Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis.

Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.

Biomarkers and short-term prognosis in COVID-19.

PURPOSE: The aim of our study was to analyse the short-term prognostic value of different biomarkers in patients with COVID-19. METHODS: We included patients admitted to emergency department with COVID-19 and available concentrations of cardiac troponin I (cTnI), D-dimer, C-reactive protein (CRP) and lactate dehydrogenase (LDH). Patients were classified for each biomarker into two groups (low vs. high concentrations) according to their best cut-off point, and 30-day all-cause death was evaluated. RESULTS: After multivariate adjustment, cTnI ≥21 ng/L, D-dimer ≥1112 ng/mL, CRP ≥10 mg/dL and LDH ≥334 U/L at admission were associated with an increased risk of 30-day all-cause death (hazard ratio (HR) 4.30; 95% CI 1.74-10.58; p = 0.002; HR 3.35; 95% CI 1.58-7.13; p = 0.002; HR 2.25; 95% CI 1.13-4.50; p = 0.021; HR 2.00; 95% CI 1.04-3.84; p = 0.039, respectively). The area under the curve for cTnI was 0.825 (95% CI 0.759-0.892) and, in comparison, was significantly better than CRP (0.685; 95% CI 0.600-0.770; p = 0.009) and LDH (0.643; 95% CI 0.534-0.753; p = 0.006) but non-significantly better than D-dimer (0.756; 95% CI 0.674-0.837; p = 0.115). CONCLUSIONS: In patients with COVID-19, increased concentrations of cTnI, D-dimer, CRP and LDH are associated with short-term mortality. Of these, cTnI provides better mortality risk prediction. However, differences with D-dimer were non-significant.

Use of predictive tools in the management of COVID-19 patients: a key role of clinical laboratories.

Objectives: Coronavirus disease 2019 (COVID-19) is widely spreading and represents a critical threat to global health. In the fight against this pandemic, provincial hospitals urgently need rapid diagnostic of COVID-19 infected patients to avoid collapsing of emergency units. However, the high demand of patients with severe acute respiratory symptoms limits the fast delivery of results by the gold standard method reverse transcription-polymerase chain reaction real time (rRT-PCR) for the identification of COVID-19 positive pneumonia. The principal aim is to find other useful laboratory indicators to assist rRT-PCR tests and to help controlling of this outbreak. Methods: Blood, coagulation and inflammatory parameters were collected from a total of 309 patients classified as negative (128) and positive (181) rRT-PCR test groups. Patients were classified as positive by molecular diagnostic test. Results: Leukocyte count (WBC), neutrophils count, lymphocytes count and lactate dehydrogenase (LDH) were statistically different between both groups of patients. The use of LDH/WBC ratio increases the diagnostic performance with the best area under the curve (0.783), sensibility (82%) and the best percentage (80.5%) of correctly identified COVID-19 positive patients. Conclusions: The combination of predictive LDH/WBC ratio with clinical illness features could help in medical management of patients and improve the technical resources of hospitals, especially in a critical scenario with a large shortage of medical equipment and lack of reagents for performing rRT-PCR.

Obstrucción nasal en paciente marroquí / Nasal obstruction in a Moroccan patient

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Pulmonary nodules: An unusual onset of HIV infection belatedly diagnosed.

BACKGROUND: Cryptococcosis is a generally systemic and potentially lethal fungal infection. Although HIV infection is a predisposing condition, especially if the CD4+ lymphocyte count is less than 100cells/mm3, other forms of immunosuppression may be associated with this opportunistic fungal condition, such as prolonged steroid therapy or solid organ transplantation. Pulmonary presentation must be included in the differential diagnosis of pneumonia or pulmonary neoplasia in the immunosuppressed patient. CASE REPORT: We report a case of pulmonary cryptococcosis in a non-diagnosed HIV patient. In a 44 year-old male suffering from dyspnea and chest pain the image of a pulmonary nodule was observed in a radiological finding. In the histopathological study, intracellular structures suggestive of fungal conidia, and morphologically compatible with Cryptococcus, were observed. HIV serology and cryptococcal antigen detection in serum were requested, given the possibility of cryptococcosis. Cryptococcus neoformans var. grubii was isolated from the culture of the pulmonary biopsy. The patient was finally diagnosed with pulmonary cryptococcosis and HIV-1 infection. With a proper antifungal treatment the patient evolved satisfactorily. CONCLUSIONS: The best strategy to avoid opportunistic infections such as cryptococcosis in HIV-infected patients consists of an early diagnosis and a highly active antiretroviral treatment. In our case, the diagnosis of a pulmonary infection by C. neoformans var. grubii allowed a late diagnosis of HIV-1 infection.

Pulmonary nodules: an unusual onset of HIV infection belatedly diagnosed / Nódulos pulmonares: un inicio infrecuente de la infección por VIH diagnosticada tardíamente

Background: Cryptococcosis is a generally systemic and potentially lethal fungal infection. Although HIV infection is a predisposing condition, especially if the CD4+ lymphocyte count is less than 100cells/mm3, other forms of immunosuppression may be associated with this opportunistic fungal condition, such as prolonged steroid therapy or solid organ transplantation. Pulmonary presentation must be included in the differential diagnosis of pneumonia or pulmonary neoplasia in the immunosuppressed patient. Case report: We report a case of pulmonary cryptococcosis in a non-diagnosed HIV patient. In a 44 year-old male suffering from dyspnea and chest pain the image of a pulmonary nodule was observed in a radiological finding. In the histopathological study, intracellular structures suggestive of fungal conidia, and morphologically compatible with Cryptococcus, were observed. HIV serology and cryptococcal antigen detection in serum were requested, given the possibility of cryptococcosis. Cryptococcus neoformans var. grubii was isolated from the culture of the pulmonary biopsy. The patient was finally diagnosed with pulmonary cryptococcosis and HIV-1 infection. With a proper antifungal treatment the patient evolved satisfactorily. Conclusions: The best strategy to avoid opportunistic infections such as cryptococcosis in HIV-infected patients consists of an early diagnosis and a highly active antiretroviral treatment. In our case, the diagnosis of a pulmonary infection by C. neoformans var. grubii allowed a late diagnosis of HIV-1 infection

Antecedentes: La criptococosis es una infección fúngica generalmente sistémica y potencialmente letal. Aunque la infección por VIH es una condición predisponente, especialmente si el recuento de linfocitos CD4+ es inferior a 100células/mm3, otras formas de inmunosupresión, como la terapia prolongada con esteroides o el trasplante de órgano sólido, pueden asociarse a esta micosis oportunista. La forma pulmonar debe incluirse en el diagnóstico diferencial de neumonía o neoplasia pulmonar en el paciente inmunodeprimido. Caso clínico: Presentamos un caso de criptococosis pulmonar en un paciente con VIH no diagnosticado. Varón de 44 años aquejado de disnea y dolor torácico en el que como hallazgo radiológico se observa un nódulo pulmonar. En el estudio histopatológico del mismo se observaron estructuras intracelulares sugestivas de conidias fúngicas, morfológicamente compatibles con Cryptococcus. Ante la sospecha de criptococosis se solicitó la serología de VIH y la detección en suero de antígeno criptocócico. Se aisló Cryptococcus neoformans variedad grubii de la siembra de la biopsia pulmonar. El paciente fue finalmente diagnosticado de criptococosis pulmonar e infección por VIH-1. Con el tratamiento antifúngico, el paciente evolucionó satisfactoriamente. Conclusiones: La mejor estrategia para evitar infecciones oportunistas como la criptococosis en pacientes infectados por VIH consiste en un diagnóstico precoz y un tratamiento antirretroviral de gran actividad. En este caso, el diagnóstico de infección pulmonar por C. neoformans var. grubii permitió un diagnóstico tardío de infección por VIH-1