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Chlamydia trachomatis; Sexually transmitted infection; Treatment failure Chlamydia trachomatis; Infecció de transmissió sexual; Fracàs del tractament Chlamydia trachomatis; Infección transmitida sexualmente; Fracaso del tratamiento The aim of this multicentre project (seven hospitals across the Spanish National Health Service) was to study the phenotypic and genotypic susceptibility of C. trachomatis to the main antimicrobials used (macrolides, doxycycline, and quinolones) in isolates from patients with clinical treatment failure in whom reinfection had been ruled out. During 2018–2019, 73 clinical isolates were selected. Sixty-nine clinical specimens were inoculated onto confluent McCoy cell monolayers for phenotypic susceptibility testing. The minimum inhibitory concentration for azithromycin and doxycycline was defined as the lowest concentration associated with an at least 95% reduction in inclusion-forming units after one passage in the presence of the antibiotic compared to the initial inoculum for each strain (control). Sequencing analysis was performed for the genotypic detection of resistance to macrolides, analysing mutations in the 23S rRNA gene (at positions 2057, 2058, 2059, and 2611), and quinolones, analysing a fragment of the gyrA gene, and searching for the G248T mutation (Ser83->Ile). For tetracyclines, in-house RT-PCR was used to test for the tet(C) gene. The phenotypic susceptibility testing was successful for 10 isolates. All the isolates had minimum inhibitory concentrations for azithromycin ≤ 0.125 mg/L and for doxycycline ≤ 0.064 mg/L and were considered sensitive. Of the 73 strains studied, no mutations were found at positions T2611C or G248T of the gyrA gene. We successfully sequenced 66 isolates. No macrolide resistance-associated mutations were found at positions 2057, 2058, 2059, or T2611C. None of the isolates carried the tet(C) gene. We found no evidence for genomic resistance in this large, clinically relevant dataset. This study was funded by Instituto de Salud Carlos III (ISCIII) via the project “PI17/01886” and co-funded by the European Union.

The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of microbial virus researchers in Belgium. The sixteen founders are affiliated to fourteen different research entities across academia, industry and government. Its inaugural symposium was held on 23 September 2022 in the Thermotechnical Institute at KU Leuven. The meeting program covered three thematic sessions launched by international keynote speakers: (1) virus-host interactions, (2) viral ecology, evolution and diversity and (3) present and future applications. During the one-day symposium, four invited keynote lectures, ten selected talks and eight student pitches were given along with 41 presented posters. The meeting hosted 155 participants from twelve countries. ispartof: VIRUSES-BASEL vol:15 issue:5 ispartof: location:Switzerland status: published

Chlamydia trachomatis; OmpA genotyping; Sexual behaviour Chlamydia trachomatis; Genotipado ompA; Comportamiento sexual Chlamydia trachomatis; Genotipat ompA; Comportament sexual Chlamydia trachomatis infection is an important public health problem. Our objective was to assess the dynamics of the transmission of this infection, analysing the distribution of circulating ompA genotypes and multilocus sequence types of C. trachomatis in Spain as a function of clinical and epidemiological variables. During 2018 and 2019, we genetically characterized C. trachomatis in tertiary hospitals in six areas in Spain (Asturias, Barcelona, Gipuzkoa, Mallorca, Seville and Zaragoza), with a catchment population of 3.050 million people. Genotypes and sequence types were obtained using polymerase chain reaction techniques that amplify a fragment of the ompA gene, and five highly variable genes (hctB, CT058, CT144, CT172 and pbpB), respectively. Amplicons were sequenced and phylogenetic analysis was conducted. We obtained genotypes in 636/698 cases (91.1%). Overall and by area, genotype E was the most common (35%). Stratifying by sex, genotypes D and G were more common among men, and genotypes F and I among women (p < 0.05). Genotypes D, G and J were more common in men who have sex with men (MSM) than in men who have sex with women (MSW), in whom the most common genotypes were E and F. The diversity index was higher in sequence typing (0.981) than in genotyping (0.791), and the most common sequence types were ST52 and ST108 in MSM, and ST30, ST148, ST276 and ST327 in MSW. Differences in genotype distribution between geographical areas were attributable to differences in population characteristics. The transmission dynamics varied with sexual behaviour: the predominant genotypes and most frequent sequence types found in MSM were different to those detected in MSW and women. This study was funded by Instituto de Salud Carlos III (ISCIII) through the project “PI17/01886”, and co-funded by the European Union.

An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available. ispartof: VIRUSES-BASEL vol:14 issue:10 ispartof: location:Switzerland status: published

Community-onset bloodstream infections (CO-BSI) caused by gram-negative bacilli are common and associated with significant mortality; those caused by Pseudomonas aeruginosa are associated with worse prognosis and higher rates of inadequateempirical antibiotic treatment. The aims of this study were to describe the characteristics of patients with CO-BSI caused by P. aeruginosa, to identify predictors, and to develop a predictive score for P. aeruginosa CO-BSI. Materials/methods: PROBAC is a prospective cohort including patients >14 years with BSI from 26 Spanish hospitals between October 2016 and May 2017. Patients with monomicrobial P. aeruginosa CO-BSI and monomicrobial Enterobacterales CO-BSI were included. Variables of interest were collected. Independent predictors of Pseudomonas aeruginosa CO-BSI were identified by logistic regression and a prediction score was developed. Results: A total of 78patients with P. aeruginosa CO-BSI and 2572 with Enterobacterales CO-BSI were included. Patients with P. aeruginosa had a median age of 70 years (IQR 60-79), 68.8% were male, median Charlson score was 5 (IQR 3-7), and 30-daymortality was 18.5%. Multivariate analysis identified the following predictors of CO-BSI-PA [adjusted OR (95% CI)]: male gender [1.89 (1.14-3.12)], haematological malignancy [2.45 (1.20-4.99)], obstructive uropathy [2.86 (1.13-3.02)], source of infection other than urinary tract, biliary tract or intra-abdominal [6.69 (4.10-10.92)] and healthcare-associated BSI [1.85 (1.13-3.02)]. Anindex predictive of CO-BSI-PA was developed; scores ? 3.5 showed a negative predictive value of 89% and an area under the receiver operator curve (ROC) of 0.66. Conclusions: We did not find a good predictive score of P. aeruginosa CO-BSI due to its relatively low incidence in the overall population. Our model includes variables that are easy to collect in real clinical practice and could be useful to detect patients with very low risk of P. aeruginosa CO-BSI. This work was financed by grants from the Plan Nacional de I + D+i 2013–2016-Instituto de Salud Carlos III (Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades) [PI16/01432]; and Spanish Network for Research in Infectious Diseases (REIPI) [RD16/0016/0001; RD16/0016/0008]; co-financed by the European Development Regional Fund “A way to achieve Europe”, Operative program Intelligent Growth 2014–2020.

From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (10(7), 10(5) and 10(3) copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions. UZ/KU Leuven: as National Reference Center for Respiratory Pathogens, is supported by Sciensano, which is gratefully acknowledged. We would like to acknowledge additional staff members of the participating laboratories that contributed to this study: Jean-Luc Gala, Benoit Kabamba, Elsa Wiam, Valentin Coste, Paul Blanpain, Jean Ruelle, Ari Serbetciyan, Nicolas Pinte, Ophélie Simon and the entire UCLouvain federal testing platform COVID-19 team (all affiliation 4), Aurore Demars (affiliation 7), Laura Vanden Daele (affiliation 9), Hanne Valgaeren (affiliation 22), Guillaume Bayon-Vicente (affiliation 23), Fabrice Bureau, Claire Gourzonès and Joey Schyns (affiliation 28), Stéphanie Evrard (affiliation 42), Clara Ceyssens (affiliation 58), Jorn Hellemans (affiliation 77), Bram Slechten (affiliation 86) and the entire team of the laboratory of microbiology of UZA (affiliation 89) and of the UZA Federal testing platform COVID-19 (affiliation 85) for their boundless dedication.

Bisphenol (BPA) is a key ingredient in the production of epoxy resins and some types of plastics, which can be released into the environment and alter the endocrine systems of wildlife and humans. In this study, the ability of the fungus M. roridumIM 6482 to BPA elimination was investigated. LC-MS/MS analysis showed almost complete removal of BPA from the growth medium within 72 h of culturing. Products of BPA biotransformation were identified, and their estrogenic activity was found to be lower than that of the parent compound. Extracellular laccase activity was identified as the main mechanism of BPA elimination. It was observed that BPA induced oxidative stress in fungal cells manifested as the enhancement in ROS production, membranes permeability and lipids peroxidation. These oxidative stress markers were reduced after BPA biodegradation (72 h of culturing). Intracellular proteome analyses performed using 2-D electrophoresis and MALDI-TOF/TOF technique allowed identifying 69 proteins in a sample obtained from the BPA containing culture. There were mainly structural and regulator proteins but also oxidoreductive and antioxidative agents, such as superoxide dismutase and catalase. The obtained results broaden the knowledge on BPA elimination by microscopic fungi and may contribute to the development of BPA biodegradation methods.

Viral and host immune kinetics during acute COVID-19 and after remission of acute symptoms need better characterization. SARS-CoV-2 RNA, anti-SARS-CoV-2 IgA, IgM, and IgG antibodies, and proinflammatory cytokines were measured in sequential samples from hospitalized COVID-19 patients during acute infection and six months following diagnosis. Twenty four laboratory confirmed COVID-19 patients with mild/moderate and severe COVID-19 were included. Most were males (83%) with a median age of 61 years. Twenty one percent were admitted to the intensive care unit (ICU) and eight of them (33.3%) met the criteria for severe COVID-19 disease. A delay in SARS-CoV-2 levels’ decline during the first six days of follow up, and viral load persistence until month 3 were related to severe COVID-19, but not viral load levels at the diagnosis. Higher levels of anti-SARS-CoV-2 IgA, IgM, IgG and the cytokines IL-6, IL-8 and MIP-1β at the diagnosis time were related to the severe COVID-19 outcome. Higher levels of MIP-1β, IL-1β, MIP-1α and IFN-γ were observed at month 1 and 3 during mild/moderate disease, compared to severe COVID-19. IgG persisted at low levels after six months of diagnosis. In conclusion, higher concentrations of IgA, IgM, and IgG, and IL-6, IL-8 and MIP-1β are identified as early predictors of COVID-19 severity, whereas no significant association is found between baseline SARS-COV-2 viral load and COVID-19 severity., This work was supported by the Plan Estatal de I+D+I 2013-2016 and 2017–2020 and cofinanced by the Instituto de Salud Carlos III (ISCIII)—Subdirección General de Evaluación y Fomento de la investigación del Fondo Europeo de Desarrollo Regional (FEDER), Fondo COVID19 of Instituto de Salud Carlos III (COV20/00698), RETICS, Red de Investigación en SIDA [RD16/0025/0026]; and Fundación Biomédica Galicia Sur. E.R-M. was supported by the Spanish Research Council (CSIC) and by the research grant CV20-85418 from the Consejería de Transformación Económica, Industria, Conocimiento y Universidades (Junta de Andalucía). A.P. was supported by the Instituto de Salud Carlos III, Subprograma Rio Hortega (CM20/00243). A.G.-V. was supported by the Instituto de Salud Carlos III, cofinanced by the European Development Regional Fund (“A way to achieve Europe”), Subprograma Miguel Servet (CP19/00159). E.M.M. was supported by the Instituto de Salud Carlos III, cofinanced by the European Development Regional Fund (“A way to achieve Europe”), Subprogram PFIS (FI19/00304). C.K. was supported by Fondo COVID19 of Instituto de Salud Carlos III (COV20/00823).

Profilaxi antibiòtica; Hemiartroplàstia de maluc; Infecció periprotèsica de l'articulació Profilaxis antibiótica; Hemiartroplastia de cadera; Infección de la articulación periprotésica Antibiotic prophylaxis; Hip hemiarthroplasty; Periprosthetic joint infection We review antibiotic and other prophylactic measures to prevent periprosthetic joint infection (PJI) after hip hemiarthroplasty (HHA) surgery in proximal femoral fractures (PFFs). In the absence of specific guidelines, those applied to these individuals are general prophylaxis guidelines. Cefazolin is the most widely used agent and is replaced by clindamycin or a glycopeptide in beta-lactam allergies. A personalized antibiotic scheme may be considered when colonization by a multidrug-resistant microorganism (MDRO) is suspected. Particularly in methicillin-resistant Staphylococcus aureus (MRSA) colonization or a high prevalence of MRSA-caused PJIs a glycopeptide with cefazolin is recommended. Strategies such as cutaneous decolonization of MDROs, mainly MRSA, or preoperative asymptomatic bacteriuria treatment have also been addressed with debatable results. Some areas of research are early detection protocols in MDRO colonizations by polymerase-chain-reaction (PCR), the use of alternative antimicrobial prophylaxis, and antibiotic-impregnated bone cement in HHA. Given that published evidence addressing PJI prophylactic strategies in PFFs requiring HHA is scarce, PJIs can be reduced by combining different prevention strategies after identifying individuals who will benefit from personalized prophylaxis. This work was supported by the ISCIII-Subdirección General de Evaluación y Fomento de la Investigación, through the project PI15/02161 and by the Plan Nacional de I+D+i 2013-016 and ISCIIII, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economia, Industria y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0003)-co-financed by European Development Regional Fund “A way to achieve Europe”, Operative program Intelligent Growth 2014–2020.

Fong; Infecció articular periprotèsica; Cirurgia d'intercanvi en dues etapes Hongo; Infección de la articulación periprotésica; Cirugía de recambio en dos etapas Fungus; Periprosthetic joint infection; Two-stage exchange surgery Candida periprosthetic joint infection (CPJI) is a rare and very difficult to treat infection, and high-quality evidence regarding the best management is scarce. Candida spp. adhere to medical devices and grow forming biofilms, which contribute to the persistence and relapse of this infection. Typically, CPJI presents as a chronic infection in a patient with multiple previous surgeries and long courses of antibiotic therapy. In a retrospective series of cases, the surgical approach with higher rates of success consists of a two-stage exchange surgery, but the best antifungal treatment and duration of antifungal treatment are still unclear, and the efficacy of using an antifungal agent-loaded cement spacer is still controversial. Until more evidence is available, focusing on prevention and identifying patients at risk of CPJI seems more than reasonable. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

We aimed to describe the clinical presentation, treatment, outcome and report on factors associated with mortality over a 90-day period in Clostridioides difficile infection (CDI). Descriptive, univariate, and multivariate regression analyses were performed on data collected in a retrospective case-control study conducted in nine hospitals from seven European countries. A total of 624 patients were included, of which 415 were deceased (cases) and 209 were still alive 90 days after a CDI diagnosis (controls). The most common antibiotics used previously in both groups were β-lactams, previous exposure to fluoroquinolones was significantly (p = 0.0004) greater in deceased patients. Multivariate logistic regression showed that the factors independently related with death during CDI were older age, inadequate CDI therapy, cachexia, malignancy, Charlson Index, long-term care, elevated white blood cell count (WBC), C-reactive protein (CRP), bacteraemia, complications, and cognitive impairment. In addition, older age, higher levels of WBC, neutrophil, CRP or creatinine, the presence of malignancy, cognitive impairment, and complications were strongly correlated with shortening the time from CDI diagnosis to death. CDI prevention should be primarily focused on hospitalised elderly people receiving antibiotics. WBC, neutrophil count, CRP, creatinine, albumin and lactate levels should be tested in every hospitalised patient treated for CDI to assess the risk of a fatal outcome.

Twenty-eight fungal feruloyl esterases (FAEs) were evaluated for their synthetic abilities in a ternary system of n-hexane: t-butanol: 100 mM MOPS-NaOH pH 6.0 forming detergentless microemulsions. Five main derivatives were synthesized, namely prenyl ferulate, prenyl caffeate, butyl ferulate, glyceryl ferulate, and l-arabinose ferulate, offering, in general, higher yields when more hydrophilic alcohol substitutions were used. Acetyl xylan esterase-related FAEs belonging to phylogenetic subfamilies (SF) 5 and 6 showed increased synthetic yields among tested enzymes. In particular, it was shown that FAEs belonging to SF6 generally transesterified aliphatic alcohols more efficiently while SF5 members preferred bulkier l-arabinose. Predicted surface properties and structural characteristics were correlated with the synthetic potential of selected tannase-related, acetyl-xylan-related, and lipase-related FAEs (SF1-2, -6, -7 members) based on homology modeling and small molecular docking simulations.

Phage therapy is increasingly put forward as a "new" potential tool in the fight against antibiotic resistant infections. During the "Centennial Celebration of Bacteriophage Research" conference in Tbilisi, Georgia on 26-29 June 2017, an international group of phage researchers committed to elaborate an expert opinion on three contentious phage therapy related issues that are hampering clinical progress in the field of phage therapy. This paper explores and discusses bacterial phage resistance, phage training and the presence of prophages in bacterial production strains while reviewing relevant research findings and experiences. Our purpose is to inform phage therapy stakeholders such as policy makers, officials of the competent authorities for medicines, phage researchers and phage producers, and members of the pharmaceutical industry. This brief also points out potential avenues for future phage therapy research and development as it specifically addresses those overarching questions that currently call for attention whenever phages go into purification processes for application. ispartof: Viruses vol:10 issue:4 ispartof: location:Switzerland status: published

Prescription optimization; Critically ill patients; Appropriate antibiotic Prescripció antimicrobiana; Pacients crítics; Antibiòtic adequat Prescripción antimicrobiana; Pacientes críticos; Antibiótico adecuado The emergence of antibiotic resistance poses a global health threat. High-risk patients such as those with neutropenia are particularly vulnerable to opportunistic infections, sepsis, and multidrug-resistant infections, and clinical outcomes remain the primary concern. Antimicrobial stewardship (AMS) programs should mainly focus on optimizing antibiotic use, decreasing adverse effects, and improving patient outcomes. There is a limited number of published studies assessing the impact of AMS programs on patients with neutropenia, where early appropriate antibiotic choice can be the difference between life and death. This narrative review updates the current advances in strategies of AMS for bacterial infections among high-risk patients with neutropenia. Diagnosis, drug, dose, duration, and de-escalation (5D) are the core variables among AMS strategies. Altered volumes of distribution can make standard dose regimens inadequate, and developing skills towards a personalized approach represents a major advance in therapy. Intensivists should partner antibiotic stewardship programs to improve patient care. Assembling multidisciplinary teams with trained and dedicated professionals for AMS is a priority.

E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products. Keywords: E. coli O157:H7; whole-genome sequencing; cgMLST; transmission; virulence genes; antimicrobial resistance, E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products.

Antibiotics; Pediatrics; Quality improvement Antibióticos; Pediatría; Mejora de la calidad Antibiòtics; Pediatria; Millora de la qualitat In Spain, many programs have been introduced in recent years to optimize antimicrobial stewardship in pediatric care (known as pediatric PROA). However, information on the current situation of these programs is scarce. The present study assesses current antimicrobial use in pediatric care in the hospitals of Catalonia affiliated with the VINCat pediatric PROA group. Between December 2020 and January 2021, an electronic survey related to the design and use of PROA was administered to members of PROA teams in our hospital network. The survey was conducted at 26 hospitals. Twelve percent of the hospitals had pediatric PROA in operation, 42% were included in adult PROA, and 46% carried out pediatric PROA activities but not as part of an established program. At 81%, the pediatric PROA team included a pediatrician, in 58% a pharmacist, and in 54% a microbiologist. The main activities were monitoring the use of antimicrobials and bacterial resistance. Twenty-seven percent measured indicators regularly. The VINCat Pediatric PROA group’s hospitals have implemented measures for optimizing antimicrobial stewardship, but few have a pediatric PROA program in place. Specific measures and indicators must be defined, and the resources available should be increased. The development of pediatric PROA should be monitored in the coming years.

International audience; The ever-evolving research in the field of antitubercular agents has led to the identification of several new potential drug classes. Among them, 5-phenyl-furan-2-carboxylic acids have emerged as innovative potential therapeutics, targeting iron acquisition in mycobacterial species. In our efforts to characterize the molecular interactions between these compounds and their protein target (MbtI from M. tuberculosis) by means of co-crystallization experiments, we unexpectedly obtained the structure of 5-(4-nitrophenyl)furan-2-carboxylic acid (1). Herein, we describe the preparation of the compound and its analysis by 1H NMR, 13C NMR, HRMS, and SC-XRD.

Breast cancer; Response biomarkers; Secretome Càncer de mama; Biomarcadors de resposta; Secretoma Cáncer de mama; Biomarcadores de respuesta; Secretoma There is a great need for non-invasive tools that inform of an early molecular response to cancer therapeutic treatment. Here, we tested the hypothesis that proteolytically resistant proteins could be candidate circulating tumor biomarkers for cancer therapy. Proteins resistant to proteolysis are drastically under-sampled by current proteomic workflows. These proteins could be reliable sensors for the response to therapy since they are likely to stay longer in circulation. We selected manganese superoxide dismutase (SOD2), a mitochondrial redox enzyme, from a screening of proteolytic resistant proteins in breast cancer (BC). First, we confirmed the robustness of SOD2 and determined that its proteolytic resistance is mediated by its quaternary protein structure. We also proved that the release of SOD2 upon chemotherapy treatment correlates with cell death in BC cells. Then, after confirming that SOD2 is very stable in human serum, we sought to measure its circulating levels in a cohort of BC patients undergoing neoadjuvant therapy. The results showed that circulating levels of SOD2 increased when patients responded to the treatment according to the tumor shrinkage during neoadjuvant chemotherapy. Therefore, the measurement of SOD2 levels in plasma could improve the non-invasive monitoring of the therapeutic treatment in breast cancer patients. The identification of circulating biomarkers linked to the tumor cell death induced by treatment could be useful for monitoring the action of the large number of cancer drugs currently used in clinics. We envision that our approach could help uncover candidate tumor biomarkers to measure a tumor’s response to cancer therapy in real time by sampling the tumor throughout the course of treatment. This work was funded by Servier.

Phytophthora sojae is a pathogen of major agricultural importance, responsible for Phytophthora root rot (PRR) in soybean crops, which can cause significant yield losses each year. The severity of the disease depends on the soybean cultivar, its growth stage at the time of pathogen infection, and the environmental conditions. High soil moisture and temperature around 25–30 °C are favorable conditions for the development of the disease. Consequently, cultural practices are mainly limited to avoiding bad weather (high moisture) during the sowing or to promoting soil drainage. The use of chemical fungicides is restricted to seed treatments when there is a high risk of disease development. Currently the most economical option for controlling P. sojae is the use of host resistance. However, even if breeding is the main control strategy of PRR, the use of resistant cultivars leads to selection pressure on P. sojae populations, which can lead to high variability of the pathogen and therefore to its adaptation to overcome plant resistance. New strategies are therefore needed, including the use of biological control agents (BCAs). The use of BCAs (i.e., microorganisms or their metabolites) is a promising and sustainable alternative to PRR control that should be strengthened. Therefore, this review addresses the P. sojae–soybean interaction, mechanisms of pathogenicity and host resistance, as well as current and new management strategies with emphasis on the biological control of P. sojae and its associated mechanisms Instituto de Patología Vegetal Fil: Giachero, María Lorena. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Giachero, María Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Declerck, Stéphane. Université Catholique de Louvain. Mycology, Earth and Life Institute; Bélgica Fil: Marquez, Nathalie. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Marquez, Nathalie. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina

A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.

Clofazimine (CFZ) is a poorly soluble, weakly basic, small molecule antibiotic clinically used to treat leprosy and is now in clinical trials as a treatment for multidrug resistant tuberculosis and COVID-19. CFZ exhibits complex, context-dependent pharmacokinetics that are characterized by an increasing half-life in long term treatment regimens. The systemic pharmacokinetics of CFZ have been previously represented by a nonlinear, 2-compartment model incorporating an expanding volume of distribution. This expansion reflects the soluble-to-insoluble phase transition that the drug undergoes as it precipitates out and accumulates within macrophages disseminated throughout the organism. Using mice as a model organism, we studied the mechanistic underpinnings of this increasing half-life and how the systemic pharmacokinetics of CFZ are altered with continued dosing. To this end, M. tuberculosis infection status and multiple dosing schemes were studied alongside a parameter sensitivity analysis (PSA) to further understanding of systemic drug distribution. Parameter values governing the sigmoidal expansion function that captures the phase transition were methodically varied, and in turn, the systemic concentrations of the drug were calculated and compared to the experimentally measured concentrations of drug in serum and spleen. The resulting amounts of drug sequestered were dependent on the total mass of CFZ administered and the duration of drug loading. This phenomenon can be captured by altering three different parameters of an expansion function corresponding to key biological determinants responsible for the precipitation and the accumulation of the insoluble drug mass in macrophages. Through this analysis of the context dependent pharmacokinetics of CFZ, a predictive framework for projecting the systemic distribution and self-assembly of precipitated drug complexes as intracellular mechanopharmaceutical devices of this and other drugs exhibiting similarly complex pharmacokinetics can be constructed.

The adoption of carbohydrate-restrictive diets to improve health is increasing in popularity, but there is a dearth of research on individuals who choose to severely restrict or entirely exclude carbohydrates. The present study investigated the beliefs and experiences of individuals following a diet that severely limits, or entirely excludes, dietary carbohydrates, colloquially known as a ‘zero-carb’ diet, for at least 6 months. Zero-carb dieters (n = 170) recruited via a social networking site completed an online qualitative survey prompting them to discuss their motives, rationale, and experiences of following a low-carb diet. Transcripts of participants’ responses were analyzed using inductive thematic analysis. Results revealed that participants’ decision to follow a zero-carb diet was driven by health concerns and benefits. Participants expressed a strong social identity and belongingness to online zero-carb communities. Participants reported strong intentions to follow the diet indefinitely. Shortcomings of the diet centered on experienced stigma; lack of support from healthcare providers and significant others; limited access to, and high cost of, foods; and limited scientific data on the diet. Further research into the benefits and shortcomings of zero-carb diets across settings and populations is warranted, and guidelines for healthcare professionals on how to support individuals following a zero-carb diet are needed.

Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile’s genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers. Publication’s printing cost was co-financed by the European Union from the European Social Fund under the "InterDOC-STARt" project (POWR.03.02.00-00-I033/16-00).

International audience; Background. Non-polio enteroviruses (EVs) and human parechoviruses (PeVs) cause a wide range of human infections. Limited data on their true disease burden exist as standardized European-wide surveillance is lacking. Aims. Our aim is to estimate the disease burden of EV and PeV infections in Europe via establishment of standardized surveillance for hand, foot and mouth disease (HFMD) and respiratory and neurological infections caused by these viruses. We will also assess the sensitivity of assays implemented in the network of participating laboratories so that all EV and PeV types are adequately detected. Plan. The European Non-Polio Enterovirus Network (ENPEN) has developed standardized protocols for a prospective, multi-center and cross-sectional hospital-based pilot study. Protocols include guidance for diagnosis, case definition, detection, characterization and reporting of EV and PeV infections associated with HFMD and respiratory and neurological diseases. Over 30 sites from 17 European countries have already registered to this one pilot study, likely to be commenced in 2022. Benefits. This surveillance will allow European-wide comparison of data on EV and PeV infection. These data will also be used to determine the burden of EV and PeV infections, which is needed to guide the further prevention measures and policies.

Pogosta disease is a mosquito-borne infection, caused by Sindbis virus (SINV), which causes epidemics of febrile rash and arthritis in Northern Europe and South Africa. Resident grouse and migratory birds play a significant role as amplifying hosts and various mosquito species, including Aedes cinereus, Culex pipiens, Cx. torrentium and Culiseta morsitans are documented vectors. As specific treatments are not available for SINV infections, and joint symptoms may persist, the public health burden is considerable in endemic areas. To predict the environmental suitability for SINV infections in Finland, we applied a suite of geospatial and statistical modeling techniques to disease occurrence data. Using an ensemble approach, we first produced environmental suitability maps for potential SINV vectors in Finland. These suitability maps were then combined with grouse densities and environmental data to identify the influential determinants for SINV infections and to predict the risk of Pogosta disease in Finnish municipalities. Our predictions suggest that both the environmental suitability for vectors and the high risk of Pogosta disease are focused in geographically restricted areas. This provides evidence that the presence of both SINV vector species and grouse densities can predict the occurrence of the disease. The results support material for public-health officials when determining area-specific recommendations and deliver information to health care personnel to raise awareness of the disease among physicians.

Although refrigeration and modified-atmosphere packaging (MAP) allow for an extended shelf life of cooked charcuterie products, they are still susceptible to bacterial spoilage. To obtain better insights into factors that govern product deterioration, ample information is needed on the associated microbiota. In this study, sliced MAP cooked ham and cooked chicken samples were subjected to culture-dependent and culture-independent microbial analysis. In total, 683 bacterial isolates were obtained and identified from 60 samples collected throughout the storage period. For both charcuterie types, lactic acid bacteria (LAB) constituted the most abundant microbial group. In cooked ham, Brochothrix thermosphacta was highly abundant at the beginning of the shelf-life period, but was later overtaken by Leuconostoc carnosum and Lactococcus piscium. For cooked chicken products, Latilactobacillus sakei was most abundant throughout the entire period. Additionally, 13 cooked ham and 16 cooked chicken samples were analyzed using metabarcoding. Findings obtained with this method were generally in accordance with the results from the culture-dependent approach, yet they additionally demonstrated the presence of Photobacterium at the beginning of the shelf-life period in both product types. The results indicated that combining culture-dependent methods with metabarcoding can give complementary insights into the evolution of microorganisms in perishable foods.

Elderly people confined to chronic care facilities face an increased risk of acquiring infections by multidrug-resistant organisms (MDROs). This review presents the current knowledge of the prevalence and risk factors for colonization by MDROs in long-term care facilities (LTCF), thereby providing a useful reference to establish objectives for implementing successful antimicrobial stewardship programs (ASPs). We searched in PubMed and Scopus for studies examining the prevalence of MDROs and/or risk factors for the acquisition of MDROs in LTCF. One hundred and thirty-four studies published from 1987 to 2020 were included. The prevalence of MDROs in LTCF varies between the different continents, where Asia reported the highest prevalence of extended-spectrum ß-lactamase (ESBL) Enterobacterales (71.6%), carbapenem resistant (CR) Enterobacterales (6.9%) and methicillin-resistant Staphylococcus aureus (MRSA) (25.6%) and North America the highest prevalence to MDR Pseudomonas aeruginosa (5.4%), MDR Acinetobacter baumannii (15.0%), vancomycin-resistant Enterococcus spp. (VRE) (4.0%), and Clostridioides difficile (26.1%). Furthermore, MDRO prevalence has experienced changes over time, with increases in MDR P. aeruginosa and extended spectrum ß-lactamase producing Enterobacterales observed starting in 2015 and decreases of CR Enterobacterales, MDR A. baumannii, VRE, MRSA and C. difficile. Several risk factors have been found, such as male sex, chronic wounds, the use of medical devices, and previous antibiotic use. The last of these aspects represents one of the most important modifiable factors for reducing colonization with MDROs through implementing ASPs in LTCF. Yes

Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.

© 2021 by the authors. Choline kinase (ChoK) is a cytosolic enzyme that catalyzes the phosphorylation of choline to form phosphorylcholine (PCho) in the presence of ATP and magnesium. ChoK is required for the synthesis of key membrane phospholipids and is involved in malignant transformation in a large variety of human tumours. Active compounds against ChoK have been identified and proposed as antitumor agents. The ChoK inhibitory and antiproliferative activities of symmetrical bispyridinium and bisquinolinium compounds have been defined using quantitative structure–activity relationships (QSARs) and structural parameters. The design strategy followed in the development of the most active molecules is presented. The selective anticancer activity of these structures is also described. One promising anticancer compound has even entered clinical trials. Recently, ChoKα inhibitors have also been proposed as a novel therapeutic approach against parasites, rheumatoid arthritis, inflammatory processes, and pathogenic bacteria. The evidence for ChoKα as a novel drug target for approaches in precision medicine is discussed. This research was funded by CSIC, grant number PIE202020E041; and in part by the NIFA through the Agricultural Research Program at North Carolina Agricultural and Technical State University (Evans-Allen Program, project number NC.X-291-5-15-170-1).

The DNA repair endonuclease EndoMS/NucS is highly conserved in Archaea and Actinobacteria. This enzyme is able to recognize and cleave dsDNA carrying a mismatched base pair, and its activity is enhanced by the interaction with the sliding clamp of the replisome. Today, EndoMS/NucS has been established as the key protein of a non-canonical mismatch repair (MMR) pathway, acting specifically in the repair of transitions and being essential for maintaining genome stability. Despite having some particularities, such as its lower activity on transversions and the inability to correct indels, EndoMS/NucS meets the main hallmarks of a MMR. Its absence leads to a hypermutator phenotype, a transition-biased mutational spectrum and an increase in homeologous recombination. Interestingly, polymorphic EndoMS/NucS variants with a possible effect in mutation rate have been detected in clinical isolates of the relevant actinobacterial pathogen Mycobacterium tuberculosis. Considering that MMR defects are often associated with the emergence of resistant bacteria, the existence of EndoMS/NucS-defective mutators could have an important role in the acquisition of antibiotic resistance in M. tuberculosis. Therefore, a further understanding of the EndoMS/NucS-mediated non-canonical MMR pathway may reveal new strategies to predict and fight drug resistance. This review is focused on the recent progress in NucS, with special emphasis on its effect on genome stability and evolvability in Actinobacteria. Yes

The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review. Yes

30 Pág. Departamento de ​Protección Vegetal (INIA), Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis., J.C. (Joana Costa) acknowledges R&D Unit Center for Functional Ecology-Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). V.C. acknowledges support of the University of Catania PIA.CE.RI. 2020–2022 Linea 2-Research Project MEDIT-ECO. J.C. acknowledges support from AEI by RTI2018-096018-R-C31 and FEDER. O.P. and I.R. acknowledge the European Union (ERDF, EAFRD) and Réunion regional council for support. J.F.P. acknowledges support from the Department of Life Sciences and Facility Management of the Zurich University of Applied Sciences (ZHAW) in Wädenswil. D.J.S. and J.G.V. also acknowledge joint funding by a grant from BBSRC, NERC, Defra, and the Scottish Government, under the Strategic Priorities Fund Plant Bacterial Diseases programme under the project ‘Xanthomonas plants diseases: mitigating existing, emerging and future threats to UK agriculture’ (BB/T010916/1 and BB/T010908/1). The APC was funded by COST (European Cooperation in Science and technology).

The use of probiotics in reproductive-related dysbiosis is an area of continuous progress due to the growing interest from clinicians and patients suffering from recurrent reproductive microbiota disorders. An imbalance in the natural colonization sites related to reproductive health-vaginal, cervicovaginal, endometrial, and pregnancy-related altered microbiota-could play a decisive role in reproductive outcomes. Oral and vaginal administrations are in continuous discussion regarding the clinical effects pursued, but the oral route is used and studied more often despite the need for further transference to the colonization site. The aim of the present review was to retrieve the standardized protocols of vaginal probiotics commonly used for investigating their microbiota modulation capacities. Most of the studies selected focused on treating bacterial vaginosis (BV) as the most common dysbiosis; a few studies focused on vulvovaginal candidiasis (VVC) and on pretreatment during in vitro fertilization (IVF). Vaginal probiotic doses administered were similar to oral probiotics protocols, ranging from ≥107 CFU/day to 2.5 × 1010 CFU/day, but were highly variable regarding the treatment duration timing. Moderate vaginal microbiota modulation was achieved; the relative abundance of abnormal microbiota decreased and Lactobacillus species increased. Yes

Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by age, product, schedule, and syndrome. Here we systematically characterize and summarize the global landscape of routine serotype-specific IPD surveillance in PCV10/13-using countries and describe the subset that are included in PSERENADE. Of 138 countries using PCV10/13 as of 2018, we identified 109 with IPD surveillance systems, 76 of which met PSERENADE data collection eligibility criteria. PSERENADE received data from most (n = 63, 82.9%), yielding 240,639 post-PCV10/13 introduction IPD cases. Pediatric and adult surveillance was represented from all geographic regions but was limited from lower income and high-burden countries. In PSERENADE, 18 sites evaluated PCV10, 42 PCV13, and 17 both, 17 sites used a 3 + 0 schedule, 38 used 2 + 1, 13 used 3 + 1, and 9 used mixed schedules. With such a sizeable and generally representative dataset, PSERENADE will be able to conduct robust analyses to estimate PCV impact and inform policy at national and global levels regarding adult immunization, schedule, and product choice, including for higher valency PCVs on the horizon.

This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes. This issue is associated with the 6th Viruses of Microbes (VoM) conference in Guimarães (www.vom2020.org, accessed on 1 April 2021), Portugal, that was originally planned for the summer of 2020, but has, in light of the pandemic, been postponed to 18–22 July 2022.The International Society for Viruses of Microbes (ISVM) supports the biannual organization of the VoM meetings and unites researchers worldwide that study the different aspects of viruses of microbes, ranging from structural biology to ecology and from applied to fundamental science (www.isvm.org, accessed on 1 April 2021). This active and expanding research community benefits not only from the scientific exchange during the VoM meetings, but also online, such as recently during the successful virtual seminar series, iVoM, that was organized by the local organizers of the 6th VoM. The meetings and online seminar series highlight the most recent developments in the field and thus have on display “The latest conquests on Viruses of Microbes”.Studies of viruses of microbes have driven many major scientific revolutions, such as the usage of phage (derived) therapy to fight antibiotic resistance, the development of molecular biology, the discovery of the major impact of viruses on biochemical cycling and the recently, Nobel-awarded, adaptation of CRISPR-Cas for genome editing. Comparison between the virion structures, genomes and infection strategies of different viruses of microbes enables a unifying view of viruses and helps to understand how viruses originated, how they develop and how they impact life on earth.In this Special Issue, recent advances in the field of microbial virology are collected. Two reviews summarize the novel developments in understanding RNA viruses of aquatic eukaryotes [1] and on entry mechanisms of prokaryotic viruses [2]. Comparison between different viruses requires genomic evaluation tools, such as the VIRIDIC tool presented in this issue [3]. Such tools, in combination with omics approaches [4] can support study of the role of individual viral proteins in the viral infection cycle [5] and manipulation of the host cell [6,7,8]. Deciphering the role of viral proteins is important for our understanding of viral infection strategies, including host recognition [9]. Isolation of novel viruses from underexplored environments is still a prerequisite for further exploration of the viral gene repertoire and molecular characterization of viral infection [10,11].The combination of efforts, such as those bundled in this Special Issue, will allow us to entangle the strategies that individual viruses use to propagate and the mechanisms by which they impact life from individual cells to ecosystems. Microbial viruses were discovered over hundred years ago, and the more we learn about them, the more they keep surprising us. It is now an exciting time for microbial virologists, and this growing research community will surely contribute to unlocking many more secrets of these fascinating viruses.

The development of incurred reference materials containing citrinin (CIT) and their successful application in a method validation study (MVS) in order to harmonize CIT determination in food and food supplements are demonstrated. CIT-contaminated materials made of red yeast rice (RYR), wheat flour, and Ginkgo biloba leaves (GBL), as well as food supplements made of red yeast rice (FS-RYR) and Ginkgo biloba leaves (FS-GBL), were manufactured in-house via fungal cultivation on collected raw materials. The homogeneity and stability from randomly selected containers were verified according to the ISO 13528. CIT was found to be homogenously distributed and stable in all contaminated materials, with no significant degradation during the timescale of the MVS when storage was performed up to +4 °C. Next, an MVS was organized with eighteen international laboratories using the provided standard operating procedure and 12 test materials, including three RYRs (blank, &lt, 50 µg/kg, &lt, 2000 µg/kg), two wheat flours (blank, &lt, 50 µg/kg), two GBL powders (blank, &lt, 50 µg/kg), three FS-RYRs (blank, &lt, 2000 µg/kg), and two FS-GBLs (blank, &lt, 50 µg/kg). The results of seven CIT-incurred materials showed acceptable within-laboratory precision (RSDr) varying from 6.4% to 14.6% and between-laboratory precision (RSDR) varying from 10.2% to 37.3%. Evidenced by HorRat values &lt, 2.0, the results of the collaborative trial demonstrated that the applied analytical method could be standardized. Furthermore, the appropriateness of producing CIT reference materials is an important step towards food and feed quality control systems and the organization of proficiency tests.

Given the widespread use of bisphenols and parabens in consumer products, the assessment of their intake is crucial and represents the first step towards the assessment of the potential risks that these compounds may pose to human health. In the present study, a total of 98 samples of food items commonly consumed by the Spanish population were collected from different national supermarkets and grocery stores for the determination of parabens and bisphenols. Our analysis demonstrated that 56 of the 98 food samples contained detectable levels of parabens with limits of quantification (LOQ) between 0.4 and 0.9 ng g&minus, 1. The total concentration of parabens (sum of four parabens: &sum, parabens) ranged from below the LOQ to 281.7 ng g&minus, 1, with a mean value of 73.86 ng g⁻1. A total of 52% of the samples showed detectable concentrations of bisphenols. Bisphenol A (BPA) was the most frequently detected bisphenol in the food samples analysed, followed by bisphenol S (BPS) and bisphenol E (BPE). Bisphenol AF (BPAF), bisphenol B (BPB) and bisphenol P (BPP) were not found in any of the analysed samples. LOQ for these bisphenols were between 0.4 and 4.0 ng g&minus, 1.

Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis. This research study was supported by the Laboratory of Excellence ARBRE (ANR-11- LABX-0002-01), the Region Lorraine, the European Regional Development Fund and the Plant– Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research in the US DOE Office of Science. J.R. is an Agreenskills Marie Sklodowska Curie postdoctoral fellow co-funded by the European Union (CoFUND-FP7-267196). The authors greatly acknowledge Yohann Daguerre and Clément Pellegrin for assistance in setting up Laccaria–Populus co-cultures and Maarten Ottaway for English language editing of the manuscript

Pneumococcal conjugate vaccine (PCV) introduction has reduced pneumococcal meningitis incidence. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project described the serotype distribution of remaining pneumococcal meningitis in countries using PCV10/13 for least 5–7 years with primary series uptake above 70%. The distribution was estimated using a multinomial Dirichlet regression model, stratified by PCV product and age. In PCV10-using sites (N = 8, cases = 1141), PCV10 types caused 5% of cases &lt, 5 years of age and 15% among ≥5 years, the top serotypes were 19A, 6C, and 3, together causing 42% of cases &lt, 5 years and 37% ≥5 years. In PCV13-using sites (N = 32, cases = 4503), PCV13 types caused 14% in &lt, 5 and 26% in ≥5 years, 4% and 13%, respectively, were serotype 3. Among the top serotypes are five (15BC, 8, 12F, 10A, and 22F) included in higher-valency PCVs under evaluation. Other top serotypes (24F, 23B, and 23A) are not in any known investigational product. In countries with mature vaccination programs, the proportion of pneumococcal meningitis caused by vaccine-in-use serotypes is lower (≤26% across all ages) than pre-PCV (≥70% in children). Higher-valency PCVs under evaluation target over half of remaining pneumococcal meningitis cases, but questions remain regarding generalizability to the African meningitis belt where additional data are needed.

Obesogenic endocrine-disrupting chemicals, such as bisphenol A (BPA) and its analogue bisphenol S (BPS), seem to play an important role in the development of obesity, although contradictory results have been reported. The aim of the present study was to conduct a gender analysis of the factors associated with exposure to dietary bisphenols in 585 Spanish adolescents. Dietary BPA and BPS exposure was assessed using a food frequency questionnaire. Foods and macronutrients accounting for more than 95% of energy intake were selected for analysis. Stepwise regression was used to estimate the foods that most contributed to dietary bisphenol exposure in the sample. Gender-related factors associated with greater dietary bisphenol exposure were evaluated using multivariate logistic regression models. Canned tuna was the main dietary source of BPA and BPS in both adolescent boys and girls. Overweight/obese girls showed a higher risk of high dietary exposure to BPA (odds ratio (OR): 3.38, 95% confidence interval (CI): 1.25–9.07) and total bisphenols (OR: 2.81, 95% CI: 1.03–7.67) in comparison with girls with a BMI lower than 25 kg/m2 . Present results indicate a positive association of dietary exposure to both total bisphenols and BPA with being overweight/obese in adolescent girls., GP/EFSA/ENCO/380 2018/03/G04: OBEMIRISK: Knowledge platform for assessing the risk of bisphenol on gut microbiota and its role in obesogenic phenotypes: looking for biomarkers’ framework, Plan Estatal de I + D + I 2013–2016, FEDER-ISCIII PI17/01758, FEDER-Consejería de Salud y Familias, Junta de Andalucía PE-0250–2019, FEDER-Junta de Andalucía-Consejería de Transformación Económica, Industria, Conocimiento y Universidades/ Proyecto P18-RT-4247, Fundación Mapfre MAPFRE2018

Calcium chloride (CaCl2) has been widely used to maintain the quality of fresh-cut fruits and vegetables because it stabilizes and strengthens the membrane system against fungal attacks. It is mainly applied via spray coating and dip coating techniques. This study explored a method of incorporating calcium chloride extracted from eggshells in a packaging material, thermoplastic starch (TPS), via a hot-melt extrusion process. The composites were characterized by FTIR, DSC, SEM-EDX and tensile testing. FTIR confirmed the chemical reactions between CaCl2 and TPS. DSC results showed a significant decrease in the heat of fusion by adding 20 wt% of CaCl2 content in TPS, indicating a drop in the degree of crystallinity. The Young’s modulus of TPS was not significantly affected by the incorporation of 10 wt% CaCl2 (P = 0.968), but reduced notably with the addition of 20 wt% CaCl2 (P = 0.05), indicating the plasticizer effect of the CaCl2. Physiochemical analysis of fresh-cut apple slices was assessed. Samples placed on the surface of the TPS/CaCl2 composites displayed less pH reduction, reduced antioxidant activity, more weight loss and increased reducing sugar compared to the samples placed on the surface of virgin TPS films. CaCl2 released from the TPS/CaCl2 films was measured and their antimicrobial activity was confirmed by bacterial inhibitory growth assessment. Fungal growth was observed on apple slices placed on virgin TPS film by day 21 while apple slices placed on TPS/CaCl2 20 wt% composites did not support any fungal growth for 28 days. In summary, TPS and eggshell-extracted CaCl2 showed the ability to maintain the quality of fresh-cut apples, and TPS/CaCl2 10 wt% composite could be a good option as a packaging material for fresh-cut fruits due to active antimicrobial activity and maintained Young’s modulus. yes

Human gut microbiota harbors numerous microbial species with molecular enzymatic potential that impact on the eubiosis/dysbiosis and health/disease balances. Microbiota species isolation and description of their specific molecular features remain largely unexplored. In the present study, we focused on the cultivation and selection of species able to tolerate or biodegrade the endocrine disruptor bisphenol A (BPA), a xenobiotic extensively found in food plastic containers. Chemical xenobiotic addition methods for the directed isolation, culturing, Whole Genome Sequencing (WGS), phylogenomic identification, and specific gene-encoding searches have been applied to isolate microorganisms, assess their BPA metabolization potential, and describe encoded catabolic pathways. BPA-tolerant strains were isolated from 30% of infant fecal microbial culture libraries analyzed. Most isolated strains were phylogenetically related to the operational taxonomic group Bacillus amyloliquefaciens spp. Importantly, WGS analysis of microbial representative strain, Bacillus sp. AM1 identified the four complete molecular pathways involved on BPA degradation indicating its versatility and high potential to degrade BPA. Pathways for Exopolysaccharide (EPS) and Polyhydroxyalkanates (PHA) biopolymer synthesis were also identified and phenotypically confirmed by transmission electronic microscopy (TEM). These microbial biopolymers could generally contribute to capture and/or deposit xenobiotics., GP/EFSA/ENCO/380 2018/03/G04: OBEMIRISK: Knowledge platform for assessing the risk of Bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkers, FEDERInfrastructure: IE_2019-198, APC was funded by EIN-2019-103082

Pseudomonas aeruginosa is an important multidrug-resistant human pathogen by dint of its high intrinsic, acquired, and adaptive resistance mechanisms, causing great concern for immune-compromised individuals and public health. Additionally, P. aeruginosa resilience lies in the production of a myriad of virulence factors, which are known to be tightly regulated by the quorum sensing (QS) system. Anti-virulence therapy has been adopted as an innovative alternative approach to circumvent bacterial antibiotic resistance. Since plants are known repositories of natural phytochemicals, herein, we explored the anti-virulence potential of Azorella atacamensis, a medicinal plant from the Taira Atacama community (Calama, Chile), against P. aeruginosa. Interestingly, A. atacamensis extract (AaE) conferred a significant protection for human lung cells and Caenorhabditis elegans nematodes towards P. aeruginosa pathogenicity. The production of key virulence factors was decreased upon AaE exposure without affecting P. aeruginosa growth. In addition, AaE was able to decrease QS-molecules production. Furthermore, metabolite profiling of AaE and its derived fractions achieved by combination of a molecular network and in silico annotation allowed the putative identification of fourteen diterpenoids bearing a mulinane-like skeleton. Remarkably, this unique interesting group of diterpenoids seems to be responsible for the interference with virulence factors as well as on the perturbation of membrane homeostasis of P. aeruginosa. Hence, there was a significant increase in membrane stiffness, which appears to be modulated by the cell wall stress response ECF&sigma, SigX, an extracytoplasmic function sigma factor involved in membrane homeostasis as well as P. aeruginosa virulence.

Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this review, we provide a general overview about recent research on the implications of quadruplex structures in cancer, firstly gathering together DNA G-quadruplexes, RNA G-quadruplexes as well as DNA i-Motifs. Yes

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.

We evaluated the feasibility and efficacy of four existing interventions to improve adherence to them in migrants living with HIV (MLWH): directly administered antiretroviral therapy (DAART), group medical appointments (GMA), early detection and treatment of psychological distress, and peer support by trained MLWH. At baseline and after the interventions, socio-demographic characteristics, psychosocial variables, and data on HIV treatment adherence were collected. The two questionnaires were completed by 234/301 (78%) MLWH included at baseline. Detectable HIV RNA decreased (from 10.3 to 6.8%) as did internalized HIV-related stigma (from 15 to 14 points), and self-reported adherence increased (between 5.5 and 8.3%). DAART and GMA were not feasible interventions. Screening of psychological distress was feasible, however, follow-up diagnostic screening and linkage to psychiatric services were not. Peer support for and by MLWH was feasible. Within this small intervention group, results on HIV RNA &lt, 400 copies/mL (decrease of 23.6%) and outpatient clinic attendance (up to 20.4% kept more appointments) were promising.