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The virulence of methicillin-resistant Staphylococcus aureus (MRSA) and its potentially fatal outcome necessitate rapid and accurate detection of patients colonized with MRSA in healthcare settings. Using the BD Kiestra Total Lab Automation (TLA) System in conjunction with the MRSA Application (MRSA App), an imaging application that uses artificial intelligence to interpret colorimetric information (mauve-colored colonies) indicative of MRSA pathogen presence on CHROMagar chromogenic media, anterior nares specimens from three sites were evaluated for the presence of mauve-colored colonies. Results obtained with the MRSA App were compared to manual reading of agar plate images by proficient laboratory technologists. Of 1,593 specimens evaluated, 1,545 (96.98%) were concordant between MRSA App and laboratory technologist reading for the detection of MRSA growth [sensitivity 98.15% (95% CI, 96.03, 99.32) and specificity 96.69% (95% CI, 95.55, 97.60)]. This multi-site study is the first evaluation of the MRSA App in conjunction with the BD Kiestra TLA System. Using the MRSA App, our results showed 98.15% sensitivity and 96.69% specificity for the detection of MRSA from anterior nares specimens. The MRSA App, used in conjunction with laboratory automation, provides an opportunity to improve laboratory efficiency by reducing laboratory technologists' labor associated with the review and interpretation of cultures., Competing Interests: S.M., J.L., D.M., C.O., J.-M.V., and K.B. are employees of the study sponsor, Becton, Dickinson and Company, and own BD shares; these authors have no other potential conflict of interest to disclose. D.R. has received research support for this investigation. He has also performed sponsored research in collaboration with Abbott, Altona, BD, bioMerieux, Cepheid, Luminex, Hardy Diagnostics, HelixBind, Hologic, Qiagen, Q-Linea, Roche, Specific Diagnostics, Cleveland Diagnostics, Thermo Fisher, & Vela Diagnostics; served as an advisor for Roche, Thermo Fisher, Luminex/DiaSorin, Seegene; received travel funds from Cepheid; and owns equity in Next Gen Diagnostics. M.D. has received research support for this investigation. P.P. and C.E.G. do not have conflicts of interest to disclose. E.M. has received research support for this investigation and is a sponsored speaker for BD.

Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome. IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis , but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection., Competing Interests: The authors declare no conflict of interest.

Clinical Microbiology Open (CMO), a meeting supported by the American Society for Microbiology's Clinical and Public Health Microbiology Committee (CPHMC) and Corporate Council, provides a unique interactive platform for leaders from diagnostic microbiology laboratories, industry, and federal agencies to discuss the current and future state of the clinical microbiology laboratory. The purpose is to leverage the group's diverse views and expertise to address critical challenges, and discuss potential collaborative opportunities for diagnostic microbiology, through the utilization of varied resources. The first and second CMO meetings were held in 2018 and 2019, respectively. Discussions were focused on the diagnostic potential of innovative technologies and laboratory diagnostic stewardship, including expansion of next-generation sequencing into clinical diagnostics, improvement and advancement of molecular diagnostics, emerging diagnostics, including rapid antimicrobial susceptibility and point of care testing (POCT), harnessing big data through artificial intelligence, and staffing in the clinical microbiology laboratory. Shortly after CMO 2019, the coronavirus disease 2019 (COVID-19) pandemic further highlighted the need for the diagnostic microbiology community to work together to utilize and expand on resources to respond to the pandemic. The issues, challenges, and potential collaborative efforts discussed during the past two CMO meetings proved critical in addressing the COVID-19 response by diagnostic laboratories, industry partners, and federal organizations. Planning for a third CMO (CMO 2022) is underway and will transition from a discussion-based meeting to an action-based meeting. The primary focus will be to reflect on the lessons learned from the COVID-19 pandemic and better prepare for future pandemics.

In non-endemic settings, transfusion-transmitted malaria (TTM) is rare but potentially fatal and becoming more common with globalization. We present two pediatric cases that demonstrate donor screening using questionnaires is subject to error and that TTM should be considered with fever following numerous transfusions in children, particularly sickle cell patients., (© The Author(s) 2021. Published by Oxford University Press on behalf of The Journal of the Pediatric Infectious Diseases Society.)

Nucleic acid amplification testing (NAAT) for SARS-CoV-2 is the standard approach for confirming COVID-19 cases. This study compared results between two emergency use authorization (EUA) NAATs, with two additional EUA NAATs utilized for discrepant testing. The limits of detection (LOD) for the BD SARS-CoV-2 reagents for the BD MAX system (MAX SARS-CoV-2 assay), the bioMérieux BioFire respiratory panel 2.1 (BioFire SARS-CoV-2 assay), the Roche cobas SARS-CoV-2 assay (cobas SARS-CoV-2 assay), and the Hologic Aptima SARS-CoV-2 assay Panther (Aptima SARS-CoV-2 assay) NAAT systems were determined using a total of 84 contrived nasopharyngeal specimens with 7 target levels for each comparator. The positive and negative percent agreement (PPA and NPA, respectively) of the MAX SARS-CoV-2 assay, compared to the Aptima SARS-CoV-2 assay, was evaluated in a postmarket clinical study utilizing 708 nasopharyngeal specimens collected from suspected COVID-19 cases. Discordant testing was achieved using the cobas and BioFire SARS-CoV-2 NAATs. In this study, the measured LOD for the MAX SARS-CoV-2 assay (251 copies/ml; 95% confidence interval [CI], 186 to 427) was comparable to the cobas SARS-CoV-2 assay (298 copies/ml; 95% CI, 225 to 509) and the BioFire SARS-CoV-2 assay (302 copies/ml; 95% CI, 219 to 565); the Aptima SARS-CoV-2 assay had an LOD of 612 copies/ml (95% CI, 474 to 918). The MAX SARS-CoV-2 assay had a PPA of 100% (95% CI, 97.3% to 100.0%) and an NPA of 96.7% (95% CI, 94.9% to 97.9%) compared to the Aptima SARS-CoV-2 assay. The clinical performance of the MAX SARS-CoV-2 assay agreed with another sensitive EUA assay.

In-system clinical laboratories have proven themselves to be a fundamentally important resource to their institutions during the COVID-19 pandemic of the past year. The ability to provide SARS-CoV-2 molecular testing to our hospital system allowed us to offer the best possible care to our patients, and to support neighboring hospitals and nursing homes. In-house testing led to significant revenue enhancement to the laboratory and institution, and attracted new patients to the system. Timely testing of inpatients allowed the majority who did not have COVID-19 infection to be removed from respiratory and contact isolation, conserving valuable personal protective equipment and staff resources at a time that both were in short supply. As 2020 evolved and our institution restarted delivery of routine care, the availability of in-system laboratory testing to deliver both accurate and timely results was absolutely critical. In this article, we attempt to demonstrate the value and impact of an in-system laboratory during the COVID-19 pandemic. A strong in-house laboratory service was absolutely critical to institutional operational and financial success during 2020, and will ensure resiliency in the future as well., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

In March 2020, NorthShore University Health System laboratories mobilized to develop and validate polymerase chain reaction based testing for detection of SARS-CoV-2. Using laboratory data, NorthShore University Health System created the Data Coronavirus Analytics Research Team to track activities affected by SARS-CoV-2 across the organization. Operational leaders used data insights and predictions from Data Coronavirus Analytics Research Team to redeploy critical care resources across the hospital system, and real-time data were used daily to make adjustments to staffing and supply decisions. Geographical data were used to triage patients to other hospitals in our system when COVID-19 detected pavilions were at capacity. Additionally, one of the consequences of COVID-19 was the inability for patients to receive elective care leading to extended periods of pain and uncertainty about a disease or treatment. After shutting down elective surgeries beginning in March of 2020, NorthShore University Health System set a recovery goal to achieve 80% of our historical volumes by October 1, 2020. Using the Data Coronavirus Analytics Research Team, our operational and clinical teams were able to achieve 89% of our historical volumes a month ahead of schedule, allowing rapid recovery of surgical volume and financial stability. The Data Coronavirus Analytics Research Team also was used to demonstrate that the accelerated recovery period had no negative impact with regard to iatrogenic COVID-19 infection and did not result in increased deep vein thrombosis, pulmonary embolisms, or cerebrovascular accident. These achievements demonstrate how a coordinated and transparent data-driven effort that was built upon a robust laboratory testing capability was essential to the operational response and recovery from the COVID-19 crisis., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Members of the genus Corynebacterium are increasingly recognized as pathobionts and can be very resistant to antimicrobial agents. Previous studies have demonstrated that Corynebacterium striatum can rapidly develop high-level daptomycin resistance (HLDR) (MIC, ≥256 μg/ml). Here, we conducted a multicenter study to assay for this in vitro phenotype in diverse Corynebacterium species. Corynebacterium clinical isolates ( n  = 157) from four medical centers were evaluated. MIC values to daptomycin, vancomycin, and telavancin were determined before and after overnight exposure to daptomycin to identify isolates able to rapidly develop daptomycin nonsusceptibility. To investigate assay reproducibility, 18 isolates were evaluated at three study sites. In addition, the stability of daptomycin nonsusceptibility was tested using repeated subculture without selective pressure. The impact of different medium brands was also investigated. Daptomycin nonsusceptibility emerged in 12 of 23 species evaluated in this study ( C. afermentans , C. amycolatum , C. aurimucosum , C. bovis , C. jeikeium , C. macginleyi , C. pseudodiphtheriticum , C. resistens , C. simulans , C. striatum , C. tuberculostearicum , and C. ulcerans ) and was detected in 50 of 157 (31.8%) isolates tested. All isolates displayed low (susceptible) MIC values to vancomycin and telavancin before and after daptomycin exposure. Repeated subculture demonstrated that 2 of 9 isolates (22.2%) exhibiting HLDR reverted to a susceptible phenotype. Of 30 isolates tested on three medium brands, 13 (43.3%) had differences in daptomycin MIC values between brands. Multiple Corynebacterium species can rapidly develop daptomycin nonsusceptibility, including HLDR, after a short daptomycin exposure period., (Copyright © 2021 American Society for Microbiology.)

Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have risen to these challenges, provide recommendations for managing the current pandemic, and outline the steps we can take as a community to better prepare for future pandemics., (Copyright © 2020 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Clinical microbiology laboratories face challenges with workload and understaffing that other clinical laboratory sections have addressed with automation. In this issue of the Journal of Clinical Microbiology , M. L. Faron, B. W. Buchan, R. F. Relich, J. Clark, and N. A. Ledeboer (J Clin Microbiol 58:e01683-19, 2020, https://doi.org/10.1128/JCM.01683-19) evaluate the performance of automated image analysis software to screen urine cultures for further workup according to their total number of CFU. Urine cultures are the highest volume specimen type for most laboratories, so this software has the potential for tremendous gains in laboratory efficiency and quality due to the consistency of colony quantification., (Copyright © 2020 American Society for Microbiology.)

Seasonal influenza virus causes significant morbidity and mortality each year. Point-of-care (POC) testing using rapid influenza diagnostic tests (RIDTs), immunoassays that detect viral antigens, are often used for diagnosis by physician offices and urgent care centers. These tests are rapid but lack sensitivity, which is estimated to be 50 to 70%. Testing by PCR is highly sensitive and specific, but historically these assays have been performed in centralized clinical laboratories necessitating specimen transport and increasing the time to result. Recently, Clinical Laboratory Improvement Amendments (CLIA)-waived, POC PCR influenza assays have been developed with >95% sensitivity and specificity compared to centralized PCR assays. To determine the clinical impact of a POC PCR test for influenza, we compared antimicrobial prescribing patterns of one urgent care location using the Cobas LIAT Influenza A/B assay (LIAT assay; Roche Diagnostics, Indianapolis, IN) to other urgent care centers in our health system using traditional RIDT, with negative specimens being reflexed to PCR. Antiviral prescribing was lower in patients with a negative LIAT PCR result (2.3%) than in patients with a negative RIDT result (25.3%; P < 0.005). Antivirals were prescribed more often in patients that tested positive by LIAT PCR (82.4%) than in those testing positive by either RIDT or reflex PCR (69.9%; P < 0.05). Antibacterial prescriptions for patients testing negative by LIAT PCR were higher (44.5%) than for those testing negative by RIDT (37.7%), although the difference was not statistically significant. In conclusion, having results from a PCR POC test during the clinic visit improved antiviral prescribing practices compared to having rapid results from an RIDT., (Copyright © 2019 American Society for Microbiology.)

Blood cultures are one of the most common and most important tests performed in clinical microbiology laboratories. Variables and technology that improve and speed the recovery of blood stream pathogens have been published in the Journal of Clinical Microbiology since its inception in 1975. Despite the importance of blood cultures, little research has focused on the turnaround time of blood culture reports. In this issue of the Journal of Clinical Microbiology, Y. P. Tabak et al. (J Clin Microbiol 56:e00500-18, 2018, https://doi.org/10.1128/JCM.00500-18) report the results of an investigation of Gram stain, organism identification, and susceptibility report turnaround times for 165,593 blood cultures from 13 laboratories. These data provide a starting point for clinical laboratories to establish targets for blood culture result reporting., (Copyright © 2018 American Society for Microbiology.)

To examine the role of the fibrinolytic system in LPS-induced airway disease, we compared the effect of a chronic LPS challenge in plasminogen activator inhibitor-deficient (C57BL/6JPAI-1-/-) mice and wild-type (WT) C57BL/6J mice. Physiological and biological assessments were performed, immediately after, and 4 wk after an 8-wk exposure to LPS or saline. Immediately after the LPS exposure, WT mice had increased estimates of airway reactivity to methacholine compared with C57BL/6JPAI-1-/- mice; however, airway inflammation was similar in both LPS-exposed groups. Significant increases in both active transforming growth factor (TGF)-beta1 and active matrix metalloproteinase (MMP)-9 was detected after LPS exposure in WT but not C57BL/6JPAI-1-/- mice. C57BL/6JPAI-1-/- mice showed significantly less TGF-beta1 in the lavage and higher MMP-9 in the lung tissue than WT mice at the end of exposure and 4 wk later. After LPS exposure, both WT and C57BL/6JPAI-1-/- mice had substantial expansion of the subepithelial area of the medium [diameter (d) = 90-129 microm]- and large (d > 129 microm)-size airways when compared with saline-exposed mice. Subepithelial fibrin deposition was prevalent in WT mice but diminished in C57BL/6JPAI-1-/-. PAI-1 expression by nonciliated bronchial epithelial cells was enhanced in LPS-exposed WT mice compared with the saline-exposed group. Four weeks after LPS inhalation, airway hyperreactivity and the expansion of the subepithelial area in the medium and large airways persisted in WT but not C57BL/6JPAI-1-/- mice. We conclude that an active fibrinolytic system can substantially alter the development and resolution of the postinflammatory airway remodeling observed after chronic LPS inhalation.