Present and Future Non-Culture-Based Diagnostics: Stewardship Potentials and Considerations

The medical microbiologist plays a key role in the transition from culture-based to molecular test methods for diagnosis of infectious diseases. They must understand the scientific and technical bases underlying these tests along with their associated benefits and limitations and be able to educate administrators and patient providers on their proper use. Coordination of testing practices between clinical departments and the spectrum of public health and research laboratories is essential to optimize health care delivery.

Temporal Dynamics of Nasopharyngeal and Tracheal SARS-CoV-2 Cycle Thresholds in COVID-19 Patients with Tracheostomy

In this study of 45 patients with COVID-19 undergoing tracheostomy, nasopharyngeal and tracheal cycle threshold (Ct) values were analyzed. Ct values rose to 37.9 by the time of tracheostomy and remained >35 postoperatively, demonstrating that persistent test positivity may not be associated with persistent transmissible virus in this population.

System-wide transcriptome damage and tissue identity loss in COVID-19 patients

The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.

Performance Evaluation of the MatMaCorp COVID-19 2SF Assay for the Detection of SARS-CoV-2 from Nasopharyngeal Swabs

The coronavirus disease 2019 (COVID-19) pandemic has taken an unprecedented toll on clinical diagnostic testing, and the need for PCR-based testing remains to be met. Nucleic acid amplification testing (NAAT) is the recommended method for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to the inherent advantages in sensitivity and specificity. In this study, we evaluated the performance of the MatMaCorp COVID-19 2SF test, a reverse transcription-PCR (RT-PCR) assay for the qualitative detection of SARS-CoV-2 from nasopharyngeal (NP) swabs, run on the Solas 8 instrument (MatMaCorp, Lincoln, NE). The Solas 8 device is portable, and the kit is a lab-in-a-box design which provides reagents in a shelf-stable lyophilized powder format. A total of 78 remnant clinical specimens were used to evaluate the COVID-19 2SF test. Sixty-two clinical specimens originally tested by the Xpert Xpress SARS-CoV-2 assay (Cepheid, Inc., Sunnyvale, CA) were used to evaluate the clinical accuracy of the COVID-19 2SF test. The negative percent agreement (NPA) was 100% (95% confidence interval [CI], 83.9% to 100%), and the positive percent agreement (PPA) was 85.4% (95% CI, 70.8% to 94.4%). Sixteen remnant specimens positive for other common respiratory pathogens (FilmArray respiratory panel 2.0; BioFire, Salt Lake City, UT) were assayed on the Solas 8 device to evaluate specificity. No cross-reactivity with other respiratory pathogens was identified. The unique lab-in-a-box design and shelf-stable reagents of the MatMaCorp COVID-19 2SF test offer laboratories a rapid option for a diagnostic NAAT for SARS-CoV-2 that can help meet diagnostic needs. IMPORTANCE The demand for molecular testing for COVID-19 remains to be met. This study of the MatMaCorp Solas 8 device and COVID-19 test provides the first evaluation of this platform.

Performance Evaluation of the MatMaCorp COVID-19 2SF Assay for the Detection of SARS-CoV-2 from Nasopharyngeal Swabs

The coronavirus disease 2019 (COVID-19) pandemic has taken an unprecedented toll on clinical diagnostic testing, and the need for PCR-based testing remains to be met. Nucleic acid amplification testing (NAAT) is the recommended method for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to the inherent advantages in sensitivity and specificity. In this study, we evaluated the performance of the MatMaCorp COVID-19 2SF test, a reverse transcription-PCR (RT-PCR) assay for the qualitative detection of SARS-CoV-2 from nasopharyngeal (NP) swabs, run on the Solas 8 instrument (MatMaCorp, Lincoln, NE). The Solas 8 device is portable, and the kit is a lab-in-a-box design which provides reagents in a shelf-stable lyophilized powder format. A total of 78 remnant clinical specimens were used to evaluate the COVID-19 2SF test. Sixty-two clinical specimens originally tested by the Xpert Xpress SARS-CoV-2 assay (Cepheid, Inc., Sunnyvale, CA) were used to evaluate the clinical accuracy of the COVID-19 2SF test. The negative percent agreement (NPA) was 100% (95% confidence interval [CI], 83.9% to 100%), and the positive percent agreement (PPA) was 85.4% (95% CI, 70.8% to 94.4%). Sixteen remnant specimens positive for other common respiratory pathogens (FilmArray respiratory panel 2.0; BioFire, Salt Lake City, UT) were assayed on the Solas 8 device to evaluate specificity. No cross-reactivity with other respiratory pathogens was identified. The unique lab-in-a-box design and shelf-stable reagents of the MatMaCorp COVID-19 2SF test offer laboratories a rapid option for a diagnostic NAAT for SARS-CoV-2 that can help meet diagnostic needs. IMPORTANCE The demand for molecular testing for COVID-19 remains to be met. This study of the MatMaCorp Solas 8 device and COVID-19 test provides the first evaluation of this platform.

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.

Rapid Implementation of Severe Acute Respiratory Syndrome Coronavirus 2 Emergency Use Authorization RT-PCR Testing and Experience at an Academic Medical Institution

An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time RT-PCR test offered in the NewYork-Presbyterian Hospital system following the Emergency Use Authorization issued by the US Food and Drug Administration. Nasopharyngeal and sputum specimens (n = 174) were validated using newly designed dual-target real-time RT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting SARS-CoV-2 in upper respiratory tract and lower respiratory tract specimens. Accuracy testing demonstrated excellent assay agreement between expected and observed values and comparable diagnostic performance to reference tests. The limit of detection was 2.7 and 23.0 gene copies per reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1694 upper respiratory tract specimens from 1571 patients revealed increased positivity in older patients and males compared with females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing 3 weeks later. Herein, we demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarize clinical data from early in the epidemic in New York City.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.

2290. Identification of Pathogens in Synovial Fluid Samples With an Automated Multiplexed Molecular Detection System

Background

Bone and Joint Infections (BJI) have high morbidity and are difficult to treat infections. Culture-based diagnosis is limited in its ability to recover fastidious bacteria and because several organisms can be involved; culture times of up to two weeks may be necessary for certain bacteria. The sensitivity of culture is also negatively impacted by antibiotics received before surgery. Alternatively, molecular methods offer a promising improvement for the diagnosis of BJI. The goal of this study was to evaluate a development version of Biofire^® Bone and Joint Infection (BJI) Panel (bioMerieux SA, BioFire Diagnostics, LLC) using synovial fluid samples.

Methods

121 synovial fluid specimens were collected from patients with suspected bone and joint infection in a pilot evaluation. All specimens were collected and tested in culture by the sites using their standard of care practices; in parallel, a leftover volume of 200 µL was tested on the BJI panel. BJI panel results were then compared with culture and discordant results were investigated using a comparator assay (PCR/sequencing).

Results

49 synovial fluid specimens (40%) were positive by culture vs. 72 with the BJI panel (59%). Of the 97 positive detections by the BJI panel, 58 were concordant with culture; the 39 additional organism detections were in majority confirmed by PCR/sequencing. Lastly, two false negative results corresponding to the same sample are under investigation.

Conclusion

The BJI Panel was able to identify most of the pathogens detected by culture. The majority of additional detections observed were confirmed by PCR/sequencing. While sites are currently enrolling more synovial fluids samples, these preliminary data suggest that a multiplexed molecular test may be more sensitive than culture to detect pathogens in synovial fluid specimens.

The data presented in this abstract have not been reviewed by FDA or other regulatory agencies for In Vitro Diagnostic use.

Disclosures

B. Pons, bioMerieux: Employee, Salary. C. Jay, bioMerieux: Employee, Salary. T. Martin, bioMerieux: Employee, Salary. I. Sothier, bioMerieux: Employee, Salary. H. Savelli, bioMerieux: Employee, Salary. B. Kensinger, bioFire a bioMerieux company: Employee, Salary. F. Laurent, BioFire (bioMerieux company): Investigator, Research support. L. Abad, BioFire (bioMerieux company): Investigator, Research support. C. Murphy, BioFire (bioMerieux company): Investigator, Research support. A. Craney, BioFire (bioMerieux company): Investigator, Research support. B. Schmitt, BioFire (bioMerieux company): Investigator, Research support. A. Waggoner, BioFire (bioMerieux company): Investigator, Research support. S. Butler-Wu, BioFire (bioMerieux): Investigator, Research support. C. Costales, BioFire (bioMerieux company): Investigator, Research support. J. Bien-Bard, BioFire (bioMerieux): Investigator, Research support. J. Mestas, BioFire (bioMerieux): Investigator, Research support. J. Esteban, BioFire (bioMerieux): Investigator, Research support. L. Salar-Vidal, BioFire (BioMerieux company)): Investigator, Research support. A. Harrington, BioFire (bioMerieux company): Investigator, Research support. S. Collier, BioFire (BioMerieux Company): Investigator, Research support. A. Leber, BioFire (bioMerieux company): Investigator, Research support. K. Everhart, BioFire (bioMerieux company): Investigator, Research support. J. M. Balada-Llasat, BioFire (bioMerieux company): Investigator, Research support. J. Horn, BioFire (bioMerieux company): Investigator, Research support. S. Magro, bioMerieux: Employee, Salary. K. Bourzac, BioFire a bioMerieux company: Employee, Salary.

Optimization of a β-Lactam Scaffold for Antibacterial Activity via the Inhibition of Bacterial Type I Signal Peptidase

β-Lactam antibiotics, one of the most important class of human therapeutics, act via the inhibition of penicillin-binding proteins (PBPs). The unparalleled success in their development has inspired efforts to develop them as inhibitors of other targets. Bacterial type I signal peptidase is evolutionarily related to the PBPs, but the stereochemistry of its substrates and its catalytic mechanism suggest that β-lactams with the 5S stereochemistry, as opposed to the 5R stereochemistry of the traditional β-lactams, would be required for inhibition. We report the synthesis and evaluation of a variety of 5S penem derivatives and identify several with promising activity against both a Gram-positive and a Gram-negative bacterial pathogen. To our knowledge these are the first 5S β-lactams to possess significant antibacterial activity and the first β-lactams imparted with antibacterial activity via optimization of the inhibition of a target other than a PBP. Along with the privileged status of their scaffold and the promise of bacterial signal peptidase I (SPase) as a target, this activity makes these compounds promising leads for development as novel therapeutics.

Not just an antibiotic target: Exploring the role of type I signal peptidase in bacterial virulence

The looming antibiotic crisis has prompted the development of new strategies towards fighting infection. Traditional antibiotics target bacterial processes essential for viability, whereas proposed antivirulence approaches rely on the inhibition of factors that are required only for the initiation and propagation of infection within a host. Although antivirulence compounds have yet to prove their efficacy in the clinic, bacterial signal peptidase I (SPase) represents an attractive target in that SPase inhibitors exhibit broad-spectrum antibiotic activity, but even at sub-MIC doses also impair the secretion of essential virulence factors. The potential consequences of SPase inhibition on bacterial virulence have not been thoroughly examined, and are explored within this review. In addition, we review growing evidence that SPase has relevant biological functions outside of mediating secretion, and discuss how the inhibition of these functions may be clinically significant.

The inhibition of type I bacterial signal peptidase: Biological consequences and therapeutic potential

The general secretory pathway has long been regarded as a potential antibiotic drug target. In particular, bacterial type I signal peptidase (SPase) is emerging as a strong candidate for therapeutic use. In this review, we focus on the information gained from the use of SPase inhibitors as probes of prokaryote biology. A thorough understanding of the consequences of SPase inhibition and the mechanisms of resistance that arise are essential to the success of SPase as an antibiotic target. In addition to the role of SPase in processing secreted proteins, the use of SPase inhibitors has elucidated a previously unknown function for SPase in regulating cleavage events of membrane proteins.

Streptomyces: a screening tool for bacterial cell division inhibitors

Cell division is essential for spore formation but not for viability in the filamentous streptomycetes bacteria. Failure to complete cell division instead blocks spore formation, a phenotype that can be visualized by the absence of gray (in Streptomyces coelicolor) and green (in Streptomyces venezuelae) spore-associated pigmentation. Despite the lack of essentiality, the streptomycetes divisome is similar to that of other prokaryotes. Therefore, the chemical inhibitors of sporulation in model streptomycetes may interfere with the cell division in rod-shaped bacteria as well. To test this, we investigated 196 compounds that inhibit sporulation in S. coelicolor. We show that 19 of these compounds cause filamentous growth in Bacillus subtilis, consistent with impaired cell division. One of the compounds is a DNA-damaging agent and inhibits cell division by activating the SOS response. The remaining 18 act independently of known stress responses and may therefore act on the divisome or on divisome positioning and stability. Three of the compounds (Fil-1, Fil-2, and Fil-3) confer distinct cell division defects on B. subtilis. They also block B. subtilis sporulation, which is mechanistically unrelated to the sporulation pathway of streptomycetes but is also dependent on the divisome. We discuss ways in which these differing phenotypes can be used in screens for cell division inhibitors.

Towards a new science of secondary metabolism

Secondary metabolites are a reliable and very important source of medicinal compounds. While these molecules have been mined extensively, genome sequencing has suggested that there is a great deal of chemical diversity and bioactivity that remains to be discovered and characterized. A central challenge to the field is that many of the novel or poorly understood molecules are expressed at low levels in the laboratory-such molecules are often described as the 'cryptic' secondary metabolites. In this review, we will discuss evidence that research in this field has provided us with sufficient knowledge and tools to express and purify any secondary metabolite of interest. We will describe 'unselective' strategies that bring about global changes in secondary metabolite output as well as 'selective' strategies where a specific biosynthetic gene cluster of interest is manipulated to enhance the yield of a single product.

Chemical perturbation of secondary metabolism demonstrates important links to primary metabolism

Bacterially produced secondary metabolites are used as antibiotics, anticancer drugs, and for many other medicinal applications. The mechanisms that limit the production of these molecules in the laboratory are not well understood, and this has impeded the discovery of many important compounds. We have identified small molecules that remodel the yields of secondary metabolites in many actinomycetes and show that one set of these molecules does so by inhibiting fatty acid biosynthesis. This demonstrates a particularly intimate relationship between this primary metabolic pathway and secondary metabolism and suggests an approach to enhance the yields of metabolites for discovery and biochemical characterization.

Bacterial transmembrane proteins that lack N-terminal signal sequences

Tail-anchored membrane proteins (TAMPs), a class of proteins characterized by their lack of N-terminal signal sequence and Sec-independent membrane targeting, play critical roles in apoptosis, vesicle trafficking and other vital processes in eukaryotic organisms. Until recently, this class of membrane proteins has been unknown in bacteria. Here we present the results of bioinformatic analysis revealing proteins that are superficially similar to eukaryotic TAMPs in the bacterium Streptomyces coelicolor. We demonstrate that at least four of these proteins are bona fide membrane-spanning proteins capable of targeting to the membrane in the absence of their N-terminus and the C-terminal membrane-spanning domain is sufficient for membrane targeting. Several of these proteins, including a serine/threonine kinase and the SecE component of the Sec translocon, are widely conserved in bacteria.

A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria

The luxCDABE operon of the bioluminescent bacterium Photorhabdus luminescens has proven to be a superb transcriptional reporter. It encodes a luciferase (LuxA and LuxB) and the enzymes that produce its substrate (LuxC, LuxD and LuxE) so cells that express the cluster emit the 490-nm light spontaneously. The sequence of these genes is AT-rich (>69%) and for this and other reasons, they are not expressed efficiently in high-GC bacteria like Streptomyces coelicolor. We therefore constructed a synthetic luxCDABE operon encoding the P. luminescens Lux proteins optimized for expression in high-GC bacteria. We tested the genes using transcriptional fusions to S. coelicolor promoters having well-established expression profiles during this organism's life cycle. The hrdB gene encodes a housekeeping sigma factor; while ramC is important for the formation of the spore-forming cells called aerial hyphae and whiE is required for the production of a grey, spore-associated pigment that is deposited in the walls of developing spores. Using these fusions we demonstrated that our synthetic lux genes are functional in S. coelicolor and that they accurately report complex developmental gene expression patterns. We suggest that this lux operon and our procedure for generating synthetic high-GC genes will be widely useful for research on high-GC bacteria.