Background: The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified via culture or the BioFire® FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in the ICU and the concordance between these techniques. Methods: This was a prospective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 h and on mechanical ventilation for no longer than 24 h in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed via conventional culture and the FA-PNEU. Coinfection was defined as the identification of a respiratory pathogen using the FA-PNEU or cultures. Serum samples of leukocytes, C-reactive protein, and procalcitonin were taken on the first day of intubation. We analyzed the empirical antibiotics and the changes in antibiotic management according to the results of the FA-PNEUM and cultures. Results: Of 110 patients whose samples underwent both methods, FA-PNEU- and culture-positive samples comprised 24.54% versus 17.27%, respectively. Eighteen samples were positive in both techniques, 82 were negative, 1 was culture-positive with a negative FA-PNEU result, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by the FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%), and those detected by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1%, and when stratified by microorganism, it was between 92.7 and 100%. The positive predictive value (PPV) was between 50 and 100% and were lower for Enterobacter cloacae and Staphylococcus aureus. The negative predictive value (NPV) was high (between 99.1 and 100%); MecA/C/MREJ had a specificity of 94.55% and an NPV of 100%. The inflammatory response tests showed no significant differences between patients whose samples were positive and negative for both techniques. Sixty-one patients (55.45%) received at least one dose of empirical antibiotics. Conclusions: The overall concordance was 90.1%, and it was between 92.7% and 100% when stratified by microorganisms. The positive predictive value was between 50 and 100%, with a very high NPV.

Adverse events in critical care: Search and active detection through the Trigger Tool

Background: High levels of different cytokines have been associated in COVID-19 as predictors of mortality; however, not all studies have found this association and its role to cause multi-organ failure and death has not been fully defined. This study aimed to investigate the association of the levels of 10 cytokines with mortality in patients with COVID-19 admitted to the intensive care unit (ICU).Materials and methods: This is a case-control study nested within a cohort of patients with COVID-19 who were on mechanical ventilation and were not hospitalized for more than 48 h across nine ICUs in Medellín, Colombia. Serum samples were collected upon admission to the ICU and 7 days later and used to measure cytokine levels.Results: Upon admission, no differences in mortality between the cytokine levels were observed when comparisons were made quantitatively. However, in the multivariate analysis, patients with median IL-1β levels <1.365 pg/ml showed an increase in mortality (OR = 3.1; 1.24<7.71; p = 0.015). On day 7 in the ICU, IL-1β median levels were lower (0.34 vs. 2.41 pg/ml, p = 0.042) and IL-10 higher (2.08 vs. 1.05 pg/ml, p = 0.009) in patients who died. However, in the multivariate analysis, only IL-12p70 was associated with mortality (OR = 0.23; 0.07<0.73; p = 0.012). The mean difference in the levels between day 1 and day 7 decreased in both IFN-γ (3.939 pg/ml, p < 0.039) and in IL-18 (16.312 pg/ml, p < 0.014) in the patients who died. A low IL-1β/IL-10 ratio was associated with mortality on both day 1 and day 7, while an IL-1β/IL-10 ratio below the cut-off on day 7 was associated with decreased survival. The lowest TNFα/IL-10 ratio was associated with mortality only on day 7.Conclusion: At the time of admission, patients with median IL-1β levels lower than 1.365 pg/ml had increased mortality. An IL-1β/IL-10 ratio 1.666 pg/ml was associated with decreased survival.

Few studies have analyzed the role of the lung microbiome in the diagnosis of pulmonary coinfection in ventilated ICU COVID-19 patients. We characterized the lung microbiota in COVID-19 patients with severe pneumonia on invasive mechanical ventilation using full-length 16S rRNA gene sequencing and established its relationship with coinfections, mortality, and the need for mechanical ventilation for more than 7 days. This study included 67 COVID-19 ICU patients. DNA extracted from mini-bronchoalveolar lavage fluid and endotracheal aspirates was amplified by PCR with specific 16S primers (27F and 1492R). General and relative bacterial abundance analysis was also conducted. Alpha diversity was measured by the Shannon and Simpson indices, and differences in the microbiota were established using beta diversity. A linear discriminant analysis (LDA) effect size algorithm was implemented to describe biomarkers. Streptococcus spp. represented 51% of the overall microbial abundance. There were no differences in alpha diversity between the analyzed variables. There was variation in bacterial composition between samples that had positive and negative cultures. The genera Veillonella sp., Granulicatella sp., Enterococcus sp. and Lactiplantibacillus sp., with LDA scores > 2, were biomarkers associated with negative cultures. Rothia sp., with an LDA score > 2, was a biomarker associated with mortality.

Introducción. El coronavirus del SARS-CoV-2 ha sido una de las pandemias más significativas de la era moderna. Es un coronavirus con alta tasa de mutación, lo que genera variantes con cambios en la proteína espícula (spike), que dificulta su contención. La vigilancia genómica es crucial para adaptar estrategias de salud pública y vacunación, especialmente en los países de ingresos bajos y medios, donde el impacto ha sido considerable.Objetivo. Identificar variantes virales y sus presentaciones clínicas en una cohorte prospectiva de pacientes hospitalizados con infección por SARS-CoV-2 entre octubre de 2021 y febrero de 2023.Materiales y métodos. Se recopilaron datos demográficos, historial médico, estado de vacunación y progresión clínica. Se hizo secuenciación del genoma viral en muestras de hisopados nasales confirmadas con la prueba de reacción en cadena de la polimerasa en tiempo real con transcripción inversa para clasificar las cepas y detectar variantes.Resultados. De 63 muestras positivas para SARS-CoV-2, la variante predominante fue ómicron (84 %), seguida de la delta (14 %). La variante delta presentó la mayor proporción de enfermedad grave (100 % casos críticos) comparada con ómicron (30 % casos críticos). Se identificaron mutaciones en la proteína espícula en cuatro categorías (A-D), junto con mutaciones específicas del gen S.Conclusión. Los patrones de mutación observados coinciden con los reportes globales, con mayor seriedad clínica en la variante delta. Se identificaron mutaciones en la proteína espiga que confieren propiedades distintivas al virus. Estos hallazgos resaltan la necesidad de la vigilancia genómica continua para comprender la dinámica de la infección y orientar las estrategias de salud pública.

Background: Despite hybrid and vaccine-induced immunity, SARS-CoV-2 continues to cause disease. The characterization of humoral and cellular immune responses is essential for guiding prevention strategies and booster dose policies; Methods: A prospective cohort study was conducted with 131 hospitalized patients with confirmed COVID-19 in the Aburrá Metropolitan Valley, Colombia. Clinical and immunological data were evaluated on days 1–3, days 5–7, days 8–12, and 4–5 months after diagnosis. Humoral immunity was assessed by enzyme-linked immunosorbent assay (ELISA), chemiluminescent microparticle immunoassay (CMIA), and neutralization testing, and cellular immunity by CD4⁺/CD8 T-cell responses. Results: vaccinated patients had higher baseline levels of IgG and neutralizing antibody positivity than unvaccinated patients (ELISA 89.1% vs. 60.0%; CMIA 86.4% vs. 50.0%; neutralizing antibodies 88.2% vs. 65.0%), but cases of severe disease occurred in both groups. Adults aged ≥65 years had higher antibody positivity, but severe disease persisted. Mortality at 28 days was 7.6%, mainly among critically ill patients with comorbidities. Antibodies persisted at 4–5 months but were lower in those with severe acute disease. Those who received the booster dose showed stronger CD4⁺/CD8⁺ activation (notably against the Omicron variant) than unvaccinated/partially vaccinated patients. Conclusions: Vaccination improved humoral and cellular responses, but severe breakthrough infections still occurred, particularly in high-risk patients.