Differential gene expression analysis of common target genes for the detection of SARS-CoV-2 using real time-PCR.

COVID-19 currently is the main cause of the severe acute respiratory disease and fatal outcomes in human beings worldwide. Several genes are used as targets for the detection of SARS-CoV-2, including the RDRP, N, and E genes. The present study aimed to determine the RDRP, N, and E genes expressions of SARS-CoV- 2 in clinical samples. For this purpose, 100 SARS-CoV-2 positive samples were collected from diagnostic laboratories of Mazandaran province, Iran. After RNA extraction, the real-time reverse transcription PCR (real-time RT-PCR) assay was performed for differential gene expressions' analysis of N, E, and RDRP. The threshold cycle (Ct) values for N, RDRP, and E targets of 100 clinical samples for identifying SARS-CoV-2 were then evaluated using quantitative real-time PCR (qRT-PCR). This result suggests N gene as a potential target for the detection of the SARS-CoV-2, since it was observed to be highly expressed in the nasopharyngeal or oropharynges of COVID-19 patients (P < 0.0001). Herein, we showed that SARS-CoV- 2 genes were differentially expressed in the host cells. Therefore, to reduce obtaining false negative results and to increase the sensitivity of the available diagnostic tests, the target genes should be carefully selected based on the most expressed genes in the cells.

Surgery without preoperative histological confirmation of lung cancer: what is the current clinical practice?

BACKGROUND: There are discordances in the guidelines regarding the need to acquire histological diagnosis before surgical treatment of (presumed) lung cancer. Preoperative histological confirmation is always encouraged in this setting to prevent unnecessary surgery or when sublobar resection for small-sized tumors is considered. The aim of this retrospective cohort study was to assess the proportion of patients undergoing lung cancer resection in the Netherlands without preoperative pathological confirmation, based on the intraoperative pathological diagnosis (IOD) rate, and to determine characteristics that may influence IOD frequency. METHODS: Data on 10,226 patients, who underwent surgical treatment for lung cancer from 2010 to 2015, were retrieved from the Netherlands National Cancer Registry. We registered an IOD when the date of diagnosis equaled the date of the first surgical intervention. Tabulations and multivariable logistic regression were used to identify predictive parameters for IOD. RESULTS: 36% of surgical procedures were classified as IOD, and decreased with increasing tumor size and extent of surgery (57% for segmentectomy, 39% for lobectomy and 11% for pneumonectomy). IOD was more frequently observed in adenocarcinoma (41%), varied between hospitals from 13% to 66% and was less common when patients were referred from a hospital where thoracic surgery was not performed. Previous history of cancer did not affect IOD. CONCLUSIONS: More than one-third of patients with suspected lung cancer in the Netherlands was operated without preoperative histological confirmation. There was significant variation in IOD rates between different hospitals, which deserves further detailed analysis when striving for uniform surgical quality of care for patients with lung cancer.

Risk Assessment After a Severe Hospital-Acquired Infection Associated With Carbapenemase-Producing Pseudomonas aeruginosa.

Importance: Resistance of gram-negative bacilli to carbapenems is rapidly emerging worldwide. In 2016, the World Health Organization defined the hospital-built environment as a core component of infection prevention and control programs. The hospital-built environment has recently been reported as a source for outbreaks and sporadic transmission events of carbapenemase-producing gram-negative bacilli from the environment to patients. Objective: To assess risk after the identification of an unexpected, severe, and lethal hospital-acquired infection caused by carbapenemase-producing Pseudomonas aeruginosa in a carbapenemase-low endemic setting. Design, Settings, and Participants: A case series study in which a risk assessment was performed on all 11 patients admitted to the combined cardiothoracic surgery and pulmonary diseases ward and the hospital-built environment in the Radboud University Medical Center, the Netherlands, in February 2018. Exposures: Water and aerosols containing carbapenemase-producing (Verona integron-mediated metallo-ß-lactamase [VIM]) P aeruginosa. Main Outcomes and Measures: Colonization and/or infection of patients and/or contamination of the environment after the detection of 1 patient infected with carbapenemase-producing (VIM) P aeruginosa. Results: A total of 5 men (age range, 60-84 years) and 6 women (age range, 55-74 years) were admitted to the combined cardiothoracic surgery and pulmonary diseases ward. The risk assessment was performed after carbapenemase-producing (VIM) P aeruginosa was unexpectedly detected in a man in his early 60s, who had undergone a left-sided pneumonectomy and adjuvant radiotherapy. No additional cases (colonization or infection) of carbapenemase-producing (VIM) P aeruginosa were detected. Plausible transmission of carbapenemase-producing P aeruginosa from the hospital environment to the patient via the air was confirmed by whole-genome sequencing, which proved the relation of Pseudomonas strains from the patient, the shower drains in 8 patient rooms, 1 sink, and an air sample. Conclusions and Relevance: This study suggests that rethinking the hospital-built environment, including shower drains and the sewage system, will be crucial for the prevention of severe and potential lethal hospital-acquired infections.