Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing

Carbapenem resistance is a major concern in the management of antibiotic-resistant Pseudomonas aeruginosa infections. The direct prediction of carbapenem-resistant phenotype from genotype in P. aeruginosa isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in P. aeruginosa make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622 P. aeruginosa isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in P. aeruginosa, including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in P. aeruginosa from clinical samples by the key gene features selected and prediction models constructed, 72 P. aeruginosa-positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72 P. aeruginosa-positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive P. aeruginosa were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of P. aeruginosa, the carbapenem resistance of P. aeruginosa could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant P. aeruginosa.

Stress hyperglycemia ratio is associated with systemic inflammation and clinical outcomes in diabetic inpatients with pneumonia on admission

BACKGROUNDS

Stress hyperglycemia ratio (SHR) reflects the acute blood glucose change in response to acute illnesses or injuries, including pneumonia. We aimed to investigate the associations of SHR with systemic inflammation and clinical outcomes in diabetic inpatients with pneumonia on admission.

METHODS

A multicenter and retrospective study was conducted among diabetic inpatients with pneumonia on admission via electronic medical records from 2013 to 2019 in Ruijin Hospital, Shengjing Hospital, and China-Japan Friendship Hospital.

RESULTS

The study included 1631 diabetic inpatients with pneumonia on admission. Patients of the fourth quartile (Q4) of SHR on admission showed significantly elevated systemic inflammation compared with those of the first quartile (Q1), second quartile (Q2), or third quartile (Q3) of SHR, including more white blood cells (9.1 × 10⁹ /L in Q4 vs 7.6 × 10⁹ /L in Q1, 7.9 × 10⁹ /L in Q2, and 8.0 × 10⁹ /L in Q3, p < .001), higher neutrophil-to-lymphocyte ratio (7.0 in Q4 vs 3.6 in Q1, 3.8 in Q2, and 4.0 in Q3, p < .001), higher C-reactive protein (52.8 mg/L in Q4 vs 18.9 mg/L in Q1, p < .001; 52.8 mg/L in Q4 vs 28.6 mg/L in Q2, p = .002), higher procalcitonin (0.22 ng/mL in Q4 vs 0.10 ng/mL in Q1, 0.09 ng/mL in Q2, and 0.11 ng/mL in Q3, p < .001), and higher D-dimer (0.67 mg/L in Q4 vs 0.47 mg/L in Q1, 0.50 mg/L in Q2, and 0.47 mg/L in Q3, p < .001). Excluding patients with hypoglycemia on admission in the analyses, there were still distinct J-shaped associations between SHR and adverse clinical outcomes in patients with different severity of pneumonia, especially in those with CURB-65 score for pneumonia severity (Confusion, blood Urea nitrogen, Respiratory rate, Blood pressure) ≥ 2. In the multivariable regression model, predictive value for adverse clinical outcomes was higher when SHR was taken as a spline term than as quartiles in all patients (area under curve 0.831 vs 0.822, p = .040), and when SHR as a spline term instead of fasting blood glucose was included in patients with CURB-65 ≥ 2 (area under curve 0.755 vs 0.722, p = .027).

CONCLUSIONS

SHR was correlated with systematic inflammation and of J-shaped associations with adverse clinical outcomes in diabetic inpatients with pneumonia of different severity. The inclusion of SHR in the blood glucose management of diabetic inpatients may be beneficial, especially for the prevention of potential hypoglycemia or the recognition of relative glucose insufficiency in those with severe pneumonia or high hemoglobin A_1C .

Corticosteroid therapy for coronavirus disease 2019-related acute respiratory distress syndrome: a cohort study with propensity score analysis

BACKGROUND

The impact of corticosteroid therapy on outcomes of patients with coronavirus disease 2019 (COVID-19) is highly controversial. We aimed to compare the risk of death between COVID-19-related ARDS patients with corticosteroid treatment and those without.

METHODS

In this single-center retrospective observational study, patients with ARDS caused by COVID-19 between January 20, 2020, and February 24, 2020, were enrolled. The primary outcome was 60-day in-hospital death. The exposure was prescribed systemic corticosteroids or not. Time-dependent Cox regression models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) for 60-day in-hospital mortality.

RESULTS

A total of 382 patients [60.7 ± 14.1 years old (mean ± SD), 61.3% males] were analyzed. The median of sequential organ failure assessment (SOFA) score was 2.0 (IQR 2.0-3.0). Of these cases, 94 (24.6%) patients had invasive mechanical ventilation. The number of patients received systemic corticosteroids was 226 (59.2%), and 156 (40.8%) received standard treatment. The maximum dose of corticosteroids was 80.0 (IQR 40.0-80.0) mg equivalent methylprednisolone per day, and duration of corticosteroid treatment was 7.0 (4.0-12.0) days in total. In Cox regression analysis using corticosteroid treatment as a time-varying variable, corticosteroid treatment was associated with a significant reduction in risk of in-hospital death within 60 days after adjusting for age, sex, SOFA score at hospital admission, propensity score of corticosteroid treatment, comorbidities, antiviral treatment, and respiratory supports (HR 0.42; 95% CI 0.21, 0.85; p = 0.0160). Corticosteroids were not associated with delayed viral RNA clearance in our cohort.

CONCLUSION

In this clinical practice setting, low-dose corticosteroid treatment was associated with reduced risk of in-hospital death within 60 days in COVID-19 patients who developed ARDS.

Coagulopathy is a major extrapulmonary risk factor for mortality in hospitalized patients with COVID-19 with type 2 diabetes

INTRODUCTION

To investigate the risk factors for the death in patients with COVID-19 with type 2 diabetes mellitus (T2DM).

RESEARCH DESIGN AND METHODS

We retrospectively enrolled inpatients with COVID-19 from Wuhan Jinyintan Hospital (Wuhan, China) between December 25, 2019, and March 3, 2020. The epidemiological and clinical data were compared between non-T2DM and T2DM or between survivors and non-survivors. Univariable and multivariable Cox regression analyses were used to explore the effect of T2DM and complications on in-hospital death.

RESULTS

A total of 1105 inpatients with COVID-19, 967 subjects with without T2DM (n=522 male, 54.0%) and 138 subjects with pre-existing T2DM (n=82 male, 59.4%) were included for baseline characteristics analyses. The complications were also markedly increased in patients with pre-existing T2DM, including acute respiratory distress syndrome (ARDS) (48.6% vs 32.3%, p<0.001), acute cardiac injury (ACI) (36.2% vs 16.7%, p<0.001), acute kidney injury (AKI) (24.8% vs 9.5%, p<0.001), coagulopathy (24.8% vs 11.1%, p<0.001), and hypoproteinemia (21.2% vs 9.4%, p<0.001). The in-hospital mortality was significantly higher in patients with pre-existing T2DM compared with those without T2DM (35.3% vs 17.4%, p<0.001). Moreover, in hospitalized patients with COVID-19 with T2DM, ARDS and coagulopathy were the main causes of mortality, with an HR of 7.96 (95% CI 2.25 to 28.24, p=0.001) for ARDS and an HR of 2.37 (95% CI 1.08 to 5.21, p=0.032) for coagulopathy. This was different from inpatients with COVID-19 without T2DM, in whom ARDS and cardiac injury were the main causes of mortality, with an HR of 12.18 (95% CI 5.74 to 25.89, p<0.001) for ARDS and an HR of 4.42 (95% CI 2.73 to 7.15, p<0.001) for cardiac injury.

CONCLUSIONS

Coagulopathy was a major extrapulmonary risk factor for death in inpatients with COVID-19 with T2DM rather than ACI and AKI, which were well associated with mortality in inpatients with COVID-19 without T2DM.

2019 novel coronavirus of pneumonia in Wuhan, China: emerging attack and management strategies

An ongoing outbreak of 2019-nCoV pneumonia was first identified in Wuhan, Hubei province, China at the end of 2019. With the spread of the new coronavirus accelerating, person-to-person transmission in family homes or hospitals, and intercity spread of 2019-nCoV occurred. At least 40,261 cases confirmed, 23,589 cases suspected, 909 cases death and 3444 cases cured in China and worldwide 24 countries confirmed 383 cases being diagnosed, 1 case death in February 10th, 2020. At present, the mortality of 2019-nCoV in China is 2.3%, compared with 9.6% of SARS and 34.4% of MERS reported by WHO. It seems the new virus is not as fatal as many people thought. Chinese authorities improved surveillance network, made the laboratory be able to recognize the outbreak within a few weeks and announced the virus genome that provide efficient epidemiological control. More comprehensive information is required to understand 2019-nCoV feature, the epidemiology of origin and spreading, and the clinical phenomina. According to the current status, blocking transmission, isolation, protection, and alternative medication are the urgent management strategies against 2019-nCoV.