Graf, Erin H.

Abstract Melioidosis, an infection caused by Burkholderia pseudomallei, has a very high risk of mortality when treated, with an even higher risk of fatality if undiagnosed or not treated appropriately. It is endemic to Asia, Australia, South America, and the Caribbean; however, the number of melioidosis cases reported in the United States has been increasing. Therefore, physicians should be aware of this clinical entity and its possible presentations. Mycotic aneurysms due to B. pseudomallei are extremely rare, accounting for ~1%–2% of cases. Here we describe a rare case of melioidosis presenting as a mycotic aneurysm in the United States, highlight the potential for diagnostic challenges and epidemiologic concerns, and provide a review of mycotic aneurysm cases due to B. pseudomallei published to date.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with more than 2 million genomes sequenced at the time of writing. The rise of more transmissible variants of concern that impact vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution.

Abstract Introduction/Objective The first human case of SARS-CoV-2 infection was reported in December of 2019. By late February 2020 evidence of community transmission in the United States was documented and soon it developed into a global pandemic. On March 11, 2020, the Mayo Clinic Arizona’s Microbiology Laboratory introduced a PCR test for diagnosis of SARS-CoV-2 infection. Even as testing demands exponentially increased, the hospital relied on timely results to assist in directing patient care. In order to provide timely results in the face of continuously emerging supply chain threats, we needed to increase our capacity for SARS-CoV-2 PCR testing by reducing technologist time and reagent waste, without impacting turnaround time or other quality metrics such as repeat rate. Methods/Case Report Technologist time was measured in hands-on time per specimen. Reagent use was defined by the volume of lysis buffer (the primary rate limiting reagent due to supply chain constraints) used per sample. Turnaround time was measured from receipt in lab until result verification and the rerun rate is the percent of specimens with an internal control (IC) failure, an indicator of specimen or process quality. Unnecessary steps were determined using a process map, spaghetti diagram and waste walk. Improvements included simplifying steps, changes to protocols and lab design. Impacts of the improvements were measured for 5 months post-implementation. Results (if a Case Study enter NA) Process improvements reduced technologist time per sample by 30.8 seconds and decreased critical reagent needs by 23.6%. Improvements led to $104,000 in just reagent savings over 5 months. Turnaround time and rerun rates were not negatively impacted. Conclusion By creating the leanest possible workflow, we were able to meet the demands for accurate and timely SARS-CoV-2 results. In future workflows, we will continue to implement lean processes and ensure the most efficient use of limited resources.

Continued replacement of the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages, and associated surges, highlights the importance of genomic surveillance to identify the next possible threats. Despite concerted efforts between clinical laboratories and public health to generate sequence data, the United States has lagged in percentage of SARS-CoV-2 cases sequenced.

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Abstract Respiratory tract infections (RTIs) drive many outpatient encounters and, despite being predominantly viral, are associated with high rates of antibiotic prescriptions. With rising antibacterial resistance, optimization of prescribing of antibiotics in outpatients with RTIs is a critical need. Fortunately, this challenge arises at a time of increasing availability of novel RTI diagnostics to help discern which patients have bacterial infections warranting treatment. Effective implementation of antibiotic stewardship is needed, but optimal approaches for ambulatory settings are unknown. Future research needs are reviewed in this summary of a research summit convened by the Infectious Diseases Society of America in the fall of 2019.

Abstract Background: Elastomeric respirators are reusable and reliable protection from infectious aerosol particles such as SARS-CoV-2. There is a lack of safety data for use in sterile fields limiting application to operating room settings where high-risk aerosol generating procedures are performed. We hypothesized an equivalent reduction in sterile field contamination would be achieved using an elastomeric respirator covered by a surgical mask as compared to a standard surgical mask or N95.Methods: Randomized controlled crossover experiment with repeat measurement comparing microbial and aerosol contamination of operating room surfaces for elastomeric respirators, elastomeric respirators covered by a surgical mask, N95, surgical mask, and no mask. 80 experiments were performed by participants with randomized order and balanced crossover to all masking groups (n=16 per masking group). Participants executed droplet and aerosol generating procedures while wearing: (Group 1) elastomeric respirator with mask, (Group 2) elastomeric respirator only, (Group 3) N95, and (Group 4) surgical mask. Positive control was established with the participant unmasked (Group 5). Contamination was measured by microbial growth on settling plates and optical particle counters (0.2+ and 2 um+ particles).Results: There was a reduction in microbial contamination at the sterile field (p<0.001) for all masks (Groups 1-4) compared to unmasked (Group 5). The mean colony forming units (CFU) at the sterile field was 0 CFUs for elastomeric respirator (+/- mask), N95, and surgical mask versus unmasked growing 1.875 CFUs. Compared to the unmasked control, the elastomeric respirator (+/- mask), N95, and surgical masks all resulted in a -0.75 difference in contamination (95% CI -0.91 to -0.48, p < 0.001). No significant difference in contamination between the elastomeric respirator (+/- mask) and a surgical mask was detected. No significant difference in particle counts (0.2 µm+ and 2.0 µm+) between the elastomeric respirator (+/- mask) and a standard surgical mask.Conclusion and Relevance: Elastomeric respirators with or without mitigation are as effective as a surgical mask and N95 for reducing contamination at the sterile field in an operating room. Consideration should be given to expanding the use of elastomeric respirators to operating rooms during high-risk aerosol generating procedures.