The increasing global burden of morbidity and mortality from chronic diseases related to poor diet quality, coupled with the unsustainable depletion of vital planetary resources by current food production systems, threatens future food security and highlights the urgent need to transition to high-quality plant-based diets as a viable solution to mitigate economic, health, and environmental challenges. Taking into consideration the significant role that fermented vegetables may play as a sustainable, healthy, long-lasting, and plant-based nutritional resource, this narrative review analyzes their production and benefits. For this purpose, the mechanisms of the fermentation process are explored, along with the importance of probiotic cultures in plant-based fermented foods, and with the implications of fermentation on food safety within the broader framework of low-impact, organic, plant-derived nutrition. Additionally, the health benefits of fermented vegetables and probiotics are examined, including their effects on mental health. Vegetable fermentation is a versatile method for enhancing food preservation, nutritional quality, and safety. This ancient practice prolongs the shelf life of perishable items, reduces the toxicity of raw ingredients, and improves digestibility. Specific starter cultures, particularly lactic acid bacteria, are essential for controlling fermentation, ensuring safety, and maximizing health benefits. Fermented vegetables, rich in probiotics, support gut health and immune function. Emerging research indicates their potential to alleviate adverse mental health symptoms such as stress and anxiety, highlighting their significance in modern dietary guidelines and chronic health management.
Simpler biological systems should be easier to understand and engineer. One way to achieve biological simplicity is through genome minimization. Here we have looked for genomic islands in the fresh water cyanobacterium Synechococcus elongatus PCC 7942 that could be used as targets for deletion for genome minimization. By using a combination of methods we have identified 184 genes that have been horizontally transferred into the genome of S. elongatus plus 127 ORFans (Figure 1). These genes have a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of a highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. We have also corroborated the existence of the largest genomic island by its lack of coverage among metagenomic sequences from a fresh water microbialite. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologous, suggesting a role for horizontal gene transfer in the evolution of sensory systems in this cyanobacteria. In parallel we have identified 1401 highly conserved genes that might be essential for cell survival and should not be deleted. These two datasets (variable and conserved genes) comprises ~11.8% and 53.6% of annotated genes in S. elongatus. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a simpler photoautotrophic cell.
Background CRF19_cpx is a complex circulating recombination form (CRF) of HIV-1. We describe the characteristics of an outbreak of the CRF19_cpx variant among treatment-naïve patients in southern Spain. Methods The study was undertaken at the Virgen de la Victoria Hospital, a reference centre for the analysis of HIV-1 genotype in Malaga (Spain). Subtyping was performed through REGA v3.0 and the relationship of our CRF19_cpx sequences, among themselves and regarding other reference sequences from the same variant, was defined by phylogenetic analysis. We used PhyML program to perform a reconstruction of the phylogeny by Maximum Likelihood method as well as further confirmation of the transmission clusters by Bayesian inference. Additionally, we collected demographic, clinical and immunovirological data. Results Between 2011 and 2016, we detected 57 treatment-naïve patients with the CRF19_cpx variant. Of these, 55 conformed a very well-defined transmission cluster, phylogenetically close to CRF19_cpx sequences from the United Kingdom. The origin of this subtype in Malaga was dated between 2007 and 2010. Over 50% of the patients presented the non-nucleoside reverse transcriptase inhibitor G190A resistance mutation. This variant was mostly represented by young adult Spanish men who had sex with men. Almost half of them were recent seroconverters, though a similar percentage was diagnosed at a late state of HIV infection. Five cases of AIDS and one non-AIDS defined death occurred during follow-up. The majority of patients treated with first-line combination antiretroviral therapy (ART) responded. Conclusions We report the largest HIV-1 CRF19_cpx cohort of treatment-naïve patients outside Cuba, almost all emerging as an outbreak in the South of Spain. Half the cases had the G190A resistance mutation. Unlike previous studies, the variant from Malaga seems less pathogenic, with few AIDS events and an excellent response to ART.
Abstract Integration of molecular, clinical, and demographic data represents a powerful tool to understand the dynamics of local HIV-1 transmission chains (TCs). The aim of our study was the phylogenetic analysis of the TCs within a HIV-1 cohort and the description of the relevant patient data within a TC. We performed a phylogenetic analysis of 757 sequences from newly HIV-1 diagnosed patients in Málaga (Southern Spain) during the period 2004–15. We used partial pol gene sequences in a preliminary phylogenetic reconstruction using the Neighbour Joining method (MEGA v6.06 program). After eliminating branches with bootstrap values <80 per cent, we constructed a new phylogeny by Maximum likelihood method (FastTree program). We considered as TC any cluster with bootstrap values ≥ 90 per cent. Patient sequences within and outside TCs were compared. Resistance mutations in the protease (PR) and reverse transcriptase (RT) sequences were analyzed using the Stanford algorithm. Four hundred and fifty-one out of 757 patients (59.6%) were grouped into fifty-three TCs, seventeen of them with five or more subjects. The largest number of patients associated within a TC was ninety. Patients younger than 40 years [odds ratio (OR) 1.75, 95% confidence interval (95% CI) 1.2–2.4, P = 0.002], men who have sex with men (MSM) (OR 2.14, 95% CI 1.3–3.2, P < 0.0001), non-Spanish (OR 1.48, 95% CI 1.0–2.1, P = 0.038), with a non-B subtype HIV-1 (OR 3.12, 95% CI 2.0–4.8, P < 0.0001), and presenting primary resistance mutations (OR 14.1, 95% CI 3.1–62.6, P = 0.001) were more likely to be associated within a cluster. Ninety-four out of 118 patients (79.6%) with transmission resistance mutations were included in some TC. The most frequent mutations associated with clusters were T69D/N, L210W, and K219E/Q, for NRTIs, K103N, and G190A/S for NNRTIs, and the I54L/M and L90M mutations for PIs. The prevalence for resistance to NNRTIs in TCs was 13.7 per cent. There were two TCs of rarer non-B subtypes: CRF19_cpx, with twenty-one individuals, sixteen of them (76.2%) with mutation G190A; and CRF51_01B with thirty-nine patients, twenty of them with the K103N mutation. Approximately 60 per cent of newly HIV-1 diagnosed patients were included in a TC. Younger patients, MSM, non-Spanish, with non-B subtype HIV-1 and primary resistance mutations were more likely to belong to a cluster. NNRTI mutations were the most frequent ones among patients in TCs. We observed two TCs represented by infrequent non-B subtypes in our area—CRF19_cpx and CRF51_01B—both of which were associated to the transmission of primary resistance.
Abstract Background Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival. Results By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems. Conclusions Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.
We aimed to describe the Hepatitis A virus (HAV) cases that arose in Malaga (Spain) in 2016 and 2017 when the European Centre for Disease Prevention and Control (ECDC) reported several outbreaks among men who have sex with men (MSM). Therefore, we conducted a retrospective study gathering demographic, clinical, and immunological data from the acute HAV patients attending our hospital between March 2016 and December 2017. Additionally, VP1/P2A region was amplified from serum samples, sequenced, and genotyped. We finally performed a phylogenetic analysis, including the HAV strains from the other European outbreaks. A total of 184 HAV cases were reported, with the highest number in March 2017. The cohort mostly comprised Spaniards (81.0%), males (84.8%), and MSM (72.3%), with a median age of 33.0 years (interquartile range (IQR) = 25.0-43.0). Most patients exhibited symptoms. In addition, a successful amplification and sequencing of the VP1/P2A region was performed in 25 out of 106 serum samples (23.6%). All the sequences belonged to the genotype IA, and 20 were phylogenetically related to VRD_521_2016, first described in the United Kingdom (UK). In conclusion, HAV cases emerged in Malaga in 2016 and 2017, showing an epidemic character phylogenetically related to the predominant strain first detected in the UK. Characteristics of the cohort were similar to those from the European outbreaks.
Introduction Sexually transmitted infections (STI) like Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) have been associated with increased risk of HIV acquisition [ 1 ]. It has been also described as a high prevalence of asymptomatic CT and NG infections in men who have sex with men (MSM) [ 2 ]. The aim of this study was to know the prevalence of CT and/or NG infections in asymptomatic HIV‐MSM and the related factors. Materials and Methods Prospective study of a cohort of asymptomatic HIV‐MSM with follow‐up in Malaga (southern Spain) during October 2012–May 2014. Patients with an opportunistic event or who received active antibiotic therapy for CT and/or NG in the previous month were excluded. All of them completed a questionnaire about sexual behaviour, barrier methods and recreational drugs use. Demographical, epidemiological, clinical, analytical and therapeutic data were also collected. Pharyngeal and rectal swabs, and urine samples were collected to be tested for CT and NG by nucleic acid amplification test (c4800 CT/NG. Roche Diagnostics, Mannheim, Germany) [ 3 ]. Statistics analysis: SPSS 17.0. Results 255 patients were asked to participate and 248 of them accepted. Median age was 37.7 (30.6–46.3) years, median time since HIV diagnosis was 47.7 (10.5–104.1) months, and median CD4 cells count was 607 (440–824) cell/µL. There were 195 (78.6%) patients on antiretroviral therapy; 81.5% of them had undetectable viral load. 80.5% of the patients had a past history of STI. Infection by CT and/or NG was diagnosed in 24 (9.7%) patients. Overall four urine samples, two pharyngeal, and 15 rectal ones were positive for CT, and five pharyngeal and five rectal swabs were positive for NG. Two patients were co‐infected by CT and NG: one with CT in urine and both in rectum, another with CT in urine and rectum and NG in pharynx. One patient presented CT in pharynx and rectum, and two patients NG in pharynx and rectum. Positive CT and/or NG tests were only related with detectable HIV viral load (OR 3.08, 95% CI 1.2–7.4; p=0.01). It was not related with sexual behaviour, nor with alcohol or recreational drugs use. Conclusions STI screening had a great acceptance in this population. There was a high prevalence of asymptomatic CT and/or NG infections. Rectum sample was the most effective one. Viral suppression could protect from these STI. Screening should be recommended in HIV‐MSM.
Abstract Background Prader–Willi syndrome (PWS), a genetically determined disorder, the most frequent cause of early onset obesity, is associated with physical and cognitive dysfunctions and behavioural disturbances; these disturbances are frequently treated with psychotropic medication. The aim of this cross‐sectional study was to describe the characteristics of the first large national sample of persons with PWS in Spain and analyse the relationships of those characteristics with key demographic and clinical factors, particularly with obesity and the regular use of psychotropic medication. Methods Participants were recruited among all members of the Spanish Prader–Willi Association who agreed to take part in the study and fulfilled its inclusion criteria. Family and patient demographic features, family size and birth order, intelligence quotient (IQ), anthropometric measures, lifestyle habits, behavioural disturbances (with the Aberrant Behavior Checklist) and clinical data, as well as use of psychotropic drugs and their side effects (with the UKU scale), were collected in genetically confirmed cases of PWS. Bivariate and logistic regression analyses were used for determining the associations of demographic and clinical factors with both obesity and the regular use of psychotropic medication. Results The cohort included 177 participants (aged 6–48 years), that is, 90 (50.8%) males and 87 (49.2%) females. Behavioural disturbances were present in a range of 75% to 93% of participants; psychotropic medication was prescribed to 81 (45.8%) of them. Number of siblings showed a direct correlation with IQ, especially among males, and inappropriate speech was more intense in only‐child females. Obesity was, in parallel, strongly associated with ascending age and with not being currently under growth hormone (GH) treatment. Participants taking any psychotropic medication were characterised by more frequent age ≥30 years, high level of hyperactivity and a psychiatric diagnosis. Conclusions Characterisation of persons with PWS in Spain confirms their physical and behavioural phenotype and supports the long‐term application of GH therapy and the rational use of psychotropic medication.
The presence of transmission clusters (TCs) and their epidemiological characteristics in a treatment-naive cohort of HIV-1 patients in southern Spain over a decade (2004–2015) were evaluated. Protease and reverse transcriptase sequences provided by each genotype test were used in the phylogenetic study, performed first by the neighbor-joining method and then confirmed by Bayesian analysis. We collected clinical, immunovirological, and demographic data for all patients included. Our cohort comprised 757 patients, 428 (56.5%) belonging to a TC. Overall, we found 123 TCs, 21 of them comprising five or more individuals and three with ≥10 sequences. Forty-three TCs (35.0%) remained active. The clustered patients were mainly men (92.8%) who had sex with men (MSM) (81.5%), Spanish (80.6%), and young adults (median age at diagnosis of 32.6 years). They had lower percentages of late diagnosis and AIDS cases (42.1% and 13.6%, respectively), whereas the presence of recent seroconverters (31.1%), HIV-1 B subtypes (79.4%), and transmission drug resistance (20.3%) increased within TCs, with regard to not-clustered individuals. Among the TCs of non-B variants, circulating recombinant forms (CRF) were predominant (87.5%), with the highest frequencies for CRF19_cpx (17.0% of non-B subtype sequences in TCs); CRF02_AG (15.9%); and CRF01_AE (9.1%). In conclusion, over half of our cohort was included within a TC. More than a third of TCs found could be considered active transmission events. Belonging to a TC was related to MSM, Spanish origin, recent seroconversion, high prevalence of resistance mutations, and B HIV subtype. Among the non-B genetic forms in TCs, we found a high prevalence of CRF19_cpx, CRF02_AG, and CRF01_AE variants.
By the middle of 2021, we are still immersed in the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The concurrence of this new pandemic in regions where human immunodeficiency virus (HIV) and tuberculosis (TB) infections possess the same epidemiological consideration, has arisen concerns about the prognosis, clinical management, symptomatology, and treatment of patients with triple infection. At the same time, healthcare services previously devoted to diagnosis and treatment of TB and HIV are being jeopardized by the urgent need of resources and attention for COVID-19 patients. The aim of this review was to collect any article considering the three conditions (HIV, TB, and SARS-CoV-2), included in PubMed/Medline and published in the English language since the beginning of the COVID-19 pandemic. We focused on detailed descriptions of the unusual cases describing the three co-infections. Eighty-four out of 184 publications retrieved met our inclusion criteria, but only three of them reported cases (five in total) with the three concomitant infections. The clinical evolution, management, and therapy of all of them were not different from mild/severe cases with exclusive COVID-19; the outcome was not worse either, with recovery for the five patients. Cases of patients with COVID-19 besides HIV and TB infections are scarce in literature, but studies deliberately embracing the triple infection as a priori inclusion criterion should be carried out in order to provide a complete understanding of joint influence.