Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.

The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.

Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population.

INTRODUCTION: Manual gating of flow cytometry (FCM) data for marrow cell analysis is a standard approach in current practice, although it is time- and labor-consuming. Recent advances in cytometry technology have led to significant efforts in developing partially or fully automated analysis methods. Although multiple supervised and unsupervised FCM data analysis algorithms have been developed, they have not been widely adopted by the clinical and research laboratories. In this study, we evaluated flowDensity, an open source freely available algorithm, as an automated analysis tool for classification of lymphocyte subsets in the bone marrow biopsy specimens. MATERIALS AND METHODS: FlowDensity-based gating was applied to 102 normal bone marrow samples and compared with the manual analysis. Independent expression of each cell marker was assessed for comprehensive expression analysis and visualization. RESULTS: Our findings showed a correlation between the manual and flowDensity-based gating in the lymphocyte subsets. However, flowDensity-based gating in the populations with a small number of cells in each cluster showed a low degree of correlation. Comprehensive expression analysis successfully identified and visualized the lymphocyte subsets. DISCUSSION: Our study found that although flowDensity might be a promising method for FCM data analysis, more optimization is required before implementing this algorithm into day-to-day workflow.

Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA.

Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015-2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2, targets of carbapenems; no effects were achieved by other ß-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

Pathology Trainee Redeployment and Education During the COVID-19 Pandemic: An Institutional Experience.

Pathology training programs throughout the United States have endured unprecedented challenges dealing with the ongoing coronavirus disease 2019 pandemic. At Houston Methodist Hospital, the Department of Pathology and Genomic Medicine planned and executed a trainee-oriented, stepwise emergency response. The focus was on optimizing workflows among areas of both clinical and anatomic pathology, maintaining an excellent educational experience, and minimizing trainee exposure to coronavirus disease 2019. During the first phase of the response, trainees were divided into 2 groups: one working on-site and the other working remotely. With the progression of the pandemic, all trainees were called back on-site and further redeployed within our department to meet the significantly increased workload demands of our clinical laboratory services. Adjustments to trainee educational activities included, among others, the organization of a daily coronavirus disease 2019 virtual seminar series. This series served to facilitate communication between faculty, laboratory managers, and trainees. Moreover, it became a forum for trainees to provide updates on individual service workflows and volumes, ongoing projects and research, as well as literature reviews on coronavirus disease 2019-related topics. From our program's experience, redeploying pathology trainees within our department during the coronavirus disease 2019 pandemic resulted in optimization of patient care while ensuring trainee safety, and importantly, helped to maintain continuous high-quality education through active involvement in unique learning opportunities.

Chlorhexidine bathing and Clostridium difficile infection in a surgical intensive care unit.

BACKGROUND: Clostridium difficile is the most common causative pathogen for hospital-acquired infections in the intensive care unit. This study evaluated the effect of chlorhexidine bathing every other day in preventing hospital-acquired C. difficile infection (CDI) using data from the CHlorhexidine Gluconate BATHing (CHG-BATH) randomized trial. METHODS: The primary endpoint was the proportion of patients acquiring CDIs among patients at risk for incident CDIs. Infections detected >48 h after randomization were classified as incident CDIs. Infections detected before or within 48 h of randomization were classified as prevalent CDIs. RESULTS: Of 38 patients (11.7%) who met criteria for potential CDI and underwent adjudication, 24 (7.4%) received oral or enema vancomycin, 18 (5.5%) had a positive C. difficile molecular assay, 14 (4.3%) received an International Classification of Diseases, Ninth Revision, Clinical Modification code for CDI, and 2 (0.6%) had possible pseudomembranous colitis on histopathology reports. The prevalence of CDI was 3.7% (6 of 164) in the soap and water arm and 4.3% (7 of 161) in the chlorhexidine arm. Compared with daily soap and water bathing, 2% chlorhexidine bathing every other day was not associated with the prevention of hospital-acquired CDI (1.3% [2 of 152] soap and water versus 2.0% [3 of 148] chlorhexidine, P = 0.68). CONCLUSIONS: It is inconclusive if there was an association between chlorhexidine bathing and incidence of CDI among surgical intensive care unit patients in this study as statistical power was limited. There are limited published data evaluating the association between chlorhexidine bathing and CDI, and this study provides data for future systematic reviews and meta-analyses.