MI, major improvement; NRS, numeric rating scale; OR, odds ratio; PR, partial remission

Acknowledgements:

AbbVie funded this study; contributed to its design; participated in data collection, analysis, and interpretation of the data; and participated in the writing, review, and approval of the abstract. No honoraria or payments were made for authorship. Medical writing support was provided by Laura Chalmers, PhD, of 2 the Nth (Cheshire, UK), and was funded by AbbVie.

Disclosure of Interests:

Marina Magrey Consultant of: Consultant for Janssen and Novartis; member of advisory boards for Eli Lilly, Janssen, Novartis, and UCB, Grant/research support from: AbbVie, Sofia Ramiro Consultant of: AbbVie, Eli Lilly, MSD, Novartis, Sanofi, and UCB, Grant/research support from: MSD, Marcelo Pinheiro Consultant of: AbbVie, Eli Lilly, Janssen, and Novartis, Tianming Gao Employee of: AbbVie employee and may own stock or options, Fabiana Ganz Employee of: AbbVie employee and may own stock or options, In-Ho Song Employee of: AbbVie employee and may own stock or options, Ana Biljan Employee of: AbbVie employee and may own stock or options, Nigil Haroon Consultant of: AbbVie, Amgen, Eli Lilly, Janssen, MSD, Novartis, Pfizer, and UCB, Martin Rudwaleit Consultant of: AbbVie, Bristol-Myers Squibb, Celgene, Eli Lilly, Janssen, MSD, Novartis, Pfizer, Roche, and UCB

AB0848 PARTICIPATION OF UNDERGRADUATE MEDICAL STUDENTS AS INVESTIGATORS IN A RHEUMATOLOGIC COHORT: IMPACT ON DEPRESSION, ANXIETY & STRESS SCALE

Background:

Mental health was widely affected during the new coronavirus pandemic. In addition, some measures adopted by most countries in order to contain the virus spread, such as isolation and social distancing, leading to the interruption of routine activities, including partial or complete interruption of face-to-face classes may be associated with increased stress, depression and anxiety among undergraduate medical students (1). From March to September, 2020, the Brazilian Society of Rheumatology carried out the Mario Pinotti II Project (MPII), a prospective, multicenter, observational cohort study designed to monitor the COVID-19 in patients with rheumatic disease on hydroxychloroquine, using periodic telephone calls performed by undergraduate medical students (2).

Objectives:

To compare the mental health status of medical students who were participating from the MPII with theirs colleagues not involved in this project.

Methods:

A web-based survey via google forms platform was developed by a panel composed of undergraduate medical students, rheumatologists, medical school professors, and a psychology professor. It included details on demographic and life habits data and domains regarding depression, anxiety and stress, using the DASS-21 (Depression, Anxiety & Stress Scale), Brazilian version. Data collection occurred from July 20th to August 31st, 2020. Statistical analysis was performed using the SPSS version 20.0. Univariate and multivariate linear regression analysis were performed to verify associations with the DASS-21, defined as dependent variable. A p-value < 0.05 was deemed as significant. This study was approved by the Institutional Research Ethics Committee.

Results:

A total of 684 undergraduate medical students were included in this study, of whom 228 as MPII volunteers (VG) and 456 as control group (CG). Median age was 23 years (IQ 21-24) and the CG was older than the VG (p<0.03). Most of them were white (68.8%) and women (63%). There were no significant differences regarding comorbidities, ethnicity, smoking status, alcohol intake and physical activity. Older age, male gender, participation of MPII study, absence of a worsening in sleep pattern during the pandemic and a lower number of prior comorbidities were associated with lower DASS21 scores, suggesting a better mental health (Table 1).

Conclusion:

Several aspects may be involved with mental health, including increased emotional maturity, gender and sleep pattern. Although with marginal independent association, medical students with participation in the MPII study had better mental health than their student colleagues not engaged with this research. Our data pointed out that voluntary participation in a research project which foresees interaction by telephone contact with rheumatic patients, professors, rheumatologists, and colleagues is associated with better mental health.

References:

[1]Meo SA, Abukhalaf AA, Alomar AA, Sattar K, Klonoff DC. Covid-19 pandemic: Impact of quarantine on medical students’ mental wellbeing and learning behaviors. Pakistan J Med Sci 2020;36(COVID19-S4):S43–8.

[2]Gomides A, Ferreira G, Kakehas A, Lacerda M, Marques C, Paiva E et al. Impact of chronic use of antimalarials on SARS-COV-2 infection in patients with immune-mediated rheumatic diseases: protocol design for a multicentric observational cohort in Brazil. JMIR Research Protocols, 2020.Preprint

Table 1.

Univariate and multivariate analysis of predictors associated to the DASS-21 in undergraduate medical students during the COVID-19 pandemic

Univariate analysisMultivariate analysisVariableB95%CIp-ValueB95%CIp-ValueAge-0.32-0.61 to -0.030.03-0.47-0.81 to -0.130.008Female gender4.883.021 to 6.76<0.001---Stable love relationship-2.49-4.35 to -0.640.008-2.5-4.4 to -0.590.01Number of previous comorbidities reported4.693.71 to 5.68<0.0014.823.73 to 5.92<0.001MP-II volunteering-2.81-4.74 to -0.860.005---Worsening in sleep pattern6.414.62 to 8.20<0.0015.013.07 to 6.96<0.001

Disclosure of Interests:

None declared

POS1252 COVID-19 IN PATIENTS WITH RHEUMATIC DISEASES ON CHRONIC USE OF HYDROXYCHLOROQUINE IN A LARGE BRAZILIAN COHORT – A 24-WEEK PROSPECTIVE STUDY

Background:

The role of chronic use of hydroxychloroquine (HCQ) in rheumatic disease (RD) patients during the SARS-CoV-2 pandemic is still subject of discussion.

Objectives:

To compare the occurrence of COVID-19 and its outcomes between RD patients on HCQ use with individuals from the same household not taking the drug during community viral transmission in an observational prospective multicenter study in Brazil.

Methods:

Participants were enrolled and monitored through 24-week (From March 29th to Sep 30th, 2020) regularly scheduled phone calls performed by trained medical professionals. Epidemiological and demographic data, as well as RD disease activity status and current treatment data, specific information about COVID-19, hospitalization, need for intensive care, and death was recorded in both groups and stored in the Research Electronic Data Capture (REDCap) database. COVID-19 was defined according to the Brazilian Ministry of Health (BMH) criteria. The statistical analysis was performed using IBM-SPSS v.20.0 software. Group comparisons were made using the Man-Whitney, Chi-Square and Fisher Exact Test, as well as multivariate regression models adjusted to confounders. Survival curves were performed using Kaplan-Meier analysis.

Results:

A total of 10,427 participants mean age (SD) of 44.04 (14.98) years were enrolled, including 6004 (57.6%) rheumatic disease patients, of whom 70.8% had systemic lupus erythematosus (SLE), 6.7% rheumatoid arthritis (RA), 4% primary Sjögren’s syndrome (pSS), 1.8% mixed connective tissue disease (DMTC), 1% systemic sclerosis (SSc) and others (15.9), including overlap syndromes. In total, 1,132 (10.8%) participants fulfilled criteria for COVID-19, being 6.7% RD patients and 4.1% controls (p=0.002). A recent influenza vaccination had a protective role (p<0.001). Moderate and severe COVID-19 included the need for hospitalization, intensive care, mechanical ventilation or death. Infection severity was not different between groups (p=0.391) (Table 1). After adjustments for multiple confounders, the main risk factors significantly associated with COVID-19 were higher education level (OR=1.29 95%CI 1.05-1.59), being healthcare professionals (OR=1.91; 95%CI 1.45-2.53), presence of two comorbidities (OR=1.31; 95%CI 1.01-1.66) and three or more comorbidities associated (OR=1.69; 95%CI 1.23-2.32). Interestingly, age >=65 years (OR=0.20; 95%CI 0.11-0.34) was negatively associated. Regarding RD, the risk factors associated with COVID-19 diagnosys were SLE (OR= 2.37; 95%CI 1.92-293), SSc (OR=2.25; 95%CI 1.05-4.83) and rituximab use (OR=1.92; 95%CI 1.13-3.26). In addition, age >=65 years (OR=5.47; 95%CI 1.7-19.4) and heart disease (OR=2.60; 95%CI 1.06-6.38) were associated with hospitalization. Seven female RD patients died, six with SLE and one with pSS, and the presence of two or more comorbidities were associated with higher mortality rate.

Conclusion:

Chronic HCQ use did not prevent COVID-19 in RD compared to their household cohabitants. Health care profession, presence of comorbidities LES, SSc and rituximab were identified as main risk factors for COVID-19 and aging and heart disease as higher risk for hospitalization. Our data suggest these outcomes could be considered to manage them in clinical practice.

Table 1.

Frequency and severity of COVID-19 in patients with rheumatic diseases on chronic use of hydroxychloroquine compared to their household controls

COVID-19 outcomesTotal(%)GroupsPPatients(%)Controls (%)DiagnosisNo9256 (89.1)5300 (88.3)3956 (90.2)0.002Yes1132 (10.9)704 (11.7)428 (9.8)SeverityMild1059 (93.6)662 (94.0)397 (92.8)0.391Moderate52 (4.6)32 (4.5)20 (4.7)Severe21 (1.9)10 (1.4)11 (2.6)

HCQ: hydroxychloroquine.

Moderate and severe COVID-19 included the need for any of the following: hospitalization, intensive care, mechanical ventilation or death.

Acknowledgements:

To the Brazilian Society of Rheumatology for technical support and rapid nationwide mobilization.

To all the 395 interviewers (medical students and physicians) who collaborated in the study and the participants

To CNPq (Number 403442/2020-6)

Disclosure of Interests:

None declared

Transferrin-functionalized lipid nanoparticles for curcumin brain delivery

Curcumin is an anti-inflammatory and antioxidant compound with potent neuroprotective activity. Due to its poor water solubility, low bioavailability, rapid elimination and the challenges for crossing and transposing the blood-brain barrier (BBB), solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) loaded with curcumin were successfully produced and functionalized with transferrin, in order to mediate the transport of these particles through the BBB endothelium to the brain. The nanosystems revealed Z-averages under 200 nm, polydispersity index below 0.2 and zeta potential around -30 mV. Curcumin encapsulation around 65 % for SLNs and 80 % for NLCs was accomplished, while the functionalized nanoparticles presented a value around 70-75 %. A stability study revealed these characteristics remained unchanged for at least 3 months. hCMEC/D3 cells viability was firstly analysed by MTT and LDH assays, respectively, and a concentration of 10 μM of curcumin-loaded nanoparticles were then selected for the subsequent permeability assay. The permeability study was conducted using transwell devices with hCMEC/D3 cells monolayers and a 1.5-fold higher permeation of curcumin through the BBB was verified. Both SLNs and NLCs are promising for curcumin brain delivery, protecting the incorporated curcumin and targeting to the brain by the addition of transferrin to the nanoparticles surface.

Quercetin lipid nanoparticles functionalized with transferrin for Alzheimer's disease

Quercetin was encapsulated in lipid nanoparticles (SLN and NLC) to take advantage of its neuroprotective properties in Alzheimer's disease. The nanoparticles were functionalized with transferrin to facilitate the passage across the blood-brain barrier through the transferrin receptors overexpressed in brain endothelial cells. NMR and FTIR confirmed the functionalization of the nanoparticles with transferrin. TEM results showed all nanoparticles presented spherical morphology. Nanoparticles exhibited size around 200 nm and zeta potential values higher than -30 mV. Quercetin entrapment efficiency was around 80-90%. LDH cytotoxicity assays in hCMEC/D3 cell line demonstrated that even for the highest concentration (30 μM) nanoparticles did not reveal cytotoxicity after 4 h of incubation. Permeability studies across hCMEC/D3 cell monolayers showed NLC permeate more the blood-brain barrier, while amyloid-beta studies demonstrated NLC-transferrin have the capacity to inhibit fibril formation. Nanoparticles seem to be suitable for brain applications, mainly for Alzheimer's disease due to inhibition of amyloid-beta aggregation.

Efficieny of Phage Intervention Against Salmonella in Meat and Poultry Processing

ObjectivesPathogen Reduction, Hazard Analysis, and Critical Control Point systems final rule mandates establishments to seek and adopt antimicrobial interventions that can help in reducing the prevalence and most probable number of Salmonella in their meat and poultry products. Bacteriophages can aid in this challenge, as they can invade and kill specific target pathogenic bacteria on food products. Effective kill by phages relies on the appropriate phage application technique. Correct dose, good distribution on the food surface area, and adequate dwell time are key factors which influence phage-bacteria contact and thereby phage efficacy. This study determined the efficacy of a commercially available phage product, PhageGuard S consisting of 2 phages, FO1a, and S16. Different pick up levels, blend and hold times (chosen based on regulatory restriction and process limitations), as well as spray versus dip treatment methods were tested.Materials and MethodsOvernight culture streptomycin resistant Salmonella enterica enterica Enteritidis C (Se13) was diluted and inoculated at a concentration of 2×104 CFU/cm2 or CFU/g on parts of chicken fillet and held for 10 min for bacterial attachment (duplicate samples per time point). Subsequently, contaminated parts were spray treated with one phage concentration (108 Plaque Forming Units/g) at 0.5%, 1% or 3% pick up (v/w) or water (control) and blended for 5, 10, and 20 min before immediate grinding and retrieval of bacteria (latter blend time sample was held for 24 h before grind). Another set of contaminated fillet parts were treated by dipping in 5% phage solution (at 1% pick up, 108 PFU/g) and held for 1, 5, 10, and 20 min, and 1 and 24 h at 40°F (4°C) before retrieval of bacteria. Enumeration of bacteria was done on selective agar plates and reductions were calculated relative to water treated control.ResultsThe application of phages 108 PFU/g via spray on chicken parts at 3% pick up and 20 min blend time resulted in 0.9 log10 CFU/g log reduction of Salmonella. Additional hold time of 24 h before grind resulted in 1.1- 1.2 log10 CFU/g kill at lower and higher pick up of 0.5% and 3%. Dip treatment resulted higher Salmonella reduction of 1.2 log10 CFU/cm2 within 5 min of 108 PFU/cm2 phage application and up to 2.3 log10 CFU/cm2 log10 reduction when held for 24 h. Overall, the spray technique, showed a dose response effect where increasing pick up and blend time resulted in an increasing Salmonella kill in ground product. However, the dip technique resulted in more effective Salmonella kill in shorter dwell time. All values are mean value of two individual experiments.ConclusionThe above results indicate that the commercially available phage solution, PhageGuard S, either via spray or dip method reduces Salmonella contamination on meat and poultry parts by 1.2 to 2.3 log10, respectively. Thereby is an effective intervention in reducing risks and allowing for increase in consumer safety. Dip technique works better than spray due to better distribution on meat surface. Longer hold and/or blend time after phage treatment results in more kill.

INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance

BACKGROUND

A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data.

RESULTS

We developed and implemented INSaFLU ("INSide the FLU"), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line "genetic requests" for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants' annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. This platform additionally flags samples as "putative mixed infections" if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional "consensus-based" influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission.

CONCLUSIONS

In summary, INSaFLU supplies public health laboratories and influenza researchers with an open "one size fits all" framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus. INSaFLU can be accessed through https://insaflu.insa.pt .

The last frontier: Coupling technological developments with scientific challenges to improve hazard assessment of deep-sea mining

The growing economic interest in the exploitation of mineral resources on deep-ocean beds, including those in the vicinity of sensitive-rich habitats such as hydrothermal vents, raise a mounting concern about the damage that such actions might originate to these poorly-know ecosystems, which represent millions of years of evolution and adaptations to extreme environmental conditions. It has been suggested that mining may cause a major impact on vent ecosystems and other deep-sea areas. Yet, the scale and the nature of such impacts are unknown at present. Hence, building upon currently available scientific information it is crucial to develop new cost-effective technologies embedded into rigorous operating frameworks. The forward-thinking provided here will assist in the development of new technologies and tools to address the major challenges associated with deep sea-mining; technologies for in situ and ex situ observation and data acquisition, biogeochemical processes, hazard assessment of deep-sea mining to marine organisms and development of modeling tools in support of risk assessment scenarios. These technological developments are vital to validate a responsible and sustainable exploitation of the deep-sea mineral resources, based on the precautionary principle.

A biomechanical analysis of prognathous and orthognathous insect head capsules: evidence for a many-to-one mapping of form to function

Insect head shapes are remarkably variable, but the influences of these changes on biomechanical performance are unclear. Among 'basal' winged insects, such as dragonflies, mayflies, earwigs and stoneflies, some of the most prominent anatomical changes are the general mouthpart orientation, eye size and the connection of the endoskeleton to the head. Here, we assess these variations as well as differing ridge and sclerite configurations using modern engineering methods including multibody dynamics modelling and finite element analysis in order to quantify and compare the influence of anatomical changes on strain in particular head regions and the whole head. We show that a range of peculiar structures such as the genal/subgenal, epistomal and circumocular areas are consistently highly loaded in all species, despite drastically differing morphologies in species with forward-projecting (prognathous) and downward-projecting (orthognathous) mouthparts. Sensitivity analyses show that the presence of eyes has a negligible influence on head capsule strain if a circumocular ridge is present. In contrast, the connection of the dorsal endoskeletal arms to the head capsule especially affects overall head loading in species with downward-projecting mouthparts. Analysis of the relative strains between species for each head region reveals that concerted changes in head substructures such as the subgenal area, the endoskeleton and the epistomal area lead to a consistent relative loading for the whole head capsule and vulnerable structures such as the eyes. It appears that biting-chewing loads are managed by a system of strengthening ridges on the head capsule irrespective of the general mouthpart and head orientation. Concerted changes in ridge and endoskeleton configuration might allow for more radical anatomical changes such as the general mouthpart orientation, which could be an explanation for the variability of this trait among insects. In an evolutionary context, many-to-one mapping of strain patterns onto a relatively similar overall head loading indeed could have fostered the dynamic diversification processes seen in insects.

Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features

Objectives: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. tri-nucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis.

Methods: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods – contingency table analysis, residual analysis, multivariate analysis (cluster analysis) – to analyze the codon bias under various aspects (degree of association, contexts and clustering).

Results: The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicansand Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples.

Conclusions: The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

New insights into the biomechanics of Legg-Calvé-Perthes' disease: The Role of Epiphyseal Skeletal Immaturity in Vascular Obstruction

Objectives

Legg–Calvé–Perthes’ disease (LCP) is an idiopathic osteonecrosis of the femoral head that is most common in children between four and eight years old. The factors that lead to the onset of LCP are still unclear; however, it is believed that interruption of the blood supply to the developing epiphysis is an important factor in the development of the condition.

Methods

Finite element analysis modelling of the blood supply to the juvenile epiphysis was investigated to understand under which circumstances the blood vessels supplying the femoral epiphysis could become obstructed. The identification of these conditions is likely to be important in understanding the biomechanics of LCP.

Results

The results support the hypothesis that vascular obstruction to the epiphysis may arise when there is delayed ossification and when articular cartilage has reduced stiffness under compression.

Conclusion

The findings support the theory of vascular occlusion as being important in the pathophysiology of Perthes disease.

Cite this article: M. Pinheiro, C. A. Dobson, D. Perry, M. J. Fagan. New insights into the biomechanics of Legg-Calvé-Perthes’ disease: The Role of Epiphyseal Skeletal Immaturity in Vascular Obstruction. Bone Joint Res 2018;7:148–156. DOI: 10.1302/2046-3758.72.BJR-2017-0191.R1.

Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

Background

Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical for decision-making.

Aim

To explore the usefulness of whole-genome sequencing (WGS) in the investigation of a P. aeruginosa outbreak, describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis.

Methods

Six patient isolates and six environmental samples from an intensive care unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS.

Findings

VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates, giving greater assurance of the transmission route between wash-hand basin water and two patients, supporting the control measures employed.

Conclusion

WGS provided detailed information without the need for further typing. When allied to epidemiological information, WGS can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and lower costs.

A Prospective Intervention in Patients with Complicated Grief

Introduction

Most reactions to grief are adaptive. However, there is the possibility that some individuals present a complicated grief disorder, where there is a pathological intensification of symptoms lasting more than 6 months, deserving special treatment.

Objectives/aims

Evaluate the effectiveness of two types of intervention in complicated grief: group intervention (GI) and cognitive-narrative (CN) therapy.

Methods

Patients in a complicated grief process were selected (n = 70), and distributed in three groups: cognitive–narrative therapy group (CNTG), group intervention group (GIG) and a control group (CG). Inclusion criteria: adults, with a reference to mourning situation, with personal meaning, for over six months and results in ICG ≥30points (cutoff). The Inventory of Complicated Grief (ICG), the Center for epidemiologic studies depression scale (CES-D) and the trauma questionnaire (ICD-11) were used. Follow-up was performed 3 months after the end of each intervention. Data analysis was performed using the statistical package from social sciences (SPSS 20).

Results

With respect to complicated grief symptoms (CGx) and depression symptoms (Dx) there were statistically significant differences between the CNTG and the CG, but not with the GIG. There was no statistically significant effect in post-traumatic symptoms (PTx), even though both interventions had a slight decrease. When the CNTG and the GIG were directly compared, there was only a statistically significant difference between PTx.

Conclusions

In our single center cohort, CNTG was a more effective intervention in complicated grief patients for CGx and Dx reduction. For PTx, no intervention was superior. Larger multi-center studies are needed to validate these results.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Pollination of Campomanesia phaea (Myrtaceae) by night-active bees: a new nocturnal pollination system mediated by floral scent

Bees are the most important diurnal pollinators of angiosperms. In several groups of bees a nocturnal/crepuscular habit developed, yet little is known about their role in pollination and whether some plants are adapted specifically to these bees. We used a multidisciplinary approach to investigate the reproductive biology and to understand the role of nocturnal/crepuscular bees in pollination of Campomanesia phaea (Myrtaceae), popularly named cambuci. We studied the floral biology and breeding system of C. phaea. We collected the floral visitors and tested the pollinators' effectiveness. We also determined the floral scents released at night and during daytime, and studied behavioural responses of crepuscular/nocturnal bees towards these scents. The flowers of cambuci were self-incompatible and had pollen as the only resource for flower visitors. Anthesis lasted around 14 h, beginning at 04:30 h at night. The flowers released 14 volatile compounds, mainly aliphatic and aromatic compounds. We collected 52 species of floral visitors, mainly bees. Nocturnal and crepuscular bees (four species) were among the most frequent species and the only effective pollinators. In field bioassays performed at night, nocturnal/crepuscular bees were attracted by a synthetic scent blend consisting of the six most abundant compounds. This study describes the first scent-mediated pollination system between a plant and its nocturnal bee pollinators. Further, C. phaea has several floral traits that do not allow classification into other nocturnal pollination syndromes (e.g. pollinator attraction already before sunrise, with pollen as the only reward), instead it is a plant specifically adapted to nocturnal bees.

Frailty Syndrome: Visceral Adipose Tissue and Frailty in Patients with Symptomatic Severe Aortic Stenosis

BACKGROUND/OBJECTIVES

In patients with severe aortic stenosis (AS), frailty is a clinically relevant measure of increased vulnerability that should be included in the preoperative risk assessment. Bioelectrical impedance analysis (BIA) derived phase angle (PA) reflects cell membrane integrity and function. Few studies are available on the relative contribution of adiposity distribution on frailty, and about the influences of frailty and visceral obesity in PA value. Therefore, we aimed to evaluate associations among frailty, visceral fat depots and PA in patients with symptomatic severe AS.

METHODS

In a cohort of patients with symptomatic severe AS and preserved ejection fraction, we examined the associations between frailty, visceral fat depots and bioelectrical impedance analysis (BIA) derived phase angle (PA); and between visceral fat and PA. Frailty was defined according the Fried et al. scale criteria and the body fat distribution was determined by multidetector computed tomography and by BIA.

RESULTS

Of the fifty-five included patients, 26 were frail (47%). Adjusting for age and gender, frailty was associated with indexed epicardial adipose tissue volume (EATVi) (the odds of frailty increased 4.1-fold per additional 100 cm3/m2 of EAT [95% confidence interval (CI) of 1.03 to 16.40, p=0.04] and with PA (OR of 0.50, 95% CI, 0.26 to 0.97, p=0.04), but not with body mass index (BMI), waist circumference (WC), indexed total, visceral and subcutaneous abdominal fat areas (TAFAi, VAFAi and SAFAi) nor with indexed mediastinal adipose tissue volume (MATVi). In an age and gender adjusted linear model, PA was inversely correlated with EATVi (β=-0.008, 95% CI, -0.016 to -0.001, p=0.03), but not with BMI, WC, nor with MATVi, VAFAi, SAFAi and TAFAi.

CONCLUSIONS

In patients with symptomatic severe AS, EATVi is associated with frailty, independently of age and gender, but not with MAFVi or VAFAi. Moreover, frailty and EATVi are associated with impaired cell membrane integrity and function assessed by PA.

Diagnostic Accuracy of 2-Dimensional Computed Tomography for Articular Involvement and Fracture Pattern of Posterior Malleolar Fractures

BACKGROUND

Up to 44% of ankle fractures have involvement of the posterior tibial margin. Fracture size and morphology are important factors to guide treatment of these fragments, but reliability of plain radiography in estimating size is low. The aim of the current study was to evaluate the accuracy of 2-dimensional computed tomography (2DCT) in the assessment of posterior malleolar fractures. Additionally, the diagnostic accuracy of 2DCT and its value in preoperative planning was evaluated.

METHODS

Thirty-one patients with 31 ankle fractures including a posterior malleolar fragment were selected. Preoperative CT scans were analyzed by 50 observers from 23 countries. Quantitative 3-dimensional CT (Q3DCT) reconstructions were used as a reference standard.

RESULTS

Articular involvement of the posterior fragment was overestimated on 2DCT by factors 1.6, 1.4, and 2.2 for Haraguchi types I, II, and III, respectively. Interobserver agreement on operative management ("to fix, or not to fix?") was substantial (κ = 0.69) for Haraguchi type I fractures, fair (κ = 0.23) for type II fractures, and poor (κ = 0.09) for type III fractures. 2DCT images led to a change in treatment of the posterior malleolus in 23% of all fractures. Surgeons would operatively treat type I fractures in 63%, type II fractures in 67%, and type III fractures in 22%.

CONCLUSION

Surgeons overestimated true articular involvement of posterior malleolar fractures on 2DCT scans. 2DCT showed some additional value in estimating the involved articular surface when compared to plain radiographs; however, this seemed not yet sufficient to accurately read the fractures. Analysis of the CT images showed a significant influence on choice of treatment in 23% with a shift toward operative treatment in 12% of cases compared to evaluating plain lateral radiographs alone.

LEVEL OF EVIDENCE

Level III, comparative study.

The lanthipeptides of Bacillus methylotrophicus and their association with genomic islands

Bacillus methylotrophicus strains are known for their potential as plant-growth promoters and as microbial pesticides that effectively control plant diseases caused by bacteria and fungi. Over the past few years, a wide diversity of their secondary metabolites has been extensively characterized. Among these are the RiPPs lanthipeptides, which are an important and growing group of notable compounds. The increasing interest in B. methylotrophicus species, accompanied by the development of high throughput sequencing techniques, has resulted in a substantial number of full genomes being available. Here, an in silico analysis was performed on these genomes in order to survey the presence of lanthipeptide biosynthetic clusters. It was found that the pan genome of B. methylotrophicus only encoded the biosynthesis of mersacidin and amylolysin, which are lanthipeptides with antibacterial activity. However, the amylolysin gene cluster identified was comprised of more genetic elements than those previously described, and it had certain features of two-peptide lantibiotics. Additionally, it was also established that the association of lanthipeptides with genomic islands (GIs) was not confined to mersacidin. This was also found for the amylolysin cluster as well as other class I and class II lanthipeptides, supporting the idea that their production is probably related to functional adaptation.

Guesstimation of posterior malleolar fractures on lateral plain radiographs

BACKGROUND

Accurate assessment of articular involvement of the posterior malleolar fracture fragments in ankle fractures is essential, as this is the leading argument for internal fixation. The purpose of this study is to assess diagnostic accuracy of measurements on plain lateral radiographs.

METHODS

Quantification of three-dimensional computed tomography (Q-3D-CT) was used as a reference standard for true articular involvement (mm(2)) of posterior malleolar fractures. One-hundred Orthopaedic Trauma surgeons were willing to review 31 trimalleolar ankle fractures to estimate size of posterior malleolus and answer: (1) what is the involved articular surface of the posterior malleolar fracture as a percentage of the tibial plafond? and (2) would you fix the posterior malleolus?

RESULTS

The average posterior malleolar fragment involved 13.5% (SD 10.8) of the tibial plafond articular surface, as quantified using Q-3D-CT. The average involvement of articular surface of the posterior malleolar fragment, as estimated by 100 observers on plain radiographs was 24.4% (SD 10.0). The factor 1.8 overestimation of articular involvement was statistically significant (p<0.001). Diagnostic accuracy of measurements on plain lateral radiographs was 22%. Interobserver agreement (ICC) was 0.61. Agreement on operative fixation, showed an ICC of 0.54 (Haraguchi type I=0.76, Haraguchi type II=0.40, Haraguchi type III=0.25).

CONCLUSIONS

Diagnostic accuracy of measurements on plain lateral radiographs to assess articular involvement of posterior malleolar fractures is poor. There is a tendency to misjudge posteromedial involvement (Haraguchi type II).

Wine fermentation microbiome: a landscape from different Portuguese wine appellations

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism

Aeromonas molluscorum Av27 cells were exposed to 0, 5 and 50 μM of TBT and the respective transcriptomes were obtained by pyrosequencing. Gene Ontology revealed that exposure to 5 μM TBT results in a higher number of repressed genes in contrast with 50 μM of TBT, where the number of over-expressed genes is greater. At both TBT concentrations, higher variations in gene expression were found in the functional categories associated with enzymatic activities, transport/binding and oxidation-reduction. A number of proteins are affected by TBT, such as the acriflavin resistance protein, several transcription-related proteins, several Hsps, ABC transporters, CorA and ZntB and other outer membrane efflux proteins, all of these involved in cellular metabolic processes, important to maintain overall cell viability. Using the STRING tool, several proteins with unknown function were related with others involved in degradation processes, such as the pyoverdine chromophore biosynthetic protein, that has been described as playing a role in the Sn-C cleavage of organotins. This approach has allowed a better understanding of the molecular effects of exposure of bacterial cells to TBT. Furthermore it contributes to the knowledge of the functional genomic aspects of bacteria exposed to this pollutant. Furthermore, the transcriptomic data gathered, and now publically available, constitute a valuable resource for comparative genome analysis.

The generalist Inga subnuda subsp. luschnathiana (Fabaceae): negative effect of floral visitors on reproductive success?

Inga species are characterised by generalist or mixed pollination system. However, this feature does not enhance reproductive rates in species with very low fruit set under natural conditions. Some ecological and genetic factors are associated with this feature, and to test the effect of massive visits on pollination success in Inga subnuda subsp. luschnathiana, we studied the efficacy of polyads deposited on stigmas of flowers isolated from visitors and polyads exposed to visitors. The proportion of polyads fixed in stigmas decreased after exposure to visitors (24 h) in comparison to stigmas isolated from visitors (hummingbirds, bees, wasps, hawkmoths and bats), and fruit set was very low. Furthermore, nectar production, sugar composition and other floral biology traits were evaluated. Increased nectar production, sugar availability and sucrose dominance during the night indicates adaptation to nocturnal visitors and supports their role as main pollinators; although the brush-flower morphology, time of anthesis, nectar dynamics and chemical composition also allow daytime visitors. Thus the species is an important resource for a diverse group of floral visitors. We conclude that excess visits (diurnal and nocturnal) are responsible for the decrease in fixed polyads in stigmas of I. subnuda subsp. luschnathiana flowers, thus contributing, with others factors, to its low fruit set. Therefore, the generalist pollination system does not result in reproductive advantages because the low fruit set in natural conditions could be the result of a negative effect of visitors/pollinators.

Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities

In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.

Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen

The results of high-resolution whole-genome sequencing data provide compelling evidence that Mycoplasma amphoriforme produces chronic relapsing infection and, importantly, is transmitted in a hospital environment.

Background. Mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community.

Methods. The bacterial load was estimated in sequential sputum samples from 9 patients by quantitative polymerase chain reaction. The genomes of all available isolates, originating from patients in the United Kingdom, France, and Tunisia, were sequenced along with the type strain. Genomic data were assembled and annotated, and a high-resolution phylogenetic tree was constructed.

Results. By using high-resolution whole-genome sequencing (WGS) data, we show that patients can be chronically infected with M. amphoriforme manifesting as a relapsing-remitting bacterial load, interspersed by periods when the organism is undetectable. Importantly, we demonstrate transmission of strains within a clinical environment. Antibiotic resistance mutations accumulate in isolates taken from patients who received multiple courses of antibiotics.

Conclusions. Mycoplasma amphoriforme isolates form a closely related species responsible for a chronic relapsing and remitting infection in PAD patients in the United Kingdom and from immunocompetent patients in other countries. We provide strong evidence of transmission between patients attending the same clinic, suggesting that screening and isolation may be necessary for susceptible patients. This work demonstrates the critical role that WGS can play in rapidly unraveling the biology of a novel pathogen.

Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites

The deep-sea hydrothermal vent mussel Bathymodiolus azoricus is a symbiont bearing bivalve that is found in great abundance at the Menez Gwen and Lucky Strike hydrothermal vent sites and in close vicinity of the Azores region near the Mid-Atlantic Ridge (MAR). The physiological relationships that vent mussels have developed with their physical and chemical environments are likely to influence global gene expression profiles providing thus the means to investigate distinct biological markers predicting the origin of Bathymodiolus sp. irrespectively of their geographical localization. Differences found at gene expression levels, and between fluorescence in situ hybridization (FISH) and 16S rRNA amplicon sequencing results provided experimental evidence for the distinction of both Menez Gwen and Lucky Strike vent mussel individuals based on bacterial and vent mussel gene expression signatures and on the constitutive distribution and relative abundance of endosymbiotic bacteria within gill tissues. Our results confirmed the presence of methanotroph endosymbionts in Menez Gwen vent mussels whereas Lucky Strike specimens seem to harbor a different bacterial morphotype when a methane monooxygenase gene specific probe was used. No qualitative differences could be visualized between Menez Gwen and Lucky Strike individuals when tested with a sulfur-oxidizing-related probe. Quantitative PCR (qPCR) studies revealed different gene expression profiles in both Menez Gwen and Lucky Strike mussel gill tissues for the immune genes selected. Genes encoding transcription factors presented noticeably low levels of fold expression whether in Menez Gwen or Lucky Strike animals whereas the genes encoding effector molecules appeared to have higher levels expression in gill tissues from Menez Gwen animals. The peptidoglycan recognition molecule encoding gene, PGRP, presented the highest level of transcriptional activity among the genes analyzed in Menez Gwen mussel gill tissues, seconded by carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both Menez Gwen and Lucky Strike mussel gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated, in Lucky Strike samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between Menez Gwen and Lucky Strike animals. A differential expression analysis of bacterial genes between Menez Gwen and Lucky Strike mussels indicated a clear expression signature in the latter animal gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at an unpredicted conservation of endosymbiont bacterial loads between Menez Gwen and Lucky Strike samples. Taken together, our results support the hypothesis that B. azoricus exhibits different transcriptional statuses while living in distinct hydrothermal vent sites may result in distinct gene expressions because of physico-chemical and/or symbiont densities differences.

The role of targeted BRCA1/BRCA2 mutation analysis in hereditary breast/ovarian cancer families of Portuguese ancestry

We report the analysis of altogether 1050 suspected hereditary breast/ovarian cancer (HBOC) families, 524 fully screened for BRCA1/BRCA2 mutations and 526 tested only for the most common mutations. Of the 119 families with pathogenic mutations, 40 (33.6%) had the BRCA2 c.156_157insAlu rearrangement and 15 (12.6%) the BRCA1 c.3331_3334del mutation, the former being specific of Portuguese ancestry and the latter showing a founder effect in Portugal. Interestingly, the two most common mutations were found in a significant proportion of the HBOC families with an a priori BRCAPRO mutation probability <10%. We recommend that all suspected HBOC families from Portugal or with Portuguese ancestry, even those fulfilling moderately stringent clinical-criteria for genetic testing, should be specifically analyzed for the two most common BRCA1/BRCA2 founder mutations, and we here present a simple method for this first tier test. Screening of the entire coding regions of BRCA1 and BRCA2 should subsequently be offered to those families with a mutation probability ≥10% if none of those founder mutations are found.

Large foot schwannoma with bone invasion - a case report

A rare case of a large foot schwannoma with an intraosseous component is presented. Due to suspicion of malignancy, an amputation had previously been proposed. When the patient presented to us, the prolonged clinical course as well as some elements of the imaging exams suggested benignancy and we decided for complete tumor excision. Intraoperative findings supported the benign character of the neoplasm and pathology would later confirm the diagnosis of a benign schwannoma. The outcome, at 18 months of follow-up was a fully functional limb. Recurrence must still be considered but malignant transformation is very rare in a solitary schwannoma and can be discounted. Solitary benign schwannomas have a negligible malignization potential independently of their size or osseous component. When benignancy is considered, primary total tumor excision, as part of a staged procedure, is a safe approach. It allows for a thorough pathologic examination and eventually for a definitive treatment.

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background

Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management.

Results

We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org.

Conclusions

This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Unravelling the diversity of grapevine microbiome

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

MOSAL: software tools for multiobjective sequence alignment

: Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of these alignments provide a potential explanation of the relationship between the sequences. We introduce MOSAL, a software tool that provides an open-source implementation and an on-line application for multiobjective pairwise sequence alignment.