Diagnostic Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid for the Diagnosis of Suspected Pneumonia in Immunocompromised Patients

Background: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in immunocompromised patients for the diagnosis of suspected pneumonia in comparation to that of conventional microbiological tests (CMTs).Methods: Sixty-nine immunocompromised patients with suspected pneumonia received both CMTs and mNGS of BALF were analyzed retrospectively. The diagnostic value was compared between CMTs and mNGS, using the clinical composite diagnosis as the reference standard. Results: Sixty patients were diagnosed of pneumonia including fifty-two patients with identified pathogens and eight patients with probable pathogens. The overall detection rate of mNGS for pathogens were higher than that of CMTs. However, a comparable diagnostic accuracy of mNGS and CMTs were found for bacterial and viral infections. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs (78% vs. 54%, P＜0.05), which mainly because of the high sensitivity of mNGS in patients with Pneumocystis jirovecii pneumonia (PJP) (100% vs. 28%, P＜0.05). Among fifty-two patients with definite pathogens, nineteen patients (37%) were identified as pulmonary mixed infection, mNGS test showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in mixed infection. Moreover, Pneumocystis jirovecii was the most common pathogen in mix infection and mNGS have identified much more co-pathogens of PJP than CMTs.Conclusions: mNGS of BALF improved the microbial detection rate of pathogens and exhibited remarkable advantages in detecting PJP and identifying mixed infections in immunocompromised patients.

Developing a Screening Procedure During the COVID-19 Pandemic: Process and Challenges Faced by a Low-Incidence Area

Purpose: To summarize the imaging results of COVID-19 pneumonia and develop a computerized tomography (CT) screening procedure for patients at our institution with malignant tumors.Methods: Following epidemiological investigation, 1,429 patients preparing to undergo anti-tumor-treatment underwent CT scans between February 17 and April 16, 2020. When CT findings showed suspected COVID-19 pneumonia after the supervisor radiologist and the thoracic experience radiologist had double-read the initial CT images, radiologists would report the result to our hospital infection control staff. Further necessary examinations, including the RT-PCR test, in the assigned hospital was strongly recommended for patients with positive CT results. The CT examination room would perform sterilization for 30 min to 1 h. If the negative results of any suspected COVID-19 pneumonia CT findings were identified, the radiologists would upload the results to our Hospital Information Systems and inform clinicians within 2 h.Results: Fifty (0.35%, 50/1,429) suspected pneumonia cases, including 29 males and 21 females (median age: 59.5 years old; age range 27–79 years), were identified. A total of 34.0% (17/50) of the patients had a history of lung cancer and 54.0 (27/50) underwent chemotherapy or targeted therapy. Forty-six patients (92.0%) had prior CT scans, and 35 patients (76.1%) with suspected pneumonia were newly seen (median interval time: 62 days). Sub-pleura small patchy or strip-like lesions most likely due to fibrosis or hypostatic pneumonia and cluster of nodular lesions were the two main signs of suspected cases on CT images (34, 68.0%). Twenty-seven patients (54.0%) had, at least once, follow-up CT scan (median interval time: 18.0 days). Only one patient had an increase in size (interval time: 8 days), the immediately RT-PCR test result was negative.Conclusion: CT may be useful as a screening tool for COVID-19 based on imaging features. But the differential diagnosis between COVID-19 and other pulmonary infection and/or non-infectious disease is very difficult due to its overlapping imaging features.The confirmed diagnosis of the COVID-19 infection should be based on the etiologic eventually. The cancer patients at a low-incidence area would continue treatment by screening carefully before admission.

Clinical utility of dual anterior nares and oropharynx MRSA screening polymerase chian reaction assay (PCR) for patients with suspected pneumonia

We reviewed the electronic health records of 1,419 inpatients with anterior nares (AN) and oropharynx (OP) MRSA PCR tests. Concordance was 96.5%. In discordant cases, AN negative–OP positive results increased detection of probable MRSA pneumonia by only 0.3%. A dual testing approach has limited utility in detecting MRSA pneumonia and increases resource utilization.

Prospective Nasal Screening for Methicillin-Resistant Staphylococcus aureus in Critically Ill Patients With Suspected Pneumonia

We carried out a prospective de-escalation study based on methicillin-resistant Staphylococcus aureus (MRSA) nasal cultures in intensive care unit patients with suspected pneumonia. Days of anti-MRSA therapy was significantly reduced in the intervention group (2 [0–3] days vs 1 [0–2] day; P < .01). Time to MRSA de-escalation was also shortened in the intervention group.

Abstract 10992: Machine Learning to Predict In-Hospital Cardiac Arrest in Patients Admitted from the Emergency Department with COVID-19 and Suspected Pneumonia

Introduction: There are only scarce models developed for stratifying the risk of cardiac arrest from COVID-19 patients presenting to the ED with suspected pneumonia. By using the machine learning (ML) approach, we aimed to develop and validate the ML models to predict in-hospital cardiac arrest (IHCA) in patients admitted from the ED. Hypothesis: We hypothesized that ML approach can serve as a valuable tool in identifying patients at risk of IHCA in a timely fashion. Methods: We included the COVID-19 patients admitted from the EDs of five hospitals in Texas between March and November 2020. All adult (≥ 18 years) patients were included if they had positive RT-PCR for SARS-CoV-2 and also received CXR examination for suspected pneumonia. Patients’ demographic, past medical history, vital signs at ED triage, CXR findings, and laboratory results were retrieved from the EMR system. The primary outcome (IHCA) was identified via a resuscitation code. Patients presented as OHCA or without any blood testing were excluded. Nonrandom splitting strategy based on different location was used to divide the dataset into the training (one urban and two suburban hospitals) and testing cohort (one urban and one suburban hospital) at around 2-to-1 ratio. Three supervised ML models were trained and performances were evaluated and compared with the National Early Warning Score (NEWS) by the area under the receiver operating characteristic curve (AUC). Results: We included 1,485 records for analysis. Of them, 190 (12.8%) developed IHCA. Of the constructed ML models, Random Forest outperformed the others with the best AUC result (0.930, 95% CI: 0.896-0.958), followed by Gradient Boosting (0.929, 95% CI: 0.891-0.959) and Extra Trees classifier (0.909, 95% CI: 0.875-0.943). All constructed ML models performed significantly better than by using the NEWS scoring system (AUC: 0.787, 95% CI: 0.725-0.840). The top six important features selected were age, oxygen saturation at triage, and lab data of APTT, lactic acid, and LDH. Conclusions: The ML approach showed excellent discriminatory performance to identify IHCA for patients with COVID-19 and suspected pneumonia. It has the potential to save more life or provide end-of-life decision making if successfully implemented in the EMR system.

A case of bacterial keratitis caused by multi-drug-resistant Shewanella algae without marine exposure

ABSTRACT Shewanella are Gram-negative rods and marine pathogens. Here, we report a case of bacterial keratitis caused by Shewanella algae without marine exposure. A 66-year-old man with suspected pneumonia was sent to the emergency department from a nursing hospital. He had been in there for 2 years in a vegetative state and could not close his eyes voluntarily. Neither the patient nor his family had experienced any marine exposure. Keratitis was suspected in his right eye. Gram-negative rods grew from swab culture and identified as S. algae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA sequencing. The patient was treated with topical tobramycin, moxifloxacin and ofloxacin as well as steroids for 14 days, and the keratitis improved. S. algae is a rare human pathogen, and most human infections involve marine exposure. This is the second report of bacterial keratitis caused by S. algae worldwide and the first in Asia.

Middle lobe syndrome: a clinical case

The term of middle lobe syndrome refers to abnormal processes that lead to the fact that due to external pressure and changes in the state of tissues, the airways are narrowed. Plain radiography in two projections is the basic method of radiological examination of patients with suspected "pneumonia" of the middle lobe. The disease develops in 6% of people with lung disorders. Middle lobe syndrome is an inconclusive clinical and radiological diagnosis. It requires clarification of the abnormal process