Different guidelines for pre-exposure prophylaxis (PrEP) eligibility estimate HIV risk differently: an incidence study in a cohort of HIV-negative men who have sex with men, Portugal, 2014-2018

IntroductionGuidelines for pre-exposure prophylaxis (PrEP) provide criteria to identify individuals at higher risk of HIV infection. We compared the ability to predict HIV seroconversion of four guidelines: the World Health Organization (WHO), the United States Public Health Service and Centers for Disease Control and Prevention (US CDC), the European AIDS Clinical Society (EACS) and the Portuguese National Health Service (PNHS).AimWe aimed to measure the association between guideline-specific eligibility and HIV seroconversion.MethodsWe studied 1,254 participants from the Lisbon Cohort of men who have sex with men with at least two evaluations between March 2014 and March 2018, corresponding to 1,724.54 person-years (PY) of follow-up. We calculated incidence rates (IR) according to each guideline eligibility definition and incident rate ratios (IRR) to test the association between eligibility at baseline and HIV seroconversion.ResultsWe found 28 incident cases (IR: 1.62/100 PY; 95% confidence interval (CI) 1.12-2.35). Guidelines' sensitivity varied from 60.7% (EACS) to 85.7% (PNHS) and specificity varied from 31.8% (US CDC) to 51.5% (EACS). IR was highest among those defined as eligible by the PNHS guideline (2.46/100 PY; IRR = 4.61; 95% CI: 1.60-13.27) and lowest for the WHO guideline (1.89/100 PY; IRR = 1.52; 95% CI: 0.69-3.35).ConclusionsBeing identified as eligible for PrEP was associated with a higher risk of infection. The magnitude of risk varied according to the guideline used. However, the number of HIV infections identified among ineligible participants highlights the potential for missing people who need PrEP.

Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature

Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.

Deep learning for drug response prediction in cancer

Predicting the sensitivity of tumors to specific anti-cancer treatments is a challenge of paramount importance for precision medicine. Machine learning(ML) algorithms can be trained on high-throughput screening data to develop models that are able to predict the response of cancer cell lines and patients to novel drugs or drug combinations. Deep learning (DL) refers to a distinct class of ML algorithms that have achieved top-level performance in a variety of fields, including drug discovery. These types of models have unique characteristics that may make them more suitable for the complex task of modeling drug response based on both biological and chemical data, but the application of DL to drug response prediction has been unexplored until very recently. The few studies that have been published have shown promising results, and the use of DL for drug response prediction is beginning to attract greater interest from researchers in the field. In this article, we critically review recently published studies that have employed DL methods to predict drug response in cancer cell lines. We also provide a brief description of DL and the main types of architectures that have been used in these studies. Additionally, we present a selection of publicly available drug screening data resources that can be used to develop drug response prediction models. Finally, we also address the limitations of these approaches and provide a discussion on possible paths for further improvement. Contact:  mrocha@di.uminho.pt.

Pre-exposure prophylaxis in a sexual health clinic for Men who Have Sex with Men in Portugal

Background

Pre-exposure prophylaxis (PrEP) is defined as the use of antiretroviral drugs to prevent HIV acquisition in uninfected individuals. Recognizing the increasing use of informal PrEP in Portugal, CheckpointLX, a community clinic targeted for MSM in Lisbon, Portugal, began offering counselling and follow-up services prior to formal introduction. This study aims to characterize PrEP users attending CheckpointLX before formal PrEP introduction in Portugal, and those who were referred to PrEP in the National Health Service (NHS) following formal approval of PrEP.

Methods

Data was collected by peer counsellors between May 2015 and September 2018 and inserted in a database. Medical care followed EACS recommendations for PrEP eligibility, initiation and follow up. For formal PrEP, the General-Directorate for Health’s PrEP guidelines checklist was used.

Results

Until the end of May 2018, CheckpointLX had a total of 90 appointments for Wild PrEP, of which 64 (71%) were first time visits. As for the 380 service users referred to the NHS, most were Portuguese (N = 318, 84%), and the mean age was 31 (8.9) years old. Condomless sex in the last six months with partners of unknown HIV status was the most common eligibility criteria (N = 59, 83%).

Conclusions

PrEP delivery should be complemented with effective information on the importance of immunization and education on safer practices of drug administration, in the scope of broader preventive sexual health care. Much remains to be done in Portugal to ensure that PrEP is available to those who need it the most. Offering PrEP at community clinics could be a first step.

Key messages

Condomless sex in the last six months with partners of unknown HIV status was the most common eligibility criteria for PrEP. PrEP delivery should be complemented with effective information on the importance of immunization and education on safer practices of drug administration.

Prevalence of gonorrhea and chlamydia in a community clinic for Men who Have Sex with Men in Portugal

Background

Men who have sex with men (MSM) are at greater risk for sexually transmitted infections (STIs). Data on MSM chlamydia and gonorrhea prevalence estimates and associated risk factors is scarce. To our knowledge, this is the first study to describe the prevalence and the determinants of both chlamydia and gonorrhea infections in MSM in Portugal.

Methods

We conducted a cross-sectional study using data from 1,832 visits to CheckpointLX, a community-based center for screening blood-borne viruses and other STIs in MSM.

Results

Overall prevalence of chlamydia or gonorrhea in our sample was 16.05%, with 14.23% coinfection and 40.73% asymptomatic presentation among those testing positive. Anorectal infection was most common for chlamydia (67.26%), followed by urethral (24.78%) and oral (19.47%) infection. Oral infection was most common for gonorrhea (55.63%), followed by anal (51.25%) and urethral (17.50%) infection. In multivariate analyses, young age (U = 94684, p = 0.014), being foreign-born (χ2=11.724, p = 0.003), reporting STI symptoms (χ2=5.316, p = 0.021), inhaled drug use (χ2=4.278, p = 0.039) and having a higher number of concurrent (χ2=18.769, p < 0.001) or total (χ2=5.988, p = 0.050) sexual partners were each associated with higher rates of chlamydia or gonorrhea infection.

Conclusions

Young and migrant MSM are a vulnerable population to STIs, as are those who use inhaled drugs and those with a higher number of concurrent or total sexual partners. Although Portugal has no guidelines on chlamydia and gonorrhea screening, our results point towards a need for greater awareness about the importance of high frequency screening for those at increased risk (i.e. every 3 to 6 months).

Key messages

Higher prevalence was found in young and migrant MSM, those with higher number of concurrent or total sexual partners, and those who use inhaled drugs. There is a need for greater awareness about the importance of high frequency STI screening for MSM at increased risk.

WebSpecmine: A Website for Metabolomics Data Analysis and Mining

Metabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool's implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies.

SamPler - a novel method for selecting parameters for gene functional annotation routines

BACKGROUND

As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotations fast and efficient. However, the (high) quality of such annotations must be guaranteed, as this is the first indicator of the genomic potential of every organism. Automatic procedures help accelerating the annotation process, though decreasing the confidence and reliability of the outcomes. Manually curating a genome-wide annotation of genes, enzymes and transporter proteins function is a highly time-consuming, tedious and impractical task, even for the most proficient curator. Hence, a semi-automated procedure, which balances the two approaches, will increase the reliability of the annotation, while speeding up the process. In fact, a prior analysis of the annotation algorithm may leverage its performance, by manipulating its parameters, hastening the downstream processing and the manual curation of assigning functions to genes encoding proteins.

RESULTS

Here SamPler, a novel strategy to select parameters for gene functional annotation routines is presented. This semi-automated method is based on the manual curation of a randomly selected set of genes/proteins. Then, in a multi-dimensional array, this sample is used to assess the automatic annotations for all possible combinations of the algorithm's parameters. These assessments allow creating an array of confusion matrices, for which several metrics are calculated (accuracy, precision and negative predictive value) and used to reach optimal values for the parameters.

CONCLUSIONS

The potential of this methodology is demonstrated with four genome functional annotations performed in merlin, an in-house user-friendly computational framework for genome-scale metabolic annotation and model reconstruction. For that, SamPler was implemented as a new plugin for the merlin tool.

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Summary

CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs.

Availability and implementation

The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp.

Prevalence of gonorrhea and chlamydia in a community clinic for men who have sex with men in Lisbon, Portugal

Men who have sex with men (MSM) are at greater risk for sexually transmitted infections (STIs). Data on MSM chlamydia and gonorrhea prevalence estimates and associated risk factors are scarce. To our knowledge, this is the first study to describe the prevalence and the determinants of both chlamydia and gonorrhea infections in MSM in Portugal. We conducted a cross-sectional study using data from 1832 visits to CheckpointLX, a community-based center for screening blood-borne viruses and other STIs in MSM. Overall prevalence of chlamydia or gonorrhea in our sample was 16.05%, with 14.23% coinfection and 40.73% asymptomatic presentation among those testing positive. Anorectal infection was most common for chlamydia (67.26%), followed by urethral (24.78%) and oral (19.47%) infection. Oral infection was most common for gonorrhea (55.63%), followed by anal (51.25%) and urethral (17.50%) infection. In multivariate analyses, young age (U = 94684, p = 0.014), being foreign-born (χ² = 11.724, p = 0.003), reporting STI symptoms (χ² = 5.316, p = 0.021), inhaled drug use (χ² = 4.278, p = 0.039) and having a higher number of concurrent (χ² = 18.769, p < 0.001) or total (χ² = 5.988, p = 0.050) sexual partners were each associated with higher rates of chlamydia or gonorrhea infection. Young and migrant MSM are a vulnerable population to STIs, as are those who use inhaled drugs and those with a higher number of concurrent or total sexual partners. Although Portugal has no guidelines on chlamydia and gonorrhea screening, our results point toward a need for greater awareness about the importance of high-frequency screening for those at increased risk (i.e., every three to six months).

Genomic imbalances defining novel intellectual disability associated loci

Background

High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID).

Results

We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed.

Conclusions

Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients.

Electronic supplementary material

The online version of this article (10.1186/s13023-019-1135-0) contains supplementary material, which is available to authorized users.

Pre-Exposure Prophylaxis Counseling in a Community Sexual Health Clinic for Men Who Have Sex with Men in Lisbon, Portugal

INTRODUCTION

Pre-exposure prophylaxis is defined as the use of antiretroviral drugs to prevent HIV acquisition in uninfected individuals. Recognizing the increasing use of informal pre-exposure prophylaxis in Portugal, CheckpointLX, a community clinic targeted to men who have sex with men in Lisbon, Portugal, began offering counselling and follow-up services prior to formal introduction. This study aims to characterize pre-exposure prophylaxis users attending CheckpointLX before formal pre-exposure prophylaxis introduction in Portugal, and those who were referred to pre-exposure prophylaxis in the National Health Service following formal approval of pre-exposure prophylaxis.

MATERIAL AND METHODS

Data was collected by peer counsellors between May 2015 and September 2018 and inserted in a database. Medical care followed the European AIDS Clinical Society recommendations for pre-exposure prophylaxis eligibility, initiation and follow-up. For formal pre-exposure prophylaxis, the General-Directorate for Health's Pre-exposure Prophylaxis guidelines checklist was used.

RESULTS

Until the end of May 2018, CheckpointLX had a total of 90 appointments for wild pre-exposure prophylaxis, of which 64 (71%) were first time visits. As for the 380 service users referred to the National Health Service, most were Portuguese (n = 318, 84%), and the mean age was 31 (8.9) years old. Condomless sex in the last six months with partners of unknown HIV status was the most common eligibility criteria (n = 59, 83%).

DISCUSSION

Pre-exposure prophylaxis delivery should be complemented with effective information on the importance of immunization and education on safer practices of drug administration, in the scope of broader preventive sexual health care.

CONCLUSION

Much remains to be done in Portugal to ensure that pre-exposure prophylaxis is available to those who need it the most. Offering pre-exposure prophylaxis at community clinics could be a first step.

Comparison of pathway analysis and constraint-based methods for cell factory design

BACKGROUND

Computational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factories. Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when compared with simulation-based CSOMs. However, since both types of methods have different underlying principles, they also imply different ways to formulate metabolic engineering problems, posing an obstacle when comparing their outputs.

RESULTS

In this work, we perform an in-depth analysis of potential strategies that can be obtained with both methods, providing a critical comparison of performance, robustness, predicted phenotypes as well as strategy structure and size. To this end, we devised a pipeline including enumeration of strategies from evolutionary algorithms (EA) and minimal cut sets (MCS), filtering and flux analysis of predicted mutants to optimize the production of succinic acid in Saccharomyces cerevisiae. We additionally attempt to generalize problem formulations for MCS enumeration within the context of growth-coupled product synthesis. Strategies from evolutionary algorithms show the best compromise between acceptable growth rates and compound overproduction. However, constrained MCSs lead to a larger variety of phenotypes with several degrees of growth-coupling with production flux. The latter have proven useful in revealing the importance, in silico, of the gamma-aminobutyric acid shunt and manipulation of cofactor pools in growth-coupled designs for succinate production, mechanisms which have also been touted as potentially useful for metabolic engineering.

CONCLUSIONS

The two main groups of CSOMs are valuable for finding growth-coupled mutants. Despite the limitations in maximum growth rates and large strategy sizes, MCSs help uncover novel mechanisms for compound overproduction and thus, analyzing outputs from both methods provides a richer overview on strategies that can be potentially carried over in vivo.

Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design

Immune responses mediated by T cells are aimed at specific peptides, designated T cell epitopes, that are recognized when bound to human leukocyte antigen (HLA) molecules. The HLA genes are remarkably polymorphic in the human population allowing a broad and fine-tuned capacity to bind a wide array of peptide sequences. Polymorphisms might generate neoepitopes by impacting the HLA-peptide interaction and potentially alter the level and type of generated T cell responses. Multiple algorithms and tools based on machine learning (ML) have been implemented and are able to predict HLA-peptide binding affinity with considerable accuracy. Challenges in this field include the availability of adequate epitope datasets for training and benchmarking and the development of fully integrated pipelines going from next-generation sequencing to neoepitope prediction and quality analysis metrics. Effectively predicting neoepitopes from in silico data is a demanding task that has been facilitated by ML and will be of great value for the future of personalized immunotherapies against cancer and other diseases.

Enhancing Low-Intensity Coaching in Parent Implemented Early Start Denver Model Intervention for Early Autism: A Randomized Comparison Treatment Trial

Short-term low intensity parent implemented intervention studies for toddlers with autism spectrum disorder (ASD) have found it difficult to demonstrate significantly improved developmental scores or autism severity compared to community treatment. We conducted a randomized comparative intent-to-treat study of a parent implemented intervention to (1) test the effects of an enhanced version on parent and child learning, and (2) evaluate the sensitivity to change of proximal versus distal measures of child behavior. We randomized 45 children with ASD, 12-30 months of age, into one of two versions of parent-implemented Early Start Denver Model (P-ESDM), the basic model, in which we delivered 1.5 h of clinic-based parent coaching weekly, and an enhanced version that contained three additions: motivational interviewing, multimodal learning tools, and a weekly 1.5-h home visit. We delivered the intervention for 12 weeks and measured child and parent change frequently in multiple settings. We found a time-by-group interaction: parents in the enhanced group demonstrated significantly greater gains in interaction skills than did parents in the non-enhanced group. Both interventions were associated with significant developmental acceleration; however, child outcomes did not differ by group. We found a significant relationship between degree of change in parental interaction skill and rate of children's improvement on our proximal measure. Parents in both groups reported satisfaction with the intervention. These findings suggest that parent skills improved more in the enhanced group than the comparison group. Children in the two groups showed similar improvements. Rate of individual parent learning was associated with greater individual child progress on a measure quite proximal to the treatment, though not on standardized assessments.

Comparative Analysis of the Adhesive Proteins of the Adult Stalked Goose Barnacle Pollicipes pollicipes (Cirripedia: Pedunculata)

Adhesion in barnacles is still poorly understood. The cement gland secretes an insoluble multi-protein complex, which adheres very strongly to a variety of substrates in the presence of water. This adhesion mechanism is bioinspiring for the engineering of new adhesive materials, but to replicate this adhesive system, the genes coding for the cement constitutive proteins must be identified and elucidated, and their products characterised. Here, the complete sequences of three cement protein (CP) genes (CP-100K, CP-52K, and CP-19K) isolated from the cement gland of the stalked barnacle Pollicipes pollicipes (order Scalpelliformes) were obtained using RACE PCR. The three genes were compared to the 23 other acorn barnacle CP genes so far sequenced (order Sessilia) to determine common and differential patterns and molecular properties, since the adhesives of both orders have visibly different characteristics. A shotgun proteomic analysis was performed on the cement, excreted at the membranous base of specimens, where the products of the three genes sequenced in the gland were identified, validating their function as CPs. A principal component analysis (PCA) was performed, to cluster CPs into groups with similar amino acid composition. This analysis uncovered three CP groups, each characterised by similar residue composition, features in secondary structure, and some biochemical properties, including isoelectric point and residue accessibility to solvents. The similarity among proteins in each defined group was low despite comparable amino acid composition. PCA can identify putative adhesive proteins from NGS transcriptomic data regardless of their low homology. This analysis did not highlight significant differences in residue composition between homologous acorn and stalked barnacle CPs. The characteristics responsible for the structural differences between the cement of stalked and acorn barnacles are described, and the presence of nanostructures, such as repetitive homologous domains and low complexity regions, and repetitive β-sheets are discussed relatively to self-assembly and adhesion.

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions

Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism.

Antimicrobial resistance and molecular characteristics of Neisseria gonorrhoeae isolates from men who have sex with men

OBJECTIVES

To analyze the susceptibility of Neisseria gonorrhoeae isolates to penicillin (Pen), cefixime (Cfm), ceftriaxone (Cro), tetracycline (Tet), ciprofloxacin (Cip), azithromycin (Azm), and spectinomycin (Spt), and to verify the presence of mutations in resistance genes.

METHODS

Antibiotic susceptibility testing was performed by Etest method on 30 N. gonorrhoeae isolates collected from the MSM (men who have sex with men) population. PCR and DNA sequencing were performed to identify mutations within the penA, mtrR, gyrA, and parC genes in intermediately resistant and fully resistant isolates.

RESULTS

N. gonorrhoeae isolates showed intermediate or full resistance to Pen (73%), Cfm (3%), Tet (60%), Cip (37%), and Azm (13%). One isolate with resistance to Cfm presented a penicillin-binding protein 2 (PBP2) mosaic XXXIV. All isolates with intermediate or full resistance to Pen (except at PBP2 mosaic) presented a D345a in PBP2. All Cip-resistant isolates had an S91F in the gyrA gene together with mutations in the parC gene. All intermediate or fully resistant isolates to substrates of the MtrCDE efflux pump had an A39T or G45D mutation in the mtrR gene or an adenine deletion within the mtrR promoter. One isolate presented a Neisseria meningitidis-like mtrR promoter sequence.

CONCLUSIONS

The results of this study are consistent with the findings of other studies and reinforce the importance of the expedient development of new therapeutic options.