Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.

[A clinical analysis of 7 cases of allergic bronchopulmonary aspergillosis].

OBJECTIVE: To study the clinical features, diagnosis and treatment of allergic bronchopulmonary aspergillosis (ABPA). METHODS: The clinical presentations, serologic results, chest radiology, pathological results and treatment of 7 patients with ABPA in Chinese PLA General Hospital were retrospectively analyzed. RESULTS: There were 4 males and 3 females, with a mean age of (33 ± 16) years. Before the diagnosis of ABPA, 6 cases had been misdiagnosed as bronchial asthma, 3 as pulmonary infection, 2 as tuberculosis and 1 as bronchiectasis. The main clinical manifestations included cough (n = 6), sputum production (n = 5), hemoptysis (n = 4), wheeze (n = 3), dyspnea(n = 3) and fever(n = 2). All cases had increased total serum IgE levels (median 3040 U/ml) and peripheral blood eosinophil count (median 0.19). Six of them showed increased peripheral eosinophil count median 1.84 × 10(9)/L, and skin test positive for Aspergillus antigen. Five of them had increased serum IgE antibodies specific to A. fumigatus (22 ± 15) kU/L, and 4 had increased serum IgG antibodies specific to A. fumigatus (108 ± 96) mg/L. The chest CT scan findings included transient or fixed pulmonary opacities, central bronchiectasis and finger-in-glove opacities. Five patients were treated with corticosteroids combined with antifungal therapy. CONCLUSIONS: Clinical features of ABPA include a history of asthma, elevation of the total serum IgE levels, presence of aspergillus IgE antibodies, peripheral eosinophilia, and transient or fixed pulmonary opacities and central bronchiectasis. Patients with asthma complicated with bronchiectasis should be routinely screened for Aspergillus skin test, and measurement of total serum IgE levels and chest CT scan are useful for confirmation of the diagnosis of ABPA. Oral glucocorticoids and anti-fungal drugs are effective in treatment of ABPA. Regular follow-up is needed for prevention of recurrence.

[Clinical analysis of non-invasive positive pressure ventilation in immunocompromised host with acute respiratory failure].

OBJECTIVE: To evaluate the value of non-invasive positive pressure ventilation (NPPV) in immunocompromised host (ICH) complicated by acute respiratory failure (ARF), and to investigate predictive variables of success with NPPV in ICH with ARF. METHODS: A retrospective study of immunocompromised patients with ARF, who were admitted to respiratory intensive care unit (RICU) from March 2008 to March 2011, was performed. Based on clinical data, univariate Logistic regression was done for prediction for independent factors affecting the success of NPPV treatment. Immunization status was assessed according to clinical outcome. RESULTS: NPPV was instituted in all 33 cases with ARF initially. Among these patients, 9 patients (27.3%) received sequential invasive mechanical ventilation (IMV, failure group) and all of them died finally; among 24 cases (72.7%) who only received NPPV (success group), 7 patients died (29.2%). There was significant difference between the two groups in mortality (P<0.01). The simplified acute physiology scoreII (SAPSII) in the success group was lower than that in the failure group (33±9 vs. 43±5, P<0.01). However, other clinical data showed no statistical significance between two groups. Univariate Logistic regression analysis identified SAPSII was the independent factor associated with the success of NPPV treatment [odds ratio (OR) =0.83, 95% confidence interval (95% CI) 0.709-0.964, P<0.05]. And SAPSII≥38 was a risk factor for the failure of NPPV [area under receiver operating characteristic (ROC) curve 0.73]. In addition, the lung injury scores (LIS) in the survival group was significantly lower than that of the death group (1.95±0.48 vs. 2.57±0.52, P<0.01), the difference was statistically significant. CD3(+) and CD8(+) T counts in the survivors were higher than that of non-survivors (CD3(+):0.73±0.16 vs. 0.41±0.20; CD8(+): 0.51±0.18 vs. 0.21±0.15, both P<0.01), and the difference was statistically significant. CONCLUSION: As an early treatment for ICH with pulmonary infections suffering from ARF, NPPV can be effective for the ICH patients suffering from severe pulmonary infection through improving hypoxemia, ameliorating respiratory distress symptoms, and avoiding complications associated with IMV when SAPSIIis less than 38. CD3(+), CD8(+), and the LIS can be used to evaluate the prognosis of those patients.

[Antimicrobial resistance and genotyping of Acinetobacter baumannii in ICU].

OBJECTIVE: To investigate the outbreak of acinetobacter baumannii in the ICU, and to explore the antimicrobial resistance characteristics of pathogens, and therefore to determine the optimal prevention strategies. METHODS: From May to June 2007, most of the cases of infection by acinetobacter baumannii in our ICU were collected. PFGE (pulsed field gel electrophoresis) and standard disk diffusion susceptibility tests were performed on the strains isolated from the patients' body fluids including sputum, blood, urine, secretion and from the ICU environment involving the patients' bed sheet, skin surface and medical staff's hands, humidification water of ventilator tubes. RESULTS: Twelve strains were resistant to imipenem and meropenem. Colistin sulphate and tigecycline showed a high rate of antimicrobial activity against the strains, the rate of susceptibility being 100% and 91.7% respectively. These strains belonged to 3 clones (clone A, B, C) and there were 2 sub-clones (A1, A2) belonging to clone A. The sub-clone A1 was isolated from the surface of unwashed medical staff's hands and patients' body fluids. From intermediate to resistance, the antimicrobial characteristics of clone A and clone B to minocycline changed over a month, and there was one strain that was resistant to tigecycline. CONCLUSION: The outbreak of acinetobacter baumannii in the ICU was caused by carbapenem resistant acinetobacter baumannii (CRAb). The delicate changes of disk diffusion susceptibility in clones A and B occurred in one month. Unwashed hands of medical staff were probably responsible for the outbreak.