Sample Processing for Metaproteomic Analysis of Human Gut Microbiota.

Human gut microbiota can be studied through the characterization of microorganisms present in feces. Metaproteomics has arisen as a good approach to investigate this vast community. However, the processing of fecal samples in order to obtain the largest number of proteins from gut microbiota to be subsequently analyzed by means of metaproteomics is a challenge. Here we describe a protocol to approach this task. It includes two main steps: the first step of humectation and dispersion of the feces, followed by the separation of microorganisms from other fecal components such as roughage and food debris, and the second step in which microbial cells are broken up and microbiota proteins recovered for MS analysis. Detailed procedures for sample preparation, protein extraction, trypsin digestion, and mass spectrometry analysis for gut microbiota samples are provided.

Candida albicans Hyphal Extracellular Vesicles Are Different from Yeast Ones, Carrying an Active Proteasome Complex and Showing a Different Role in Host Immune Response.

Candida albicans is the principal causative agent of lethal fungal infections, predominantly in immunocompromised hosts. Extracellular vesicles (EVs) have been described as crucial in the interaction of microorganisms with their host. Since the yeast-to-hypha transition is an important virulence trait with great impact in invasive candidiasis (IC), we have addressed the characterization of EVs secreted by hyphal cells (HEVs) from C. albicans, comparing them to yeast EVs (YEVs). YEVs comprised a larger population of bigger EVs with mainly cell wall proteins, while HEVs were smaller, in general, and had a much higher protein diversity. YEVs were able to rescue the sensitivity of a cell wall mutant against calcofluor white, presumably due to the larger amount of cell wall proteins they contained. On the other hand, HEVs also contained many cytoplasmic proteins related to protein metabolism and intracellular protein transport and the endosomal sorting complexes required for transport (ESCRT) pathway related to exosome biogenesis, pointing to an intracellular origin of HEVs. Interestingly, an active 20S proteasome complex was secreted exclusively in HEVs. Moreover, HEVs contained a greater number of virulence-related proteins. As for their immunogenic role, both types of EV presented immune reactivity with human sera from patients suffering invasive candidiasis; however, under our conditions, only HEVs showed a cytotoxic effect on human macrophages and could elicit the release of tumor necrosis factor alpha (TNF-α) by these macrophages. IMPORTANCE This first analysis of HEVs of C. albicans has shown clear differences between them and the YEVs of C. albicans, showing their relevance and possible use in the discovery of new diagnostic markers and treatment targets against C. albicans infections. The data obtained point to different mechanisms of biogenesis of YEVs and HEVs, as well as different involvements in cell biology and host interaction. YEVs played a more relevant role in cell wall maintenance, while HEVs were more closely related to virulence, as they had greater effects on human immune cells. Importantly, an active 20S proteosome complex was described as a fungal-EV cargo. A deeper study of its role and those of many other proteins exclusively detected in HEVs and involved in different relevant biological processes of this fungus could open up interesting new areas of research in the battle against C. albicans.

Quantitative proteome and acidic subproteome profiling of Candida albicans yeast-to-hypha transition.

Candida albicans yeast-to-hypha morphological transition is involved in the virulence strategy of this opportunistic fungal pathogen. Changes in relative abundance of the Candida proteome related to this process were analyzed using different two-dimensional differential in-gel electrophoresis (2D-DIGE)-based approaches. First, a comparative analysis of yeast and hyphal cytoplasmic proteins allowed the detection of 106 protein spots with significant variation in abundance. Sixty-one of them, corresponding to 46 proteins, were identified. As most of the differentially abundant proteins had an acidic isoelectric point, a large-scale prefractionation approach to analyze the acidic C. albicans subproteome was carried out. Ninety acidic C. albicans proteins were identified by either gel-based or nongel-based approaches. Additionally, different workflows combining preparative isoelectric focusing, Cy labeling, and narrow pH gradient 2-DE gels were tested to analyze the differences in relative protein abundance between yeast and hyphal acidic subproteomes. It was possible to identify 21 differentially abundant acidic proteins; 10 of them were not identified in the previous 2D-DIGE gels. Functional and network interaction analyses of the 56 differentially abundant proteins identified by both approaches rendered an integrated view of metabolic and cellular process reorganization during the yeast-to-hypha transition. With these results, we propose a model of metabolic reorganization.

Distinct Human Gut Microbial Taxonomic Signatures Uncovered With Different Sample Processing and Microbial Cell Disruption Methods for Metaproteomic Analysis.

The use of metaproteomics for studying the human gut microbiota can shed light on the taxonomic profile and the functional role of the microbial community. Nevertheless, methods for extracting proteins from stool samples continue to evolve, in the pursuit of optimal protocols for moistening and dispersing the stool sample and for disrupting microbial cells, which are two critical steps for ensuring good protein recovery. Here, we evaluated different stool sample processing (SSP) and microbial cell disruption methods (CDMs). The combination of a longer disintegration period of the stool sample in a tube rotator with sonication increased the overall number of identified peptides and proteins. Proteobacteria, Bacteroidetes, Planctomycetes, and Euryarchaeota identification was favored by mechanical cell disruption with glass beads. In contrast, the relative abundance of Firmicutes, Actinobacteria, and Fusobacteria was improved when sonication was performed before bead beating. Tenericutes and Apicomplexa identification was enhanced by moistening the stool samples during processing and by disrupting cells with medium-sized glass beads combined with or without sonication. Human protein identifications were affected by sonication. To test the reproducibility of these gut metaproteomic analyses, we examined samples from six healthy individuals using a protocol that had shown a good taxonomic diversity and identification of proteins from Proteobacteria and humans. We also detected proteins involved in microbial functions relevant to the host and related mostly to specific taxa, such as B12 biosynthesis and short chain fatty acid (SCFA) production carried out mainly by members in the Prevotella genus and the Firmicutes phylum, respectively. The taxonomic and functional profiles obtained with the different protocols described in this work provides the researcher with valuable information when choosing the most adequate protocol for the study of certain pathologies under suspicion of being related to a specific taxon from the gut microbiota.

The Fusarium oxysporum cell wall proteome under adhesion-inducing conditions.

Fusarium oxysporum is a soilborne fungus that causes vascular wilt disease on a wide range of crops. During initial stages of infection, fungal hyphae attach firmly to roots, penetrate the cortex and colonize xylem vessels. The mechanisms underlying root attachment are poorly understood, although it was previously shown that this process depends on Fmk1, a mitogen-activated protein kinase orthologous to the mating/filamentation mitogen-activated protein kinases Fus3/Kss1 in yeast. We investigated the hypothesis that root adhesion is mediated by fungal cell wall proteins (CWPs). To characterize the cell wall subproteome of F. oxysporum, we performed LC-MS/MS analysis of tryptic digests of purified cell walls obtained from adhesion-inducing conditions, identifying a total of 174 proteins, 19 of which contain a predicted signal peptide and 10 of which have a predicted glycosylphosphatidyl-inositol motif. 2-D DIGE was used to compare four different fractions of CWPs extracted from hyphae of the wild-type strain and the Deltafmk1 mutant. We detected 18 proteins differing significantly in abundance between the two strains. Differential expression of five of these proteins was confirmed by RT-PCR analysis. A significant fraction of the subproteome lacked functional information, highlighting the limitations in the current understanding of CWPs in F. oxysporum.

Immunoproteomic analysis of the protective response obtained from vaccination with Candida albicans ecm33 cell wall mutant in mice.

Systemic candidiasis remains a major cause of disease and death, particularly among immunocompromised patients. The cell wall of Candida albicans defines the interface between host and pathogen and surface proteins are major elicitors of host immune responses during candidiasis. The C. albicans ecm33 mutant (RML2U) presents an altered cell wall, which entails an increase in the outermost protein layer. Vaccination of BALB/c mice with RML2U mutant protected them from a subsequent lethal infection with virulent strain SC5314 in a systemic candidiasis model. Using immunoproteomics (2-DE followed by Immunoblotting) we detected 29 immunoreactive proteins specifically recognized by antibodies from vaccinated mice sera, six of which are described as immunogenic for the first time (Gnd1p, Cit1p, Rpl10Ep, Yst1p, Cys4p, Efb1p). Furthermore, identification of wild type and mutant cell surface proteome (surfome), confirmed us that the mutant surfome presented a larger number of proteins than the wild type. Interestingly, proteins exclusively identified in the mutant surfome (Met6p, Eft2p, Tkl1p, Rpl10Ep, Atp1p, Atp2p) were also detected as immunogenic, supporting the idea that their surface location enhances their immunoprotective capacity.

Proporción de infecciones oportunistas y factores de riesgo asociados a su aparición en pacientes con VIH / Proportion of opportunistic infections and risk factors associated with its appearance in patients with HIV

Antecedentes: Las infecciones oportunistas son la principal causa de morbilidad, discapaci- dad y mortalidad en pacientes con VIH, aumentando el número de hospitalizaciones y costos en la atención. Objetivo: Estimar la proporción de infecciones oportunistas e identificar los factores asociados a su aparición en pacientes con VIH atendidos en el Servicio de Atención Integral del Hospital Nacional Dr. Mario Catarino Rivas, San Pedro Sula, 2019-2020. Métodos: Estudio no experimental, analítico de casos (infección oportunista presente) y controles. Se evaluaron 40 casos y 120 controles, con un nivel de confianza de 95%, poder estadístico de 80%, con muestreo tipo aleatorio simple. Se utilizó la distribución de variables entre casos y controles para la obtención de Odds Ratio. Resultados: Las infecciones oportunistas incluyeron: 52.5% (21) tuberculosis, 15.0% (6) histoplasmosis, 12.5% (5) citomegalovirus, 10.0% (4) toxoplasmosis, 10.0% (4) candidiasis, 7.5% (3) criptococosis. El conteo de linfocitos T CD4 fue <200 cel/mm3 en 60.0% (24) de grupo casos y 10.8% (13) de grupo control. La carga viral ˃1000 copias/ml (OR 14.500 IC95% 6.109-34.415), el antecedente de abandono (OR 4.363 IC95% 1.928-9.872) y el no tomar tratamiento antirretroviral (OR 64.076 IC95% 8.063-509.165) se asociaron a infecciones oportunistas. La carga viral mayor de 1000 copias/mL predominó en el grupo de casos, y se encontró asociación de esta con la presencia de infecciones oportunistas con OR 14.500 (IC 95% 6.109-34.415, p=.0001). Conclusión: El no tomar ARV aumenta 64 veces más el riesgo de desarrollar infecciones oportunistas y el haber abandonado el tratamiento antirretroviral aumenta 4 veces más la probabilidad de desarrollar una infección oportunista. El tratamiento antirretroviral de gran actividad y el apego al mismo es la mejor estrategia para prevenir las infecciones oportunistas en pacientes infectados por el VIH...(AU)

Impacto de la implementación de inicio temprano de terapia antirretroviral en nuevos diagnósticos de VIH: estudio de casos y controles / Impact of the implementation of early initiation of antiretroviral therapy in new HIV diagnoses: case-control study

Antecedentes: En Honduras aún se prioriza asegurar la aceptación del diagnóstico de Virus de Inmunodeficiencia Humana (VIH) y la adherencia al tratamiento del Terapia Anti Retroviral (TAR), provocando retraso en su inicio, consecuencias negativas y alto riesgo de muerte. Objetivo: Evaluar el impacto del inicio temprano de TAR en pacientes con nuevos diagnósti- cos de VIH en el Hospital Nacional Mario Catarino Rivas (HNMCR). Pacientes y Métodos: Investigación analítica, observacional de casos y controles. Muestra: 62 casos que iniciaron TAR temprano, de enero a agosto del 2019 y 62 controles que iniciaron TAR en el 2018, fuera de la estrategia de inicios tempranos. Se tomaron datos de expedientes clínicos y se vacío la información en instrumento tipo cuestionario. Resultados: Se encontró más rápida vinculación al servicio y más inicios tempranos de TAR en el grupo casos (OR 19.6, IC 95% 7.2-53.0, p=0.000), una mayor captación en etapa temprana A1 (OR 3.45, IC 95% 1.36-8.59, p=0.006), un menor cambio de estadio clínico (OR 2.35, IC 95% 0.92-5.98, p= 0.070), mayor cumplimiento de evaluación psicológica (OR 8.15, IC 95% 3.42-19.4, p=0.000), menor riesgo de infecciones oportunistas (OR 3.01, IC 95% 1.34-6.74, p=0.006), menor riesgo de hospita- lización (OR 1.33, IC 95% 0.46-3.84, p=0.596), mayor tamizaje de IO (p=0.000). Conclusión /Recomendación: El inicio del TAR en los primeros 7 días posterior al diagnóstico aporta beneficios clínicos y profilácticos, mejorando la calidad de vida y disminuyendo la transmisibilidad del virus. Se recomienda protocolizar los inicios tempranos como estrategia de atención a los nuevos diagnósticos de VIH...(AU)

The Cell Wall Protein Ecm33 of Candida albicans is Involved in Chronological Life Span, Morphogenesis, Cell Wall Regeneration, Stress Tolerance, and Host-Cell Interaction.

Ecm33 is a glycosylphosphatidylinositol-anchored protein in the human pathogen Candida albicans. This protein is known to be involved in fungal cell wall integrity (CWI) and is also critical for normal virulence in the mouse model of hematogenously disseminated candidiasis, but its function remains unknown. In this work, several phenotypic analyses of the C. albicans ecm33/ecm33 mutant (RML2U) were performed. We observed that RML2U displays the inability of protoplast to regenerate the cell wall, activation of the CWI pathway, hypersensitivity to temperature, osmotic and oxidative stresses and a shortened chronological lifespan. During the exponential and stationary culture phases, nuclear and actin staining revealed the possible arrest of the cell cycle in RML2U cells. Interestingly, a "veil growth," never previously described in C. albicans, was serendipitously observed under static stationary cells. The cells that formed this structure were also observed in cornmeal liquid cultures. These cells are giant, round cells, without DNA, and contain large vacuoles, similar to autophagic cells observed in other fungi. Furthermore, RML2U was phagocytozed more than the wild-type strain by macrophages at earlier time points, but the damage caused to the mouse cells was less than with the wild-type strain. Additionally, the percentage of RML2U apoptotic cells after interaction with macrophages was fewer than in the wild-type strain.

Resistencia antirretroviral en pacientes con virus de inmuno- deficiencia humana en Hospital Nacional Mario Catarino Rivas / Resistance to antiretroviral drugs in patients with human immunodeficiency virus in Mario Catarino Rivas National Hospital

Introducción: La terapia antirretroviral de primera línea utilizada en el país desde hace varios años, consiste en un inhibidor de la transcriptasa reversa no nucleósido con dos inhibidores de la transcriptasa reversa nucleósidos, está asociada al fallo terapéutico y se ha reportado resis- tencia a la misma. Objetivo: conocer la resistencia a la terapia antirretroviral de primera línea en pacientes tratados por Virus de Inmunodeficiencia Humana en Hospital Nacional Mario Catarino Rivas desde octubre 2016 al 2017. Pacientes y métodos: Investigación observacio- nal, descriptiva; tipo cohorte transversal, retrospectiva. Población de 313 pacientes a quienes se le realizó prueba de genotipo, de los cuales se tomaron como muestra 291 pacientes distri- buidos por grupos: sin previa exposición a antirretrovirales, pediátricos, con 12 meses de trata- miento y 48 o más meses de tratamiento a quienes se les realizó prueba de genotipo. Resulta- dos: Hubo amplificación en el 52% (152) de los pacientes, de los cuales el 56% (85) presentó resistencia a tratamiento antirretroviral, con prevalencia de resistencia de inhibidores de trans- criptasa reversa análogo de nucleósidos del 75% (64), los inhibidores de transcriptasa reversa no nucleósidos (ITRNN) con 89% (76) y los inhibidores de proteasa del 15% (13). Se encontró una prevalencia de resistencia primaria del 19% en pacientes de diagnóstico nuevo. Conclu- sión: Se recomienda el cambio de primera línea de terapia antirretroviral ya que se identifica- ron mutaciones de resistencia a los ITRNN en un 91% en los pacientes con diagnóstico recien- te y sin exposición a ARV. La OMS recomienda retirar los ITRNN como primera línea e incluir fármacos con mejor barrera genética, cuando los niveles de resistencia para los ITRNN sean >10%...(AU)

Candida albicans Ecm33p is important for normal cell wall architecture and interactions with host cells.

Candida albicans ECM33 encodes a glycosylphosphatidylinositol-linked cell wall protein that is important for cell wall integrity. It is also critical for normal virulence in the mouse model of hematogenously disseminated candidiasis. To identify potential mechanisms through which Ecm33p contributes to virulence, we investigated the interactions of C. albicans ecm33Delta mutants with endothelial cells and the FaDu oral epithelial cell line in vitro. The growth rate of blastospores of strains containing either one or no intact copies of ECM33 was 50% slower than that of strains containing two intact copies of ECM33. However, all strains germinated at the same rate, forming similar-length hyphae on endothelial cells and oral epithelial cells. Strains containing either one or no intact copies of ECM33 had modestly reduced adherence to both types of host cells, and a markedly reduced capacity to invade and damage these cells. Saccharomyces cerevisiae expressing C. albicans ECM33 did not adhere to or invade epithelial cells, suggesting that Ecm33p by itself does not act as an adhesin or invasin. Examination of ecm33Delta mutants by transmission electron microscopy revealed that the cell wall of these strains had an abnormally electron-dense outer mannoprotein layer, which may represent a compensatory response to reduced cell wall integrity. The hyphae of these mutants also had aberrant surface localization of the adhesin Als1p. Collectively, these results suggest that Ecm33p is required for normal cell wall architecture as well as normal function and expression of cell surface proteins in C. albicans.

The GPI-anchored protein CaEcm33p is required for cell wall integrity, morphogenesis and virulence in Candida albicans.

Ecm33p is a widely distributed fungal protein with functional relevance, clearly demonstrated by ecm33Delta mutant phenotypes, mainly related to the cell wall. Homology searches with Saccharomyces cerevisiae genes identified Candida albicans Ecm33p, as well as the two other proteins of its family: Pst1p and the product of YCL048w. C. albicans Ecm33p is a 423 aa protein which has the typical features of cell-surface GPI proteins and is able to complement S. cerevisiae ecm33Delta cell wall defects. Heterozygous (RML1) and homozygous (RML2) mutants of CaECM33 were obtained, as well as a single and a double reintegrant (RML3 and RML4, respectively). Caecm33 mutant strains displayed an aberrant morphology, being more rounded and bigger than the wild-type, suggesting morphogenetic defects. They also exhibited cell wall defects, with enhanced sensitivity to different compounds that interfere in polymerization of cell wall components (Calcofluor white, Congo red and hygromycin B) and a marked tendency to flocculate extensively. In addition, CaEcm33p is required for normal C. albicans yeast-to-hyphae transition in vitro. In liquid medium (5 % serum), the transition was delayed in Caecm33 mutants, and after 24 h the culture contained very abnormal large and rounded cells. On solid medium (10 % serum, Spider or SLADH) RML2 failed to produce hyphae and media invasiveness. CaECM33 showed a gene dosage effect, demonstrated by the intermediate phenotype of the heterozygous mutants RML1 and confirmed by Northern blot analysis. Furthermore, CaEcm33p is also involved in C. albicans virulence. In a murine systemic model of infection, 100 % mouse survival and no kidney or brain colonization were obtained 30 days after infection with 10(6) Candida cells of any homozygous or heterozygous Caecm33Delta mutant tested. In contrast, all mice infected with parental or RML4 (two CaECM33 copies reintegrated) strains died in a few days, showing that, in these conditions, two CaECM33 copies were required for virulence.